Data from: Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice

Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain.

系统发育树（Phylogenetic trees）可揭示细菌内共生谱系（endosymbiotic lineages）的起源，并探明其与宿主的协同演化（co-evolution）模式。尽管分类群采样（taxon sampling）可显著影响系统发育推断与协同演化推断，但当前绝大多数内共生菌关系假说均基于少量已获取的细菌序列。本研究探讨了γ-变形菌纲（Gammaproteobacteria）序列的不同采样策略，如何影响寄生吸虱（昆虫纲：Phthirapatera：Anoplura）内共生菌谱系数量的估算结果。本研究结合新获取的与已发表的细菌16S rDNA序列，以及来自其他γ-变形菌纲的42000余条16S rDNA序列，对吸虱内共生菌的谱系数量进行了估算。本研究还开展了参数化与非参数自展（bootstrapping）实验，以探究系统发育误差与不确定性对上述估算结果的影响。16S rDNA序列的采样会对吸虱内共生菌多样性的估算产生影响，直至达到遗传多样性阈值——该阈值的大小取决于采样策略。以最大化16S rDNA序列多样性为目标的采样策略，相较于随机采样现有16S rDNA序列的策略，效率更高。尽管模拟结果验证了吸虱存在多支内共生菌谱系的估算结果，但自展分析结果表明，内共生菌起源的确切数量仍未明确。