Genomic responses to selection for tame/aggressive behaviors in the silver fox (<i>Vulpes vulpes</i>)

Wang, Xiaozhu; Pipes, Lenore; Trut, Lyudmila N.; Herbeck, Yury; Vladimirova, Anastasiya V.; Гулевич, Р. Г.; Kharlamova, Anastasiya V.; Johnson, Jennifer L.; Acland, Gregory M.; Kukekova, Anna V.; Clark, Andrew G.

doi:10.1101/228544

Cited by 26 publications

(54 citation statements)

References 55 publications

(39 reference statements)

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“…Another strong candidate region is the protocadherin gene cluster, associated with neuronal functions in humans and mice [75][76][77], and shown to be under positive selection in domesticated cats and foxes [78,79]. GRoSS identifies this region as under selection in the Romanian Grey breed terminal branch.…”

Section: Discussionmentioning

confidence: 99%

“…They have been implicated in mental retardation and epilepsy in humans [76] and in fear-conditioning and memory in mice [77], and have also been shown to be under selection in cats [78]. Genes of the protocadherin family have also been detected to have expression and allele frequency differences consistent with adaptation in an analysis of tame and aggressive foxes [79].…”

Section: Cattle Breeding: Morphology Tameness and Milk Yieldmentioning

confidence: 99%

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Identifying loci under positive selection in complex population histories

Refoyo-Martínez

Fonseca

Halldórsdóttir

et al. 2018

Preprint

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Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called Graph-aware Retrieval of Selective Sweeps (GRoSS )-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.

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Section: Discussionmentioning

confidence: 99%

Section: Cattle Breeding: Morphology Tameness and Milk Yieldmentioning

confidence: 99%

Identifying loci under positive selection in complex population histories

Refoyo-Martínez

Fonseca

Halldórsdóttir

et al. 2018

Preprint

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“…Consistent with this, genomic studies highlight evidence of selection upon genes associated with neural crest development, in e.g. domesticated foxes [3], horses [4] and dogs [5]. However, genes associated with neural crest development were only a subset of many showing selective signatures, complicating assessment of the single developmental source hypothesis for DS phenotypes.…”

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confidence: 90%

Morphology does not covary with predicted behavioural correlations of the domestication syndrome in dogs

Wheat

Bijl

2019

Preprint

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11 Domesticated animals display suites of morphological, behavioural and physiological 12 differences compared to their wild ancestors, a phenomenon known as the 13 domestication syndrome (DS). Domestication experiments, and the convergent 14 patterns seen across domesticated species, have been adduced to support a singular 15 developmental source for the DS. Specifically, the suite of DS traits are hypothesized 16 to arise via selection solely upon tameness [1] resulting in neural crest deficit, which 17 as a developmental by-product gives rise to morphological changes such as white 18 pigmentation and floppy ears [2]. Consistent with this, genomic studies highlight 19 evidence of selection upon genes associated with neural crest development, in e.g. 20 domesticated foxes [3], horses [4] and dogs [5]. However, genes associated with 21 neural crest development were only a subset of many showing selective signatures, 22Results). Then, to test for a moderating effect of breed morphology on behaviour, we 59 designed a Bayesian phylogenetic multilevel meta-analytic model. This model uses 60 the estimated effect sizes from the correlations as its response variable and compares 61 the average effect size between morphological categories. The level of support and 62 effect of morphology were allowed to vary between the different predicted 63 associations through the inclusion of group level effects. We also accounted for 64 repeated measures from the same breeds, as well as the non-independence of breeds 65 due to shared ancestry. We performed two versions of this nested meta-analysis. To 66 test whether the presence of floppy ears, curly tails or white pigmentation predicts the 67 strength of any of the behavioural correlations, we evaluated these traits as binary 68 Supplemental information 103Supplemental information including methods, statistical analyses, two figures and 104 supplemental results can be found with this article online at [link] 105 106 Acknowledgements 107We thank Rasmus Erlandsson for designing the dog illustrations in Figure 1a. 108

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“…This set of common features, impacting on the skull/brain, the face, or the skin, but also on development (paedomorphosis and neotenous behavior, reduction of sexual dimorphism, tameness) has been hypothesized to result from the hypofunction of the neural crest (NC) (Wilkins et al 2014). Recent genomic analyses of dogs and domesticated foxes have revealed enrichments of genes linked to neural crest function (Pendleton et al, 2018;Wang et al, 2018). Signs of self-domestication in humans have increased in recent times (reviewed in Hare, 2017).…”

Section: Introductionmentioning

confidence: 99%

Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis

Benítez‐Burraco

Chekalin

Брускин

et al. 2019

Preprint

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Human evolution resulted from changes in our biology, behavior, and culture. One source of these changes has been hypothesized to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. In this paper we compare whole-genome data between Late Neolithic/Bronze Age individuals and modern Europeans and show that some genes associated with self-domestication and with neural crest development and function in mammals are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. We discuss how these changes might account for the exacerbation of features linked to self-domestication and more generally, together with other factors like dietary or social changes, for subtle changes in human cognition and behavior, including language.

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Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes)

Abstract: show significant allele frequency differences between tame and aggressive population (1% 12 FDR), including genes with a role in neural crest cell fate determination.

Cited by 26 publications

References 55 publications

Identifying loci under positive selection in complex population histories

Identifying loci under positive selection in complex population histories

Morphology does not covary with predicted behavioural correlations of the domestication syndrome in dogs

Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis

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