Ancient genomic changes associated with domestication of the horse

Librado, Pablo; Gamba, Cristina; Gaunitz, Charleen; Sarkissian, Clio Der; Pruvost, Mélanie; Albrechtsen, Anders; Fages, Antoine; Khan, Naveed; Schubert, Mikkel; Jagannathan, Vidhya; Serres‐Armero, Aitor; Kuderna, Lukas F. K.; Povolotskaya, Inna; Seguin-Orlando, Andaine; Lepetz, Sébastien; Neuditschko, Markus; Thèves, Catherine; Alquraishi, Saleh A.; Alfarhan, Ahmed H.; Al‐Rasheid, Khaled A. S.; Rieder, Stefan; Samashev, Z.; Francfort, Henri‐Paul; Benecke, Norbert; Hofreiter, Michael; Ludwig, Arne; Keyser, Christine; Marquès-Bonet, Tomàs; Ludes, Bertrand; Crubézy, Éric; Leeb, Tosso; Willerslev, Eske; Orlando, Ludovic

doi:10.1126/science.aam5298

Cited by 203 publications

(186 citation statements)

References 148 publications

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“…A corollary of this scenario regards the mutation load, which hitherto has been regarded as a “cost of domestication.” Under a continuous erosion of genetic diversity through repeated bottlenecks, we should expect a pattern in which mutation load increases over time. This notion is supported by recent findings in which the mutation load in horses was found to increase some time after domestication (Librado et al., ). In the case of sorghum, mutation load was found to increase over time and significantly correlate with signals of selection (Smith et al., ).…”

Section: Resultsmentioning

confidence: 99%

A re‐evaluation of the domestication bottleneck from archaeogenomic evidence

Allaby

Ware

Kistler

2018

Evolutionary Applications

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Domesticated crops show a reduced level of diversity that is commonly attributed to the “domestication bottleneck”; a drastic reduction in the population size associated with subsampling the wild progenitor species and the imposition of selection pressures associated with the domestication syndrome. A prediction of the domestication bottleneck is a sharp decline in genetic diversity early in the domestication process. Surprisingly, archaeological genomes of three major annual crops do not indicate that such a drop in diversity occurred early in the domestication process. In light of this observation, we revisit the general assumption of the domestication bottleneck concept in our current understanding of the evolutionary process of domestication.

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Section: Resultsmentioning

confidence: 99%

A re‐evaluation of the domestication bottleneck from archaeogenomic evidence

Allaby

Ware

Kistler

2018

Evolutionary Applications

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“…Recent studies of ancient DNA extracted from ancient maize, for example, have made it possible to track the appearance of specific domestication genes in this important crop plant as it moved from the heartland of initial domestication in southwestern Mexico up through central Mexico and into the southwestern USA [94,140,141]. Another recent study of ancient DNA extracted from horse skeletal remains finds evidence of enrichment for genes involved in androgen and steroid hormone receptor binding indicative of the selective pressures for behavioural and cognitive changes central to animal domestication [142]. This same study also found evidence for enrichment of genes affecting tissues and cell types derived from the neural crest that lends support for the hypothesis that the neural crest development is involved in the variety of associated traits commonly found in domestic animals [73].…”

Section: Directionalitymentioning

confidence: 99%

Domestication as a model system for the extended evolutionary synthesis

Zeder

2017

Interface Focus.

119

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One of the challenges in evaluating arguments for extending the conceptual framework of evolutionary biology involves the identification of a tractable model system that allows for an assessment of the core assumptions of the extended evolutionary synthesis (EES). The domestication of plants and animals by humans provides one such case study opportunity. Here, I consider domestication as a model system for exploring major tenets of the EES. First I discuss the novel insights that niche construction theory (NCT, one of the pillars of the EES) provides into the domestication processes, particularly as they relate to five key areas: coevolution, evolvability, ecological inheritance, cooperation and the pace of evolutionary change. This discussion is next used to frame testable predictions about initial domestication of plants and animals that contrast with those grounded in standard evolutionary theory, demonstrating how these predictions might be tested in multiple regions where initial domestication took place. I then turn to a broader consideration of how domestication provides a model case study consideration of the different ways in which the core assumptions of the EES strengthen and expand our understanding of evolution, including reciprocal causation, developmental processes as drivers of evolutionary change, inclusive inheritance, and the tempo and rate of evolutionary change.

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“…Admittedly, genealogies for significant candidate genomic regions identified by whole‐genome scans can be reconstructed and used to specify the branch on which a sweep most likely occurred (as in Fariello et al., ). Nonetheless, with a growing interest in evolutionary histories of ancestral populations (Basu, Sarkar‐Roy, & Majumder, ; Fraser, Künstner, Reznick, Dreyer, & Weigel, ; Johnson & Voight, ; Jones et al., ; Librado et al., ; Lindo et al., ; Mondal et al., ; Racimo et al., ), it is important to develop methods that can directly address hypotheses about shared ancestral selection, as they will permit ease of interpretation of candidate signals, and may exhibit improved power over methods that are not designed for this specific purpose.…”

Section: Introductionmentioning

confidence: 99%

Fast and robust detection of ancestral selective sweeps

Cheng

DeGiorgio

2017

Molecular Ecology

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There are few methods tailored for detecting signals of positive selection in populations directly ancestral to multiple descendent populations. We introduce the ancestral branch statistic (ABS), a four-population summary statistic for identifying selective sweeps occurring in the direct ancestor of a pair of populations. Simulations show that ABS performs at least as well as, and often better under model violations, than the complementary likelihood approach of 3P-CLR across diverse selection scenarios and parameter values. We first applied ABS to contemporary human genomic data to identify genes that may have been adaptive in ancestral East Asian populations, uncovering the well-established candidate EDAR, as well as a novel candidate SLC35F3, which encodes a putative thiamine transporter that may have been involved in adaptation to eating polished grains. Next, we performed scans with ancient European genomic data to reexamine evidence of recent positive selection in ancestral Europeans. The MCM6/LCT cluster and the SLC45A2 and HERC2 genes are strong outliers, agreeing with previous studies. Novel candidates, such as SLC30A9 and CYP1A2, may have been involved in adaptation to local nutrient sufficiency and lifestyle changes. Finally, we provide open-source software, CalcABS, which can perform genomic scans of ancestral sweeps with ABS from population allele frequency data.

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Ancient genomic changes associated with domestication of the horse

Cited by 203 publications

References 148 publications

A re‐evaluation of the domestication bottleneck from archaeogenomic evidence

A re‐evaluation of the domestication bottleneck from archaeogenomic evidence

Domestication as a model system for the extended evolutionary synthesis

Fast and robust detection of ancestral selective sweeps

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