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[QUOTE]Originally posted by Tukuler: [QB] Those "humps" look nothing like those of full bred Zebu cattle to me. [list] [*]we now find strong evidence of [URL=http://underline]exportations from the Indian subcontinent[/URL] to China and southeast Asia, [URL=http://underline]India to Africa[/URL], Africa to the Iberian Peninsula and Mediterranean Europe, India to the Americas, and Europe to the Americas (Figures 4 and ​and5,5, discussed in detail in the following subsections). [/list] [...] [list] [*]The second factor that we believe underlies the divergence of African taurine is a high level of [URL=http://underscore]wild African auroch [30], [31] introgression[/URL]. Principal component (Figure 1), phylogenetic trees (Figures 2 and ​and3),3), and admixture (Figure 6) analyses all reveal the African taurines as being the most diverged of the taurine populations. Because of this divergence, it has been hypothesized that there was a third domestication of cattle in Africa [32]–[36]. If there was a third domestication, African taurine would be sister to the European and Asian clade. When no migration events were fit in the TreeMix analyses, African cattle were the most diverged of the taurine populations (Figures 2 and ​and3),3), but [URL=http://underline]when admixture was modeled to include 17 migrations, all African cattle, except for East African Shorthorn Zebu and Zebu from Madagascar which have high indicine ancestry[/URL], were sister to European cattle and were less diverged than Asian or Anatolian cattle (Figure 4), thus ruling out a separate domestication. Our phylogenetic network (Figure 4) shows that there was not a third domestication process, rather there was a single origin of domesticated taurine (Asian, African, and European all share a recent common ancestor denoted by an asterisk in Figure 4, with Asian cattle sister to the rest of the taurine lineage), followed by admixture with an ancestral population in Africa (migration edge a in Figure 4, which is consistent across 6 separate TreeMix runs, Figure S4). This ancestral population (origin of migration edge a in Figure 4) was approximately halfway between the common ancestor of indicine and the common ancestor of taurine. We conclude that [URL=http://underline]African taurines received as much as 26% (estimated as 0.263 in the network, p-value<2.2e-308) of their ancestry from admixture with wild African auroch, with the rest being Fertile Crescent domesticate in origin[/URL]. Although three other migration edges originate from the branch between indicine and taurine (such as edge b), all of the receiving populations show indicine ancestry in the ADMIXTURE models. But African auroch are extinct and samples were not available for the ADMIXTURE model, thus the admixed auroch ancestry of African taurines cannot specifically be discovered by this model [27], [37] and [URL=http://underline]African taurine, especially Lagune, are depicted as having a single ancestry without indicine influence[/URL] (Figures 5 and ​and6,6, see f3 and f4 statistics reported later). Unlike ADMIXTURE, TreeMix can model admixture from an unsampled population by placing a migration edge more basal along a branch of the phylogeny, in this case African auroch. [/list] [...] [list] [*][b]Indicine admixture in Africa[/b] African cattle also demonstrate a geographical gradient of indicine ancestry [47]. Taurine cattle in western Africa possess from 0% to 19.9% indicine ancestry (Figures 5 and ​and6,6, LAG, ND1, ND2, NDAM, BAO, OUL, SOM), with an average of 3.3%. [URL=http://underline]Moving from west to east and from south to central Africa, the percent of indicine ancestry increases from 22.7% to 74.1%[/URL] (Figures 5 and ​and6,6, ZFU, ZBO, ZMA, BORG, TULI, BOR, SHK, ZEB, ANKW, LAMB, an AFR), with an average of 56.9%. As we increased values of K to 10, 15, and 20 (Figures S8, S9, S10), we revealed [URL=http://underscore]two clusters of indicine ancestry possibly resulting from the previously suggested two waves of indicine importation into Africa, the first occurring in the second millennium BC[/URL] and the second during and after the Islamic conquests [25], [34], [48]. The presence of two separate clades of African cattle in Figure 4 also supports the idea of two waves of indicine introgression. [/list] [b]Jared E. Decker[/b] et al[i] Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle[/i] PLoS Genet. Mar 2014; 10(3): e1004254. See also http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967955/figure/pgen-1004254-g005/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967955/figure/pgen-1004254-g006/ [/QB][/QUOTE]
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