Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g. cospeciation, host-switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites’ diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.

寄生虫多样性构成了地球生物多样性的核心组成部分，其形成受诸多演化过程调控，例如协同成种（cospeciation）、宿主转换（host-switching）等。为厘清塑造寄生虫多样性的各类过程的效应，结合深层（系统发育（phylogenetic））与浅层（种群（population））两类研究视角为最优研究方案。为此，我们开发了一套全新分析流程，从寄生于新大陆地鸠（New World ground-doves）的体虱（body lice）全基因组序列中提取系统发育与种群遗传学数据。基于该数据构建的系统发育树，为体虱提供了一致性强、分辨率极高的物种类群演化关系。通过比对体虱与新大陆地鸠的系统发育树，我们发现在长期演化尺度下，二者的系统发育拓扑结构整体一致。诸多体虱类群（涵盖物种类群与种群）均表现出极高的宿主特异性（host-specificity），这表明新大陆地鸠的物种分化是其寄生虫多样性形成的主要驱动因素。但少数属于泛化种（generalists）的体虱类群，其种群结构却符合生物地理学（biogeography）分布模式。这意味着同域宿主（sympatric hosts）间的扩散对体虱多样性存在一定影响，但在更深的时间尺度下，寄生虫最终会按照宿主物种进行分化聚类。综上，本研究结果表明，多类因素共同塑造了该类寄生虫的多样性分布模式，且这些因素的效应会随演化尺度的不同而发生变化。我们所采用的整合研究方法，是揭示上述多样性模式的关键，且该方法有望在其他相关研究中得到广泛应用。