Conner William R, Delaney Emily K, Bronski Michael J, Ginsberg Paul S, Wheeler Timothy B, Richardson Kelly M, Peckenpaugh Brooke, Kim Kevin J, Watada Masayoshi, Hoffmann Ary A, Eisen Michael B, Kopp Artyom, Cooper Brandon S, Turelli Michael
Department of Evolution and Ecology, University of California, Davis, CA 95616, USA; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA(1).
Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
Mol Phylogenet Evol. 2021 May;158:107061. doi: 10.1016/j.ympev.2020.107061. Epub 2020 Dec 31.
The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution - even when complete genome sequences are available - as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.
芒山果蝇物种组是一个包含94个命名物种的进化枝，与模式物种黑腹果蝇密切相关。芒山果蝇物种组分布在亚洲、非洲和澳大拉西亚的广泛地理区域。该组物种具有广泛的形态、交配行为和内共生体关联，这使得这个进化枝对于比较分析很有用。我们使用来自42个可用物种的基因组数据来估计芒山果蝇物种组内的系统发育和相对分歧时间，以及它与黑腹果蝇的相对分歧时间。为了评估我们系统发育推断的稳健性，我们使用3组不重叠的每组20个单拷贝编码序列，并使用贝叶斯方法和最大似然方法分析所有60个基因。我们的分析支持该组的单系性。除了一个单一物种——白马果蝇的位置不确定外，我们的分析还支持芒山组内提出的所有七个亚组的单系性。我们的系统发育树图和相对时间线图提供了一个高度解析的物种树，不一致性仅限于树中较深的相对短分支的估计。相比之下，芒山果蝇冠群相对于其与黑腹果蝇分歧的年龄估计，严重依赖于关于各分支分子进化速率变化的先验假设，因此尚未得到可靠确定。我们讨论了限制系统发育分辨率的方法学问题——即使有完整的基因组序列可用——以及当前系统发育对于理解这个进化枝的进化和生物地理历史的效用。
