Reply to Wang et al.: Sequencing datasets do not refute Central Asian domestication origin of dogs

Shannon, Laura M.; Boyko, Ryan H.; Castelhano, Marta G.; Corey, Elizabeth; Hayward, Jessica J.; McLean, Corin; White, Mary H.; Said, Mounir R. Abi; Anita, Baddley A.; Bondjengo, Nono Ikombe; Calero, Jorge; Galov, Ana; Hedimbi, Marius; Imam, Bulu; Khalap, Rajashree; Lally, Douglas; Masta, Andrew; Oliveira, Kyle C.; Pérez, Lucía Pérez; Randall, Julia; Tam, Nguyen Minh; Trujillo-Cornejo, Francisco J.; Valeriano, Carlos; Sutter, Nathan B.; Todhunter, Rory J.; Bustamante, Carlos D.; Boyko, Adam R.

doi:10.1073/pnas.1600618113

Cited by 1 publication

(3 citation statements)

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“…These LD patterns were called into question by an analysis that added LD data from East Asian village dogs based upon whole-genome sequencing, which found they had lower LD than Central Asian village dogs (50). However, this finding was attributed to negative bias in LD estimates arising from the low-coverage nature of these genome sequences (51).…”

Section: Regional Modelmentioning

confidence: 99%

“…Notably, there is substantial geographic structure in Chinese wolves, which can add to diversity of dogs that are geographically overlapping with them (15,20). Admixture from Asian wolves into dogs would elevate metrics of genetic diversity in ways that do not reflect their genetic ancestry and may be a problem for studies that do not use explicit demographic models that account for admixture (e.g., 48,51).…”

Section: The Admixture Problemmentioning

confidence: 99%

“…As bottlenecks associated with breed formation strongly reduce genetic diversity (2,22,44,67,68) and increase LD, this is not an appropriate comparison. Sequencing strategies can also influence LD patterns, such as a negative bias when inferences are based on low-coverage data (51). Finally, there is the problem of biological versus statistical significance.…”

Section: Demography Genetic Diversity and Linkage Disequilibriummentioning

confidence: 99%

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Deciphering the Origin of Dogs: From Fossils to Genomes

Freedman

Wayne

2017

Annu. Rev. Anim. Biosci.

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Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements. In addition, because the domestication of dogs occurred in the relatively recent past, much of the observed polymorphism may be shared between dogs and wolves, limiting the power to distinguish between alternative models of dog history. Greater insight into the domestication process will require explicit tests of alternative models of domestication through the joint analysis of whole genomes from modern lineages and ancient wolves and dogs from across Eurasia.

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Section: Regional Modelmentioning

confidence: 99%