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The potential role of chromosomal inversions in the persistence of small, isolated populations of Brook Trout (Salvelinus fontinalis)
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  • Cait Nemeczek,
  • Maria Lisette Delgado Aquije,
  • Meg Smith,
  • John MacMillan,
  • Mallory Van Wyngaarden,
  • Daniel Ruzzante
Cait Nemeczek
Dalhousie University

Corresponding Author:[email protected]

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Maria Lisette Delgado Aquije
Dalhousie University
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Meg Smith
Dalhousie University
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John MacMillan
Nova Scotia Department of Fisheries and Aquaculture
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Mallory Van Wyngaarden
Dalhousie University
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Daniel Ruzzante
Dalhousie University
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Abstract

Understanding the role of structural variants such as chromosomal inversions in local adaptation among small, isolated populations is an important addition to robust conservation strategies, as most studies investigating inversions to date have been conducted on high gene flow systems. Brook Trout (Salvelinus fontinalis), an economically important top sportfish, is extremely vulnerable to thermal stress. Local adaptation with respect to this trait warrants investigation as climate change accelerates the loss of cold-stream ecosystems. We performed low-coverage whole genome sequencing (lcWGS) on N=192 Brook Trout from nine small, isolated streams in Nova Scotia, Canada. Using the indirect structural variant detection framework, we detected four potential chromosomal inversions in the three westernmost populations which differ from all other streams in water temperature, streamflow, and surficial geology. These genomic regions exhibited high linkage disequilibrium (LD) and principal component analyses (PCA) revealed the presence of three karyotypes (inverted and non-inverted homokaryotype, and heterokaryotype). Heterozygosity was lowest among inverted homokaryotypes, providing further support of the presence of inversions. Mitogenome analyses suggest that a single glacial lineage recolonized the region. The mtDNA haplotypes of individuals carrying potential inversions were shared among individuals with two copies of non-inverted chromosomal regions, suggesting these inversions were derived post-recolonization. These novel inversions comprised genes involved in different biological processes including thermal adaptations.