物种起源导论03_家养条件下的变异(2)

Hypotheses
Two major hypotheses, suggesting either a single origin of cultivated rice or multiple, geographically independent domestications from its wild ancestor, have been proposed.
Jason P. Londo, Yu-Chung Chiang, Kuo-Hsiang Hung, Tzen-Yuh Chiang, and Barbara A. Schaal Department of Biology, Washington University, St. Louis, MO 63130;§Department of Life Sciences, Pingtung University of Science and Technology, Pingtung, Taiwan 912; and¶ Department of Life Sciences, Cheng Kung University, Tainan, Taiwan 701
设得兰马 Shetland
Thoroughbred 纯血马
Asian Breeds
Akhal Teké 阿克哈-塔克马
Arabian Horse阿拉伯马
Caspian Pony 里海小型马
Malwari horse 马尔瓦尔马
Khuzestan Arab horse（图片未见） Thai Pony 泰国小型马（图片未见）
普氏野马 Przewalski's horses (Equus caballus przewalskii)
Nature Genetics 36(4), 2004
All stallions carried the same Y-chromosome haplotype. Limited polymorphism is not a general feature of equine nuclear DNA. By determining the orthologous X- and Y-chromosome sequence in donkey, strong statistical support for lower levels of variability on Y than on X in horse. ―We sequenced one male Przewalski's horse for all Y-chromosome fragments and found that it differed from all domestic horses at six nucleotide positions over the 14.3 kb and also had a 7-bp deletion. ―
马
斑马
驯鹿
麋鹿
绵羊 加拿大盘羊
牛
非洲水牛
山羊
落基山山羊
?
橡树
PNAS. 2006. 103: 9578-9583
Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa 普通野生稻的系统发育地理学研究 揭示了亚洲栽培稻经历过多次独立驯化
The gene regions selected: 3 gene regions, one of chloroplast and two of nuclear. (1) atpB-rbcL A gene region of chloroplast a maternally inherited marker, contains a good representation of genetic variation in cultivated and wild rice. (2) p-VATPase A region of a nuclear pseudogene , under little selective constraint, a neutral region. (3) SAM S-腺苷甲硫氨酸合成酶基因 (S-adenosyl methionine synthetase) A functional nuclear gene, a representative of gene regions that have been influenced by the forces of selection.
Objectives
(1) To examine the DNA sequence variation in cultivated and wild rice (2) To examine the geographic pattern of cultivated and wild haplotypes (3) To determine the number of potential domestication events and precise geographical locations of domestication
The data suggest that using a limited number of stallions in breeding may be traditional breeding practice and thus date back to the initial phase of horse domestication. In general, food production is maximized if most males are consumed and females are left for reproduction; such a sex bias in exploitation of several domestic animals is suggested from archaeological records. The observations do not exclude the possibility that the equine Y chromosome was low in variability before the time of domestication.
家养条件下的变异 (续) ——典型案例
European Breeds
Ardennais 阿登纳斯马（重型马）
Connemara 康尼马拉马
Exmoor 埃克斯穆尔马
Fjord 挪威峡湾马
Gotland horse哥德兰马
Icelandic horse 冰岛马
North-Swedish horse 北方瑞典马
新月沃地
野生四倍体二粒小麦 Triticum dicoccoides
小麦 Wheat
野生大麦 Hordeum spontaneum
大麦 barley
豌豆 peas
小扁豆 lentils
野高粱 Sorghum bicolor ssp. verticilliflorum
1-3 domestication events
Study System —— Phylogeographic approch
(1) To examine the variations between the haplotypes of cultivated and wild rice.
(2) To construct haplotype network base on genetic diversity and genetic distance. (3) To draw conclusions from genetic and scussion DNA Sequence Variation
aligned base pairs polymorphic sites
atpB-rbcL p-VATPase SAM
801 1, 300 1,166
50 66 53
6.24% 5.07% 4.55%
Tests of neutrality
高粱 Sorghum bicolor var. bicolor
Although the domestication of rice from its wild ancestor Oryza rufipogon is documented and occurred somewhere in east Asia, the number of domestications and precise geographical location of domestication are debated.
Asian wild rice
Oryza nivara
Oryza rufipogon
Cultivated rice
粳稻 O. sativa ssp. japonica
籼稻 O. sativa ssp. indica
药用野生稻 O. officinalis Wall ex Watt
The Background of Genus Oryza
Based on Y-chromosome data, the split between Przewalski's horse and domestic horses is estimated to have occurred 120,000 −240,000 years ago. As this is long before wild horses were domesticated (6,000 years ago), wild horses may have had Ychromosome variability before domestication. A randomization test provided strong statistical support for a significant difference in Y-chromosome polymorphism levels between horses and humans (P < 0.0001).