Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.

/pdf/current-perspectives-and-the-future-of-domestication-studies-1k2zua6l88.pdf

Current perspectives and the future of domestication studies

Jack Harlan was a polymath. His life-long study of crop evolution combined plant sciences, archaeology, systematics, genetics, and conservation, leaving a legacy of five decades of influential publications that explored all aspects of crop plants – their origins, their dispersal, and their continued and future role in supporting the Earth’s burgeoning populations. To Harlan, agriculture was not an invention or the product of a single big idea. Instead, he saw agricultural origins in terms of a long co-evolutionary process involving humans and plants that grew out of “many independent tentatives in many locations that fused over time to produce effective food production systems” (Harlan 1995). Harlan’s remarkable body of published work contains only one short encyclopedia entry on the subject of animal domestication (Harlan 1994). He was, in fact, somewhat dismissive of the contribution of animal domesticates to humankind’s food supply stating that “(a)nimals are not essential, plants supply over 90% of the food consumed by humans” (Harlan 1995). Jack Harlan would likely agree, however, that understanding livestock evolution requires the same breadth of focus that he brought to the study of crop evolution. Here I follow Harlan’s example in a consideration of domestic animals, bringing together information from animal sciences, genetics, and archaeology to explore the multiple pathways leading to animal domestication and the implications of these pathways for current and future relationships between humans and their animal partners.

9 Pathways to Animal Domestication

Domestication is an ongoing co-evolutionary process rather than an event or invention. Recent zooarchaeological and animal genetics research has prompted a thorough revision of our perspectives on the history of domestic animals in Africa. Genetic analyses of domestic animal species have revealed that domestic donkeys are descended from African ancestors, opened a debate over the contribution of indigenous aurochs to African domestic cattle, revealed an earlier and possibly exogenous origin of the domestic cat, and reframed our vision of African dogs. Genetic diversity studies and mapping of unique traits in African cattle, sheep, goats, pigs and chickens indicate adaptations to regional environmental challenges and suggest hitherto unknown and complex patterns of interactions both among Africans and with Southwest Asia and other Asian regions on the Indian Ocean. This article argues against the static perspective on domestication as invention and for viewing it as a dynamic, locally based and continuing process.

/pdf/domesticating-animals-in-africa-implications-of-genetic-and-4uh20orwd0.pdf

Domesticating Animals in Africa: Implications of Genetic and Archaeological Findings

Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0–4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1–3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

https://www.pnas.org/content/pnas/111/52/18655.full.pdf

Speciation with Gene Flow in Equids Despite Extensive Chromosomal Plasticity

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

/pdf/ancient-dna-from-nubian-and-somali-wild-ass-provides-4jwqixqmx1.pdf

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Reassessing the evolutionary history of ass-like equids: Insights from patterns of genetic variation in contemporary extant populations

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Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Reassessing the evolutionary history of ass-like equids: Insights from patterns of genetic variation in contemporary extant populations