CHAPTER 1 Gene Trees, Species Trees, and Species Networks
生物学英语教程10 18 19 20 23 24原文及翻译
10: The nature of viruses has been apparent only within the last half century, and the first step on this path of discovery was taken by the Russian botanist Dmitri Lvanovsky in 1892 when he studying the tobacco mosaic disease.Viruses are very small entities, ranging in size from 0.02 to 0.3 microns. Unlike the organisms making up the five taxonomic kingdoms of the living world, viruses are acellular, they don’t consist of cells and conduct energy metabolism-they don’t produce ATP and incapable of fermentation , cellular respiration or photosynthesis. As for these, the questions of the viruses origin arise. Do they represent a primitive ‘nearly living’ stage in the evolution of life? Or are they organisms which have lost all cellular components except the nucleus? Could viruses simply be fragments of genetic material derived from cellular organisms? No one really knows the answers to these questions, but we do know that viruses have been around for a long time, and that almost every form of life is susceptible to viral attack.The basic units of a virus consist of nucleic acid surrounded by a capsid or coat, composed of one or at most a few kinds of proteins. These proteins are so assembled as to give the virion a characteristic shape. As they bud through host cell membranes, many animal viruses also acquire a membrane consisting of lipids and proteins, and many bacterial viruses have specialized ‘tails’made of protein. The viral nucleic acid is usually a single molecule and may be composed of either DNA or RNA, but not both. DNA or RNA can be double-stranded or single-stranded.Viruses are obligate intracellular parasite, that is why they must depend upon specific hosts for their reproduction and development. The cells of animals, plants and bacteria can all serve as hosts to viruses. Animal viruses attach to special sites on the plasma membrane of the host cell and are then taken up by endocytosis. A given virus can infect only those cells that have a receptor site for that virus. After the membrane breaks down, the viral protein capsid is broken down by cellular enzymes before the viral nucleic acid, in addition, the viral nucleic acid serves to direct the synthesis of new capsid protein by the protein-synthesizing system of the host, and the capsid combine with new viral nucleic acid spontaneously; and in due course, the new virions are released by the host cell.Plant viruses and bacteriophages must get through a cell wall as well as the host plasma membrane. Infection of a plant usually results from attack by a virion-laden insect vector. The insect uses its proboscis to penetrate the cell wall, and the virions the escape from the insect into the plant. Bacterial viruses are often equipped with tail assemblies that inject the nucleic acid into the host bacterium while the protein coat remains outside. Once inside the host cell, the virus genes takes over the metabolic machinery of the cell and generate their own.Sometimes, viral DNA does not immediately take control of the host metabolism, but insert itself into the host chromosome and present as ‘silent’ provirus until the host cell is exposed to some environmental insult, such as ultraviolet light or radiation.If the viral nucleic acid is RNA, replication needs special enzymes to make the process of RNA-to-RNA synthesis occurs. Some RNA viruses called retroviruses do not carry outRNA-to-RNA transcription. Instead, their RNA is transcribed into DNA is immediately, this reaction is catalyzed by reverse transcriptase, then newly formed DNA is inserted into host DNA and then transcribed into RNA and at last new viruses are produced.After replication and combination, most viruses are released by lysis of the host cell. But in other cases, like that of the retroviruses, viruses are released by extrusion, a process similar tobudding thereby the virus becomes enveloped in a small piece of cell membrane as it moves out of the cell. Lysis result in the destruction of the cell, but extrusion allows the cell to remain alive and continue to produce new viruses for a long period of time.A common way to classify viruses is to separates them first on the nature of the nucleic acid component (DNA or RNA) and then on whether the nucleic acid in the virion is single-ordouble-stranded. Further levels of classification depend on such factors as the overall shape of the virus and the symmetry of the capsid. Most capsid may be categorized as helical, icosahedral and so on. Another level of categorization is based on the presence or absence of membranous envelope around the virion; still further subdivision relies on capsid size and other criteria.18: Within a cell, energy is needed at every stage to drive the reactions that keep life in normal states. On the earth, almost all the energy that fuels life today comes from the sun and is captured in the process of photosynthesis by plants. Most nonphotosynthetic organisms obtain energy by ingesting photosynthetic organisms or others that have themselves ingested photosynthetic organisms, and the energy stored by photosynthesis is usually released through a process known as respiration. In this chapter, we shall discuss these two processes.Photosynthesis is a logical starting point for our discussion of the basic energy transformation of life. In simple terms photosynthesis consists of the reduction of atmospheric CO2 to carbonhydrate by use of light energy, with an associated release of oxygen from water. This reaction can be summarized by the following generalized equation.Like many other physiological processes, photosynthesis consists of a number of sequential steps:①trapping of light energy by chloroplasts; pigments other than chlorophyll(e.g carotenoids)play an accessory role in photosynthesis by transferring energy to chlorophyll a. ②splitting of water and release of high-energy electrons and o2.③electron transfer leading to generation of chemical energy in the form of ATP and the reducing power as NADPH2.④terminal steps involving expenditure of energy of ATP and the reducing power of NADPH2 to fix CO2 molecules, and finally convert this compounds into more complex carbohydrates, such as sucrose, starch, cellulose and so on.Carbon dioxide is an exceedingly energy-poor compound, whereas carbohydrates isenergy-rich. Photosynthesis, then, converts light energy into chemical energy. In chemical terms, the energy is said to be stored by the addition of one more electron-stores energy in the substance being reduced.Although, photosynthesis can occur in any chlorophyll-containing parts of the plant, leaves that expose the greatest area of green tissue to the light are the principal organs of photosynthesis. Through a microscope it can be seen that the outer surfaces of the leaf have a layer of epidermis, which is covered by waxy layer of cuticle. The region between the upper and lower epidermis constitutes the mesophyll portion of the leaf. The cells of mesophyll contain many chloroplasts, which is the organelles that photosynthesis takes place. The CO2 required for photosynthesis can enter through some holes called stomata between the spaces of mesophyll cell. Chloroplast is bounded by two concentric membrane and a third set of internal membranes that form a series of flattened, interconnected sacs known as thylakoids, where chlorophyll moleculesand most of the electron-transport-chain molecules are located. The light reaction, in which light energy is trapped and converted into chemical energy, takes place on the thylakoid membrane. The dark reaction, in which CO2 is reduced to carbohydrates, occurs in the more fluid stroma that surrounds the thylakoid sacs.19: It is evident that the phenomenon of inheritance and variation is of universal important in the living world. To understand it, we must explore how hereditary material expresses itself in new combinations, and whether principles can be formulated about so complex event. This exploration is the study of the branch of biology known as genetics.Some of the basic concepts of heredity grew out of experiments performed by Gregor Mendel in the mid-1800s. Mendel spent most of his lifetime as a monk in an Austrian monastery and during this time he cultivated garden peas, and did a series of experiments to study inheritance in plants. We now know that owing to his elaborate design, unique technique, Mendel formulated two excellent Laws of Inheritance from his breeding experiments on the garden peas: one is the Law of Segregation, the other is the Law of Independent Assortment.The Law of Segregation emphasize on single traits and it can be stated as follows: the inheritance of each individual trait is determined by hereditary factors (genes), each organism possesses two inheritance factors for each character, when gametes are formed, the two factors separate into separated gametes. An offspring formed by the fusion of two gametes therefore receives one factor for each character from each parent. The Law of Independent Assortment involving two or more traits and states that during gametes formation, when two or more genes are involved in a cross, the alleles of one gene are inherited independently of the alleles of another gene. His great achievement laid a solid foundation for the genetics. In order to further understanding of these two laws, some details can be known either:1.Hereditary traits are controlled by discrete units that pass unchanged from generationto generation. For example, the trait white flower seems to disappear in the F1generation, but reappears on the F2 progeny, and that there are no intermediate colors,only red or white.2.Each trait is produced by two hereditary factors. This is a necessary assumption toaccount for the way in which a trait such as flower color appears in successivegenerations in a predictable ratio.3.When two contrasting hereditary factors are present in an organism, such asred-flower color and white-flower color, only one will be expressed. one will bedominant and the other recessive. In the case of the peas, red-flower color isdominant to white-flower color since only the hereditary character of red shows onthe F1 generation.4.Each parent contributes only one of the hereditary factors to each gamete. Moreover,as a consequence of segregation, equal numbers of gametes each kind are formed.5.when gametes unite at the fertilization, the two hereditary factors are broughttogether. Fertilization is a random union in the sense that equal numbers of thedifferent kinds of gametes are produced and it is a matter of chance how they willpair. This being true it should be possible, on a probability basis, to predict the ratioof various characteristics in the offspring. In the flower color experiment, forexample, the ratio of approximately three red-flowered plants to each white-floweredplant conform the expected or predicted ratio of 3 to 1.Today, Mendel’s theories seem rather obvious in the light of the discovery of DNA, genes, chromosomes and meiosis. But it should be remembered that Mendel did his work before all of these theories. He arrived at his great conclusions purely by reasoning from the patterns of inheritance he detected in his experiments. Of course, we know that a variety of influence, including environment, interaction of one gene with another, can cause the appearancechanges, and a single gene may have multiple effects on explaining the phenomenon of the testimony to the strength of the Mendel’s conclusions.20: we know that when a cell divides it must first duplicate the genetic information contained in its chromosomes, so that each daughter cell receive its own copy from the parental cell, but how the genetic information copied on a molecular level? Since 1928, Frederick Griffith published his experiments on pneumococci, a series of experiments led to the realization that DNA is the genetic material. Soon after then, scientists proposed that the linear order of nucleotides in DNA determines the order of amino acids in polypeptides, and therefore determines the structure and function of proteins. This work is now so well established that it is called the central dogma of molecular biology. The dogma states that the information contained in DNA molecules is transferred to RNA molecules, and then from the RNA molecules the information is expressed in the structure of proteins. A summary of this process is: DNA molecule is known to be composed of two nucleotide chains, each nucleotide are joined by covalent bonds between the sugar of one nucleotide and the phosphate group of the next nucleotide in the sequence. The nitrogenous bases are side groups of the chains, the two chains are held together by hydrogen bonds between nitrogenous bases (adenine=thymine and guanine= cytosine) in opposite directions, then, the ladder like double-chained molecule is coiled into a double helix. During replication, the two chains of the DNA separated, and each chain acts as a template for the synthesis of its new partner according to base pairing principle. This process is much like one might unzip a zipper and then produce two complete double-chained molecules, each identical in base sequence to the mother DNA molecule.The transcription of DNA into RNA begins when the enzyme of RNA polymerase binds to a sequence of nucleotides on the DNA called the promoter. Next, the two strands of DNA are separated, and one strand serves as the template for the formation of a complementary strand of RNA. RNA polymerase moves along the DNA and joins the complementary ribonucleotides to the growing RNA strand, one by one. The enzyme works only in the 3’ to 5’direction on its DNA template, assembling RNA in the 5’ to 3’ direction. This process is much like the replication of DNA, with one important difference. When DNA replication, once begin, usually copies all DNA in the cell, whereas RNA synthesis transcribes only selected proteins of the DNA. When the polymerase reaches a termination signal on the DNA, it leaves the DNA chain, and the RNA also detached.Sine DNA molecules are double-stranded, any section of DNA could, in principle, betranscribed into two different RNA molecules, one complementary to each strand. In practice, only one of the strands is transcribed in any one segment of DNA. The orientation of the promoter indicates which strand is to be transcribed because the promoter reads ‘correctly’ only on that strand. The codes for some genes lie on one DNA strand, and codes for other genes lie on its partner.There are four major stages in protein synthesis:1.activation: each amino acid is first activated by reacting with a molecule of ATP. Theactivated amino acid is then attached to its own particular tRNA molecule with theaid of an enzyme(a synthetase) that is specific for that particular amino acid and thatparticular tRNA molecule.2.initiation: this stage consists of three steps:①mRNA, which carries the informationnecessary to synthesize one protein molecule, attached to the 40s ribosome. ②theanticodon of the first tRNA binds to the codon of the mRNA that represents theinitiation signal. ③the 60s ribosome now combines with 40s body. The 60s bodyhas two binding site: one is P site where the growing peptide chain will bind, theother is A site where the incoming tRNA will bring the next amino acid in.3.elongation: at this point the A site is vacant, and each of the 20 tRNA can come inand try to fit itself in. but only one can be the right anticodon that corresponds to thenext codon on the mRNA. In the next elongation, the whole ribosome moves onecodon along the mRNA. Simultaneously with this move, the dipeptide is translocatedfrom the A site to the P site, while the empties tRNA dissociates and goes back to thetRNA pool to pick up another amino acid. After the translocation, the A site isassociated with the next codon on the mRNA. These elongation steps are repeateduntil the last amino acid is attached.4.termination: after the last translocation, the next codon reads ‘stop’ (UAA,UAG orUGA). No more amino acid can be added. Releasing factors then cleave thepolypeptide chain from the last tRNA in a mechanism not yet fully understood. ThetRNA itself is released from the P site, and the whole mRNA is released from theribosome.23：within multiple-cellular organisms, cells of different tissues divide at very differentrates, this process is strictly controlled so that cells divide only when necessary. Occasionally, however, the genetic control fail, a cell begins to grow and divide without restrain, until its offspring begin to crowed surrounding cells and interfere with tissue functions. The alteration has spawned a tumor. Tumor cells divide not only at a horrendous rate, but not respond to the controls telling them when to stop. They will not stop as long as conditions for growthremain favorable. If the tumor cells remain localized, it is said to be benign. Sometimes,however, a tumor cell can metastasize and then grow and divide in other organs of the body, such tumor cells are said to be malignant, or cancerous by definition. A cancer cell has the following characteristics:1.Almost all cancer cells have an abnormal number of chromosomes.2.Cancer cells tend to have a rather spherical shape, making them more mobile thannormal cells.3.Profound abnormalities in the plasma membrane. Membrane transport andpermeability are amplified. Some proteins at the surface are lost or altered, and newone appears.4.Profound changes in the cytoplasm. The cytoskeleton shrinks, becomesdisorganized, or both. Enzyme activity shifts.5.Abnormal growth and division.6.Diminished capacity for adhesion to substrates. Secretions needed for adhesiondwindle; cells cannot become properly anchored in the parent tissue.Our current understanding of cancer suggests that most cancer arise from a single abnormal cell, but how this cell produced? According to multistep hypothesis, we know that the development of a cancer is a long-term process, and it is a result of several independent genetic mutations occurring in the same cell that convert a normal cell into a malignant cell. These mutations can be caused by mutagenic agents known as carcinogens. Carcinogens include numberous natural and synthetic compounds, X-rays, gamma rays and ultraviolet radiation, which may cause single base changes, deletions, insertions and result in cancerous.Genes that cause cancer are called oncogenes. Research results show that more than fifty oncogenes have now been isolated from a variety of animals. In each case, an identical gene sequence, called a proto-oncogene, has been discovered in the normal DNA of the host animal—and the cells carrying them rarely become cancerous. Proto-oncogenes, which is highly conserved in diverse species, is an inherent parts of vertebrate DNA, and it codes for proteins necessary in normal cell functioning. It may become cancer-causing genes only on those occasions when specific mutations altered its structure or its expression.How oncogene-encoded proteins induce cancer? In normal cells, extracellular signals trigger cell division. At the very least, signaling mechanisms of the pathways controlling division must include the following:①growth factors (molecules that carry growth signals from one cell to another);②signal receptors at the membrane surface of the receiving cell;③molecules that transmit signals from the cell surface to specific targets inside. As to cancerous cells, these mechanism is destroyed, this may be generally foreshadows cell division and then cause it cancerous.24: within the past three decades the ability to alter the genetic characteristics of organisms has been enhanced by the advent of modern recombinant DNA technology. The aim of this technology is to impart some new characteristics or functions to an organism by transferring into its cells the DNA of a different organism. This technology can make an organism obtain desired characteristics or functions in short spans, so it has far-reaching potential and has been widely used in agriculture, medicine and so on. Four basic steps are involved in recombinant DNA technology.First, DNA from the donor organisms is cut into small, manageable pieces. To do this, special enzymes are required, the enzymes that cut DNA are called restriction enzymes, each of which hasthe capability to recognize a specific nucleotide base sequence and to cut each DNA strand whenever the sequence occurs. After cutting, there would be a mixture of DNA segments with‘sticky ends’. Of all these fragments, only one may be of interest.The second step in this technology involves joining the pieces of DNA to a vector that acts as a carrier to transport the gene into a new host cell. There are two types of vectors are commonly used: plasmids and bacteriophages. Plasmids are small, circular DNA molecules in the cytoplasm of bacteria and can replicate independently. The initial procedure is similar by using these two vectors: the donor DNA and ‘vector’ DNA are cut with the same restriction enzyme to create the same sticky ends, then the two types of DNA are mixed, complementary base pairing occurs between the sticky ends, and the ends are joined by ligase. But when bacteriophages act as vectors, some protein are to be added next, the protein then combine with the DNA to form bacteriophages, the bacteriophages then infect other bacterial cells by attaching to the cells and injecting their DNA, and this process is called transduction.Once inside the bacteria, the plasmid or bacteriophage replicates autonomously to produce many copies of itself and the foreign DNA it carries. These copies are sometimes referred to as a gene library. Because thousands of identical copies can be produced, the entire library must be searched to find the one clone that has the desired gene. Generally, there are several techniques, including radioactive probe and specific antibody, are used to solve these problems. When the copies have been identified, the bacteria with the desired gene can be cultured, creating limitless numbers of bacteria.Plasmids and bacteriophages are useful vectors to transport DNA into bacterial cells, but such vectors cannot normally enter eukaryotic cell. How can we do about this next? At present, using microinjection, shotgun procedure or bacterium agrobacterium can insert genes into host cells. Of all these methods, microinjection and shotgun techniques have been successfully used in introducing DNA into plant cell or animal cell. But unfortunately, both two ways have a very low success rate. The bacterium agrobacterium can infects a plant cell efficiently and inserts its plasmids into the host’s chromosomes, but not all plants are susceptible to the crown gall bacterium. So we can select considerable ways to cope with special questions.Of course, it must be remembered that getting the DNA into the cell is only the beginning, so at last, we must use proper control elements to stimulate transcription and allow the host cells to multiple large numbers of descendants, and the descendants are screened to commercially utilize.Although, the recombinant DNA technology seems difficult, genetically engineered plants with herbicide-insect and disease-resistance are come into fruit, and gene transfers to domesticated animals have given us many advantages. Looking towards future, some researchers have suggested using this technology to transfer genes for the fixation of atmospheric nitrogen into crop plants, thus eliminating the need for the application of nitrogenous fertilizers.翻译10：病毒病毒的性质在过去的半个世纪已明显，以及在这一发现道路上的第一步是由俄罗斯植物学家DmitriLvanovsky在1892年时研究的烟草花叶疾病。
研究生学位英语考试试题
2005年1月份研究生学位课英语统考试题Paper OnePart I ：Listening Comprehension (25 minutes, 20 points )Section A (1 point each)1.A: He refuses to help the woman. B: He can‘t handle the equipment by himself.C: He thinks some other people can do it better.D; He thinks the equipment is too heavy for the woman.2.A: His colleagues have contributed a lot. B: All of his colleagues congratulated him.C. The award has been given to his colleagues. D He doesn‘t deserve the honor.3. A: He dislike Jack‘s name. B He doesn‘t care who Jack is.C He doesn‘t know Jack well.D He dislikes Jack.4. A: The man is cracking a joke on her.B It is impossible to buy a genuine antique for so little money.C The man is out of his mind about the old vase.D The man has run into a great fortune.5. A: He can‘t find a good idea about the problem. B He feels hopeless about the project.C He has encountered another problem.D He is going to give up the project.6. A: It is worthwhile. B It has a very tight schedule.C It was a waste of time.D It took him too much time on the road.7. A: It‘s useless to talk to the professor. B The professor is often unfair.C The man has done well enough.D The man can‘t be be tter next time.8. A The man should not say things like that. B The man should fight back.C The man should show his anger openly.D The man should not complain openly.9. A: She was injured in the shoulder. B She disliked the people who attended the party.C She was laughed at for her behaviour.D She was unpopular at the party.Section B (1 point each)Mini-talk One10. A: Improving the conditions of farm animals. B: Increasing the production of farm animals.C: Regulating the food marketing system.D: Regulating the food stores and restaurant chains.11. A: Because they want to save more money. B: Because they want the hens to lay more eggs.C Because they want the hens to grow more lean meat.D Because they want to sell the hens at a better price.12. A: Chickens should be kept in clean places. B: Pigs should be housed in large metal boxes.C: Farm animals should be slaughtered in factories.D Farm animals should be killed without feeling pain.Mini-talk Two13. A: Under the mountains is the state of Nevada.B: At the power centers in almost forty states.C: Under the deep ocean . D Near the inactive volcanoes.14. A: People object to burying it at the power centers.B: The power centers have no more space to store it.C: It is very dangerous to bury it in populous areas.D: The new site is the estate of the federal government.15. A; There are active volcanoes nearby. B: Some people still live in the area.C: The area is close to Las Vegas. D The area is geographically unsafe.Section C (1 point each)You will hear the recording twice. At the end of the talk there will be a 3-minute pause, during which time you are asked to write down your answers briefly on the Answer Sheet. You now have 25 seconds to read the questions (请在录音结束后把16-20题的答案抄写在答题纸上.) 16．What percentage of plant and animal species on Earth do rain forests contain?17. What critical role do rain forests play besides being home to animals and plants?18. How much has global output of carbon dioxide increased in the past century?19. To be classified as a rain forest, how should the trees look?20. How large is the size of the rain forest in South America?Part I Vocabulary Section A1.This student was expelled from school because he had forged some documents for overseasstudy.A frustratedB formulatedC fabricatedD facilitated2.Opinion polls suggest that the approval rate of the president is on the increase.A agreementB consensus Cpermission D support3. A man of resolve will not retreat easily from setbacks or significant challenges.A pull outB pull upC pull inD pull over4. As few household appliances are now perfect, this minor defect is negligible.A detectableB triflingC inexcusableD magnificent5. The U.S. athletes topped the gold medal tally for the 3rd straight time this summer.A directB proceedingC verticalD successive6. Despite tremendous achievement, formidable obstacles to development will persist.A difficultB sustainableC externalD unpredictable7. Moderate and regular exercise can boost the rate of blood circulation and metabolism.A restrictB reduceC increaseD stabilize8. The manager is seeking some cost-effective methods that can call forth their initiative .A efficientB conventionalC economicalD unique.9. The report proposes that students be allowed to work off their debt through community service.A pay offB get offC dispose ofD run off10. It was a tragic love affair that only gave rise to pain.A brought forwardB brought aboutC brought downD brought inSection B :11. As females in their 40s tend to ____ weight, they are to go in for outdoor activities.A take onB hold onC carry onD put on12. The shop-owner took a load of ____-crusted bread and handed it to the child.A fragileB crispC vagueD harsh13. The excessive hospitality ____ the local officials failed to leave us assured.A on the point ofB on the grounds ofC on the advice ofD on the part of14.These intelligence officers tried a ___ of persuasion and force to get the information they wanted.A combinationB collaborationC convictionD confrontation15. The terminally ill patient lying in the ___ care unit was kept alive on life support.A apprehensiveB intensiveC extensiveD comprehensive16. The very sound of our national anthem being played at the awarding ceremony is ____.A ice-breakingB eye-catchingC painstakingD soul-touching17. Leading universities in China prefer to enroll ___ brilliant high school students.A intellectuallyB intelligiblyC intelligentlyD intimately18. When a heavy vehicle is ___ in the mud, the driver has to ask for help.A involvedB stuckC interferedD specialized19. A risk or effect may diminish ___, but it may also increase for some reason.A at willB over timeC under wayD so far20. It‘s in your best ____ to quit smoking, for you have some breathing problems.A sakeB benefitC advantageD interestPart II. Cloze―Techno-stress‖----frustration arising from pressure to use new technology----is said to be 21 , reports Maclean‘s magazine of Canada. Studies point to causes that 22 ―the never-ending process of learning how to use new technologies to the 23 of work and home life as a result of 24 like e-mail, call-forwarding and wireless phones.‖ How can you cope? Experts recommend setting 25 . Determine whether using a particular device will really simplify life or merely add new 26 . Count on having to invest time to learn a new technology well enough to realize its full benefits. ― 27 time each day to turn the technology off,‖ and devote time to other things afforded or deserving 28 attention. ―People start the day by making the 29 mistake of opening their e-mail, instead of wo rking to a plan,‖ notes Vancouver productivity expert Dan Stamp. ―The best hour and a half of the day is spent on complete30 .‖21. A descending B narrowing C mounting D widening22. A pass on B range from C deal with D give up23. A confusion B construction C contribution D conduction24. A creations B promotions C productions D innovations25. A laws B boundaries C deadlines D barriers26. A convenience B advantages C flexibility D complexity27. A Put forward B Put across C Put aside D Put up28. A prior B major C senior D superior29. A fragmental B fictional C fractional D fundamental30. A relaxation B entertainment C rubbish D hobbyPart III. Reading ComprehensivePassage OneThe study of genetics has given rise to a profitable new Industry called biotechnology. As the name suggests, it blends biology and modern technology through such techniques as genetic engineering. Some of the new biotech companies, as they are called, specialize in agriculture and are working enthusiastically to patent seeds that give a high yield, that resist disease, drought, and frost, and that reduce the need for hazardous chemicals. If such goals could be achieved, it would be most beneficial. But some have raised concern about genetically engineered crops.―In nature, genetic diversity is created within certain limits,”says the book Genetic Engineering, Food, and Our Environment.―A rose can be crossed with a different kind of rose, but a rose will never cross with a potato…‖ Genetic engineering, on the other hand, usually involves taking genes from one species and inserting them into another in an attempt to transfer adesired property or character. This could mean, for example, selecting a gene which leads to the production of a chemical with antifreeze properties from an arctic fish, and joining it into a potato or strawberry to make it frost-resistant. It is now possible for plants to be engineered with genes taken from bacteria, viruses, insects, animals or even humans.In essence, then, biotechnology allows humans to break the genetic walls that separate species.Like the green revolution, what some call the gene revolution contributes to the problem of genetic uniformity---some say even more so because geneticists can employ techniques such as cloning and tissue culture, processes that produce perfectly identical copies, or clones. Concerns about the erosion of biodiversity, therefore, remain. Genetically altered plants, however, raise new issues, such as the effects that they may have on us and the environment. ―We are flying blindly into a new era of agricultural biotechnology with high hopes, few constraints, and little idea of the potential outcomes,‖ said science writer Jeremy Rifkin.31. According to the author, biotech companies are ______A mostly specialized in agriculture.B those producing seeds of better propertiesC mainly concerned about the genetically engineered crops.D likely to have big returns in their business.32. Now biotech products are made ____.A within the limits of natural genetics .B by violating laws of natural genetics.C without the interference of humans.D safer than those without the use of biotechnology33. In nature, genetic diversity is created ____A by mixing different speciesB within the species itselfC through natural selectionD through selection or contest34.Biotechnoly has made it possible ____A for us to solve the food shortage problem in the world.B for plants to be produced with genes of humans.C for humans to assume the cold-resistant property.D to grow crops with the taste of farm animals.35. According to the author, with the development of biotechnology ____A the species of creatures will be reduced. D we will suffer from fewer and fewer diseases.B our living environment will be better than it is now.C humans will pay for its side effect.36. T he author‘s attitude towards genetic engineering can best be described ____A optimisticB pessimisticC concernedD suspiciousPassage TwoThe practice of capital punishment is as old as government itself. For most of history, it has not been considered controversial. Since ancient times most governments have punished a wide variety of crimes by death and have conducted executions as a routine part of the administration of criminal law. However, in the mid-18th century, social critics in Europe began to emphasize the worth of the individual and to criticize government practices they considered unjust, including capital punishment. The controversy and debate whether government should utilize the death penalty continue today.The first significant movement to abolish the death penalty began during the era known as the Age of Enlightenment. In 1764 Italian jurist and philosopher Cesare Beccaria published An Essay on Crimes and Punishments. Many consider this influential work the leading document in the early campaign capital punishment. Other individuals who campaigned against executions duringthis period include French authors V oltaire and Denis Diderot, British philosophers David Hume and Adam Smith, and political theorist Thomas Paine in the United States.Critics of capital punishment argue that it is cruel and inhumane, while supporters consider it a necessary form of revenge for terrible crimes. Those who advocates the death penalty declare that it is a uniquely effective punishment that prevents crime. However, advocates and opponents of the death penalty dispute the proper interpretation of statistical analyses of its preventing effect. Opponents of capital punishment see the death penalty as a human right issue involving the proper limits of governmental power. In contrast, those who want governments to continue to execute tend to regard capital punishment as an issue of criminal justice policy. Because of these alternative viewpoint, there is a profound difference of opinion not only about what is the right answer on capital punishment, but also about what type of question is being asked when the death penalty becomes a public issue.37. We can learn from the first paragraph that in ancient times _________A death penalty had been carried out before government came into being.B people thought it was right for the government to conduct executions.C death penalty was practiced scarcely in European countries.D many people considered capital punishment unjust and cruel.38. Why was capital punishment questioned in the mid-18th century in Europe?A People began to criticize their government.B The government was unjust in this period.C People began to realize the value of life.D Social critics were very active at that time.39. Italian jurist and philosopher Cesare Beccaria ____A was the first person to question the rightness of death penalty.B was regarded as an important author criticizing capital punishment.C was the first person who emphasized the worth of the individuals.D first raised the theory against capital punishment.40. Critics of capital punishment insist that it ___.A violates human rights regulations.B is an ineffective punishment of the criminalsC is just the revenge for terrible crimes.D involves killing without mercy.41. The advocates and opponents of the death penalty _____A agree that it is a human rights issueB agree that it can prevent crimes.C explain its statistical analyses differentlyD think that they are asked different types of questions.42. The author‘s attitude towards capital punishment can be summarized as _____A supportiveB criticalC neutralD contradictoryPassage ThreeBears mostly live alone, except for mothers and their babies, and males and females during mating season. Bears form temporary groups only in exceptional circumstances, when food is plentiful in a small area. Recent evidence also suggests that giant pandas may form small social groups, perhaps because bamboo is more concentrated than the patchy food resources of other bear species. Other bears may live alone but exist in a social network. A male and female may live in an area partly shared in common----although they tolerate each other, each defends its range from other bears of the same sex. Male young usually leave their mothers to live in other areas, but female young often live in a range that is commonly shared with that of their mother.The key to a bear‘s survival is finding enough food to satisfy the en ergy demands of its largesize. Bears travel over huge territories in search of food, and they remember the details of the landscape they cover. They use their excellent memories to return to locations where they have had success finding food in past years or seasons. Most bears are able to climb trees to chase small animals or gain access to additional plant vegetation. The exceptions are polar bears and large adult brown bears----their heavy weight makes it difficult for them to climb trees.Bears that live in regions with cold winters spend the coldest part of the year asleep in sheltered dens, including brown bears, American and Asiatic black bears, and female polar bears. Pregnant females give birth in the winter in the protected surroundings of these dens. After fattening up during the summer and fall when food is abundant, the bears go into this winter home to conserve energy during the part of the year when food is scarce. Winter sleep differs from hibernation in that a bear is easily aroused from sleep. In addition, a bear‘s body temperature drops only a few degrees in its winter sleep. In contrast, a true hibernator undergoes more extensive changes in bodily functions. For instance, the body temperature of the Arctic ground squirrel drops from 380C to as low as -30C.43. Most bears live alone because _________A they don‘t want to keep a social network.B each bear feeds on different kinds of food.C male and female bears can‘t tolerate each other.D they don‘t want other bears to share th eir food.44.According to the passage, bears of the same sex ____A can get along with each other peacefully.B share their range with each other.C live in an area partly shared in common.D can‘t live peacefully in the same area.45.As is told about bears in the passage, we know that _____A it is easy for bears to find enough food if they can climb trees.B a bear can long remember where it has found food.C all except polar bears are able to climb trees to catch their prey.D all except polar bears and adult brown bears feed on small animals.46. Bears sleep in their sheltered dens in cold winter because ____A their babies need to be born in a cold and protected surrounding.B they need to fatten themselves up in the cold season.C they need to convert their fat into energy in winter.D they can‘t find enough food in the cold season.47. Winter sleep differs from hibernation in that _______A animals in hibernation don‘t wake up easily.B animals in hibernation are aroused regularly for energy supply.C the body temperature of animals in winter sleep doesn‘t change.D animals in winter sleep experience drastic changes in bodily functions.48. The passage is mainly about ___.A the species of bearsB the food category of bearsC the winter sleep of bearsD the behavior of bearsPassage FourThe young man who came to the door--- he was about thirty, perhaps, with a handsome, smiling face---- didn‘t seem to find my lateness offensive, and led me into a larg e room. On one side of the room sat half a dozen women, all in white; they were much occupied with a beautiful baby, who seemed to belong to the youngest of the women. On the other side of the room sat seven or eightmen, young, dressed in dark suits, very much at ease, and very imposing. The sunlight came into the room with the peacefulness that one remembers from rooms in one‘s early childhood--- a sunlight encountered later only in one‘s dreams. I remember being astounded by the quietness, the ease, the peace , and the taste. I was introduced, they greeted me with a genuine cordiality and respect ---and the respect increased my fright, for it meant that they expected something of me that I knew in my heart, for their sakes, I could not give ---and we sat down. Elijah Muhammad was not in the room. Conversation was slow , but not as stiff as I had feared it would be. They kept it going, for I simply did not know which subjects I could acceptably bring up. They knew more about me and read more of what I had written, than I had expected , and I wondered what they made of it all, what they took my usefulness to be. The women were carrying on their own conversations, in low tones; I gathered that they were not expected to take part in male conversations. A few women kept coming in and out of the room, apparently making preparations for dinner. We, the men, did not plunge deeply into any subject, for, clearly, we were all waiting for the appearance of Elijah. Presently, the men, one by one, left the room and returned. Then I was asked if I would like to wash, and I, too, walked down the hall to the bathroom. Shortly after I came back, we stood up, and Elijah entered. I don‘t know what I had expected to see. I had read some of his speeches, and had heard fragments of others on the radio and on television, so I associated him with strength. But, no ----the man who came into the room was small and slender, really very delicately put together, with a thin face, large warm eyes, and a most winning smile. Something came into the room with him ---- his worshipers‘ joy at seeing him, his joy at seeing them. It was the kind of encounter one watches with a smile simply because it is so rare that people enjoy one another.49.Which of the following is the best alternative word f or ―imposing‖?A EnthusiasticB HostileC ImpressiveD Anxious50. Which word best describes the atmosphere in the room?A TranquilB SolemnC ChaoticD Stressful51.How did the author feel when he was greeted with respect?A DelightedB AstonishedC EmbarrassedD Scared52. Which of the following statements is true about the author?A He talked little.B He was puzzledC He enjoyed the conversationD He got more respect than he deserved.53. The man didn‘t get deeply involved in any subject because they ____A had little knowledgeB didn‘t know one another well.C wanted to relax themselvesD awaited the arrival of someone important54. What can we learn about Elijah?A He was admired by others.B He was very handsome.C He was a man with determinationD He was happy to give speeches.Passage FiveSingapore‘s Mixed Reality Lab is working on new ways of interacting with computers, including wearable devices and virtual war room that will allow officials to work together online as if they were all in one place. Its director is a spiky-haired Australian, a postmodern match for the fictional British agent James Bond‘s tool man, Q.It is funded by the Defense Science & Technology Agency, which controls half the $ 5 billion defense budget, and sponsors hundreds of research projects every year. The agency came to worldwide attention last year when it took justone day to customize a thermal scanner in order to detect travelers with high fever, helping to stem the spread of SARS.DSTA is now working on a range of projects that are attracting attention in both the commercial and military worlds. It devised an air-conditioning system that harnesses melting ice and cool seawater to conserve electricity at the new Changi Naval Base, and could have broad civilian applications.Singapore can easily afford Western hardware, but off-the-shelf products are often unsuitable for the tropical conditions in Southeast Asia. For example, the DSTA is funding development of an anti-chemical-weapons suit that works not as a shield, but as a sort of weapon. The Singapore garments, made of a revolutionary plastic-like material that is much lighter and cooler than traditional fabrics, actually degrade suspect substance on contact.Much of the agency‘s work is geared toward helping this resource-poor city-state overcome its natural limitations, says its director R&D, William Lau Yue Khei. Conserving manpower is one of the agency‘s most critical assignmen ts, because Singapore is a nation of 5 million people dwarfed by larger neighbors, including Indonesia and Malaysia. Right now, the biggest DSTA project is computerizing a stealth warship so that it can run on half the usual crew. Making equipment lighter is a particular agency specialty, because the universal military rule of thumb is that a soldier should carry no more than one third his body weight, and that seems that smaller Singaporean soldiers should carry no more than 24 kilos, or 20 percent less than Europeans, says DSTA project manager Choo Hui Weing. One such program: the Advanced Combat Man System, has produced a lightweight handguard that controls an integrated laser range finder, digital compass and a targeting camera. Top that, Q.55. It can be inferred from the passage that Q is probably________A a mechanic in James Bond‘s garage.B a fictional Australian with spiky hair.C a director of the Advanced Combat Man SystemD An imaginary engineer who invents advanced equipment.56. Which of the following statements concerning DSTA true?A It became world-known for its high efficiency in preventing the SARS spread.B It funds numerous research programs, including Mixed Reality lab.C It devised an air-conditioning system now widely used in households.D It takes credit for conserving electricity at the new Changi Naval Base.57. The suit described in the third paragraph can be used as a sort of weapon mainly because ___A it is made of a new material resembling plastics.B it can reduce harmful effects of chemicals on it.C it has been adapted to the tropical weather there.D its light weight allows soldiers to carry more equipment.58. Which of the following is Not mentioned as a disadvantage of Singapore?A Smaller soldiersB Smaller populationC Limited defense budgetD Limited natural resources59. The Advance Combat Man System is mentioned in the last paragraph mainly to show ____A what DSTA has done to meet the country‘s special needs.B how sophisticated the equipments designed by DSTA can be.C why it is difficult for Q to compete with CHoo Hui Weing .D how Singapore‘s technology is superior to that of the British.60. The main purpose of the passage is to ____A analyze Singapore‘s defense system.B summarize the contributions of DSTA.C introduce the technical advantages of a small country.D describe the roles and achievements of a government agency.Paper Two Part IV TranslationSection AQuitting smoking is more of a matter of willpower than of individual choice, for smoking is widely recognized as addictive. Although counseling and medication can increase the odds that a smoker quits permanently, the best way to avoid dilemmas is never to take up smoking to begin with.The irreversible effects of cigarette smoking vary in intensity and are related both to the amount and duration of exposure and the age at which the person is initially exposed. This report challenges the notion that a few years of exposure to smoking will have no lasting harmful consequences. We hope to discourage this prevalent but vital habit and suggest that tobacco-related health effects decline substantially as time away from smoking increases. Section B人们越来越意识到开发环保型产品的重要性. 为实现长期可持续发展, 发达国家应不惜代价减少温室气体的排放. 如果目前全球变暖的速度保持不变, 东京和伦敦等大城市从地球上消失的可能性将是20年前的10倍.Part V Writingwrite a compositions of no less than 150 words under the title of “Knowledge from books and knowledge from experience” . Your composit ion should be based on the following outline:1Compare and contrast knowledge gained from experience with knowledge gained from books. 2．Explain which source is more important?Answer1-10 CDABD, ACCAB, 11-20 DBDAB, DABBD 21-30 CBADB, DCADC31-40 DBBBA, CBCBD, 41-50 CCDDB, DADCA 51-60 DADAD, CBCABTranslation : Section BThere is a growing realization/awareness that developing environment-protecting products really counts. To fulfil the long-term and substantial development, developed countries should at all costs decrese the emission of greenhouse gases. If the speed of global warming nowadays continues, the probability of disappearance from the earth to such big cities as Tokyo and London will be 10 times as fast as that of 20 years ago.2005年6月研究生学位英统考试题Paper OnePart I Listening Comprehension（25 minutes, 20 points ）Section A (1 point each)1.A: To ask his boss for leave. B: To work in his place.C To meet his friend at the airport.D To cover his absence from his boss.2. A; He doesn’t want to go to the show, as he is not interested in it.B: He is not free to go to the fashion show with the woman.C He can’t go with the woman, as he has to finish his paper.D he can’t go with the woman, as he has a pile of paperwork to do.3. A: He has been pretty busy. B: He has been mad.。
第四讲 基因识别
系统发育树重建分析步骤
多序列比对（自动比对，手工比对） 建立取代模型（建树方法） 建立进化树 进化树评估
The Source Below Come From:
Bioinformatics Sequence and Genome Analysis
❖ 关键问题是如何提高一个识别算法的敏 感性（sensitivity，Sn）和特异性 （specificity，Sp）。
3、基因识别的主要方法
两大类识别方法： ❖ 从头算方法（或基于统计的方法）
根据蛋白质编码基因的一般性质和特征进行识别， 通过统计值区分外显子、内含子及基因间区域
❖ 基于同源序列比较的方法
以上两个概念代表了两个不同的进化事件 用于分子进化分析中的序列必须是直系同源 的，才能真实反映进化过程。
趋同进化的基因
(genes have converged function by separate evolutionary paths)
异源基因或水平转移基因
(xenologous or horizontally transferred genes)
内容提要
❖ 分子进化分析介绍 ❖ 系统发育树重建方法 ❖ Phylip软件包在分子进化分析中的应用
分子进化研究的目的
从物种的一些分子特性出发，从而了 解物种之间的生物系统发生的关系。
蛋白和核酸序列 通过序列同源性的比较进而了解基因的进 化以及生物系统发生的内在规律。
系统发育树是什么？
对一组实际对象的世系关系的描述（如基 因，物种等）。
1.Fitch-Margoliash Method（FM法） 2. Neighbor-Joining Method (NJ法/邻接法) 3. Neighbors Relaton Method(邻居关系法) 4.Unweighted Pair Group Method (UPGMA法)
05-Molecular Phylogeny(生物信息学国外教程2010版)
Fig. 7.3 Page 220
Historical background: insulin
By the 1950s, it became clear that amino acid substitutions occur nonrandomly. For example, Sanger and colleagues noted that most amino acid changes in the insulin A chain are restricted to a disulfide loop region. Such differences are called “neutral” changes (Kimura, 1968; Jukes and Cantor, 1969). Subsequent studies at the DNA level showed that rate of nucleotide (and of amino acid) substitution is about sixto ten-fold higher in the C peptide, relative to the A and B chains.
To Darwin, the struggle for existence induces a natural selection. Offspring are dissimilar from their parents (that is, variability exists), and individuals that are more fit for a given environment are selected for. In this way, over long periods of time, species evolve. Groups of organisms change over time so that descendants differ structurally and functionally from their ancestors.
最新TPO31阅读文本答案及译文
Geographic isolation also can proceed slowly, over great spans of time. We find evidence of such extended events in the fossil record, which affords glimpses into the breakup of formerly continuous environments. For example, during past ice ages, glaciers advanced down through North America and Europe and gradually cut off parts of populations from one another. When the glacier retreated, the separated populations of plants and animals came into contact again. Some groups that had descended from the same parent population were no longer reproductively compatible — they had evolved into separate species. In other groups, however, genetic divergences had not proceeded so far, and the descendants could still interbreed — for them, reproductive isolation was not completed, and so speciation had not occurred.
罡哥GMAT 阅读
2013年4月25日逻辑冲刺课讲稿Reading ComprehensionACarotenoids, a family of natural pigments, form an important art of the colorful signals used by many animals. Animals acquire carotenoids either directly (from the plants and algae that produce them) or indirectly (by eating insects) and store them in a variety of tissues. Studies of several animal species have shown that when choosing mates, females prefer males with brighter carotenoid-based coloration. Owens and Olson hypothesize that the presence of carotenoids, as signaled by coloration, would be meaningful in the context of mate selection if carotenoids were either rare or required for health. The conventional view is that carotenoids are meaningful because they are rare: healthier males can forage for more of the pigments than can their inferior counterparts. Although this may be true, there is growing evidence that carotenoids are meaningful also because they are required: they are used by the immune system and for detoxification processes that are important for maintaining health. It may be that males can use scarce carotenoids either for immune defense and detoxification or for attracting females. Males that are more susceptible to disease and parasites will have to use their carotenoids to boost their immune systems, whereas males that are genetically resistant will use fewer carotenoids for fighting disease and will advertise this by using the pigments for flashy display instead.rmation in the passage suggests that which of the following is true ofcarotenoids that a male animal uses for detoxification processes?2013年4月25日逻辑冲刺课讲稿2.The passage suggests that relatively bright carotenoid-based coloration is asignal of which of the following characteristics in males of certain animal species?3.According to the "conventional view" referred to in the highlighted text of thepassage, brighter carotenoid-based coloration in certain species suggests that an individual2013年4月25日逻辑冲刺课讲稿BThe dry mountain ranges of the Western united states contain rocks dating back 440 to 510 million years, to the Ordovician period, and teeming with evidence of tropical marine life. This rock record provides clues about one of the most significant radiations (periods when existing life-forms gave rise to variations that would eventually) evolve into entirely new species) in the history of marine invertebrates. During this radiation the number of marine biological families increased greatly, and these families included species that would dominate the marine ecosystems of the area for the next 215 million years. Although the radiation spanned tens of millions of years, major changes in many species occurred during a geologically short time span within the radiation and, furthermore, appear to have occurred worldwide, suggesting that external events were major factors in the radiation. And , in fact, there is evidence of major ecological and geological changes during this period: the sea level dropped drastically and mountain ranges were formed, in this instance, rather than leading to large-scale extinctions, these kinds of environmental changes may have resulted in an enriched pattem of habitats and nutrients, which in turn gave rise to the Ordovician radiation. However, the actual relationship between these environmental factors and the diversification of life forms is not yet fully understood.1、The passage is primarily concerned with2013年4月25日逻辑冲刺课讲稿2、Which of the following can be inferred from the passage regarding the geologic changes that occurred during Ordovician period?3、Which of the following best describes the function of last sentence of the passage ?C2013年4月25日逻辑冲刺课讲稿A key decision required of advertising managers is whether a "hard-sell" or "soft-sell" strategy is appropriate for a specific target market. The hard-sell approach involves the use of direct, forceful claims regarding the benefits of the advertised brand over competitors' offerings. In contrast, the soft-sell approach involves the use of advertising claims that imply superiority more subtlyOne positive aspect of the hard-sell approach is its use of very simple and straightforward product claims presented claims presented as explicit conclusions, with little room for confusion regarding the advertiser's message. However, some consumers may resent being told what to believe and some may distrust the message. Resentment and distrust often lead to counter argumentation and to boomerang effects where consumers come to believe conclusions diametrically opposed to conclusions endorsed in advertising claims, By contrast, the risk of boomerang erects is greatly reduced with soft-sell approaches. One way to implement the soft-sell approach is to provide information that implies the main conclusions the advertiser wants the consumer to draw, but leave the conclusions themselves unstated. Because consumers are invited to make up their own minds, implicit conclusions reduce the risk of resentment ,distrust, and counter argumentation.Recent research on consumer memory and judgment suggests another advantage of implicit conclusions. Beliefs or conclusions that are self-generated are more accessible from memory than beliefs from conclusions provided explicitly by other individuals, and thus have a greater impact on judgment and decision making. Moreover, self-generated beliefs are often perceived as more accurate and valid than the beliefs of others, because other individuals may be perceived as less less knowledgeable, or may be perceived as manipulative or deliberately misleading. Despite these advantages, implicit conclusions may mot always be more effective than explicit Conclusions. One risk is that some consumers may fail to draw their own conclusions and thus miss the point of the message. .Inferential activity is likely only when consumers are motivated and able to engage in effortful cognitive processes. Another risk is that some conSummers may draw conclusions Other than2013年4月25日逻辑冲刺课讲稿the one intended ,Even if inferential activity is likely there is no guarantee that consumers will follow the path provided by the advertiser. Finally, a third risk is that consumers may infer the intended conclusion but question the validity of their inference.1、The primary purpose of the passage is to2、it can be inferred from the passage that the research mentioned in thehighlighted text supports which of the following statements ?3、It can be inferred from the passage that one situation in which the boomerangeffect often occurs is when consumersdiscussed in the last paragraph if they were able to provideD2013年4月25日逻辑冲刺课讲稿Over the last 150 years, large stretches of salmon habitat have been eliminated by human activity: mining, livestock grazing, timber harvesting, and agriculture as well as recreational and urban development. The numerical effect is obvious: there are fewer salmon in degraded regions than in pristine ones; however, habitat loss also has the potential to reduce genetic diversity. This is most evident in cases where it results in the extinction of entire salmon populations. Indeed, most analysts believe that some kind of environmental degradation underlies the demise of many extinct salmon populations. Although some rivers have been recolonized, the unique genes of the original populations have been lost.Large-scale disturbances in one locale also have the potential to alter the genetic structure of populations in neighboring areas, even if those areas have pristine habitats. Why? Although the homing instinct of salmon to their natal stream is strong, a fraction of the fish returning from the sea(rarely more than 15 percent) stray and spawn in nearby streams. Low levels of straying are crucial, since the process provides a source of novel genes and a mechanism by which a location can be repopulated should the fish there disappear. Yet high rates of straying can be problematic because misdirected fish may interbreed with the existing stock to such a degree that any local adaptations that are present become diluted. Straying rates remain relatively low when environmental conditions are stable, but can increase dramatically when streams suffer severe disturbance. The 1980 volcanic eruption of Mount Saint Helens, for example, sent mud and debris into several tributaries of the Columbia River. For the next couple of years, steelhead trout (a species included among the salmonids) returning from the sea to spawn were forced to find alternative streams. As a consequence, their rates of straying, initially 16 percent, rose to more than 40 percent overall.Although no one has quantified changes in the rate of straying as a result of the disturbances caused by humans, there is no reason to suspect that the effect would be qualitatively different than what was seen in the aftermath of the Mount Saint Helens eruption. Such a dramatic increase in straying from damaged areas to more1.The primary purpose of the passage is toreturn to their natal streams in order to spawn provides a mechanism by whichon salmon populations?highlighted text) most likely in order to1、Which of the following most accurately describes the organization of the passage?Earth's mantle 2.5 to 4 billion years ago?3、Which of the following most accurately states the main point of the passage?FWhile acknowledging that there are greater employment opportunities for Latin American women in cities than in the countryside, social science theorists have2013年4月25日逻辑冲刺课讲稿continued to argue that urban migration has unequivocally hurt women's status. However, the effects of migration are more complex than these theorists presume. For example, effects can vary depending on women's financial condition and social class. Brazilian women in the lowest socioeconomic class have relatively greater job opportunities and job security in cities than do men of the same class, although there is no compelling evidence that for these women the move to the city is a move out of poverty. Thus, these women may improve their status in relation to men but at the same time may experience no improvement in their economic standing.In addition, working outside the home, which is more common in urban than in rural areas, helps women in the lowest socioeconomic class make contacts to extend exchange networks—the flow of gifts, loans, or child care from those who currently have access to resources to those who do not. Moreover, poor women working in urban areas actively seek to cultivate long-term employer employee relations. When an emergency arises that requires greater resources than an exchange network can provide, these women often appeal for and receive aid from their wealthy employers. However, the structure of many poor women's work—often a labor force of one in an employer's home—makes it difficult for them to organize to improve their economic conditions in general.Not surprisingly, then, Latin American women in the lowest socioeconomic class differ in their opinions about the effects of urban migration on their lives. Some find urban living, with access to electricity and running water, an improvement and would never return to the countryside. Others, disliking the overcrowding and crime, would return to the countryside if there were work opportunities for them there. Thus, urban life has had both negative and positive impacts on women's lives. In general, urban migration has not provided economic prosperity or upward mobility for women in the lowest socioeconomic class, despite their intelligent and energetic utilization of the resources available to them.1、In the first paragraph, the author refers to the experiences of Brazilian womenmost probably in order to2、Which of the following best summarizes the main point of the passage?employment for Latin American women in the lowest socioeconomic group? influenced by the2013年4月25日逻辑冲刺课讲稿difference in the effects of urban migration on men and women of the same social and economic classG(The following was excerpted from material written in 1988.)2013年4月25日逻辑冲刺课讲稿For over a decade the most common policy advice given to developing countries by international development institutions has been to copy the export-oriented path of the newly industrializing countries, the celebrated NIC's. These economies—Brazil, Hong Kong, Mexico, Singapore, South Korea, and Taiwan burst into the world manufacturing market in the late 1960's and the 1970's; by 1978 these six economies, along with India, enjoyed unequaled growth rates for gross national product and for exports, with exports accounting for 70 percent of the developing world's manufactured exports. It was, therefore, not surprising that dozens of other countries attempted to follow their model, yet no countries—with the possible exceptions of Malaysia and Thailand—have even approached their success. In "No More NIC's," Robin Broad and John Cavanagh search for the reasons behind these failures, identifying far-reaching changes in the global economy—from synthetic substitutes for commodity exports to unsustainable levels of foreign debt—as responsible for a glut economy offering little room for new entrants. Despite these changes, the authors maintain, the World Bank and the International Monetary Fund—the foremost international development institutions—have continued to promote the NIC path as the way for heavily indebted developing countries to proceed. And yet the futility of this approach should, according to the authors, be all too apparent so many years into a period of reduced growth in world markets.1.Given the information in the passage, which of the following is a true statementabout the NIC's?2.The author of the passage most clearly implies that Broad and Cavanagh disagree with the World Bank and the International Monetary Fund about which of the following?The ways in which the global economy has changed in recent yearsThe causes of the unsustainable levels of foreign debt that the developing countries have incurred in recent yearsThe level of foreign debt that should be maintained by developing countriesThe degree to which international development institutions should monitor the growth of developing countriesThe degree to which heavily indebted developing countries should emphasize exports in their overall economic strategy3.The author mentions Malaysia and Thailand in order toHHistorians who study European women of the Renaissance try to measure2013年4月25日逻辑冲刺课讲稿"independence," "options," and other indicators of the degree to which the expression of women's individuality was either permitted or suppressed.Influenced by Western individualism, these historians define a peculiar form of personhood: an innately bounded unit, autonomous and standing apart from both nature and society. An anthropologist, however, would contend that a person can be conceived in ways other than as an "individual." In many societies a person's identity is not intrinsically unique and self-contained but instead is defined within a complex web of social relationships.In her study of the fifteenth-century Florentine widow Alessandra Strozzi, a historian who specializes in European women of the Renaissance attributes individual intention and authorship of actions to her subject. This historian assumes that Alessandra had goals and interests different from those of her sons, yet much of the historian's own research reveals that Alessandra acted primarily as a champion of her sons' interests, taking their goals as her own. Thus Alessandra conforms more closely to the anthropologist's notion that personal motivation is embedded in a social context. Indeed, one could argue that Alessandra did not distinguish her personhood from that of her sons. In Renaissance Europe the boundaries of the conceptual self were not always firm and closed and did not necessarily coincide with the boundaries of the bodily self.1.In the first paragraph, the author of the passage mentions a contention that wouldbe made by an anthropologist most likely in order to2.According to the passage, much of the research on Alessandra Strozzi done bythe historian mentioned in the second paragraph (the highlighted text) supports which of the following conclusions?3.The passage suggests that the historian mentioned in the second paragraph (thehighlighted text) would be most likely to agree with which of the following assertions regarding Alessandra Strozzi?ISocial learning in animals is said to occur when direct or indirect social2013年4月25日逻辑冲刺课讲稿interaction facilitates the acquisition of a novel behavior. It usually takes the form of an experienced animal (the demonstrator) performing a behavior such that the naive animal (the observer) subsequently expresses the same behavior sooner, or more completely, than it would have otherwise. One example of social learning is the acquisition of preferences for novel foods.Some experiments have suggested that among mammals, social learning facilitates the identification of beneficial food items, but that among birds, social learning helps animals avoid toxic substances. For example, one study showed that when red-wing blackbirds observed others consuming a colored food or a food in a distinctly marked container and then becoming ill, they subsequently avoided food associated with that color or container. Another experiment showed that house sparrows consumed less red food after they observed others eating red food that was treated so as to be noxious. Studies on nonavian species have not produced similar results, leading researchers to speculate that avian social learning may be fundamentally different from that of mammals.But Sherwin's recent experiments with domestic hens do not support the notion that avian social learning necessarily facilitates aversion to novel foods that are noxious or toxic. Even when demonstrator hens reacted with obvious disgust to a specific food, via vigorous head shaking and bill wiping, there was no evidence that observers subsequently avoided eating that food. Sherwin's research team speculated that ecological or social constraints during the evolution of this species might have resulted in there being little benefit from the social learning of unpalatability, for instance, selective pressures for this mode of learning would be reduced if the birds rarely encountered noxious or toxic food or rarely interacted after eating such food, or if the consequences of ingestion were minimal. In a related experiment, the same researchers showed that if observer hens watched demonstrator hens react favorably to food of a particular color, then observer hens ate more food of that color than they ate of food of other colors. These results confirmed that avian species can develop preferences for palatable food through social learning.2013年4月25日逻辑冲刺课讲稿2、According to the passage, which of the following is true of the experimentson domestic hens conducted by Sherwin's research team?3、It can be inferred that the author of the passage would be most likely to agree with which of the following statements regarding the results of the recent experiments conducted by Sherwin's research team?JScientists studying the physiology of dinosaurs have long debated whether2013年4月25日逻辑冲刺课讲稿dinosaurs were warm- or cold-blooded. Those who suspect they were warm blooded point out that dinosaur bone is generally fibro-lamellar in nature; because fibro-lamellar bone is formed quickly, the bone fibrils, or filaments, are laid down haphazardly. Consistent with their rapid growth rate, warm-blooded animals, such as birds and mammals, tend to produce fibro-lamellar bone, whereas reptiles, which are slow growing and cold-blooded, generally produce bone in which fibrils are laid down parallel to each other. Moreover, like the bone of birds and mammals, dinosaur bone tends to be highly vascularized, or filled with blood (20) vessels. These characteristics, first recognized in the 1930's, were documented in the 1960's by de Ricqlès, who found highly vascular ized, fibro-lamellar bone in several groups of dinosaurs. In the 1970's, Bakker cited these characteristics as evidence for the warm-bloodedness of dinosaurs. Although de Ricqlès urged caution, arguing for an intermediate type of dinosaur physiology, a generation of paleontologists has come to believe that dinosaur bone is mammalian like.In the 1980's, however, Bakker's contention began to be questioned, as a number of scientists found growth rings in the bones of various dinosaurs that are much like those in modern reptiles. Bone growth in reptiles is periodic in nature, producing a series of concentric rings in the bone, not unlike the growth rings of a tree. Recently, Chinsamy investigated the bones of two dinosaurs from the early Jurassic period (208-187 million years ago), and found that these bones also had growth rings; however, they were also partially fibro-lamellar in nature. Chinsamy's work raises a question central to the debate over dinosaur physiology: did dinosaurs form fibro-lamellar bone because of an innately high metabolic rate associated with warm-bloodedness or because of periods of unusually fast growth that occurred under favorable environmental conditions? (Although modern reptiles generally do not form fibro-lamellar bone, juvenile crocodiles raised under optimal environmental conditions do.) This question remains unanswered; indeed, taking all the evidence into account, one cannot make a definitive statement about dinosaur physiology on the basis of dinosaur bone. It may be that dinosaurs had an intermediate pattern of2013年4月25日逻辑冲刺课讲稿bone structure because their physiology was neither typically reptilian, mammalian, nor avian.1、According to the passage, the discovery of growth rings in the bones of certaindinosaurs served to undermine which of the following claims?2、The author of the passage mentions bone growth patterns in juvenile crocodiles most likely in order toKAlthough recent censure of corporate boards of directors as "passive" and2013年4月25日逻辑冲刺课讲稿"supine" may be excessive, those who criticize board performance have plenty of substantive ammunition. Too many corporate boards fail in their two crucial responsibilities of overseeing long-term company strategy and of selecting. evaluating, and determining appropriate. compensation of top management. Attimes, despite disappointing corporate performance, compensation of chief executive officers reaches indefensibly high levels, Nevertheless, suggestions that the government should legislate board reform are premature. There are ample opportunities for boards themselves to improve corporate performance.Most corporate boards' compensation committees focus primarily on peer-group comparisons. They are content if the pay of top executives approximates that of the executives of competing firms with comparable short-term earnings or even that of executives of competing firms of comparable size. However, mimicking the compensation policy of competitors for the sake of parity means neglecting the value of compensation as a means of stressing long-term performance. By tacitly detaching executive compensation policy from long-term performance, committees harm their companies and the economy as a whole. The committees must develop incentive compensation policies to emphasize long-term performance. For example a board's compensation committee can, by carefully proportioning straight salary and such short-term and long-term incentives as stock options, encourage top management to pursue a responsible strategy.their executives?2013年4月25日逻辑冲刺课讲稿requiring that corporate boards undergo reform?3.Which of the following best describes the organization of the passage?LIn colonial Connecticut between 1670 and 1719, women participated in one of2013年4月25日逻辑冲刺课讲稿every six civil cases, the vast majority of which were debt-related. Women's participation dropped to one in ten cases after 1719, and to one in twenty by the 1770's. however, as Cornelia Hughes Dayton notes in Women Before the Bar: Gender, Law, and Society in Connecticut, 1639-1789, these statistics are somewhat deceptive: in fact, both the absolute numbers and the percentage of adult women participating in civil cases grew steadily throughout the eighteenth century, but the legal activity of men also increased dramatically, and at a much faster rate. Single, married, and widowed women continued to pursue their own and their husbands' debtors through legal action much as they had done in the previous century, but despite this continuity, their place in the legal system shifted dramatically. Men's commercial interests and credit networks became increasingly far-flung, owing in part to the ability of creditors to buy and sell promissory notes (legal promises to pay debts). At the same time, women's networks of credit and debt remained primarily local and personal. Dayton contends that, although still performing crucial economic services in their communities—services that contributed to the commercialization of the colonial economy—women remained for the most part outside the new economic and legal culture of the eighteenth century.1.The passage is primarily concerned with2.According to the passage, compared with women in eighteenth-centuryConnecticut, men were3.The passage suggests that which of the following best compares the economicconcerns of women with those of men toward the close of the eighteenth Century in colonial Connecticut?MIn 1975 Chinese survey teams remeasured Mount Everest, the highest of the2013年4月25日逻辑冲刺课讲稿Himalayan mountains. Like the British in 1852, they used the age-old technique of "carrying in" sea level: surveyors marched inland from the coast for thousands of miles, stopping at increments of as little as a few feet to measure their elevation, and marking each increment with two poles. To measure the difference in elevation between poles, surveyors used an optical level—a telescope on a level base—placed halfway between the poles. They sighted each pole, reading off measurements that were then used to calculate the change in eleva tion over each increment. In sight of the peaks the used theodolites—telescopes for measuring vertical and horizontal angles—to determine the elevation of the summit.The Chinese, however, made efforts to correct for the errors that had plagued the British. One source of error is refraction, the bending of light beams as they pass through air layers of different temperature and pressure. Because light traveling. down from a summit passes through many such layers, a surveyor could sight a mirage rather than the peak itself. To reduce refraction errors, the Chinese team carried in sea level to within five to twelve miles of Everest's summit, decreasing the amount of air that light passed through on its way to their theodolites. The Chinese also launched weather balloons near their theodolites to measure atmospheric temperature and pressure changes to better estimate refraction errors. Another hurdle is the peak's shape. When surveyors sight the summit. there is a risk they might not all measure the same point. In 1975 the Chinese installed the first survey beacon on Everest, a red reflector visible through a theodolite for ten miles, as a reference point. One more source of error is the unevenness of sea level. The British assumed that carrying in sea level would extend an imaginary line from the shore along Earth's curve to a point beneath the Himalaya. In reality, sea level varies according to the irregular interior of the planet. The Chinese used a gravity meter to correct for local deviations in sea level.1.It can be inferred from the passage that refraction would be most likely to causeerrors in measurements of a mountain's elevation under which of the following。
高中生物必修二第一章
高中生物必修二第一章**高中生物必修二第一章：遗传与进化****Genetics and Evolution**Genetics, as a branch of biology, focuses on the study of inheritance and variation of traits in organisms. It delves into the mechanisms underlying the transmission of genetic information from one generation to the next.遗传学作为生物学的一个分支，主要研究生物体中性状的遗传和变异，深入探索遗传信息从一代传递到另一代的机制。
Chapter one of the compulsory high school biology textbook II introduces the fundamental concepts of genetics, starting with the discovery of Mendel's laws of inheritance. Mendel's experiments with peas revolutionized our understanding of how traits are passed down from parents to offspring.高中生物必修二第一章介绍了遗传学的基本概念，从孟德尔遗传定律的发现开始。
孟德尔的豌豆实验彻底改变了我们对性状如何从父母传递给后代的理解。
The chapter goes on to explain the basic structure and function of DNA, the carrier of genetic information. DNA's double helix structure, discovered by Watson and Crick, provides a stable platform for the storage and replication of genetic material.接着，这一章解释了遗传信息的载体——DNA的基本结构和功能。
人民大2023农林国际学术交流英语 PPTUnit 1 Gene Editing
G__M5O__
It is a plant, animal, microorganism or other organisms whose genetic makeup has been modified in a laboratory using genetic engineering or transgenic technology.
2. Can you arrange them in chronological order?
B-C-A
Part I History of Gene Editing
Timeline Method and Technique selective breeding discovery of DNA
Detailed Information It can strengthen ____u_s_e__f1u_l_t_r_a_i_t_s___ in plants and animals, but never truly understand ___h_o2w___i_t. worked
Part II The Working Principles of CRISPR-Cas9
Can you retell the working principles of CRISPR after watching the video clip?
Part II The Working Principles of CRISPR-Cas9
This creates combinations of plant, animal, bacterial and virus genes that do not occur in nature or through traditional crossbreeding methods.
[农业]基因树冲突与系统发育基因组学研究
![[农业]基因树冲突与系统发育基因组学研究](https://img.taocdn.com/s3/m/44e4901a6d85ec3a87c24028915f804d2b1687bd.png)
植物分类学报 46 (6): 795–807 (2008) doi: 10.3724/SP.J.1002.2008.08081 Journal of Systematics and Evolution (formerly Acta Phytotaxonomica Sinica) 基因树冲突与系统发育基因组学研究邹新慧 葛颂*(系统与进化植物学国家重点实验室, 中国科学院植物研究所北京 100093)Conflicting gene trees and phylogenomicsXin-Hui ZOU Song GE*(State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China) Abstract With more and more sequence data available, it has been a widespread practice to apply multiple genes to reconstruct phylogenies at different hierarchical levels. The phenomenon of conflicting gene trees has accordingly become a remarkable and difficult problem. It is increasingly understood that the difference between gene tree and species tree and the causes behind should be fully appreciated in molecular phylogenetic studies. In this paper, we have explored the major causes resulting in conflicting gene trees, including stochastic errors, systematic errors and biological factors. We also introduced a newly developed discipline, phylogenomics, and demonstrated its power and great potential in resolving difficult phylogenetic problems using our recent phyloge-nomic study of Oryza as an example. Furthermore, we discussed some strategies and approaches in elucidating conflicting gene trees and provided some suggestions and recommendations for molecular phylogenetic studies using multiple genes.Key words conflicting gene trees, gene tree, molecular phylogenetics, phylogenomics, species tree.摘要随着越来越多的基因序列被运用于系统发育重建中, 随之产生的基因树冲突已成为分子系统发育研究中日益突出的问题。
森林进化论作文素材摘抄
森林进化论作文素材摘抄英文回答：Forest Evolution: An Essay on the Resilience and Adaptation of Ecosystems.Forests, with their intricate tapestry of life, have borne witness to eons of evolutionary change. Over millions of years, these vast and dynamic ecosystems have adapted to a myriad of environmental challenges, shaping the planet's geography and supporting countless species. The study of forest evolution provides valuable insights into the resilience and plasticity of life on Earth.One key factor driving forest evolution is environmental selection pressures. As climates fluctuate and disturbances occur, forests must adapt to survive. For example, in regions prone to wildfires, tree species have evolved thick bark and deep roots to resist extreme heat and flames. In areas with high rainfall, forests havedeveloped dense canopies to intercept and disperse water, preventing soil erosion and flooding.Another important aspect of forest evolution is coevolution. Trees and other organisms within forests form complex relationships that influence their mutual adaptation. Mycorrhizal fungi, for instance, establish symbiotic associations with tree roots, providing essential nutrients in exchange for carbohydrates. This mutually beneficial relationship has been instrumental in the diversification of both tree species and fungal species.Furthermore, genetic diversity plays a crucial role in forest resilience. Populations with high genetic diversity are more likely to possess individuals with adaptive traits that can withstand environmental changes. In forests, genetic diversity is maintained through processes such as gene flow, migration, and random mutations.Additionally, disturbances act as a catalyst for forest evolution. While disturbances such as fires, storms, and insect outbreaks can cause immediate damage, they alsocreate opportunities for new species to colonize and establish themselves. These disturbances can alter the composition and structure of forests, fostering diversity and resilience.Finally, human activities have had a significant impact on forest evolution. Deforestation, fragmentation, and climate change have altered the distribution and composition of forests worldwide. Understanding the consequences of human activities on forest evolution is essential for developing effective conservation strategies.中文回答：森林进化论，生态系统适应与恢复力的探讨。
演化后的生物,一小段作文
演化后的生物,一小段作文英文回答：Evolution has played a significant role in shaping the diverse range of organisms that inhabit our planet today. Through the process of natural selection, species have adapted and changed over time to better survive and reproduce in their environments. This has resulted in the emergence of new species and the extinction of others.One example of a species that has evolved is the giraffe. Over time, giraffes have developed long necks in order to reach leaves on tall trees for food. This adaptation has allowed them to thrive in their habitat and avoid competition with other herbivores. Another example is the peppered moth, which evolved dark coloration during the Industrial Revolution to blend in with the soot-covered trees, providing them with protection from predators.Evolution is not limited to physical characteristics,but also includes behavioral changes. For instance, birds have developed complex mating rituals and songs to attract mates. These behaviors have evolved over time and arecrucial for reproductive success.In addition to adaptation, evolution also involves the process of speciation. This occurs when a population of organisms becomes isolated from others of the same species and undergoes genetic changes that lead to the formation of a new species. This can happen through geographic isolation, where physical barriers such as mountains or bodies ofwater prevent gene flow, or through reproductive isolation, where individuals within a population are no longer able to successfully mate with each other.Evolution is an ongoing process, and organisms continue to evolve in response to changing environments andselective pressures. This can be seen in the development of antibiotic resistance in bacteria, where the overuse of antibiotics has led to the survival and reproduction of resistant strains.中文回答：进化在塑造我们今天星球上各种多样的生物方面起着重要作用。
树木的繁衍英文作文
树木的繁衍英文作文英文：As a tree, my main goal in life is to reproduce and ensure the survival of my species. There are two main ways that trees can reproduce: through seeds and through vegetative propagation.Seeds are the most common way that trees reproduce. Trees produce seeds that are dispersed by wind, water, or animals. When a seed lands in a suitable environment, it can germinate and grow into a new tree. Some trees, like the maple tree, produce seeds with wings that allow them to travel far distances before landing.Vegetative propagation is another way that trees can reproduce. This method involves the growth of new trees from parts of the parent tree, such as roots, stems, or leaves. Some trees, like the aspen tree, can grow new trees from their roots, creating large clonal colonies.Both methods of reproduction have their advantages and disadvantages. Seed production allows for genetic diversity and adaptation to changing environments, but it alsorequires a lot of energy and resources from the parent tree. Vegetative propagation allows for rapid reproduction andthe creation of large colonies, but it can also lead to a lack of genetic diversity and vulnerability to diseases.Overall, as a tree, my ability to reproduce isessential for the survival of my species. Whether through seeds or vegetative propagation, I must continue to produce offspring to ensure the continuation of my lineage.中文：作为一棵树，我的主要目标是繁衍后代，确保我的物种的生存。
园林树木种质资源的特点
园林树木种质资源的特点English.Characteristics of Plant Genetic Resources in Arboriculture.Plant genetic resources (PGR) in arboriculture refer to the diversity of genetic material found in tree speciesused for landscaping and urban greening. This diversity encompasses the range of genes, alleles, and genotypes that contribute to the traits and characteristics of these trees. Understanding the characteristics of PGR in arboricultureis crucial for effective conservation, management, and utilization of tree species.1. Genetic Diversity:Arboricultural PGR exhibits high levels of genetic diversity due to various factors, including:Wide Geographical Distribution: Tree species in arboriculture are often distributed across diverse geographic regions, leading to adaptation to different environmental conditions and the accumulation of unique genetic variations.Long Generation Times: Trees have relatively long generation times, allowing for the accumulation of genetic differences over longer periods.Outcrossing: Many tree species in arboriculture are outcrossing, meaning they require cross-pollination between different individuals. This promotes genetic recombination and increases diversity.2. Local Adaptation:Arboricultural PGR often exhibits local adaptation, with specific genotypes being better suited to particular environmental conditions within a region. This adaptation results from natural selection pressures, such as climate, soil conditions, and biotic interactions. Local adaptationis crucial for the resilience and survival of trees intheir specific environments.3. Phenotypic Variation:The genetic diversity of arboricultural PGR manifestsin a wide range of phenotypic variations, including:Morphological Characteristics: Tree size, shape, leaf form, and bark texture are influenced by genetic factors, resulting in diverse aesthetic qualities.Disease Resistance: Genetic variation contributes to differences in susceptibility or resistance to pests and diseases, which is critical for tree health and longevity.Environmental Tolerance: Trees exhibit varying tolerances to environmental stressors such as drought, heat, cold, and pollution, influenced by their genetic makeup.4. Economic and Cultural Value:Arboricultural PGR has significant economic andcultural value:Timber Production: Tree species are used for timber production, and genetic diversity ensures the availability of trees with desirable traits for specific uses.Aesthetic Enhancement: Trees contribute to the aesthetic appeal of urban areas, and their geneticdiversity allows for the selection of visually pleasing and diverse landscapes.Cultural Significance: Some tree species hold cultural or historical significance, and their genetic conservation preserves these cultural values.5. Conservation and Management:The conservation and management of arboricultural PGR are essential for maintaining genetic diversity and ensuring the availability of trees for future generations:Ex Situ Conservation: Gene banks, botanical gardens, and seed banks play a crucial role in preserving genetic material for research and reforestation efforts.In Situ Conservation: Protecting natural populations of tree species in their original habitats is vital for maintaining genetic diversity and ecosystem services.Genetic Improvement: Selective breeding programs can enhance desirable traits in trees, such as disease resistance, growth rate, and drought tolerance.Understanding the characteristics of PGR in arboriculture is fundamental to the sustainable management and conservation of tree species. It allows arborists, urban planners, and conservationists to make informed decisions about species selection, genetic conservation, and breeding programs. Preserving and utilizing the genetic diversity of arboricultural PGR ensures the resilience, beauty, and ecological benefits of trees in our urban and natural environments.中文回答：园林树木种质资源的特点。
基因9Chapter 1
初中生物英语词汇
初中生物英语词汇一、细胞(Cell)1. 细胞膜 (Cell membrane)- 定义：包围和保护细胞的薄膜，控制物质的进出。
- 示例：The cell membrane allows nutrients to enter the cell.2. 细胞核 (Cell nucleus)- 定义：细胞的控制中心，包含遗传物质 DNA。
- 示例：The cell nucleus controls all the activities of the cell.3. 基因 (Gene)- 定义：生物体传递给后代的遗传信息单位。
- 示例：Genes determine the traits and characteristics of an organism.二、遗传(Genetics)1. 遗传学 (Genetics)- 定义：研究遗传现象和规律的学科。
- 示例：Genetics helps us understand how traits are passed from one generation to another.2. 遗传物质 (Genetic material)- 定义：决定物种遗传特性的DNA和RNA。
- 示例：The genetic material carries the instructions for the development and functioning of organisms.3. 遗传变异 (Genetic variation)- 定义：个体之间遗传特征的差异。
- 示例：Genetic variation is important for the survival and adaptation of a species.三、进化(Evolution)1. 进化论 (Theory of evolution)- 定义：生物种类在长时间内发生的变化和适应环境的过程。
2. 适应性 (Adaptation)- 定义：生物体对环境变化做出的结构或行为上的调整。
基因组学16
16. Molecular PhylogeneticsLearning outcomesWhen you have read Chapter 16, you should be able to:•Recount how taxonomy led to phylogeny and discuss the reasons why molecular markers are important in phylogenetics•Describe the key features of a phylogenetic tree and distinguish between inferred trees, true trees, gene trees and species trees•Explain how phylogenetic trees are reconstructed, including a description of DNA sequence alignment, the methods used to convert alignment data into a phylogenetic tree, and how the accuracy of a tree is assessed•Discuss, with examples, the applications and limitations of molecular clocks•Give examples of the use of phylogenetic trees in studies of human evolution and the evolution of the human and simian immunodeficiency viruses•Describe how molecular phylogenetics is being used to study the origins of modern humans, and the migrations of modern humans into Europe and the New WorldIf genomes evolve by the gradual accumulation of mutations, then the amount of difference in nucleotide sequence between a pair of genomes should indicate how recently those two genomes shared a common ancestor. Two genomes that diverged in the recent past would be expected to have fewer differences than a pair of genomes whose common ancestor is more ancient. This means that by comparing three or more genomes it should be possible to work out the evolutionary relationships between them. These are the objectives of molecular phylogenetics.16.1. The Origins of Molecular PhylogeneticsMolecular phylogenetics predates DNA sequencing by several decades. It is derived from the traditional method for classifying organisms according to their similarities and differences, as first practiced in a comprehensive fashion by Linnaeus in the 18th century. Linnaeus was a systematicist not an evolutionist, his objective being to place all known organisms into a logical classification which he believed would reveal the great plan used by the Creator - the Systema Naturae. However, he unwittingly laid the framework for later evolutionary schemes by dividing organisms into a hierarchic series of taxonomic categories, starting with kingdom and progressing down through phylum, class, order, family and genus to species. The naturalists of the 18th and early 19th centuries likened this hierarchy to a ‘tree of life' (Figure 16.1), an analogy that was adopted by Darwin (1859) in The Origin of Species as a means of describing the interconnected evolutionary histories of living organisms. The classificatory scheme devised by Linnaeus therefore became reinterpreted as a phylogeny indicating not just the similarities between species but also their evolutionary relationships.Whether the objective is to construct a classification or to infer a phylogeny, the relevant data are obtained by examining variable characters in the organisms being compared. Originally, these characters were morphological features, but molecular data were introduced at a surprisingly early stage. In 1904 Nuttall used immunological tests to deduce relationships between a variety of animals, one of his objectives being to place humans in their correct evolutionary position relativeto other primates, an issue that we will return to in Section 16.3.1. Nuttall's work showed that molecular data can be used in phylogenetics, but the approach was not widely adopted until the late 1950s, the delay being due largely to technical limitations, but also partly because classification and phylogenetics had to undergo their own evolutionary changes before the value of molecular data could be fully appreciated. These changes came about with the introduction of phenetics and cladistics(Box 16.1), two novel phylogenetic methods which, although quite different in their approach, both place emphasis on large datasets that can be analyzed by rigorous mathematical procedures. The difficulty in obtaining large mathematical datasets when morphological characters are used was one of themain driving forces behind the gradual shifttowards molecular data, which have threeadvantages compared with other types ofphylogenetic information:Figure 16.1. The tree of life. An ancestral speciesis at the bottom of the ‘trunk' of the tree. As timepasses, new species evolve from earlier ones sothe tree repeatedly branches until we reach thepresent time, when there are many speciesdescended from the ancestor.16.1. Phenetics and cladisticsPhenetics, when first introduced (Michener and Sokal, 1957), challenged the prevailing view that classifications should be based on comparisons between a limited number of characters that taxonomists believed to be important for one reason or another. Pheneticists argued that classifications should encompass as many variable characters as possible, these characters being scored numerically and analyzed by rigorous mathematical methods.Cladistics (Hennig, 1966) also emphasizes the need for large datasets but differs from phenetics in that it does not give equal weight to all characters. The argument is that in order to infer the branching order in a phylogeny it is necessary to distinguish those characters that provide a good indication of evolutionary relationships from other characters that might be misleading. This might appear to take us back to the pre-phenetic approach but cladistics is much less subjective: rather than making assumptions about which characters are ‘important', cladistics demands that the evolutionary relevance of individual characters be defined. In particular, errors in the branching pattern within a phylogeny are minimized by recognizing two types of anomalous data.•Convergent evolution or homoplasy occurs when the same character state evolves in two separate lineages. For example, both birds and bats possess wings, but bats are more closely related to wingless mammals than they are to birds (see Figure A). The character state ‘possession of wings' is therefore misleading in the context of vertebrate phylogeny.•Ancestral character states must be distinguished from derived character states. An ancestral (or plesiomorphic) character state is one possessed by a remote common ancestor of a group of organisms, an example being five toes in vertebrates. A derived (or apomorphic) character state is one that evolved from the ancestral state in a more recentcommon ancestor, and so is seen in only a subset of the species in the group being studied.Among vertebrates, the possession of a single toe, as displayed by modern horses, is a derived character state (see Figure B). If we did not realize this then we might conclude that humans are more closely related to lizards, which like us have five toes, rather than to horses.Phenetics and cladistics have had an uneasy relationship over the last 40 years. Most of today's evolutionary biologists favor cladistics, even though a strictly cladistic approach throws up some apparently counter-intuitive results, a notable example being the conclusion that the birds should not have their own class (Aves) but be included among the reptiles.Box 16.1. Phenetics and cladisticsPhenetics, when first introduced (Michener and Sokal, 1957), challenged the prevailing view that classifications should be based on comparisons between a limited number of characters that taxonomists believed to be important for one reason or another. Pheneticists argued that classifications should encompass as many variable characters as possible, these characters being scored numerically and analyzed by rigorous mathematical methods.Cladistics (Hennig, 1966) also emphasizes the need for large datasets but differs from phenetics in that it does not give equal weight to all characters. The argument is that in order to infer the branching order in a phylogeny it is necessary to distinguish those characters that provide a good indication of evolutionary relationships from other characters that might be misleading. This might appear to take us back to the pre-phenetic approach but cladistics is much less subjective: rather than making assumptions about which characters are ‘important', cladistics demands that the evolutionary relevance of individual characters be defined. In particular, errors in the branching pattern within a phylogeny are minimized by recognizing two types of anomalous data.•Convergent evolution or homoplasy occurs when the same character state evolves in two separate lineages. For example, both birds and bats possess wings, but bats are more closely related to wingless mammals than they are to birds (see Figure A). The character state ‘possession of wings' is therefore misleading in the context of vertebrate phylogeny.•Ancestral character states must be distinguished from derived character states. An ancestral (or plesiomorphic) character state is one possessed by a remote common ancestor of a group of organisms, an example being five toes in vertebrates. A derived (or apomorphic) character state is one that evolved from the ancestral state in a more recent common ancestor, and so is seen in only a subset of the species in the group being studied.Among vertebrates, the possession of a single toe, as displayed by modern horses, is a derived character state (see Figure B). If we did not realize this then we might conclude that humans are more closely related to lizards, which like us have five toes, rather than to horses.Phenetics and cladistics have had an uneasy relationship over the last 40 years. Most of today's evolutionary biologists favor cladistics, even though a strictly cladistic approach throws up some apparently counter-intuitive results, a notable example being the conclusion that the birds should not have their own class (Aves) but be included among the reptiles.•When molecular data are used, a single experiment can provide information on many different characters: in a DNA sequence, for example, every nucleotide position is a character with four character states, A, C, G and T. Large molecular datasets can therefore be generated relatively quickly.•Molecular character states are unambiguous: A, C, G and T are easily recognizable and one cannot be confused with another. Some morphological characters, such as those based on the shape of a structure, can be less easy to distinguish because of overlaps between different character states.•Molecular data are easily converted to numerical form and hence are amenable to mathematical and statistical analysis.The sequences of protein and DNA molecules provide the most detailed and unambiguous data for molecular phylogenetics, but techniques for protein sequencing did not become routine until the late 1960s, and rapid DNA sequencing was not developed until 10 years after that. Early studies therefore depended largely on indirect assessments of DNA or protein variations, using one of three methods:•Immunological data, such as those obtained by Nuttall (1904), involve measurements of the amount of cross-reactivity seen when an antibody specific for a protein from one organism is mixed with the same protein from a different organism. Remember that in Section 12.2.1 we learned that antibodies are immunoglobulin proteins that help to protect the body against invasion by bacteria, viruses and other unwanted substances by binding to these ‘antigens'. Proteins also act as antigens, so if human β-globin, for example, is injected into a rabbit then the rabbit makes an antibody that binds specifically to that protein. The antibody will also cross-react with β-globins from other vertebrates, because these β-globins have similar structures to the human version. The degree of cross-reactivity depends on how similar the β-globin being tested is to the human protein, providing the similarity data used in the phylogenetic analysis.•Protein electrophoresis is used to compare the electrophoretic properties, and hence degree of similarity, of proteins from different organisms. This technique has proved useful for comparing closely related species and variations between members of a single species.•DNA-DNA hybridization data are obtained by hybridizing DNA samples from the two organisms being compared. The DNA samples are denatured and mixed together so thathybrid molecules form. The stability of these hybrid molecules depends on the degree of similarity between the nucleotide sequences of the two DNAs, and is measured by determining the melting temperature (see Figure 5.8), a stable hybrid having a higher melting temperature than a less stable one. The melting temperatures obtained with DNAs from different pairs of organisms provide the data used in the phylogenetic analysis.By the end of the 1960s these indirect methods had been supplemented with an increasing number of protein sequence studies (e.g. Fitch and Margoliash, 1967) and during the 1980s DNA-based phylogenetics began to be carried out on a large scale. Protein sequences are still used today in some contexts, but DNA has now become by far the predominant molecule. This is mainly because DNA yields more phylogenetic information than protein, the nucleotide sequences of a pair of homologous genes having a higher information content than the amino acid sequences of the corresponding proteins, because mutations that result in non-synonymous changes alter the DNA sequence but do not affect the amino acid sequence (Figure 16.2). Entirely novel information can also be obtained by DNA sequence analysis because variability in both the coding and non-coding regions of the genome can be examined. The ease with which DNA samples for sequence analysis can be prepared by PCR (Section 4.3) is another key reason behind the predominance of DNA in modern molecular phylogenetics.Figure 16.2. DNA yields more phylogenetic information thanprotein. The two DNA sequences differ at three positions but theamino acid sequences differ at only one position. These positionsare indicated by green dots. Two of the nucleotide substitutions aretherefore synonymous and one is non-synonymous (see Figure 14.11).As well as DNA sequences, molecular phylogenetics also makes use of DNA markers such as RFLPs, SSLPs and SNPs (Section 5.2.2), particularly for intraspecific studies such as those aimed at understanding migrations of prehistoric human populations (Section 16.3.2). Later in this chapter we will consider various examples of the use of both DNA sequences and DNA markers in molecular phylogenetics, but first we must make a more detailed study of the methodology used in this area of genome research.16.2. The Reconstruction of DNA-based Phylogenetic TreesThe objective of most phylogenetic studies is to reconstruct the tree-like pattern that describes the evolutionary relationships between the organisms being studied. Before examining the methodology for doing this we must first take a closer look at a typical tree in order to familiarize ourselves with the basic terminology used in phylogenetic analysis.16.2.1. The key features of DNA-based phylogenetic treesA typical phylogenetic tree is shown in Figure 16.3A. This tree could have been reconstructed from any type of comparative data, but as we are interested in DNA sequences we will assume that the tree shows the relationships between four homologous genes, called A, B, C and D. The topology of this tree comprises four external nodes, each representing one of the four genes thatwe have compared, and two internal nodes representing ancestral genes. The lengths of the branches indicate the degree of difference between the genes represented by the nodes. The degree of difference is calculated when the sequences are compared, as described in Section 16.2.2.The tree in Figure 16.3A is unrooted, which means that it is only an illustration of the relationships between A, B, C and D and does not tell us anything about the series of evolutionary events that led to these genes. Five different evolutionary pathways are possible, each depicted by a different rooted tree, as shown in Figure 16.3B. To distinguish between them the phylogenetic analysis must include at least one outgroup, this being a homologous gene that we know is less closely related to A, B, C and D than these four genes are to each other. The outgroup enables the root of the tree to be located and the correct evolutionary pathway to be identified. The criteria used when choosing an outgroup depend verymuch on the type of analysis that isbeing carried out. As an example, let ussay that the four homologous genes inour tree come from human, chimpanzee,gorilla and orangutan. We could thenuse as an outgroup the homologousgene from another primate, such as thebaboon, which we know frompaleontological evidence branchedaway from the lineage leading to human,chimpanzee, gorilla and orangutanbefore the time of the common ancestorof those four species (Figure 16.4).Figure 16.3. Phylogenetic trees. (A)An unrooted tree with four externalnodes. (B) The five rooted trees that canbe drawn from the unrooted tree shownin part A. The positions of the roots areindicated by the numbers on the outlineof the unrooted tree.We refer to the rooted tree that weobtain by phylogenetic analysis as aninferred tree. This is to emphasize that itdepicts the series of evolutionary eventsthat are inferred from the data that wereanalyzed, and may not be the same asthe true tree, the one that depicts theactual series of events that occurred.Sometimes we can be fairly confident that the inferred tree is the true tree, but most phylogenetic data analyses are prone to uncertainties which are likely to result in the inferred tree differing in some respects from the true tree. In Section 16.2.2 we will look at the various methods used to assign degrees of confidence to the branching pattern in an inferred tree, and later in the chapterwe will examine some of the controversies that havearisen as a result of the imprecise nature of phylogeneticanalysis.Figure 16.4. The use of an outgroup to root aphylogenetic tree. The tree of human, chimpanzee, gorillaand orangutan genes is rooted with a baboon gene becausewe know from the fossil record that baboons split awayfrom the primate lineage before the time of the commonancestor of the other four species. For more informationon phylogenetic analysis of humans and other primates seeSection 16.3.1.Figure 16.5. The difference betweena gene tree and a species tree.Gene trees are not the same as speciestreesThe tree shown in Figure 16.4illustrates a common type of molecularphylogenetics project, where theobjective is to use a gene tree,reconstructed from comparisonsbetween the sequences of orthologousgenes (those derived from the sameancestral sequence; see page 196), tomake inferences about theevolutionary history of the speciesfrom which the genes are obtained.The assumption is that the gene tree,based on molecular data with all itsadvantages, will be a more accurateand less ambiguous representation ofthe species tree than that obtainable bymorphological comparisons. Thisassumption is often correct, but it doesnot mean that the gene tree is the sameas the species tree. For that to be the case, the internal nodes in the gene and species trees would have to be precisely equivalent. However, they are not equivalent, because:•An internal node in a gene treerepresents the divergence of anancestral gene into two genes withdifferent DNA sequences: this occurs bymutation (Figure 16.5A).•An internal node in a species treerepresents a speciation event (Figure16.5B): this occurs by the population ofthe ancestral species splitting into twogroups that are unable to interbreed, forexample, because they aregeographically isolated.Figure 16.6. Mutation might precedespeciation, giving an incorrect time for aspeciation event if a molecular clock is used.See the text for details. Based on Li (1997).The important point is that these two events - mutation and speciation - are not expected to occur at the same time. For example, the mutation event could precede the speciation. This would mean that, to begin with, both alleles of the gene are present in the unsplit population of the ancestral species (Figure 16.6). When the population split occurs, it is likely that both alleles will still be present in each of the two resultinggroups. After the split, the newpopulations evolve independently. Onepossibility is that the results of randomgenetic drift (see Box 16.3) lead to oneallele being lost from one populationand the other being lost from the otherpopulation. This establishes the twoseparate genetic lineages that we inferfrom phylogenetic analysis of the genesequences present in the modern speciesresulting from the continued evolutionof the two populations.Figure 16.7. A gene tree can have adifferent branching order from aspecies tree. In this example, the genehas undergone two mutations in theancestral species, the first mutationgiving rise to the ‘blue' allele and thesecond to the ‘green' allele. Randomgenetic drift in association with the twosubsequent speciations results in the red allele lineage appearing in species A, the green allele lineage in species B and the blue allele lineage in species C. Molecular phylogenetics based on the gene sequences will reveal that the red-blue split occurred before the blue-green split, giving the gene tree shown on the right. However, the actual species tree is different, as shown on the left. Based on Li (1997).How do these considerations affect the equivalence of the gene and species trees? There are various implications, two of which are as follows:•If a molecular clock (Section 16.2.2) is used to date the time at which the gene divergence took place, then it cannot be assumed that this is also the time of the speciation event. If the node being dated is ancient, say 50 million or more years ago, then the error may not be noticeable. But if the speciation event is recent, as when primates are being compared, then the date for the gene divergence might be significantly different to that for the speciation event.•If the first speciation event is quickly followed by a second speciation event in one of the two resulting populations, then the branching order of the gene tree might be different from that of the species tree. This can occur if the genes in the modern species are derived from alleles that had already appeared before the first of the two speciation events, as illustrated in Figure 16.7.16.2.2. Tree reconstructionIn this section we will look at how tree reconstruction is carried out with DNA sequences, concentrating on the four steps in the procedure:•Aligning the DNA sequences and obtaining the comparative data that will be used to reconstruct the tree;•Converting the comparative data into a reconstructed tree;•Assessing the accuracy of the reconstructed tree;•Using a molecular clock to assign dates to branch points within the tree.Sequence alignment is the essential preliminary to tree reconstructionThe data used in reconstruction of a DNA-based phylogenetic tree are obtained by comparing nucleotide sequences. These comparisons are made by aligning the sequences so that nucleotide differences can be scored. This is the critical part of the entire enterprise because if the alignment is incorrect then the resulting tree will definitely not be the true tree.The first issue to consider is whether the sequences being aligned are homologous. If they are homologous then they must, by definition, be derived from a common ancestral sequence (Section 7.2.1) and so there is a sound basis for the phylogenetic study. If they are not homologous then they do not share a common ancestor. The phylogenetic analysis will find a common ancestor because the methods used for tree reconstruction always produce a tree of some description, even if the data are completely erroneous, but the resulting tree will have no biological relevance. With some DNA sequences - for example, the β-globin genes of different vertebrates - there is no difficulty in being sure that the sequences being compared are homologous, but this is not always the case, and one of the commonest errors that arises during phylogenetic analysis is the inadvertent inclusion of a non-homologous sequence.Once it has been established that two DNA sequences are indeed homologous, the next step is to align the sequences so that homologous nucleotides can be compared. With some pairs of sequences this is a trivial exercise (Figure 16.8A), but it is not so easy if the sequences are relatively dissimilar and/or have diverged by the accumulation of insertions and deletions as well as point mutations. Insertions and deletions cannot be distinguished when pairs of sequences are compared so we refer to them as indels. Placing indels at their correct positions is often the most difficult part of sequence alignment (Figure 16.8B).Figure 16.8. Sequence alignment. (A)Two sequences that have not divergedto any great extent can be aligned easilyby eye. (B) A more complicatedalignment in which it is not possible todetermine the correct position for anindel. If errors in indel placement aremade in a multiple alignment then thetree reconstructed by phylogeneticanalysis is unlikely to be correct. In this diagram, the red asterisks indicate nucleotides that are the same in both sequences.Some pairs of sequences can be aligned reliably by eye. For more complex pairs, alignment might be possible by the dot matrix method (Figure 16.9). The two sequences are written out on the x- and y-axes of a graph, and dots placed in the squares of the graph paper at positions corresponding to identical nucleotides in the two sequences. The alignment is indicated by a diagonal series of dots, broken by empty squares where the sequences have nucleotide differences, and shifting from one column to another at places where indels occur.Figure 16.9. The dot matrix techniquefor sequence alignment. The correctalignment stands out because it forms adiagonal of continuous dots, broken atpoint mutations and shifting to a differentdiagonal at indels.More rigorous mathematical approaches tosequence alignment have also been devised.The first of these is the similarity approach( Needleman and Wunsch, 1970), whichaims to maximize the number of matchednucleotides - those that are identical in thetwo sequences. The complementary approach is the distance method (Waterman et al., 1976), in which the objective is to minimize the number of mismatches. Often the two procedures will identify the same alignment as being the best one.Usually the comparison involves more than just two sequences, meaning that a multiple alignmentis required. This can rarely be done effectively with pen and paper so, as in all steps in a phylogenetic analysis, a computer program is used. For multiple alignments, Clustal is often the most popular choice ( Jeanmougin et al., 1998). Clustal and other software packages for phylogenetic analysis are described in Technical Note 16.1.Technical note 16.1. Phylogenetic analysisSoftware packages for construction of phylogenetic trees.Few sets of DNA sequences are simple enough to be converted into phylogenetic trees entirely by hand. Virtually all research in this area is carried out by computer with the aid of any one of a variety of software packages designed specifically for one or other of the steps in tree reconstruction.One of the easiest to use and most popular packages is Clustal, which was originally written in 1988 and has undergone several upgrades in the intervening years ( Jeanmougin et al., 1998). Clustal is primarily a program for carrying out multiple alignments of protein or DNA sequences, which it is able to do very effectively provided that the sequences being compared do not contain extensive internal repeat motifs. Clustal is usually used in conjunction with NJplot, a simple program for tree reconstruction by the neighbor-joining method. One important advantage of Clustal and NJplot is that they do not require huge amounts of computer memory and so can be run on small PCs or Macintosh computers.More comprehensive software packages enable the researcher to choose between a variety of different methods for tree reconstruction and to carry out more sophisticated types of phylogenetic analysis. The most widely used of these packages are PAUP (Swofford, 1993) and PHYLIP (Felsenstein, 1989). The tree-building programs in PAUP are often looked upon as the most accurate ones currently available and are able to handle relatively large datasets ( Eernisse, 1998). PHYLIP has the advantage of including a number of software tools not readily available from other sources. Other popular packages include PAML ( Yang, 1997), MacClade, and HENNIG86.Converting alignment data into a phylogenetic treeOnce the sequences have been aligned accurately, an attempt can be made to reconstruct the phylogenetic tree. To date nobody has devised a perfect method for tree reconstruction, and several different procedures are used routinely. Comparative tests have been run with artificialdata, for which the true tree is known, but these havefailed to identify any particular method as being betterthan any of the others ( Felsenstein, 1988).Figure 16.10. A simple distance matrix. The matrixshows the evolutionary distance between each pair ofsequences in the alignment. In this example theevolutionary distance is expressed as the number ofnucleotide differences per nucleotide site for eachsequence pair. For example, sequences 1 and 2 are 20nucleotides in length and have four differences,corresponding to an evolutionary difference of 4/20 =0.2. Note that this analysis assumes that there are nomultiple substitutions (also called multiple hits).。
园艺英语词汇
Amphiploid双倍体Amphidiploid双二倍体Autotetraploid同源四倍体Allotetraploid异源四倍体Allohexaploid异源六倍体Allopolyploid异源多倍体Autopolyploid同源多倍体Natural selection自然选择Euploid整倍体Aneuploid非整倍体Wild relatives野生亲缘种Plant introduction引种Heritability遗传力Transgressive inheritance超亲遗传Quantitative inheritance数量遗传Qualitative inheritance质量遗传(Fertility) Restoring gene育性基因Additive effect加性效应Dose effect剂量效应Dominant effect显性效应Male sterile gene雄性不育基因Gene transfer转基因Genic sterility基因性不育Mutation突变mutant突变体Mutational site突变位点Hot spot (in mutation)突变热点Biochemical mutation生化诱变karyotype核型Cytoplasmic mutation细胞质突变bud mutation芽变Mutation frequency突变频率Addition line附加系Substitution line代换系Translocation line易位系Somatic hybridization体细胞杂交Homogeneity同质性Heterogeneity异质性Xenia异粉性Metaxenia后生异粉性Male parent父本Female parent母本Progeny后代Filial generation子代，杂交后代Cross杂交Hybrid杂种，杂合物Cross breeding (Hybridization)杂交育种Pure line breeding (Pure line selection) 纯系育种Single cross单交Heterosis (hybrid vigor)杂交优势Heterobeltiosis超亲杂交优势Test cross测交Double cross双杂交Top cross顶交Back cross回交Recurrent parent轮回亲本Non-recurrent parent非回交亲本Reciprocal cross正反交，互交Selfing自交Inbreeding (Close breeding)近交Outbreeding远交，杂交繁殖Cross pollination异花授粉Self-pollination自花授粉Self-fertilization自花受精Artificial pollination人工授粉Mixed pollination混合授粉haploid breeding单倍体育种Distant hybrid远缘杂交Strain (Line)系Breeding for disease resistance 抗病育种Apomixis无融合生殖Cultivar (Variety)栽培品种Variety certification品种鉴定Landrace Variety registration 本地品种记录Improved variety改良品种Commercial variety商业品种Introduced variety引进品种Kingdom界Phylum门Class纲SubclassxxFamily科Genus属Species种Germplasm种质Fruit atlas果树图集Germplasm resources种质资源Germplasm of fruit tree果树种质Germplasm resources of fruits果树种质资源Germplasm resources file种质资源档案Exploration of germplasm resources种质资源勘查Wild species野生种Cultivar栽培品种Variety变种Maintenance of germplasm resources species种质资源保存Kindred wild National fruit germplasm repository国家果树种质库Passport data基本数据Strain株系、品系Classification of fruit plants果树分类Characterization鉴定Fruit cultivar inventory果树栽培品种目录Monograph of fruit trees果树专著Degeneration of cultivars品种退化Origin of cultivated fruits果树栽培品种的起源Cultivated species栽培品种Palynology characterization孢粉学特征鉴定Science of germplasm resources种质资源学Biodiversity生物多样性Science of germplasm resources of fruit 果树种质资源学Variety test品种试验Identification of characters性状鉴定Early stage evaluation早期鉴定Carbon (C)Hydrogen (H)Oxygen (O)Nitrogen (N)Phosphorous (P)Potassium (K)Calcium (Ca)Zinc (Zn)Magnesium (Mg)Sulphur (S)Sodium (Na)Iron (Fe)Manganese (Mn)Copper (Cu)Boron(B)Chloride (Cl)Molybdenum(Mo)Fertilizer肥料Diagnosis诊断Fertigation施肥灌溉Nutrient balance营养平衡Element元素Starch淀粉The balanced fertilization平衡施肥Beneficial element有益元素Essential element必需元素Carbohydrate碳水化合物Assimilate吸收，同化Photosynthate 光合产物Ion离子Deficiency缺乏Mineral nutrition矿质营养Toxicity毒性Physiological disorder生理失调Manure施肥Green manure绿色肥料Organic manure有机肥Inorganic无机肥Cover crops 覆盖作物cash crop商品作物Pomology果树学Deciduous fruit tree落叶果树Annual vegetable crop一年生蔬菜Biennial vegetable crop两年生蔬菜Perennial vegetable crop多年生蔬菜Aquatic水生的Vegetables蔬菜Ornamental horticulture观赏园艺学Flower arrangement花卉装饰Flower decoration花卉装饰landscape design景观设计Landscape gardening传统园林学The standard leaf sample标准叶样Rhizosphere根际Stress胁迫Tolerance耐受性The standard values of leaf mineral elements标准xx矿质元素值mineral elements矿质元素Photosynthesis光合作用ChlorophyllxxSpray喷洒Nutrient养分Content含量，内容物Concentration浓度Solution溶液Soil application土壤施肥Foliar application叶面施肥Solution culture液体培养abortion败育agarxxanther花粉apical顶端的auxin生长素axillary bud腋芽callus，calli愈伤组织cellular totipotency细胞全能性cellulase纤维素酶cellulose纤维素centrifuge离心chloroplastxxchromosome doubling染色体加倍colony细胞团，菌落cybrid(cytoplasmic hybrid)胞质杂种cytokin细胞分裂素cytoplasm细胞质degeneration败育dedifferentiation脱分化redifferentiation再分化dihaploid二单倍体diploid二倍体dissect剥离dormancy休眠eliminate除去embryo胚胎embryoid胚状体embryogenesis胚胎发生方式epidermis表皮，上表皮excise切除explants外植体filter paper滤纸agarose琼脂糖germplasm种质global embryo球型胚hormone激素interspecific种间的intraspecific种内的in vitro体外in vivo活体meristem分生组织meristem culture茎尖培养micropagation微繁microspore小孢子monocotyledon/monocots单子叶植物nod culture茎段培养organelle细胞器organogenesis器官发生方式osmotic渗透的plantlet小植株，苗pollen culture花粉培养pollinate授粉somatic embryo体细胞胚somatic hybridization体细胞杂交somatic hybrid 体细胞杂种stem茎sterile distilled water蒸馏水sterilization消毒stock plant母株subculture继代sucrose蔗糖terminal bud顶芽transfer转移virus eradication脱毒Gene基因IntronxxExon外显子Operon操纵子Replicon复制子Promoter启动子Ribonucleic acidRNANucleotide核酸Amino acid氨基酸Protein蛋白质Mutant突变体Mutation突变Splicing剪接Ligase连接酶Kinase激酶Transcriptional factor转录因子Genome基因组Action spectrum光谱Photoautotroph光合自养生物Photoheterotroph光合异养生物Absorption吸收Bioassay生物测定Phytotron人工气候室Photoreduction光还原Photooxidation光氧化Thermal death point(TDP)热[致]死点Lignification木质化Optimum temperature最适温度Photochemical induction光化学感应After-effect后效Transmembrane potential跨膜电位Reaction center反应中心Gross photosynthesis总光合作用率Net (Apparent) photosynthesis净光合Law of limiting factor限制因素定律Photosystem光系统Quantum efficiency量子效率Photosynthetically active radiation (PAR)光合成有效辐射Assimilation同化作用Dissimilation异化作用Compensation point补偿点Light reaction光反应Dark reaction暗反应Photolysis光解作用Photophosphorylation光合磷酸化Light saturation point光饱和点Respiration呼吸作用Aerobic respiration有氧呼吸Anaerobic respiration厌氧呼吸Photorespiration光呼吸Dark respiration暗呼吸Cyanide-resistant respiration抗氰呼吸Climacteric呼吸跃变Metabolism新陈代谢Catabolism分解代谢（异化作用）Anabolism合成代谢Secondary metabolism次级代谢Electron transport电子传递Electron carrier电子载体Terminal oxidase末端氧化酶Terminal electron acceptor末端电子受体Antitranspirant抗蒸腾，抗蒸腾剂Plasmolysis质壁分离Physiological drought生理干旱Soil permeability土壤渗透性Water requirement水分需求Osmotic pressure渗透压diffusion coefficient 扩散系数Percolation (leakage)渗透Guttation伤流现象Bleeding伤流wilting coefficient萎蔫系数Turgor pressure膨胀压water potential水势Permanent wilting永久萎蔫Wilting萎蔫Hypertonic solution高渗溶液Hypotonic solution低渗溶液Isotonic solution等渗溶液Temporary wilting临时萎蔫Osmotic pressure渗透压Nitrogen fixation固氮作用Permeability渗透性Permeable membrane渗透膜Physiological acidity生理酸度Physiological alkalinity生理碱度Acropetal translocation顶向运输Bidirectional translocation基向运输Ring gridling环割Partioning分配Root pressure根压Symplast共质体Apoplast质外体Aging老化Tropism向性Apical dominance顶端优势Critical period临界期Taxis趋避性Nasty感性GeotropismxxPhotropismxxThreshold value临界值Stress胁迫Lodging倒伏Earliness早熟Lateness迟误Physiological maturity成熟度。
- 1、下载文档前请自行甄别文档内容的完整性，平台不提供额外的编辑、内容补充、找答案等附加服务。
- 2、"仅部分预览"的文档,不可在线预览部分如存在完整性等问题,可反馈申请退款(可完整预览的文档不适用该条件!)。
- 3、如文档侵犯您的权益，请联系客服反馈,我们会尽快为您处理(人工客服工作时间：9:00-18:30)。
CHAPTER1Gene Trees,Species Trees,and SpeciesNetworksLuay Nakhleh Derek RuthsDepartment of Computer ScienceRice UniversityHouston,TX77005,USA{nakhleh,druths}@Hideki InnanUniversity of Texas Health Science Center at HoustonHouston,TX77030,USAHideki.Innan@1.1IntroductionThe availability of whole-genome sequence data has provided a rich resource of deep insights into many biological,medical and pharmaceutical problems and ap-plications,and is promising even more.Yet,along with these insights and promises, genomic data have given rise to many challenging problems,mainly due to the quan-tity and heterogeneity of such data.One of these major challenges is the phylogenetic analysis of multiple gene datasets that whole genomes provide.Phylogeny,i.e.,the evolutionary history of a set of organisms,has become an indis-pensable tool in the post-genomic era.Emerging techniques for handling essential biological tasks(e.g.,genefinding,comparative genomics,and haplotype inference) are usually guided by an underlying phylogeny.The performance of these techniques, therefore,depends heavily on the quality of the phylogeny.Almost all phylogenetic methods,however,assume that evolution is a process of strict divergence that can be modeled by a phylogenetic tree.While the tree model gives a satisfactoryfirst-order approximation for many families of organisms,other families exhibit evolutionary events that cannot be represented by a tree.In particular,the evolutionary history of bacterial genomes is characterized by the occurrence of processes such as hor-izontal gene transfer(HGT)—transfer of genetic material across the boundaries of of distantly related species—and inter-specific recombination—exchange of genetic material.Further,hybrid speciation occurs among various groups of plants,fish,and12GENE TREES,SPECIES TREES,AND SPECIES NETWORKS frogs.In the presence of such evolutionary processes,the evolutionary relationship of a set of organisms is modeled by a phylogenetic network.Accurate reconstruction of these processes bears significant impact on many do-mains.The Tree of Life—the phylogeny of all organisms on Earth—is one of the grand challenges in evolutionary biology.The prokaryotic branch of this tree is be-lieved to have a large number of horizontal gene transfer events,in addition to re-combination events.Efforts to reconstruct a phylogeny for the prokaryotic branch may prove futile without developing phylogenetic network models and reconstruc-tion methods.A significant aspect of these complex evolutionary mechanisms is their contribu-tion to microbial genome diversification.Like all forms of life,bacteria undergoes evolution.However,unlike many other organisms,bacterial evolution is not one of strict divergence.Recombination usually occurs within populations;in bacteria,how-ever,recombination occurs among different strains.Further,HGT is ubiquitous in the prokaryotic branch of the Tree of Life.Ho(2002)has recently written of the various health risks that recombination and HGT pose,including:(1)antibiotic resistance genes spreading to pathogenic bacteria,(2)disease-associated genes spreading and recombining to create new viruses and bacteria that cause diseases,and(3)transgenic DNA inserting into human cell,triggering cancer.Hence,detecting and reconstruct-ing these processes in bacteria play a major role in developing effective antibiotics, and bears a great impact on human health.Biologists have long acknowledged the presence of these processes,their signifi-cance,and their effects.The computational research community has responded in recent years and proposed a plethora of methods for reconstructing complex evolu-tionary histories.The general theme of most existing methods can be summarized by:construct gene trees and reconcile them(this is known as the separate analysis approach).Gene tree reconciliation presents two major issues,namely identifying the(biological)source of incongruence,and(computationally)reconciling the trees. Many processes may lead to incongruent gene trees:(1)Stochastic factors,such as wrong assumptions,insufficient data,incomplete sam-pling,and differential rates of sequence evolution across lineages.These factors do not violate the tree model of organismal evolutionary relationships;rather,the incon-gruence they cause must be eliminated in the early stages of phylogenetic analyses.(2)Intra-species factors,such as gene loss and duplication.Although these events may lead to incongruent gene trees,they do not violate the tree model of organismal evolutionary relationships.(3)Inter-species factors,such as horizontal gene transfer(whose rate is very high among prokaryotic organisms),and inter-specific recombination.These events result in networks of relationships,rather than trees of relationships.In this work,we review the intra-and inter-species factors that cause gene tree incon-gruence and discuss current approaches for resolving these phenomena,with focus on non-treelike evolution.Further,we address extensions to the coalescent model to address non-treelike evolution.The rest of the chapter is organized as follows.InGENE TREE INCONGRUENCE3 Section1.2we illustrate some of the processes that lead to incongruence gene trees. In Section1.3we review existing methods for addressing gene tree incongruence caused by gene loss and duplication(intra-species factors).In Section1.4,we de-scribe the phylogenetic network model and discuss the problem of reconciling gene trees into species networks.In Section1.5we propose approaches for extending the coalescent model to incorporate non-treelike evolutionary processes.We conclude the chapter in Section1.6.1.2Gene Tree IncongruenceA gene tree is a model of how a gene evolves through duplication,loss,and nu-cleotide substitution.As a gene at a locus in the genome replicates and its copies are passed on to more than one offspring,branching points are generated in the gene tree.Because the gene has a single ancestral copy,barring recombination,the re-sulting history is a branching tree(Maddison(1997)).Sexual reproduction and mei-otic recombination within populations break up the genomic history into many small pieces,each of which has a strictly treelike pattern of descent(Hudson(1983b); Hein(1990);Maddison(1995)).Thus,within a species,many tangled gene trees can be found,one for each nonrecombined locus in the genome.A species tree de-picts the pattern of branching of species lineages via the process of speciation.When reproductive communities are split by speciation,the gene copies within these com-munities likewise are split into separate bundles of descent.Within each bundle,the gene trees continue branching and descending through time.Thus,the gene trees are contained within the branches of the species phylogeny(Maddison(1997)).Gene trees can differ from one another as well as from the species tree.Disagree-ments(incongruence)among gene trees may be an artifact of the data and/or meth-ods used(stochastic factors).Various studies show the effects of stochastic factors on the performance of phylogenetic tree reconstruction methods(e.g.,Hillis et al. (1993);Hillis&Huelsenbeck(1994,1995);Nakhleh et al.(2001a,b,2002);Moret et al.(2002)).Stochastic factors confound the accurate reconstruction of evolution-ary relationships,and must be handled in thefirst stage of a phylogenetic analysis. Incongruence among gene trees due to intra-or inter-species processes,on the other hand,is a reflection of true biological processes,and must be handled as such. Whereas eukaryotes evolve mainly though lineal descent and mutations,bacteria ob-tain a large proportion of their genetic diversity through the acquisition of sequences from distantly related organisms,via horizontal gene transfer(HGT)or recombi-nation(Ochman et al.(2000)).Views as to the extent of HGT and recombination in bacteria vary between the two extremes,with most views being in the middle (Doolittle(1999b,a);Kurland et al.(2003);et al.(2002);Hao&Golding(2004); et al.(2004);Nakamura et al.(2004)).However,there is a common belief that re-combination and HGT,among other processes,form the essence of prokaryotic evo-lution.Further,these two are the main processes(in addition to random mutations) by which bacteria develop resistance to antibiotics(e.g.,Lewis(1995);Ho(2002);4GENE TREES,SPECIES TREES,AND SPECIES NETWORKS A B C g a g b g c A B C g a g b g c (a)(b)A B C g a g b g c DuplicationA B C g a g b gc(c)(d)A B C g a gb gc G a G b Gc(e)Figure 1.1(a)Gene tree that agrees with the species tree.(b)Gene tree that disagrees with the species tree due to gene loss and duplication.(c)Gene tree that disagrees with the species tree due to HGT.(d)An inter-specific recombination event in which genetic material is exchanged between species B and C .(e)A hybrid speciation event that leads to two incongruent gene trees.Enright et al.(2002);Paulsen et al.(2003)).Gene transfer and exchange are consid-ered a primary explanation of incongruence among bacterial gene phylogenies and a significant obstacle to reconstructing the prokaryotic branch of the Tree of Life (Daubin et al.(2003)).We illustrate some of the scenarios that may lead to gene tree incongruence in Figure1.1.The species (or,organismal)tree is represented by the “tubes”;it has A and B as sister taxa whose most recent common ancestor (MRCA)is a sister taxon of C .Figure 1.1(a)shows a gene evolving within the branches of the same species tree;in this case,the topologies of the gene and species trees agree (the topology of this gene tree is shown in Figure 1.2(a)).In Figure 1.1(b)we show an example of how intra-species processes may lead to incongruent gene trees.The figure shows a gene evolving within the branches a species tree with one duplication event and three losses.Note that the species tree differs from the gene tree;based on this gene,BGENE TREE INCONGRUENCE 5g b g c g a G cG b G a (a)(b)(c)(d)Figure 1.2(a)The tree of the gene whose evolution is shown in Figure 1.1(a),and Figure1.1(e).(b)The tree of the genes whose evolution is shown in Figures 1.1(b)and 1.1(c).(c)The tree of the gene involved in the recombination event shown in Figure 1.1(d).(e)The tree of the gene involved in the hybrid speciation event shown in Figure 1.1(e).and C are sister taxa and their MRCA is a sister of taxon A .This gene tree is shown in Figure 1.2(b).Another event that may cause incongruence between the species tree and the gene tree is HGT.In the case of HGT,shown in Figure 1.1(c),genetic material is trans-ferred from one lineage to another.Sites that are not involved in a horizontal transfer are inherited from the parent (as in Figure 1.2(a)),while other sites are horizontally transferred from another species (as in Figure 1.2(b)).In the case of inter-specific recombination,as illustrated in Figure 1.1(d),some ge-netic material is exchanged between pairs of species;in this example,species B and C exchange genetic material.The genes involved in this exchange have an evolu-tionary history (shown in Figure 1.2(c))that is incongruent with that of the species.In hybrid speciation,two lineages recombine to create a new species.We can dis-tinguish diploid hybridization ,in which the new species inherits one of the two ho-mologs for each chromosome from each of its two parents—so that the new species has the same number of chromosomes as its parents,and polyploid hybridization ,in which the new species inherits the two homologs of each chromosome from both parents—so that the new species has the sum of the numbers of chromosomes of its parents.Under this last heading,we can further distinguish allopolyploidization ,in which two lineages hybridize to create a new species whose ploidy level is the sum of the ploidy levels of its two parents (the expected result),and auto-polyploidization ,a regular speciation event that does not involve hybridization,but which doubles the ploidy level of the newly created lineage.Prior to hybridization,each site on each homolog has evolved in a tree-like fashion,although,due to meiotic recombination,different strings of sites may have different histories.Thus,each site in the homologs of the parents of the hybrid evolved in a tree-like fashion on one of the trees induced by (contained inside)the network representing the hybridization event.Figure 1.1(e)shows a network with one hybrid.Each site evolves down exactly one of the two trees shown in Figures 1.2(a)and 1.2(d).Notice that in the case of intra-species processes (gene loss and duplication),infer-ring the species tree from a set of potentially conflicting gene trees is a problem of reconciling the gene trees and explaining their differences through duplications and losses of genes.Therefore,in this case,despite the potential incongruence among the species and gene trees,the species phylogeny is still a tree (Mirkin et al.(1995);Page6GENE TREES,SPECIES TREES,AND SPECIES NETWORKS (1990,1994);Eulenstein et al.(1998)).However,in the case of recombination,HGT, and hybrid speciation,the evolutionary history of the organismal genomes cannot be represented by phylogenetic trees;rather,phylogenetic networks are the appropriate model(Hallett&Lagergren(2001);Moret et al.(2004)).1.3Trees Within Trees:The Gene Tree Species Tree ProblemVarious reports of instances and effects of gene loss and duplication exist in the literature(e.g.,Moore(1995);Nichols(2001);Ruvolo(1997)).When losses and duplications are the only processes acting on the genes,a mathematical formulation of the gene tree reconciliation problem is as follows:Definition1.1(The Gene Tree Reconciliation Problem)Input:Set T of rooted gene trees,a cost w D for duplications,and a cost w L for losses.Output:Rooted tree T with each gene tree t∈T mapped onto T,so as to mini-mize the sum w D n D+w L n L,where n D is the total number of duplications and n L is the total number of losses,over all genes.This problem was shown to be NP-hard by Fellows et al.(1998)and Ma et al. (1998).Heuristics for the problem exist,but these do not solve the optimization problem(see Ma et al.(1998);Page&Charleston(1997a)).Variousfixed-parameter approaches have been proposed by Stege(1999a);Hallett&Lagergren(2000)and some variants can be approximated to within a factor of2and shown by Ma et al. (1998).When loss and duplication are the only processes acting on the genes,two different questions can be posed,depending on the input data:1.Gene tree reconciliation problem—when the gene trees are known and the speciestree is known,what is the best set of duplication and loss events that reconcile each gene tree with the species tree?2.Species tree construction problem—when the gene trees are known,but the evolu-tionary relationships among the species involved is not known,can the gene trees provide the information necessary to derive an estimate of the species tree? Both of these questions require the assumption of a certain model of gene duplication and loss.The complexity of the gene-tree reconciliation problem is determined by the model chosen,whereas the general species tree construction problem is NP-hard under all commonly used models of gene duplication and loss.The simplest version of either problem uses a duplication-only model(i.e.,losses do not occur).During the period between years1995and2000,this was a commonly used model(Eulenstein et al.(1996);Page&Charleston(1997b);Page(1998);Eu-lenstein(1997);Stege(1999b);Ma et al.(1998);Zhang(1997);Ma et al.(2000)).TREES WITHIN NETWORKS:THE GENE TREE SPECIES NETWORK PROBLEM7 Under the duplication-only model,the gene tree reconciliation problem has linear-time solutions(Zhang(1997);Eulenstein(1997)),as well as other polynomial-time algorithms that report better performance on real biological datasets(Zmasek&Eddy (2001)).The species tree construction problem is NP-hard,as was shown by Maet al.(1998).Different approaches have been taken to solving the species tree con-struction problem including heuristics(Page&Charleston(1997b)),approximation algorithms(Ma et al.(2000)),andfixed parameter tractable algorithms obtained by parameterizing by the number of gene duplications separating a gene tree from the species tree(Stege(1999b)).The other common model used is the more general duplication-loss model,which admits both duplication and loss events within gene trees.The gene tree reconcil-iation problem has been shown to be polynomial-time under conditions where the evolution of the sequences themselves are not considered(Arvestad et al.(2004); Chen et al.(2000);Durand et al.(2005));if this is taken into account,the prob-lem becomes NP-hard(Fellows et al.(1998);Ma et al.(1998)).Various efficient heuristics for the problem are currently available(Arvestad et al.(2003,2004)). Early work on the gene tree reconciliation problem under this model borrowed tech-niques from biogeography and host/parasite evolution(Charleston(2000);Page& Charleston(1998)).1.4Trees Within Networks:The Gene Tree Species Network ProblemAs described in Section1.2,when events such as horizontal gene transfer,hybrid speciation,or recombination occur,the evolutionary history can no longer be mod-eled by a tree;rather,phylogenetic networks are the appropriate model in this case.In this section,we describe the phylogenetic network model and approaches for re-constructing networks from gene trees.1.4.1Terminology and notationGiven a(directed)graph G,let E(G)denote the set of(directed)edges of G andV(G)denote the set of nodes of G.Let(u,v)denote a directed edge from nodeu to node v;u is the tail and v the head of the edge and u is a parent of v.The indegree of a node v is the number of edges whose head is v,while the outdegree ofv is the number of edges whose tail is v.A node of indegree0is a leaf(often calleda tip by systematists).A directed path of length k from u to v in G is a sequenceu0u1···u k of nodes with u=u0,v=u k,and∀i,1≤i≤k,(u i−1,u i)∈E(G);we say that u is the tail of p and v is the head of p.Node v is reachable from u in G,denoted u;v,if there is a directed path in G from u to v;we then also say that u is an ancestor of v.A cycle in a graph is a directed path from a vertex backto itself;trees never contain cycles:in a tree,there is always a unique path between two distinct vertices.Directed acyclic graphs(or DAGs)play an important role onour model;note that every DAG contains at least one vertex of indegree0.A rooted8GENE TREES,SPECIES TREES,AND SPECIES NETWORKS directed acyclic graph,in the context of this paper,is then a DAG with a single node of indegree0,the root;note that all all other nodes are reachable from the root by a(directed)path of graph edges.We denote by r(T)the root of tree T and byL(T)the leaf set of T.Let T be a rooted phylogenetic tree over set S of taxa,and let S ⊆S.We denote by T(S )the minimal rooted subtree of T that connects all the element of S .Furthermore,the restriction of T to S ,denote T|S is the rooted subtree that is obtained from T(S )by suppressing all vertices(except for the root) whose number of incident edges is2.Let S be a maximum-cardinality set of leaves such that T1|S =T2|S ,for two trees T1and T2;we call T1|S (equivalently,T2|S ) the maximum agreement subtree of the two trees,denoted MAST(T1,T2).A clade of a tree T is a complete subtree of T.Let T =MAST(T1,T2);then,T1−T is the set of all maximal clades whose pruning from T1yields T (we define T2−T similarly).In other words,there do not exist two clades u and u in T1−T such that either u is a clade in u ,or u is a clade in u.We say that node x reaches node y in tree T if there is a directed path from x to y in T.We denote the root of a clade t by r(t).We say that clade t1reaches clade t2(both in tree T)if r(t1)reaches r(t2).The sibling of node x in tree T is node y,denoted sibling T(x)=y whenever x and y are children of the same node in T.We denote by T x the clade rooted at node x in T.The least common ancestor of a set X of taxa in tree T,denoted lca T(X)is the root of the minimal subtree of T that contains the leaves of X.The edge incoming into node x in tree T is denoted by inedge T(x).1.4.2Phylogenetic networksMoret et al.(2004)modeled phylogenetic networks using directed acyclic graphs (DAGs),and differentiated between“model”networks and“reconstructible”ones. Model networks A phylogenetic network N=(V,E)is a rooted DAG obeying certain constraints.We begin with a few definitions.Definition1.2A node v∈V is a tree node if and only if one of these three condi-tions holds:•indegree(v)=0and outdegree(v)=2:root;•indegree(v)=1and outdegree(v)=0:leaf;or•indegree(v)=1and outdegree(v)=2:internal tree node.A node v is a network node if and only if we have indegree(v)=2and outdegree(v)= 1.Tree nodes correspond to regular speciation or extinction events,whereas network nodes correspond to reticulation events(such as hybrid speciation and horizontal gene transfer).We clearly have V T∩V N=∅and can easily verify that we have V T∪V N=V.TREES WITHIN NETWORKS:THE GENE TREE SPECIES NETWORK PROBLEM9 Definition1.3An edge e=(u,v)∈E is a tree edge if and only if v is a tree node;it is a network edge if and only if v is a network node.The tree edges are directed from the root of the network towards the leaves and the network edges are directed from their tree-node endpoint towards their network-node endpoint.A phylogenetic network N=(V,E)defines a partial order on the set V of nodes. We can also assign times to the nodes of N,associating time t(u)with node u;suchan assignment,however,must be consistent with the partial order.Call a directed path p from node u to node v that contains at least one tree edge a positive-time directed path.If there exists a positive-time directed path from u to v,then we must have t(u)<t(v).Moreover,if e=(u,v)is a network edge,then we must havet(u)=t(v),because a reticulation event is effectively instantaneous at the scale of evolution;thus reticulation events act as synchronization points between lineages.Definition1.4Given a network N,two nodes u and v cannot co-exist(in time)if there exists a sequence P= p1,p2,...,p k of paths such that:•p i is a positive-time directed path,for every1≤i≤k;•u is the tail of p1,and v is the head of p k;and•for every1≤i≤k−1,there exists a network node whose two parents are the head of p i and the tail of p i+1.Obviously,if two nodes x and y cannot co-exist in time,then a reticulation event between them cannot occur.Definition1.5A model phylogenetic network is a rooted DAG obeying the follow-ing constraints:1.Every node has indegree and outdegree defined by one of the four combinations(0,2),(1,0),(1,2),or(2,1)—corresponding to,respectively,root,leaves,inter-nal tree nodes,and network nodes.2.If two nodes u and v cannot co-exist in time,then there does not exist a networknode w with edges(u,w)and(v,w).3.Given any edge of the network,at least one of its endpoints must be a tree node.Reconstructible networks Definition1.5of model phylogenetic networks assumes that complete information about every step in the evolutionary history is available. Such is the case in simulations and in artificial phylogenies evolved in a laboratory setting—hence our use of the term model.When attempting to reconstruct a phylo-genetic network from sample data,however,a researcher will normally have only incomplete information,due to a combination of extinctions,incomplete sampling, and abnormal model conditions.Extinctions and incomplete sampling have the same consequences:the data do not reflect all of the various lineages that contributed tothe current situation.Abnormal conditions include insufficient differentiation along10GENE TREES,SPECIES TREES,AND SPECIES NETWORKS edges,in which case some of the edges may not be reconstructible,leading to poly-tomies and thus to nodes of outdegree larger than2.All three types of problems may lead to the reconstruction of networks that violate the constraints of Definition1.5. (The distinction between a model phylogeny and a reconstructible phylogeny is com-mon with trees as well:for instance,model trees are always rooted,whereas recon-structed trees are usually unrooted.In networks,both the model network and the reconstructed network must be rooted:reticulations only make sense with directed edges.)Clearly,then,a reconstructible network will require changes from the defini-tion of a model network.In particular,the degree constraints must be relaxed to allow arbitrary outdegrees for both network nodes and internal tree nodes.In addition,the time coexistence property must be reconsidered.There are at least two types of problems in reconstructing phylogenetic networks. First,slow evolution may give rise to edges so short that they cannot be reconstructed, leading to polytomies.This problem cannot be resolved within the DAG framework,so we must relax the constraints on the outdegree of tree nodes.Secondly,missing data may lead methods to reconstruct networks that violate indegree constraints or time coexistence.In such cases,we can postprocess the reconstructed network to restore compliance with most of the constraints in the following three steps:1.For each network node w with outdegree larger than1,say with edges(w,v1),...,(w,v k),add a new tree node u with edge(w,u)and,for each i,1≤i≤k, replace edge(w,v i)by edge(u,v i).2.For each network node w whose parents u and v violate time coexistence,addtwo tree nodes w u and w v and replace the two network edges(u,w)and(v,w) by four edges:the two tree edges(u,w u)and(v,w v)and the two network edges (w u,w)and(w v,w).3.For each edge(u,v)where both u and v are network nodes,add a new tree nodew and replace the edge(u,v)by the two edges(u,w)and(w,v).The resulting network is consistent with the original reconstruction,but now satisfiesthe outdegree requirement for network nodes,obeys time coexistence(the introduc-tion of tree edges on the paths to the network node allow arbitrary time delays),andno longer violates the requirement that at least one endpoint of each edge be a tree node.Moreover,this postprocessing is unique and quite simple.We can thus definea reconstructible network in terms similar to a model network.Definition1.6A reconstructible phylogenetic network is a rooted DAG obeying the following constraints:1.Every node has indegree and outdegree defined by one of the three(indegree,outdegree)combinations(0,x),(1,y),or(z,1),for x≥1,y≥0,and z≥2—corresponding to,respectively,root,other tree nodes(internal nodes and leaves),and network nodes.2.If two nodes u and v cannot co-exist in time,then there does not exist a networknode w with edges(u,w)and(v,w).3.Given any edge of the network,at least one of its endpoints must be a tree node.TREES WITHIN NETWORKS:THE GENE TREE SPECIES NETWORK PROBLEM11 Definition1.7A network N induces a tree T if T can be obtained from N by the following two steps:1.For each network node in N,remove all but one of the edges incident into it;and2.for every node v such that indegree(v)=outdegree(v)=1,the parent of vis u,and the child of v is w,remove v and the two edges(u,v)and(v,w),andadd new edge(u,w)(this is referred to in the literature as the forced contractionoperation).For example,the network N shown in Figure1.1(e)induces both trees shown in Figure1.2(a)and Figure1.2(d).1.4.3Reconstructing networks from gene treesFrom a graph-theoretic point of view,the problem can be formulated as pure phylo-genetic network reconstruction(Moret et al.(2004);Nakhleh et al.(2004,2005)).In the case of HGT,and despite the fact the evolutionary history of the set of organ-isms is a network,Lerat et al.(2003)showed that an underlying species tree canstill be inferred.In this case,a phylogenetic network is a pair(T,Ξ),where T is the species(organismal)tree,andΞis a set of HGT edges whose addition to T resultsin a phylogenetic network N that induces all the gene trees.The problem can be formulated as follows.Definition1.8(The HGT Reconstruction Problem)Input:A species tree ST and a set G of gene trees.Output:SetΞof minimum cardinality whose addition to ST yields phylogeneticnetwork N that induces each of the gene trees in G.However,in the case of hybrid speciation,there is no underlying species tree;insteadthe problem is one of reconstructing a phylogenetic network N that induces a givenset of gene trees.Definition1.9(The Hybrid Speciation Reconstruction Problem)Input:A set G of gene trees.Output:A Phylogenetic network N with minimum number of network nodes thatinduces each of the gene trees in G.The minimization criterion reflects the fact that the simplest solution is sought;inthis case,the simplest solution is one with the minimum number of HGT or hybrid speciation events.We illustrate this point with the example species tree ST in Figure1.3(a)and the gene tree GT in Figure1.3(b).Assume that the actual HGT events thattook place are the one depicted in Figure1.3(c).Nonetheless,the scenario depicted。