Establishing the validity of domestication genes using DNA from ancient chickens

Abstract

Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone.selective sweep | breed formation | animal domestication | Gallus gallus | cultural history

A domestication related mutation in the thyroid stimulating hormone receptor gene (TSHR) modulates photoperiodic response and reproduction in chickens

“…Another scenario is that the mutation became fixed through strong artificial selection during the past 500 years (Girdland Flink et al, 2014). Our genotyping showed that birds sampled from eight out of nine Swedish landrace breeds were homozygous for the domestic d/d alleles and only two from one breed were heterozygous.…”

“…Studies of ancient chicken DNA from different archeological sites in Europe have shown that the TSHR mutation was fixed already in Classical Greek chickens (Girdland Flink et al, 2014).…”

“…A missense mutation causing a non-conservative amino acid substitution was suggested as the candidate mutation in the sweep (Rubin et al, 2010). Ancient DNA studies have shown that the mutation was present already in classical Greek chickens which indicates that it is old, but data also suggest that the sweep allele was not fixed in European chickens until much later in time, and took place only 500 years ago due to strong human-mediated selection (Girdland Flink et al, 2014).…”

Chicken domestication : Effects of tameness on brain gene expression and DNA methylation

“…Initially, the captive chicken is thought to have been used for cock fighting [46]. Data from medieval sources suggest that the selection for production traits in chickens did not start until the 16 th or 17 th century [59], with selection for variation in TSHR, thyroid-stimulating hormone receptor, a mutation affecting seasonal reproduction [60,61]. Up until the beginning of the 20 th century, the chicken was a dual purpose animal with the same breed used for both meat and egg production.…”

Chicken project gets off the ground

“…But DNA from chickens recovered at archaeological sites across Europe, spanning the period from around 280 bc to ad 1800, has turned that idea on its head. In an analysis published last month, Larson's team reported that none of 25 ancient chickens would have had yellow legs, and that just 8 out of 44 birds carried two copies of the TSHR variant 3 . So even 200 years ago, chickens may have been very different from those we know today.…”