Genetic Architecture Underlying Nascent Speciation-The Evolution of Eurasian Pigs under Domestication.

Speciation is a process whereby the evolution of reproductive barriers leads to isolated species. Although many studies have addressed large-effect genetic footprints in the advanced stages of speciation, the genetics of reproductive isolation in nascent stage of speciation remains unclear. Here, we show that pig domestication offers an interesting model for studying the early stages of speciation in great details. Pig breeds have not evolved the large X-effect of hybrid incompatibility commonly observed between "good species." Instead, deleterious epistatic interactions among multiple autosomal loci are common. These weak Dobzhansky-Muller incompatibilities confer partial hybrid inviability with sex biases in crosses between European and East Asian domestic pigs. The genomic incompatibility is enriched in pathways for angiogenesis, androgen receptor signaling and immunity, with an observation of many highly differentiated cis-regulatory variants. Our study suggests that partial hybrid inviability caused by pervasive but weak interactions among autosomal loci may be a hallmark of nascent speciation in mammals.

Origins of Polynesian Pigs Revealed by Mitochondrial Whole Genome Ancient DNA.

Domestic pigs (Sus scrofa) were first transported to Polynesia through a series of long-distance voyages ultimately linked to the Neolithic expansion of Austronesian-speaking people out of Asia. The descendants of the founding pigs belong to a rare mtDNA group referred to as the "Pacific Clade" that may have originated in peninsular or island Southeast Asia. We report the first whole genome mtDNA from domestic pigs from any of the remote islands of the Pacific. In this brief report, we describe the close link we discovered between ancient mtDNA from archaeological specimens from across Polynesia and from that of modern pigs in northern peninsular Southeast Asia, specifically southern China's Yunnan Province. More complete mtDNA coverage in commensal animals is necessary to improve our picture of the settlement of Polynesia (ca. 2800-700 years before the present) and specify the route, or routes, that pigs took from northern peninsular Southeast Asia.

Ancient DNA reveals the maternal genetic history of East Asian domestic pigs.

Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generate 42 complete mitochondrial DNA sequences from ∼7500- to 2750-year-old individuals from the Yellow River basin. Our results show that the maternal genetic continuity of East Asian domestic pigs dates back to at least the Early to Middle Neolithic. In contrast, the Near Eastern ancestry in European domestic pigs saw a near-complete genomic replacement by the European wild boar. The majority of East Asian domestic pigs share close haplotypes, and the most recent common ancestor of most branches dates back to less than 20,000 years before present, inferred using new substitution rates of whole mitogenomes or combined protein-coding regions. Two major population expansion events of East Asian domestic pigs coincided with changes in climate, widespread adoption of introduced crops, and the development of agrarian societies. These findings add to our understanding of the maternal genetic composition and help to complete the picture of domestic pig evolutionary history in East Asia.

Pigs as Pets: Early Human Relations with the Sulawesi Warty Pig (Sus celebensis).

The Sulawesi warty pig (S. celebensis) is a wild and still-extant suid that is endemic to the Indonesian island of Sulawesi. It has long been theorised that S. celebensis was domesticated and/or deliberately introduced to other islands in Indonesia prior to the advent of the Neolithic farming transition in the region. Thus far, however, there has been no empirical support for this idea, nor have scientists critiqued the argument that S. celebensis was a pre-Neolithic domesticate in detail. Here, it is proposed that early foragers could have formed a relationship with S. celebensis that was similar in essence to the close association between Late Pleistocene foragers in Eurasia and the wild wolf ancestors of domestic dogs. That is, a longstanding practice of hunter-gatherers intensively socialising wild-caught S. celebensis piglets for adoption into human society as companion animals ('pets') may have altered the predator-prey dynamic, brought aspects of wild pig behaviour and reproduction under indirect human selection and control, and caused changes that differentiated human-associated pigs from their solely wild-living counterparts.