Data from: Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North American songbird, using next-generation sequencing. Additionally, we reassess previous phylogeographic studies within the group. Based on ~30 million sequencing reads and more than 16 000 single-nucleotide polymorphisms in 41 individuals, we identified a strong positive relationship between genetic differentiation and chromosome size, with a negative relationship between genetic diversity and chromosome size. A combination of selection and drift may explain these patterns, although we found no evidence for selection. Because the observed genomic patterns are very similar between widespread, allopatric clades, it is unlikely that selective pressures would be so similar across such different ecological conditions. Alternatively, the accumulation of fixed differences between lineages and loss of genetic variation within lineages due to genetic drift alone may explain the observed patterns. Due to relatively higher recombination rates on smaller chromosomes, larger chromosomes would, on average, accumulate fixed differences between lineages and lose genetic variation within lineages faster, leading to the patterns observed here in C. americana.

随着可对大量个体的数千个基因座开展测序的技术方法问世，系统地理学（phylogeographic）研究的推断能力得到显著提升，同时拓展了其应用于全新研究问题的潜力。在鸣禽类群中，极强的染色体间同线性（inter-chromosomal synteny）特征、已公开的鸣禽基因组序列，以及可从大量个体中获取数千个遗传基因座的技术条件，使得研究者能够开展跨染色体的谱系间分化与谱系内多样性研究。本研究以分布广泛的北美鸣禽北美旋木雀（*Certhia americana*）为研究对象，借助下一代测序技术探究其分化与多样性模式；同时重新评估该类群此前开展的系统地理学研究。基于对41个个体的约3000万条测序读段与超过16000个单核苷酸多态性（single-nucleotide polymorphism, SNP）位点，本研究发现遗传分化与染色体大小呈显著正相关，而遗传多样性与染色体大小则呈负相关。尽管本研究未检测到选择作用的相关证据，但选择与遗传漂变的共同作用或可解释上述基因组模式。鉴于分布广泛且地理隔离的支系间观测到的基因组模式高度相似，在差异如此显著的生态环境条件下，选择压力不太可能保持如此高度的一致性。与之相对，仅由遗传漂变导致的谱系间固定差异积累与谱系内遗传变异丢失，或可完美解释本研究观测到的上述模式。由于较小染色体的重组率相对更高，平均而言，较大染色体的谱系间固定差异积累速度与谱系内遗传变异丢失速度均更快，这也正是北美旋木雀（*C. americana*）中观测到上述基因组模式的原因。