Linnen Catherine R, Farrell Brian D
Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
Syst Biol. 2008 Dec;57(6):876-90. doi: 10.1080/10635150802580949.
Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between individual gene trees, both of which are common in groups that diverged recently and/or rapidly, make it impossible to infer a species tree using methods that are designed to estimate gene trees. Therefore, in this study, we estimate relationships between members of the lecontei species group using four approaches that are intended to estimate species, not gene, trees: (1) minimize deep coalescences (MDC), (2) shallowest divergences (SD), (3) Bayesian estimation of species trees (BEST), and (4) a novel approach that combines concatenation with monophyly constraints (CMC). Multiple populations are sampled for most species and all four methods incorporate this intraspecific variation into estimates of interspecific relationships. We investigate the sensitivity of each method to taxonomic sampling, and, for the BEST method, we assess the impact of prior choice on species-tree inference. We also compare species-tree estimates to one another and to a morphologically based hypothesis to identify clades that are supported by multiple analyses and lines of evidence. We find that both taxonomic sampling and method choice impact species-tree estimates and that, for these data, the BEST method is strongly influenced by Theta and branch-length priors. We also find that the CMC method is the least sensitive to taxonomic sampling. Finally, although interspecific genetic variation is low due to the recent divergence of the lecontei group, our results to date suggest that incomplete lineage sorting and interspecific gene flow are the main factors complicating species-tree inference in Neodiprion. Based on these analyses, we propose a phylogenetic hypothesis for the lecontei group. Finally, our results suggest that, even for very challenging groups like Neodiprion, an underlying species-tree signal can be extracted from multi-locus data as long as intraspecific variation is adequately sampled and methods that focus on the estimation of species trees are used.
食针叶锯蜂属（Neodiprion）的锯蜂为研究生殖隔离的起源和维持提供了绝佳机会，但要获得用于食针叶锯蜂物种形成比较研究的系统发育估计却颇具困难。具体而言，单个基因树内部的非单系性以及基因树之间的不一致性，这两种情况在近期和/或快速分化的类群中都很常见，使得无法使用旨在估计基因树的方法来推断物种树。因此，在本研究中，我们使用四种旨在估计物种树而非基因树的方法来估计莱康特锯蜂物种组各成员之间的关系：（1）最小化深度合并（MDC），（2）最浅分歧（SD），（3）物种树的贝叶斯估计（BEST），以及（4）一种将串联与单系性约束相结合的新方法（CMC）。大多数物种都采样了多个种群，并且所有四种方法都将这种种内变异纳入种间关系的估计中。我们研究了每种方法对分类群采样的敏感性，对于BEST方法，我们评估了先验选择对物种树推断的影响。我们还将物种树估计相互比较，并与基于形态学的假设进行比较，以识别得到多种分析和多条证据支持的分支。我们发现分类群采样和方法选择都会影响物种树估计，并且对于这些数据，BEST方法受Theta和分支长度先验的强烈影响。我们还发现CMC方法对分类群采样最不敏感。最后，尽管由于莱康特锯蜂组近期的分化，种间遗传变异较低，但我们目前的结果表明，不完全谱系分选和种间基因流是使食针叶锯蜂物种树推断复杂化的主要因素。基于这些分析，我们提出了莱康特锯蜂组的系统发育假设。最后，我们的结果表明，即使对于像食针叶锯蜂这样极具挑战性的类群，只要充分采样种内变异并使用专注于估计物种树的方法，就可以从多基因座数据中提取潜在的物种树信号。
