Data from: A flicker of hope: genomic data distinguish Northern Flicker taxa despite low levels of divergence

Next-generation sequencing technologies are increasingly being employed to
explore patterns of genomic variation in avian taxa previously
characterized using morphology and/or traditional genetic markers. The
hybridization dynamics of the Northern Flicker complex have received
considerable attention, primarily due to the conspicuous plumage
differences among these birds and the geographically extensive hybrid zone
between the Red-shafted (Colaptes auratus cafer) and Yellow-shafted
(Colaptes auratus auratus) flickers in the Great Plains region of North
America. However, no traditional molecular techniques have been able to
differentiate these 2 morphologically well-defined taxa from one another,
or conclusively from the closely related Gilded Flicker (Colaptes
chrysoides). Here, we use a next-generation sequencing approach to assess
the genetic diversity and evolutionary history of these 3 taxa. We confirm
the overall low levels of differentiation found using traditional
molecular markers, but are able to distinguish between the 3 taxa for the
first time, using a dataset of thousands of SNP loci distributed across
the genome. Through demographic modeling and phylogenetic reconstructions,
we find that Red-shafted and Yellow-shafted flickers are likely sister
taxa, and that their divergence from the Gilded Flicker was comparatively
older. The low level of divergence and lack of fixed differences in our
dataset between Red-shafted and Yellow-shafted flickers, in particular,
suggests whole-genome re-sequencing may be necessary to assess the
dynamics of their hybridization and identify the genetic basis of their
striking differences in plumage.

新一代测序技术正日益被应用于探究此前依托形态学及/或传统遗传标记开展分类的鸟类类群的基因组变异模式。北扑翅鴷复合种（Northern Flicker complex）的杂交动态已获得学界广泛关注，这主要源于该类群鸟类间显著的羽色差异，以及北美大平原地区红肋扑翅鴷（Colaptes auratus cafer）与黄肋扑翅鴷（Colaptes auratus auratus）之间广泛分布的杂交带。然而，传统分子技术无法区分这两个形态学定义明确的类群，也无法确凿地将其与亲缘关系密切的金胸扑翅鴷（Colaptes chrysoides）区分开来。本研究采用新一代测序技术，对这三个类群的遗传多样性与演化历史进行评估。本研究证实了传统分子标记所检测到的整体较低的分化水平，但首次利用全基因组分布的数千个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点数据集，实现了对这三个类群的区分。通过种群动态模型构建与系统发育重建，本研究发现红肋与黄肋扑翅鴷大概率为姊妹类群，且二者与金胸扑翅鴷的分化时间相对更早。尤为值得注意的是，本研究数据集显示红肋与黄肋扑翅鴷之间分化程度极低且不存在固定差异，这表明若要探究二者的杂交动态并阐明其显著羽色差异的遗传基础，全基因组重测序或许是必要的手段。