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Climate change is threatening aquatic populations with rapid changes in habitat salinity and temperature. Locally adapted alleles along environmental gradients, along with low but sufficient gene flow, could provide crucial genetic variation to adapt to future climate change and rescue populations from extinction. Thus, we explored whether planktonic populations exhibit genomic signatures of selection and gene flow across salinity and temperature gradients in the Baltic Sea and North Sea region. LocationBaltic Sea, North Sea region. MethodsWe performed whole‐genome sequencing of 11 populations of the copepodEurytemora affinisproper along salinity and temperature gradients. We determined signatures of population structure, admixture, and natural selection by analysing single nucleotide polymorphism (SNP) frequencies across populations using TreeMix, PoPoolation2, poolfstat, and BayPass. ResultsWe found significant population genomic signatures of selection associated with salinity and temperature gradients using BayPass XTX and environmental association tests, consistent with local adaptation. Several ion transport functional categories (GO terms) were significantly associated with the salinity gradient across all populations, whereas only one GO term, ‘prostaglandin biosynthetic process’, was significantly associated with the temperature gradient in the North Sea region. We found clear population structure with PoPoolation2 and TreeMix. We also found signals of admixture between populations with poolfstat and TreeMix, consistent with the presence of gene flow. Site‐frequency spectra (SFS) of candidate SNPs tested against simulated SFS distributions revealed an excess of intermediate frequency alleles within a few populations. Main ConclusionsThe interplay between local adaptation and gene flow had not been fully explored in passive holoplankton dispersers. Many of the same ion transporter genes showed signatures of selection as in our prior studies, but in this case across a metapopulation ofE. affinisspanning a broad geographic range. The presence of locally adapted alleles along with gene flow across environmental gradients could provide genetic substrate for natural selection, enabling populations to adapt to future climate change.
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This content will become publicly available on June 1, 2027
Summer Rainfall Drives Adaptation with Gene Flow in a Widespread Butterfly
ABSTRACT Understanding how environmental variation interacts with gene flow to shape population genomic patterns is a central goal in evolutionary biology. We investigated how geographic and environmental differences impact genetic variation in the clouded sulfur butterfly (Colias philodice eriphyle) by conducting whole‐genome resequencing across replicated transects consisting of paired high‐ and low‐elevation sites on both sides of a major mountain range. Despite sampling across steep environmental gradients, we found no evidence of discrete population structure, providing support for high connectivity across the region or recent divergence with limited drift. Nonetheless, significant isolation by distance—strongest in eastern populations—revealed that geographic distance may impose limits on gene flow, and genetic diversity was also elevated in the east. Genotype‐environment association analyses identified more than 16,000 loci associated with elevation, precipitation, and solar radiation. Our redundancy analysis identified precipitation as the strongest predictor of adaptive genomic differentiation, and candidate genes included those linked to melanization and thermoregulation (e.g.,THandyellow). These results demonstrate that even in a largely panmictic population, environmental variation can maintain regional‐scale signals of local adaptation. Because insects are declining globally and remain underrepresented in genomic monitoring, conducting whole‐genome analyses in a widespread species provides valuable context for assessing how insects today persist across such diverse landscapes and their potential for withstanding future environmental change.
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- Award ID(s):
- 2508266
- PAR ID:
- 10710106
- Publisher / Repository:
- Molecular Ecology / Wiley
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 35
- Issue:
- 12
- ISSN:
- 0962-1083
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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