Department of Biology, University of Miami, Coral Gables, FL 33146, USA; Smithsonian Tropical Research Institute, 0843-03092 Balboa, Ancon, Panama; Museo de Zoología, Escuela de Biología, Universidad de Costa Rica, 11502 San José, Costa Rica.
University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA.
Mol Phylogenet Evol. 2022 Aug;173:107510. doi: 10.1016/j.ympev.2022.107510. Epub 2022 May 13.
Disentangling the evolutionary relationships of rapidly radiating clades is often challenging because of low genetic differentiation and potentially high levels of gene flow among diverging taxa. The genus Sporophila consists of small Neotropical birds that show, in general, relatively low genetic divergence, but particularly high speciation rates and pronounced variation in secondary sexual traits (e.g., plumage color), which can be important in generating premating reproductive isolation. In cases like these, the use of genome-wide sequence data can increase the resolution to uncover a clade's evolutionary history. Here, we used a phylogenomic approach to study the evolutionary history and genetic structure of the Variable Seedeater superspecies complex, which includes S. corvina, S. intermedia, and S. americana. Using ∼25,000 genome-wide single nucleotide polymorphisms (SNPs), we confirmed that the Variable Seedeater superspecies complex is monophyletic. However, a phylogenetic reconstruction based on a mitochondrial marker (ND2) resulted in a discordant tree topology, particularly in the position of Wing-barred Seedeater S. americana, which might be due to a mitochondrial capture event. Our results suggest historical gene flow among lineages, particularly between species with conflicting topologies. Among the four phenotypically variable S. corvina subspecies, our structure analyses identified three main distinct genetic groups (K = 3), and that the entirely black subspecies, S. c. corvina, is derived from within a pied-colored clade. Further, we inferred widespread gene flow across the whole species' distribution, including between subspecies. However, gene flow was about 100 times lower at the geographic boundaries of the entirely black and the pied subspecies, suggesting an important role for plumage divergence in limiting gene flow. Overall, our findings suggest that the early diversification of the Sporophila genus occurred rapidly despite historical gene flow between lineages and that divergence in plumage color possibly influences the extent of gene flow among taxa.
解析快速辐射进化枝的系统发育关系通常具有挑战性，因为在分化的分类群之间存在低遗传分化和潜在的高水平基因流。Sporophila 属由小型新热带鸟类组成，这些鸟类总体上表现出相对较低的遗传分化，但表现出较高的物种形成率和明显的次要性征（例如，羽毛颜色）变异，这可能在产生交配前生殖隔离方面很重要。在这种情况下，使用全基因组序列数据可以提高分辨率，以揭示进化枝的历史。在这里，我们使用系统基因组学方法来研究可变种子食者超种复合体的进化历史和遗传结构，该复合体包括 S. corvina、S. intermedia 和 S. americana。使用约 25000 个全基因组单核苷酸多态性（SNP），我们证实可变种子食者超种复合体是单系的。然而，基于线粒体标记（ND2）的系统发育重建导致了不和谐的树拓扑，特别是在翼条纹种子食者 S. americana 的位置，这可能是由于线粒体捕获事件。我们的结果表明，在进化枝之间存在历史基因流，特别是在拓扑结构冲突的物种之间。在四个表型可变的 S. corvina 亚种中，我们的结构分析确定了三个主要的遗传群体（K=3），并且完全黑色的亚种 S. c. corvina 是从斑驳色支系中衍生出来的。此外，我们推断整个物种分布范围内存在广泛的基因流，包括亚种之间。然而，在完全黑色和斑驳亚种的地理边界处，基因流约低 100 倍，这表明羽毛分化在限制基因流方面起着重要作用。总体而言，我们的研究结果表明，尽管在进化枝之间存在历史基因流，但 Sporophila 属的早期多样化发生得很快，并且羽毛颜色的分化可能会影响分类群之间基因流的程度。
