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.

中文翻译：

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锯蝇属 Neodiprion 物种树推断方法的比较（膜翅目：Diprionidae）

Neodiprion 属中以针叶树为食的锯蝇为研究繁殖障碍的起源和维持提供了极好的机会，但事实证明，获得 Neodiprion 物种形成比较研究的系统发育估计很困难。具体而言，个体基因树内部的非单一性和不一致（这两种情况在最近和/或迅速分化的群体中很常见）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而非基因树的方法来估计 lecontei 物种组成员之间的关系：（1）最小化深度合并（MDC），（2）最浅的分歧（SD）， (3) 物种树的贝叶斯估计（BEST），(4) 一种将串联与单系约束 (CMC) 相结合的新方法。大多数物种对多个种群进行抽样，所有四种方法都将这种种内变异纳入种间关系的估计中。我们调查了每种方法对分类抽样的敏感性，并且对于 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，以识别由多种分析和证据线支持的进化枝。我们发现分类抽样和方法选择都会影响物种树估计，对于这些数据，BEST 方法受到 Theta 和分支长度先验的强烈影响。我们还发现 CMC 方法对分类抽样最不敏感。最后，尽管由于 lecontei 组最近的分歧，种间遗传变异很低，但我们迄今为止的结果表明，不完整的谱系分类和种间基因流是使 Neodiprion 中物种树推断复杂化的主要因素。基于这些分析，我们提出了 lecontei 组的系统发育假设。最后，我们的结果表明，即使对于像 Neodiprion 这样非常具有挑战性的群体，只要充分采样种内变异并使用专注于物种树估计的方法，也可以从多基因座数据中提取潜在的物种树信号。我们迄今为止的结果表明，不完整的谱系分类和种间基因流是使 Neodiprion 物种树推断复杂化的主要因素。基于这些分析，我们提出了 lecontei 组的系统发育假设。最后，我们的结果表明，即使对于像 Neodiprion 这样非常具有挑战性的群体，只要充分采样种内变异并使用专注于物种树估计的方法，也可以从多基因座数据中提取潜在的物种树信号。我们迄今为止的结果表明，不完整的谱系分类和种间基因流是使 Neodiprion 物种树推断复杂化的主要因素。基于这些分析，我们提出了 lecontei 组的系统发育假设。最后，我们的结果表明，即使对于像 Neodiprion 这样非常具有挑战性的群体，只要充分采样种内变异并使用专注于物种树估计的方法，也可以从多基因座数据中提取潜在的物种树信号。