College of Life Sciences, China Jiliang University, Hangzhou, P.R. China.
School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom.
Genome Biol Evol. 2023 Nov 1;15(11). doi: 10.1093/gbe/evad193.
The lizard Teira dugesii exhibits morphological divergence between beach and inland habitats in the face of gene flow, within the volcanic island of Madeira, Portugal. Here, we analyzed genomic data obtained by genotyping-by-sequencing, which provided 16,378 single nucleotide polymorphisms (SNPs) from 94 individuals sampled from 15 sites across Madeira. Ancient within-island divergence in allopatry appears to have mediated divergence in similar species within other Atlantic islands, but this hypothesis was not supported for T. dugesii. Across all samples, a total of 168 SNPs were classified as statistical outliers using pcadapt and OutFLANK. Redundancy analysis (RDA) revealed that 17 of these outliers were associated with beach/inland habitats. The SNPs were located within 16 sequence tags and 15 of these were homologous with sequences in a 31 Mb region on chromosome 3 of a reference wall lizard genome (the remaining tag could not be associated with any chromosome). We further investigated outliers through contingency analyses of allele frequencies at each of four pairs of adjacent beach-inland sites. The majority of the outliers detected by the RDA were confirmed at two pairs of these matched sites. These analyses also suggested some parallel divergence at different localities. Six other outliers were associated with site elevation, four of which were located on chromosome 5 of the reference genome. Our study lends support to a previous hypothesis that divergent selection between gray shingle beaches and inland regions overcomes gene flow and leads to the observed morphological divergence between populations in these adjacent habitats.
面对基因流，葡萄牙马德拉火山岛上的蜥蜴 Teira dugesii 在海滩和内陆生境中表现出形态上的分化。在这里，我们分析了通过测序基因型获得的基因组数据，这些数据来自马德拉群岛 15 个地点的 94 个个体，共提供了 16378 个单核苷酸多态性（SNP）。在同域发生的古老岛内分化似乎介导了其他大西洋岛屿内相似物种的分化，但这一假设不适用于 T. dugesii。在所有样本中，共有 168 个 SNP 被 pcadapt 和 OutFLANK 归类为统计异常值。冗余分析（RDA）显示，其中 17 个异常值与海滩/内陆生境有关。SNP 位于 16 个序列标签内，其中 15 个与参考壁虎基因组第 3 号染色体上 31 Mb 区域的序列同源（其余标签无法与任何染色体相关联）。我们通过在四个相邻的海滩-内陆对位点的每个位点的等位基因频率进行 contingency 分析进一步研究了异常值。RDA 检测到的大多数异常值在其中两对匹配位点得到了证实。这些分析还表明在不同地点存在一些平行的分化。另外六个异常值与地点海拔有关，其中四个位于参考基因组的 5 号染色体上。我们的研究支持了先前的假设，即灰卵石滩和内陆地区之间的分歧选择克服了基因流，导致了这些相邻生境中种群的观察到的形态分化。
