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- Barmentlo, Niek W. G., et al.
(författare)
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Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States
- 2024
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Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X.
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Tidskriftsartikel (refereegranskat)abstract
- Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa x domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high-density single-nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation.
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| 2. |
- Lord, Edana, 1993-
(författare)
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Investigating the impacts of Late Pleistocene climate change on Arctic mammals using palaeogenomics
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The climatic fluctuations of the Late Pleistocene likely had a large impact on the evolutionary history of Arctic species. Palaeogenomics is a useful tool to shed light on how past populations responded to these climatic shifts and the associated ice sheet dynamics and sea level change. Here, I have used modern and ancient DNA data from four Arctic mammals in order to investigate the impacts of Late Pleistocene climate on their evolutionary histories, from population dynamics and demography, to speciation and gene flow, adaptation, and genome erosion. In Paper I, using ancient mitogenomes from across their Late Pleistocene range, I showed that the Eurasian collared lemming (Dicrostonyx torquatus) had a dynamic Late Pleistocene population structure in Europe. Furthermore, the Eemian interglacial likely led to a bottleneck in collared lemmings, after which the species diversified during the Last Glacial period. Nuclear genome data from a modern individual in northeastern Siberia suggests population stability in northeastern Siberia during the Holocene. In Paper II, I sequenced the nuclear genome of a ~18,500 year old woolly rhinoceros (Coelodonta antiquitatis) and used this in combination with mitochondrial data to explore the demographic history of the species. There was little geographic structuring in the northeast Siberian population, and stability in their effective population size just prior to extinction, which may indicate a subsequent rapid decline towards extinction, likely associated with the Bølling-Allerød interstadial. Additionally, I found that this species had mutations in TRPA1, a gene involved in temperature sensitivity. In a third study (Paper III), I used whole genome data from modern and ancient true lemmings (Lemmus sp.) to determine that the Norwegian lemming (L. lemmus) has one of the youngest speciation times (~37-34 ka BP) of mammals. Norwegian lemmings have mutations in genes involved in coat colour, colour perception, fat transport and reproduction, and likely evolved their unique colouration as a result of isolation after the recolonisation of Fennoscandia. Finally, we examined the consequences of long-term small effective population size in muskox (Ovibos moschatus) using 107 modern nuclear genomes and one 21,000 year old Siberian genome (Paper IV). While muskox survived the warming at the end of the Late Pleistocene, the successive founder events experienced during its colonisation of the Canadian Arctic and Greenland reduced the genetic diversity to some of the lowest values observed in mammals. However, the results suggest that the long-term small population size likely led to purging of strongly deleterious alleles in the muskox, allowing them to persist to today with limited evidence of inbreeding depression. From a technical point, this thesis presents four de-novo genome assemblies, and the first whole nuclear genomes for these Arctic species. Taken together, the results in this thesis show that the climatic fluctuations, in particular the Eemian interglacial and Bølling-Allerød interstadial, along with sea level change and the formation and retreat of ice sheets during the Last Glacial Maximum have influenced the evolutionary histories of these four Arctic mammals.
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