Genetic diversity in global chicken breeds as a function of genetic distance to the wild populations

Abstract

26Migration of populations from their founder population is expected to cause a reduction in 27 genetic diversity and facilitates population differentiation between the populations and their 28 founder population as predicted by the theory of genetic isolation by distance. Consistent with 29 that, a model of expansion from a single founder predicts that patterns of genetic diversity in 30 populations can be well explained by their geographic expansion from the founders, which is 31 correlated to the genetic differentiation. To investigate this in the chicken, we have estimated the 32 relationship between the genetic diversity in 172 domesticated chicken populations and their 33 genetic distances to wild populations. We have found a strong inverse relationship whereby 34 87.5% of the variation in the overall genetic diversity of domesticated chicken can be explained 35 by the genetic distance to the wild populations. We also investigated if different types of SNPs 36 and genes present similar patterns of genetic diversity as the overall genome. Among different 37 SNP classes, the non-synonymous ones were the most deviating from the overall genome. 38However, the genetic distances to wild populations still explained more variation in domesticated 39 chicken diversity in all SNP classes ranging from 81.7 to 88.7%. The genetic diversity seemed to 40 change at a faster rate within the chicken in genes that are associated with transmembrane 41 transport, protein transport and protein metabolic processes, and lipid metabolic processes. In 42 general, such genes are flexible to be manipulated according to the population needs. On the 43 other hand, genes which the genetic diversity hardly changes despite the genetic distance to the 44 wild populations are associated with major functions e.g. brain development. Therefore, changes 45 in the genes may be detrimental to the chickens. These results contribute to the knowledge of 46 different evolutionary patterns of different functional genomic regions in the chicken.47 48Author summary 49 The chicken was first domesticated about 6000 B.C. in Asia from the jungle fowl. Following 50 domestication, chickens were taken to different parts of the world mainly by humans. 51Evolutionary forces such as selection and genetic drift have shaped diversification within the 52 chicken species. In addition, new breeds or strains have been developed from crossbreeding 53 programs facilitated by man. These events, together with other breeding practices, have led to 54 genomic alterations causing genetic differentiation between the domesticated chickens and their 55 ancestral/wild population as well as manipulation of the genetic diversity within the 56 domesticated chickens. We investigated the relationship between 172 domesticated chicken 57 populations from different selection, breeding and management backgrounds and their genetic 58 distance to the wild type chickens. We found that the genetic diversity within the populations 59 decreases with the increasing genetic distances to the wil...

Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

“…However, despite this intensive sampling, only the Near East is suggested as a site of cat domestication indicating a pattern of dispersal outwards from regions like the Levant and the Nile Valley, while elsewhere in the world lacks this pattern (Vigne et al 2004;Driscoll et al 2007;Lipinski et al 2008). For other domesticated species, isolation by distance testing and genetic diversity measurements reveal a pattern of expansion from the domesticated founders (Ramachandran et al 2005;Scheu et al 2015;Malomane et al 2021).…”

“…This pattern of isolation by distance, with the highest levels of diversity near sites of domestication, is observed in other species. Chickens, like cats, dispersed from a domestication center by human-mediated migration, and the majority of genetic diversity variation is explained by genetic distance to the wild populations (Malomane et al 2021). Village dogs, like random-bred cats, are considered to be free-breeding with minimal admixture due to isolation and have escaped human-mediated inbreeding (Shannon et al 2015).…”

Insights on the historical biogeography of Philippine native pigs and its relationship with Continental domestic and wild boars

“…Population differentiation usually occurs when there is migration of a certain population away from its founder population which leads to a reduction in genetic diversity as predicted by the theory of Genetic Isolation by Distance. Moreover, an expansion model from a single founder predicts that patterns of genetic diversity in populations can be thoroughly explained by their geographic expansion from the founders, concomitant to genetic differentiation [65].…”