More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)

A central question concerning data collection strategy for molecular phylogenies has been, is it better to increase the number of characters or the number of taxa sampled to improve the robustness of a phylogeny estimate? A recent simulation study concluded that increasing the number of taxa sampled is preferable to increasing the number of nucleotide characters, if taxa are chosen specifically to break up long branches. We explore this hypothesis by using empirical data from noctuoid moths, one of the largest superfamilies of insects. Separate studies of two nuclear genes, elongation factor-1α (EF-1α) and dopa decarboxylase (DDC), have yielded similar gene trees and high concordance with morphological groupings for 49 exemplar species. However, support levels were quite low for nodes deeper than the subfamily level. We tested the effects on phylogenetic signal of (1) increasing the taxon sampling by nearly 60%, to 77 species, and (2) combining data from the two genes in a single anal...关于分子系统发育（molecular phylogenies）的数据收集策略，核心争议问题始终是：为提升系统发育推断的稳健性，究竟应增加性状数量，还是扩大采样类群规模？近期一项模拟研究指出，若类群选取专门用于破除长支，则扩大采样类群数量优于增加核苷酸性状（nucleotide characters）数量。本研究以昆虫最大超科之一的夜蛾总科昆虫（noctuoid moths）的实证数据为基础，对该假说展开验证。此前已有两项针对两个核基因——延伸因子-1α（elongation factor-1α，EF-1α）与多巴脱羧酶（dopa decarboxylase，DDC）——的独立研究，其构建的基因树结果相似，且与49个代表物种的形态学类群划分高度一致，但亚科层级以上的深层节点支持率均较低。本研究测试了两种操作对系统发育信号（phylogenetic signal）的影响：(1) 将类群采样规模扩大近60%，增至77个物种；(2) 将两个基因的数据合并进行单...