Jiang Zhiyong, Song Gang, Luo Xu, Zhang Dezhi, Lei Fumin, Qu Yanhua
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
Evol Lett. 2023 Mar 16;7(2):99-111. doi: 10.1093/evlett/qrad005. eCollection 2023 Apr 1.
Speciation is fundamental for building and maintaining biodiversity. The formation of the highly differentiated genomic regions between diverging taxa has been interpreted as a result of divergence with gene flow, linked selection, and reduction in recombination. It is challenging to unravel these nonexclusive processes in shaping genomic divergence. Here, we investigate the relative roles of these processes in shaping genomic differentiation in a montane bird, the Green-backed Tit (). Our genetic structure and demographic analyses identify that four genetic lineages diverge between 838 and 113 thousand years ago and there is evidence of secondary gene flow. The highly divergent genomic regions do not increase with the divergence time, as we found that the old lineages show relatively fewer numbers and smaller sizes of highly differentiated regions than the young divergent lineages (numbers, 118-138 vs. 156-289; sizes, 5.9-6.9 vs. 7.8-14.5 megabase). Across the genome, the outlier windows show a reduction in nucleotide diversity, absolute genetic divergence, and recombination rate, suggesting recurrent selection in regions with low recombination being the major driver of genomic divergence. Finally, we show that secondary gene flow tends to affect the highly differentiated genomic regions if these regions are less likely to be the targets of selection. Altogether, our study shows how common ancestry, recurrent selection, low recombination rate, and gene flow have contributed to the emergence of genomic islands at different stages of speciation.
物种形成是构建和维持生物多样性的基础。不同分类群之间高度分化的基因组区域的形成被解释为是分歧与基因流、连锁选择以及重组减少的结果。在塑造基因组分歧的过程中，厘清这些并非相互排斥的过程具有挑战性。在这里，我们研究了这些过程在一种山地鸟类——绿背山雀（Parus monticolus）基因组分化形成过程中的相对作用。我们的遗传结构和种群动态分析表明，四个遗传谱系在83.8万至11.3万年前出现分歧，并且存在二次基因流的证据。高度分化的基因组区域并没有随着分歧时间的增加而增多，因为我们发现，与年轻的分歧谱系相比，古老谱系中高度分化区域的数量相对较少，大小也较小（数量，118 - 138个对156 - 289个；大小，5.9 - 6.9兆碱基对与7.8 - 14.5兆碱基对）。在整个基因组中，异常窗口显示核苷酸多样性、绝对遗传分歧和重组率降低，这表明在低重组区域的反复选择是基因组分歧的主要驱动因素。最后，我们表明，如果高度分化的基因组区域不太可能成为选择目标，二次基因流往往会对其产生影响。总之，我们的研究展示了共同祖先、反复选择、低重组率和基因流如何在物种形成的不同阶段促成了基因组岛的出现。
