Cattle demographic history modelled from autosomal sequence variation

Abstract

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus, with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus. Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.

Evaluating the accuracy of genomic prediction of growth and wood traits in twoEucalyptusspecies and their F1hybrids

“…When crossbred data is not available, separate purebred training populations can be used either separately or combined depending on the correlation of LD phase between the pure lines [61], which in turn is in part determined by the time of divergence between the populations. Compared to bovine breeds that belong to the same species and have diverged relatively recently (<300KYA) [62], the estimated divergence time between the two Eucalyptus species used in our study is much older, estimated at 2-5 MYA [63]. We therefore don't expect much correlation of LD phase between the two species and it is thus not surprising that training on the combined pure species sets with validation in F 1 hybrids resulted in poor PA. To the best of our knowledge, our results are the first ones to provide an initial look at the issue of genomic prediction from pure species to interspecific hybrids and our results indicate that, consistent with theoretical expectations, models have to be trained using hybrids if one is to predict phenotypes in hybrid selection candidates.…”

Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection

“…A panel of 10 African (Ndama, Somba, Lagune) B. taurus, 18 European (Aberdeen Angus, Friesian, Norwegian Red, German Black, Highland, Alentejana, Mertolenga, Romagnola, Sikias, Anatolian Black) B. taurus, and 11 Indian (Hariana, Tharparkar, Sahiwal, Ongole) B. indicus were sequenced as previously described (21). Plains bison (Bison bison) was used as an outgroup.…”

“…The locus shows a high level of linkage disequilibrium throughout the 4 kbp sequenced. Interestingly, each of these behaviors was extreme when viewed within the context of results for a total of 18 loci that were wholly or partially resequenced in similar continental cohorts (21,22) (Table S2). These included TNFAIP8L1, a second immunogene also targeted from under the chromosome 7 QTL peak, which gave no outlying behavior, plus several other loci of immunological consequence (e.g., several interleukins and Toll-like receptors), some of which also give indications of adaptive history.…”

Evaluating the roles of directed breeding and gene flow in animal domestication

“…In contrast to pigs, there is no genetic support for interbreeding of domestic taurine cattle with wild cattle as herders moved across Europe (74), the one exception being data from Italy, where ancient mtDNA suggests female aurochs may have been recruited into domestic herds. The picture is different for South Asia, where high autosomal diversity indicates repeated crossing of domestic zebu cattle with wild males and females (75). Multiple mitochondrial lineages represent either two separate domestications or, again, recruitment of wild animals into domestic zebu herds (68).…”