Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome
Abstract The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptatio...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2020-10-01
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| Series: | Evolution Letters |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/evl3.189 |
| _version_ | 1797711600373727232 |
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| author | Aryn P. Wilder Stephen R. Palumbi David O. Conover Nina Overgaard Therkildsen |
| author_facet | Aryn P. Wilder Stephen R. Palumbi David O. Conover Nina Overgaard Therkildsen |
| author_sort | Aryn P. Wilder |
| collection | DOAJ |
| description | Abstract The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median FST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change. |
| first_indexed | 2024-03-12T07:09:27Z |
| format | Article |
| id | doaj.art-abea97cdcdc54a43b8c39ceeb2310577 |
| institution | Directory Open Access Journal |
| issn | 2056-3744 |
| language | English |
| last_indexed | 2024-03-12T07:09:27Z |
| publishDate | 2020-10-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Evolution Letters |
| spelling | doaj.art-abea97cdcdc54a43b8c39ceeb23105772023-09-02T23:14:24ZengOxford University PressEvolution Letters2056-37442020-10-014543044310.1002/evl3.189Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genomeAryn P. Wilder0Stephen R. Palumbi1David O. Conover2Nina Overgaard Therkildsen3Department of Natural Resources Cornell University Ithaca New York 14853Department of Biology, Hopkins Marine Station Stanford University Pacific Grove California 93950Department of Biology University of Oregon Eugene Oregon 97403Department of Natural Resources Cornell University Ithaca New York 14853Abstract The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median FST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.https://doi.org/10.1002/evl3.189Clinedivergent selectiongene flowlinkage disequilibriumsupergenes |
| spellingShingle | Aryn P. Wilder Stephen R. Palumbi David O. Conover Nina Overgaard Therkildsen Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome Evolution Letters Cline divergent selection gene flow linkage disequilibrium supergenes |
| title | Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome |
| title_full | Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome |
| title_fullStr | Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome |
| title_full_unstemmed | Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome |
| title_short | Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome |
| title_sort | footprints of local adaptation span hundreds of linked genes in the atlantic silverside genome |
| topic | Cline divergent selection gene flow linkage disequilibrium supergenes |
| url | https://doi.org/10.1002/evl3.189 |
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