Genomics of domestication in chicken and cattle

Two recent studies attempt to understand the process of adaptive evolution in domestication and artificial selection by characterizing (a) sweeps, and their association with phenotypes in extant hybrid lines (Sheng et al. 2015), and (b) phylogenomic position of an extinct wild ancestor (Park et al. 2015).
Sheng et al. (2015) – Selection in Virginia chicken lines

HWS and LWS lines from the Virginia chicken experiment. Image courtesy:

Artificial selection experiments provide a classic means to study the genomic consequences of accelerated adaptive evolution, and differentiating between standing genetic variation and novel polymorphisms that contribute to the evolution of advantageous phenotypes. Sheng et al. (2015) estimate the genome-wide effects of long-term bi-directional selection on 56-day body weight in experimental populations of Virginia chicken lines, derived from a common ancestral population, and characterize sweeps contributing to adaptive evolution. Specifically, by genotyping (at 106 sweep loci, previously identified to be fixed for alternate alleles) and phenotyping a large F15 line (Advanced Intercrossed Line – AIL) of hybrids from body weight variant lines, Sheng et al. (2015) report (1) 99 sweeps to be potentially adaptive, (2) most identified alternate alleles at sweeping loci were associated with increased weight, (3) significant association of the length of sweeping loci with strength of selection, (4) sweeping alleles were likely present in the ancestor, thus stressing the role of standing genetic variation in adaptive evolution.

A large number of loci, each having small allele-substitution effects, were major contributors to the selectable additive variance during adaptation. The loci that were fixed in the divergent lines after 40 generations of selection contributed much of the variation in the base population, thus providing empirical support for earlier work that has suggested that initial selection response is likely to result from selection on standing genetic variation…In summary, these results provide not only novel insights to the genetics contributing to the gradual, continued, long-term response to selection in the Virginia lines, but also to the fundamental genetic mechanisms contributing to selection and adaptation.

Park et al. 2015 – Evolutionary history of wild aurochs

Extinct wild aurochs (Bos primigenius) skeleton. Image courtesy:

Domestication of the now extinct wild auroch, Bos primigenius gave rise to two the now extant cattle species, Bos taurus and Bos indicus, previously reported to have occurred in the Near East and Southwest Asia. Park et al. (2015) sequence the genome of B. primigenius from bone powders extracted from six well preserved aurochs bones of the CPC98 sample. Upon alignment the B. taurus genome, the CPC98 sample was determined to be from a male, and > 5 million variants were identified, with > 2 million SNP’s passing quality filters. A maximum likelihood phylogenetic tree constructed using ~15k SNP’s across the CPC98 sample, and 1228 extant B. taurus and B. indicus cattle supports separate domestic origins of the two extant species, and the CPC98 sample as an outgroup to the modern B. taurus clade, also corroborated by a PCA. Analyses of population structure however reveal the presence of three putative subpopulations (European, African, and zebu) in the CPC98 sample, indicating that several of the allelic variants now private to extant clades may have been present more widely prior to domestication. ABBA-BABA tests of genomic admixture between aurochs and extant European taurine cattle also provide significant support for gene flow from the now extinct B. primigenius into European cattle, also shown by their TreeMix analyses. HKA tests of selection in the B. taurus lineage identified several regions under positive selection, and characterized several functional elements involved in neurobiology, muscle development and function, and immune response genes.

First 2 PC’s of variation using SNP data from B. taurus, B. indicus, and B. primigenius lines. Image courtesy: Park et al. (2015)

Sequencing data from the aurochs genome provides an important reference for testing hypotheses regarding the genetic consequences of recent artificial and natural selection in modern cattle. In addition, future analyses of whole-genome sequences from modern animals and additional aurochs samples will refine the catalogue of genomic loci that contribute to key functional traits in domestic cattle.

Sheng, Z, et al. (2015) Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment. Genome Biology. DOI: 10.1186/s13059-015-0785-z
Park, S, et al. (2015) Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biology. DOI: 10.1186/s13059-015-0790-2

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