ORCID Profile
0000-0001-8000-3639
Current Organisation
University of York
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Publisher: Proceedings of the National Academy of Sciences
Date: 12-08-2019
Abstract: Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig s les and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
Publisher: Cold Spring Harbor Laboratory
Date: 18-07-2019
DOI: 10.1101/706226
Abstract: Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic ersity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in genus Anser have been domesticated providing excellent opportunity for joint study of domestication and hybridization. Until now, knowledge on the details of the goose domestication process has come from archaeological findings and historical writings supplemented with few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the greylag goose ( Anser anser ). Our dataset consisted of 58 wild greylags s led around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that ergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that greylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable ( 10%) ancestry with Chinese domestic geese that is derived from the swan goose Anser cygnoid . We show that domestication process can progress despite continued and pervasive gene flow from the wild form. Reproductive isolation between conspecific wild and domestic populations is a cornerstone of the domestication process, yet gene flow between such wild and domestic populations has been frequently documented. European domestic geese and their wild progenitor (greylags) co-occur and can hybridize and we show that they represent a particularly persuasive case where wild and domestic populations are not isolated gene pools. Our study makes a first genome-based estimate of goose domestication, which up to now has mostly relied on archaeological findings and historical writings. We show ongoing gene flow between greylags and European domestic geese following domestication, but we also observe a surprisingly large contribution of Chinese domestic geese (a separate species) to the genetic make-up of European domestic geese.
Publisher: Proceedings of the National Academy of Sciences
Date: 17-07-2023
Publisher: The Royal Society
Date: 10-2015
Abstract: Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB , both novel mutations in Gallus , allowed us to estimate a molecular rate of 3.13 × 10 −7 mutations/site/year (95% confidence interval 3.75 × 10 −8 –1.12 × 10 −6 ). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 in iduals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 27-08-2021
Abstract: Compound-specific isotope analysis of human bone collagen provides a snapshot of dietary variability at Roman Herculaneum.
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Michelle Alexander.