Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
Institute of Biodiversity, Animal Health and Comparative Medicine, School of Life Science, University of Glasgow, Glasgow, UK.
Mol Ecol. 2022 Sep;31(18):4688-4706. doi: 10.1111/mec.16625. Epub 2022 Aug 3.
Sympatric adaptive phenotypic divergence should be underlain by genomic differentiation between subpopulations. When divergence drives similar patterns of phenotypic and ecological variation within species we expect evolution to draw on common allelic variation. We investigated divergence histories and genomic signatures of adaptive divergence between benthic and pelagic morphs of Icelandic Arctic charr. Divergence histories for each of four populations were reconstructed using coalescent modelling and 14,187 single nucleotide polymorphisms. Sympatric divergence with continuous gene flow was supported in two populations while allopatric divergence with secondary contact was supported in one population; we could not differentiate between demographic models in the fourth population. We detected parallel patterns of phenotypic divergence along benthic-pelagic evolutionary trajectories among populations. Patterns of genomic differentiation between benthic and pelagic morphs were characterized by outlier loci in many narrow peaks of differentiation throughout the genome, which may reflect the eroding effects of gene flow on nearby neutral loci. We then used genome-wide association analyses to relate both phenotypic (body shape and size) and ecological (carbon and nitrogen stable isotopes) variation to patterns of genomic differentiation. Many peaks of genomic differentiation were associated with phenotypic and ecological variation in the three highly divergent populations, suggesting a genomic basis for adaptive divergence. We detected little evidence for a parallel genomic basis of differentiation as most regions and outlier loci were not shared among populations. Our results show that adaptive divergence can have varied genomic consequences in populations with relatively recent common origins, similar divergence histories, and parallel phenotypic divergence.
同域适应表型分歧应该以亚种群之间的基因组分化为基础。当分歧导致物种内表型和生态变异出现相似模式时，我们预计进化会利用共同的等位基因变异。我们研究了冰岛北极鲑底栖和浮游两种形态之间的分歧历史和适应性分歧的基因组特征。使用合并建模和 14187 个单核苷酸多态性，重建了四个种群中的每一个的分歧历史。在两个种群中支持同域分歧与连续基因流动，而在一个种群中支持异域分歧与二次接触；我们无法在第四个种群中区分人口模型。我们在种群之间沿着底栖-浮游进化轨迹检测到了表型分歧的平行模式。底栖和浮游形态之间的基因组分化模式的特点是在整个基因组中存在许多狭窄的分化峰处的异常基因座，这可能反映了基因流动对附近中性基因座的侵蚀作用。然后，我们使用全基因组关联分析将表型（身体形状和大小）和生态（碳和氮稳定同位素）变异与基因组分化模式联系起来。在三个高度分化的种群中，许多基因组分化峰与表型和生态变异相关，这表明适应性分歧有一个基因组基础。我们发现，大多数区域和异常基因座在种群之间没有共享，因此没有多少证据表明分化的基因组基础是平行的。我们的研究结果表明，在具有相对较近的共同起源、相似的分歧历史和平行的表型分歧的种群中，适应性分歧可能具有不同的基因组后果。
