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Journal article
Local adaptation and the evolution of genome architecture in threespine stickleback
Genome biology and evolution, v 14(6)
20 May 2022
PMID: 35594844
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely-related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and Lineage-Specific Genes (LSGs) were enriched around genomic islands, and that all three chromosomes harbouring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9x and 2.9x more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.
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Details
- Title
- Local adaptation and the evolution of genome architecture in threespine stickleback
- Creators
- Qiushi Li - University of CalgaryDorothea Lindtke - University of CalgaryCarlos Rodríguez-Ramírez - University of BernRyo Kakioka - University of the RyukyusHiroshi Takahashi - National Fisheries UniversityAtsushi Toyoda - National Institute of GeneticsJun Kitano - National Institute of GeneticsRachel L Ehrlich - Drexel UniversityJoshua Chang Mell - Department of Microbiology & Immunology, Drexel University College of Medicine. Philadelphia, USA. 19102Sam Yeaman - University of Calgary
- Publication Details
- Genome biology and evolution, v 14(6)
- Publisher
- Oxford University Press
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000808221200001
- Scopus ID
- 2-s2.0-85131772060
- Other Identifier
- 991019169697204721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Evolutionary Biology
- Genetics & Heredity