Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids

Plassais, Jocelyn; vonHoldt, Bridgett M.; Parker, Heidi G.; Carmagnini, Alberto; Dubos, Nicolas; Papa, Ilenia; Bevant, Kevin; Derrien, Thomas; Hennelly, Lauren; Whitaker, D. Thad; Harris, Alex C.; Hogan, Andrew N.; Huson, Heather J.; Zaibert, Victor; Linderholm, Anna; Haile, James; Fest, Thierry; Habib, Bilal; Sacks, Benjamin N.; Benecke, Norbert; Outram, Alan K.; Sablin, Mikhail; Germonpré, Mietje; Larson, Greger; Frantz, Laurent; Ostrander, Elaine A.

doi:10.1016/j.cub.2021.12.036

Cited by 33 publications

(35 citation statements)

References 85 publications

(108 reference statements)

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“…Numerous studies have documented the speci c traits acquired in domesticated animals (dog, horse, pig, cow) (Diamond, 2002;Frantz et al, 2015;Petersen et al, 2013;Warmuth et al, 2011) and plants (cabbage, corn, wheat) (Hufford et al, 2012;Mabry et al, 2021;Peng et al, 2011), as well as their genetic differentiation from wild populations and their adaptive genomic changes. For example, domesticated animals (dog, horse and cattle) have been selected for coat color, size, rapidity and docility (Liu et al, 2022;Plassais et al, 2022;Qanbari et al, 2014). On the other hand, functions essential in wild environments but unused in anthropic environments have often degenerated due to relaxed selection, for example, reductions in defense mechanisms in plants (Cornille et al, 2014;Hufford et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Bennetot

Vernadet

Perkins

et al. 2022

Preprint

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Domestication is an excellent model for studying adaptation processes, constituting recent adaptation and diversification, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese-making and is also found in other environments such as soil and plants. By analyzing whole genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three differentiated populations and we detected footprints of recombination and hybridization. The genetic diversity in the cheese clade was the lowest but remained high compared to other domesticated fungi, indicating milder bottlenecks. Commercial starter strains were scattered across the cheese clade, not constituting a single clonal lineage. The cheese clade was phenotypically differentiated from other populations, with a slower growth on all media even cheese, a prominent production of attractive cheese flavors and a lower proteolytic activity. Furthermore, cheese populations displayed contrasted phenotypes, with one cheese population producing a typical blue cheese flavor and another one displaying denser and fluffier colonies, excluding more efficiently cheese spoiler fungi. Cheese populations lost two beta lactamase-like genes, involved in xenobiotic clearance, and displayed transposable element expansion, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into three varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation.

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Section: Introductionmentioning

confidence: 99%

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Bennetot

Vernadet

Perkins

et al. 2022

Preprint

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“…Size reduction is characteristic of many animals under domestication, but the selective forces responsible for generating these changes are debated ( 20 , 21 ). Human intentionality likely drives some of these size changes, but a suite of unintentional actions and nonhuman factors is also surely at work.…”

Section: Resultsmentioning

confidence: 99%

The evolution of dog diet and foraging: Insights from archaeological canids in Siberia

et al. 2022

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Research on the evolution of dog foraging and diet has largely focused on scavenging during their initial domestication and genetic adaptations to starch-rich food environments following the advent of agriculture. The Siberian archaeological record evidences other critical shifts in dog foraging and diet that likely characterize Holocene dogs globally. By the Middle Holocene, body size reconstruction for Siberia dogs indicates that most were far smaller than Pleistocene wolves. This contributed to dogs’ tendencies to scavenge, feed on small prey, and reduce social foraging. Stable carbon and nitrogen isotope analysis of Siberian dogs reveals that their diets were more diverse than those of Pleistocene wolves. This included habitual consumption of marine and freshwater foods by the Middle Holocene and reliance on C 4 foods by the Late Holocene. Feeding on such foods and anthropogenic waste increased dogs’ exposure to microbes, affected their gut microbiomes, and shaped long-term dog population history.

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“…À partir de l'ensemble de ces résultats, les auteurs considèrent que l'allèle ancestral du gène IGF1-AS chez les canidés est l'allèle C (petite taille). L'allèle T (grande taille) serait ensuite apparu il y a plus de cinquante mille ans, car il est présent à l'état hétérozygote dans le génome de loup le plus ancien retrouvé, provenant de la région de la rivière Tirektyakh en Sibérie orientale et daté à -52 500 ans [5]. Cet allèle serait rapidement devenu majoritaire chez les loups, pour lesquels la grande taille présente un avantage sélectif, sans pour autant que l'allèle C ne disparaisse complètement de la population.…”

Section: Histoire éVolutive Des Allèles Du Gène Igf1unclassified

“…C'est à ce locus IGF1, pour lequel il a été montré qu'il était responsable d'environ 15 % de la différence de taille entre races [2], que nous allons nous intéresser maintenant. Il fait l'objet d'un article publié début 2022 [5], émanant d'une quinzaine d'équipes étatsuniennes, françaises, d'autres pays européens, russes et asiatiques et intitulé « Sélection naturelle et dirigée portant sur un variant non codant associé à la taille chez les canidés anciens et modernes » 1 . Vaste programme, qui recouvre en effet un très intéressant ensemble d'études.…”

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Chiens, loups et gènes

Jordan¹

2022

Med Sci (Paris)

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The most significant polymorphism associated with dog size occurs in the region of the IGF1 gene and concerns a single base change in a neighbouring lncRNA. The “small” (C) allele of this SNP is mostly found in small modern breeds and canids (foxes, coyotes, jackals) while the “large” (T) dominates in wolves and large dogs. However, the small allele is also present at low level in ancient wolves and is shown to represent the ancestral allele in canids, which has been recently selected in small dog breeds obtained by human selection.

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Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids

Cited by 33 publications

References 85 publications

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

The evolution of dog diet and foraging: Insights from archaeological canids in Siberia

Chiens, loups et gènes

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