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Genalpic: Conservation genomics of endangered Alpine ichthyofauna

Ilardo, B (2023) Genalpic: Conservation genomics of endangered Alpine ichthyofauna. Doctoral thesis, Liverpool John Moores University.

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Genomic erosion due to hybridisation is a problem which many endemisms face, including Italian pike Esox flaviae and marble trout Salmo marmoratus. These important freshwater species, which naturally occur in the Italian peninsula, are threatened by decades of stocking with non-native commercial lines, namely European pike Esox lucius and brown trout Salmo trutta. While supportive breeding programmes are in place for these species, screening of suitable breeders is based on traditional genetic methods such as microsatellite marker genotyping, which may have limited power to distinguish hybrids. Moreover, such markers are often surveyed through alternative laboratory protocols that can yield inconsistent results amongst research groups and hinder integration of molecular data from different local surveys on a larger biogeographical scale. In this doctoral thesis, I apply high-density Single Nucleotide Polymorphisms (SNPs) to the study of population substructure and genomic landscape within Italian pike, and I develop a large SNP panel to be implemented in a future genotyping array for large-scale genetic monitoring of Italian marble trout populations. In particular, I identified more than 20 million high-quality SNP markers from whole genome sequencing. Using these data sets, I found evidence of introgressive hybridisation in both species and reported a diminished ability of microsatellites to detect hybridisation compared to SNPs. Analyses of population structure confirm that at least four genetic clusters are present within Italian pike, and that anthropogenic translocations between geographically isolated basins have taken place. Moreover, I unveil genomic adaptations in Italian pike concerning olfactory perception, immune response and metabolism, emphasising the need to preserve the adaptive potential of endemic species. In marble trout, I filtered and validated in silico a set of more than 8 million high-quality SNPs after removing pseudo-SNPs from paralogous regions of the salmonid genome and potentially introgressed allochthonous alleles. Switching from current microsatellite-based screening to a SNP genotyping array would not only increase resolving power for hybrid detection but also produce faster results in a less invasive manner. Indeed, while current screening methods require up to a week during which time marble trout are confined in low density pools, genetic analyses with the proposed technology would reduce time of confinement by several days, resulting in lower stress levels and higher post-release survival rates in marble trout wild breeders. Findings from this study will greatly facilitate detection of genetic introgression from introduced European pike and brown trout into these Alpine endemics which will inform regional and national conservation practices.

Item Type: Thesis (Doctoral)
Uncontrolled Keywords: conservation genomics; population genetics; endangered species; next-generation sequencing; genome-wide selection scan; alpine ichthyofauna; italian pike; marble trout
Subjects: G Geography. Anthropology. Recreation > GE Environmental Sciences
Q Science > QH Natural history > QH301 Biology
Q Science > QL Zoology
Divisions: Biological & Environmental Sciences (from Sep 19)
SWORD Depositor: A Symplectic
Date Deposited: 03 Nov 2023 10:43
Last Modified: 03 Nov 2023 10:44
DOI or ID number: 10.24377/LJMU.t.00021727
Supervisors: Brown, R, Gandolfi, A, Micheletti, D and Nichols, H
URI: https://researchonline.ljmu.ac.uk/id/eprint/21727
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