IntroductiontoMolecularSystematics：分子系统学导论
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From W. P. Maddison (1997), Systematic Biology 46:527
Orthology vs. Paralogy
• DNA sequences that are at homologous loci are orthologous
• DNA sequences that are similar due to duplication but are at different loci are paralogous
• DNA code is read and converted to protein in two steps
– Transcription: DNA is copied to messenger RNA – Translation: messenger RNA is template for protein
positions = 43)
M acintosh PICT im age form at
is not supported
From Raven et al. (1999), Biology of Plants
DNA functional classes
• Coding
– Proteins (exons) – Ribosomes (RNA) – Transfer RNA
Chemistry of Genes
• DNA • Parallel strands linked together • Linear array of units called nucleotides
– Phosphate – Sugar: deoxyribose – One of four bases
• Assess orthology • Align sequences • Homology is often implicit (is this a good
thing?)
DNA Sequences and Homology
• Homology: similarity due to common descent
M acintosh PICT M acin to sh P IC T Macintosh PICT im age form at im ag e fo rm at image format is not supported is n o t su p p o rted is not supported
M a c in to s h P IC T im a g e fo rm a t
is n o t s u p p o rte d
© W. S. Judd, et al., Plant Systematics
Phylogenetic data
• Morphology
• Secondary chemistry
• “Non-coding”
– Introns – Spacers
Macintosh PICT im age form at is not supported
From Raven et al. (1999), Biology of Plants
Homology in Molecular Systematics
severed between populations • Phylogenetic relationships depicted as a tree
M acin to sh P IC T im ag e fo rm at
is n o t su p p o rted
© W. S. Judd, et al., Plant Systematics
M acin to sh P IC T im ag e fo rm at
is n o t su p p o rted
M acintosh P IC T im age form at
is not supported
M acintosh PIC T im age form at
is not supported
• Genes located in the nucleus are the nuclear genome
• Other genomes (organellar)
– Mitochondrion: mitochondrial genome – Chloroplast: plastid genome
mitochondrion
is not supported
gila monster
Macintosh PICT image format is not supported
gopher tortoise
?
kingsnake
Phylogeny
• Branching history of evolutionary lineages • New branches arise via speciation • Speciation occurs when gene flow is
Simple Sequence Alignment
Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6
GTACGTTG GTACGTTG GTACGTTG GTACATTG GTACATTG GTACATTG
– A & G are purines – C & T are pyrimidines
DNA function
• DNA is code for making proteins (and a few other molecules)
• Proteins are the structures and enzymes that catalyze biochemical reactions that are essential for the function of an organism
Introduction to Phylogenetic Systematics
Mark Fishbein
Dept. Biological Sciences Mississippi State University
13 October 2003
Which of these critters are most closely related?
• How do we assess homology of DNA sequences?
• Levels of homology
– Locus – Allele – Nucleotide position
M acintosh P IC T im age form at
is not supported
• Cytology
• Allele frequencies
} • Protein sequences
• Restriction sites
“Molecular” data
• DNA sequences
Molecular (genetic) data
• Proteins
– Serology (immunoassay) – Isozymes (electrophoretic variants) – Amino acid sequences
• How does the DNA code get translated into protein?
DNA code
• Each amino acid is coded for by at least one triplet of nucleotide bases in DNA
• Each triplet is called a codon • There are 64 possible codons (4 bases, 3
• Orthology may be best detected with a phylogenetic analysis of all sequences
Macintosh PICT image format is not supported
From Martin & Burg (2002), Systematic Biology 51:578
nucleus chloroplast
From Raven et al., 1999, Biology of Plants
Comparison of Genomes
Nuclear Mitochondrial Plastid
Size
Large
Small
Small
Number
Multiple Single
From Raven et al. (1999), Biology of Plants
DNA structure
• Paired strands are linked by bases
– A must bond with T – G must bond with C
• Each link is composed of a purine and a pyrimidine
Macintosh PICT image format is not supported
image format is notsupported
From Raven et al. (1999), Biology of Plants
Genomes
• All of the genes within a cell are the genome
• Adenine (“A”) • Cytosine (“C”) • Guanine (“G”) • Thymine (“T”)
源自文库
Macintosh PICT Macintosh PICT image format image format is notsupported is not supported
is n o t s u p p o rte d
Crossing over, duplication, and loss
M a c in to s h P IC T im a g e fo rm a t
is n o t s u p p o rte d
From Freeman and Herron (1998), Evolutionary Analysis
M acintosh PICT im age form at is not supported
purple gallinule
M acin to sh P IC T im ag e fo rm at
is n o t su p p o rted
alligator
M acintosh P IC T im age form at
Single
Shape of
Linear
Chromosomes
Ploidy
Diploid
Circular Haploid
Circular Haploid
Inheritance Biparental Uniparental Uniparental
Structural rearrangements
M a c in to s h P IC T i m a g e f o r m a t Inversion
DNA code
• A gene is a code composed of a string of nucleotide bases (A’s, C’s, G’s, T’s)
• A protein is composed of a string of amino acids (there are 20)
• DNA
– Structural (translocations, inversions, duplications)
– Restriction sites – DNA sequences
• Substitutions • Insertions/Deletions
What are genes?
Macintosh PICT
Multiple Sequence Alignment
• Goal: create data matrix in which columns are homologous positions
• Problem: sequences vary in length • Why?
– Insertions – Deletions
Orthology vs. Paralogy
• DNA sequences that are at homologous loci are orthologous
• DNA sequences that are similar due to duplication but are at different loci are paralogous
• DNA code is read and converted to protein in two steps
– Transcription: DNA is copied to messenger RNA – Translation: messenger RNA is template for protein
positions = 43)
M acintosh PICT im age form at
is not supported
From Raven et al. (1999), Biology of Plants
DNA functional classes
• Coding
– Proteins (exons) – Ribosomes (RNA) – Transfer RNA
Chemistry of Genes
• DNA • Parallel strands linked together • Linear array of units called nucleotides
– Phosphate – Sugar: deoxyribose – One of four bases
• Assess orthology • Align sequences • Homology is often implicit (is this a good
thing?)
DNA Sequences and Homology
• Homology: similarity due to common descent
M acintosh PICT M acin to sh P IC T Macintosh PICT im age form at im ag e fo rm at image format is not supported is n o t su p p o rted is not supported
M a c in to s h P IC T im a g e fo rm a t
is n o t s u p p o rte d
© W. S. Judd, et al., Plant Systematics
Phylogenetic data
• Morphology
• Secondary chemistry
• “Non-coding”
– Introns – Spacers
Macintosh PICT im age form at is not supported
From Raven et al. (1999), Biology of Plants
Homology in Molecular Systematics
severed between populations • Phylogenetic relationships depicted as a tree
M acin to sh P IC T im ag e fo rm at
is n o t su p p o rted
© W. S. Judd, et al., Plant Systematics
M acin to sh P IC T im ag e fo rm at
is n o t su p p o rted
M acintosh P IC T im age form at
is not supported
M acintosh PIC T im age form at
is not supported
• Genes located in the nucleus are the nuclear genome
• Other genomes (organellar)
– Mitochondrion: mitochondrial genome – Chloroplast: plastid genome
mitochondrion
is not supported
gila monster
Macintosh PICT image format is not supported
gopher tortoise
?
kingsnake
Phylogeny
• Branching history of evolutionary lineages • New branches arise via speciation • Speciation occurs when gene flow is
Simple Sequence Alignment
Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6
GTACGTTG GTACGTTG GTACGTTG GTACATTG GTACATTG GTACATTG
– A & G are purines – C & T are pyrimidines
DNA function
• DNA is code for making proteins (and a few other molecules)
• Proteins are the structures and enzymes that catalyze biochemical reactions that are essential for the function of an organism
Introduction to Phylogenetic Systematics
Mark Fishbein
Dept. Biological Sciences Mississippi State University
13 October 2003
Which of these critters are most closely related?
• How do we assess homology of DNA sequences?
• Levels of homology
– Locus – Allele – Nucleotide position
M acintosh P IC T im age form at
is not supported
• Cytology
• Allele frequencies
} • Protein sequences
• Restriction sites
“Molecular” data
• DNA sequences
Molecular (genetic) data
• Proteins
– Serology (immunoassay) – Isozymes (electrophoretic variants) – Amino acid sequences
• How does the DNA code get translated into protein?
DNA code
• Each amino acid is coded for by at least one triplet of nucleotide bases in DNA
• Each triplet is called a codon • There are 64 possible codons (4 bases, 3
• Orthology may be best detected with a phylogenetic analysis of all sequences
Macintosh PICT image format is not supported
From Martin & Burg (2002), Systematic Biology 51:578
nucleus chloroplast
From Raven et al., 1999, Biology of Plants
Comparison of Genomes
Nuclear Mitochondrial Plastid
Size
Large
Small
Small
Number
Multiple Single
From Raven et al. (1999), Biology of Plants
DNA structure
• Paired strands are linked by bases
– A must bond with T – G must bond with C
• Each link is composed of a purine and a pyrimidine
Macintosh PICT image format is not supported
image format is notsupported
From Raven et al. (1999), Biology of Plants
Genomes
• All of the genes within a cell are the genome
• Adenine (“A”) • Cytosine (“C”) • Guanine (“G”) • Thymine (“T”)
源自文库
Macintosh PICT Macintosh PICT image format image format is notsupported is not supported
is n o t s u p p o rte d
Crossing over, duplication, and loss
M a c in to s h P IC T im a g e fo rm a t
is n o t s u p p o rte d
From Freeman and Herron (1998), Evolutionary Analysis
M acintosh PICT im age form at is not supported
purple gallinule
M acin to sh P IC T im ag e fo rm at
is n o t su p p o rted
alligator
M acintosh P IC T im age form at
Single
Shape of
Linear
Chromosomes
Ploidy
Diploid
Circular Haploid
Circular Haploid
Inheritance Biparental Uniparental Uniparental
Structural rearrangements
M a c in to s h P IC T i m a g e f o r m a t Inversion
DNA code
• A gene is a code composed of a string of nucleotide bases (A’s, C’s, G’s, T’s)
• A protein is composed of a string of amino acids (there are 20)
• DNA
– Structural (translocations, inversions, duplications)
– Restriction sites – DNA sequences
• Substitutions • Insertions/Deletions
What are genes?
Macintosh PICT
Multiple Sequence Alignment
• Goal: create data matrix in which columns are homologous positions
• Problem: sequences vary in length • Why?
– Insertions – Deletions