Data from: Stepwise colonization of the Andes by Ruddy Ducks and the evolution of novel β-globin variants

Andean uplift played a key role in Neotropical bird diversification, yet past dispersal and genetic adaptation to high-altitude environments remain little understood. Here we use multilocus population genetics to study population history and historical demographic processes in the ruddy duck (Oxyura jamaicensis), a stiff-tailed diving duck comprising three subspecies distributed from Canada to Tierra del Fuego and inhabiting wetlands from sea level to 4500 m in the Andes. We sequenced the mitochondrial DNA, four autosomal introns and three haemoglobin genes (αA, αD, βA) and used isolation-with-migration (IM) models to study gene flow between North America and South America, and between the tropical and southern Andes. Our analyses indicated that ruddy ducks dispersed first from North America to the tropical Andes, then from the tropical Andes to the southern Andes. While no nonsynonymous substitutions were found in either α globin gene, three amino acid substitutions were observed in the βA globin. Based on phylogenetic reconstruction and power analysis, the first βA substitution, found in all Andean individuals, was acquired when ruddy ducks dispersed from low altitude in North America to high altitude in the tropical Andes, whereas the two additional substitutions occurred more recently, when ruddy ducks dispersed from high altitude in the tropical Andes to low altitude in the southern Andes. This stepwise colonization pattern accompanied by polarized βA globin amino acid replacements suggest that ruddy ducks first acclimatized or adapted to the Andean highlands and then again to the lowlands. In addition, ruddy ducks colonized the Andean highlands via a less common route as compared to other waterbird species that colonized the Andes northwards from the southern cone of South America.安第斯隆升在新热带鸟类多样化进程中发挥了关键作用，但学界对其过往的扩散事件以及对高海拔环境的遗传适应机制仍知之甚少。本研究采用多位点群体遗传学方法，对棕硬尾鸭（Oxyura jamaicensis）的种群历史与历史种群动态过程展开研究。棕硬尾鸭是一种硬尾潜水鸭，下辖3个亚种，分布范围从加拿大延伸至火地岛，栖息于安第斯山脉内从海平面至海拔4500米的湿地生境。我们对线粒体DNA、4个常染色体内含子以及3个血红蛋白基因（αA、αD、βA）进行了测序，并采用隔离-迁移（isolation-with-migration, IM）模型，解析了南北美洲种群间以及热带安第斯与南部安第斯种群间的基因流模式。分析结果显示，棕硬尾鸭的扩散路径为先从北美抵达热带安第斯山脉，随后再从热带安第斯山脉扩散至南部安第斯山脉。尽管在两个α球蛋白基因中均未发现非同义替换，但在βA球蛋白中检测到3处氨基酸替换。基于系统发育重建与功效分析结果，所有安第斯种群个体均携带的首个βA替换，是在棕硬尾鸭从北美低海拔区域扩散至热带安第斯高海拔区域时获得的；而另外两处替换则出现较晚，对应棕硬尾鸭从热带安第斯高海拔区域扩散至南部安第斯低海拔区域的过程。这种伴随βA球蛋白氨基酸极性替换的逐步定殖模式表明，棕硬尾鸭首先对安第斯高原环境完成了驯化或遗传适应，随后又适应了南部安第斯的低海拔生境。此外，与其他从南美南锥体向北扩散定殖安第斯山脉的水鸟物种相比，棕硬尾鸭的安第斯高原定殖路径较为罕见。