November 14, 2012

Pig genome + admixture into European wild boars

Of interest: 
The domestic pig (Sus scrofa) is a eutherian mammal and a member of the Cetartiodactyla order, a clade distinct from rodent and primates, that last shared a common ancestor with humans between 79 and 97 million years (Myr) ago1,2 ( Molecular genetic evidence indicates that Sus scrofa emerged in South East Asia during the climatic fluctuations of the early Pliocene 5.3–3.5 Myr ago. Then, beginning ~10,000 years ago, pigs were domesticated in multiple locations across Eurasia3 (Frantz, L. A. F. et al., manuscript submitted).

We found a clear signal for admixture between North Chinese and European populations of wild boars that we interpret as migrations across Eurasia during the later stage of the Pleistocene (Supplementary Table 24). Moreover, this hypothesis is further supported by the high value of concordance factor on the X chromosomes (Supplementary Table 20). The demographic analysis shows that the last glacial maximum (LGM)-induced bottleneck had similar magnitude in Europe and North China (Figure 2, main text). Together, these evidences suggest the existence of another (besides Asian + European) biogeographic zone for pigs, extending across North Eurasia. 
There was a strong signal for admixture from Asian into European breeds. We found that European domestic breeds such as Landrace and Large White have a significant amount of Asian genetic material (Supplementary Table 24). This admixture is likely to be due to importation of Chinese breeds into Europe (especially UK) at the onset of the 'agricultural' revolution in the late 18th and 19th century.
Nature 491, 393–398 (15 November 2012) doi:10.1038/nature11622

Analyses of pig genomes provide insight into porcine demography and evolution

Martien A. M. Groenen et al.

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.



terryt said...

"Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago"

So once mere we find species that split as long as a million years ago freely able to interbreed. How on earth does anyone still justify a belief that modern humans and Neanderthals were only just able to form hybrids?

Tom Bridgeland said...

Not all species respond the same way. It depends on where on the chromosome the mutations appear, and what kind of mutation. Even among a single species there are individuals who are not interfertile, though they are both fertile with other partners.