Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

McHugo, Gillian P.; Dover, Michael J.; MacHugh, David E.

doi:10.1186/s12915-019-0724-7

Cited by 60 publications

(53 citation statements)

References 268 publications

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“…Since their domestication, animals have occupied a wide range of roles, from simply being tolerated, to being venerated within ritual practices, to providing humans with other benefits, including food, clothing, material for construction, transportation, herding and hunting. The diversification of phenotypes evident in multiple domesticated taxa have also provided generations of biologists with a key model with which to study evolution 4,5 .…”

Section: [H1] Introductionmentioning

confidence: 99%

Animal domestication in the era of ancient genomics

et al. 2020

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The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have made possible the sequencing of whole ancient genomes and helped researchers to reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in the light of recent contributions from ancient genomics.

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Section: [H1] Introductionmentioning

confidence: 99%

Animal domestication in the era of ancient genomics

et al. 2020

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“…[ 9,10 ] These sequence data yielded insights into the evolutionary and population history of organisms. [ 11‐16 ]…”

Section: Introductionmentioning

confidence: 99%

Present‐Day DNA Contamination in Ancient DNA Datasets

Peyrégne

Prüfer

2020

BioEssays

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Present‐day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.

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“…Nuclear genomes exist for a few ancient wolves and dogs (e.g., Botigué et al., 2017; Frantz et al., 2016; Skoglund et al., 2015), but the financial support for genome sequencing ancient samples for population level characterization and composition is still beyond the resources of even the best funded nonhuman oriented laboratories. However, the future is very promising, for example, in species such as horses and cattle, we are approaching large scale characterization of ancient genomes from which the complexity of ancestry across the Late Pleistocene may be resolved and demographic models based on recent samples better tested (MacHugh, Larson, & Orlando, 2017; McHugo, Dover, & MacHugh, 2019). Ancient DNA population levels studies such as Loog et al.…”

Section: Introductionmentioning

confidence: 99%

Illuminating the mysteries of wolf history

Schweizer

Wayne

2020

Molecular Ecology

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One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter & Stewart 2009; Burbrink et al. 2016). Perhaps such continuity should not be expected as the Pleistocene is marked by episodes of climate change, glaciation and the invasions of humans into previously isolated areas. Although fossils are one of the primary sources for inferring population continuity, a problem with fossil material is that, even if similar morphological forms might exist in a place over time, they may not be from the same genetic lineage. There are now readily available methods to assess genetic continuity solely from DNA found in fossil material, provided the record is fairly continuous. In a From the Cover article in this issue of Molecular Ecology, Loog et al. (2020) apply some of these readily available methods to analyse mitochondrial genomes and model the demography of wolves over the last 50,000 years.

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Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

Cited by 60 publications

References 268 publications

Animal domestication in the era of ancient genomics

Animal domestication in the era of ancient genomics

Present‐Day DNA Contamination in Ancient DNA Datasets

Illuminating the mysteries of wolf history

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