Congrains Carlos, Zucchi Roberto A, de Brito Reinaldo A
Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ, Universidade de São Paulo - USP, Piracicaba, SP, Brazil.
Mol Phylogenet Evol. 2021 Sep;162:107200. doi: 10.1016/j.ympev.2021.107200. Epub 2021 May 11.
New sequencing techniques have allowed us to explore the variation on thousands of genes and elucidate evolutionary relationships of lineages even in complex scenarios, such as when there is rapid diversification. That seems to be the case of species in the genus Anastrepha, which shows great species diversity that has been divided into 21 species groups, several of which show wide geographical distribution. The fraterculus group has several economically important species and it is also an outstanding model for speciation studies, since it includes several lineages that have diverged recently possibly in the presence of interspecific gene flow. Our main goal is to test whether we can infer phylogenetic relationships of recently diverged taxa with gene flow, such as what is expected for the fraterculus group and determine whether certain genes remain informative even in this complex scenario. An analysis of thousands of orthologous genes derived from transcriptome datasets of 10 different lineages across the genus, including some of the economically most important pests, revealed signals of incomplete lineage sorting, vestiges of ancestral introgression between more distant lineages and ongoing gene flow between closely related lineages. Though these patterns affect the phylogenetic signal, the phylogenomic inferences consistently show that the morphologically identified species here investigated are in different evolutionary lineages, with the sole exception involving Brazilian lineages of A. fraterculus, which has been suggested to be a complex assembly of cryptic species. A tree space analysis suggested that genes with greater phylogenetic resolution have evolved under similar selection pressures and are more resilient to intraspecific gene flow, which would make it more likely that these genomic regions may be useful for identifying fraterculus group lineages. Our findings help establish relationships among the most important Anastrepha species groups, as well as bring further data to indicate that the diversification of fraterculus group lineages, and even other lineages in the genus Anastrepha, has been strongly influenced by interspecific gene flow.
新的测序技术使我们能够探索数千个基因的变异，并阐明谱系的进化关系，即使在复杂的情况下，比如快速分化时也是如此。实蝇属的物种似乎就是这种情况，该属表现出极大的物种多样性，已被划分为21个物种组，其中几个物种组具有广泛的地理分布。果实蝇组有几个具有重要经济意义的物种，它也是物种形成研究的一个杰出模型，因为它包括几个最近可能在种间基因流存在的情况下分化的谱系。我们的主要目标是测试我们是否能够推断出存在基因流的近期分化类群的系统发育关系，比如果实蝇组所预期的情况，并确定某些基因在这种复杂情况下是否仍然具有信息价值。对来自该属10个不同谱系转录组数据集的数千个直系同源基因进行分析，包括一些经济上最重要的害虫，结果揭示了不完全谱系分选的信号、较远谱系之间祖先基因渗入的痕迹以及密切相关谱系之间正在进行的基因流。尽管这些模式影响了系统发育信号，但系统基因组学推断一致表明，这里所研究的形态学鉴定物种处于不同的进化谱系中，唯一的例外是巴西的果实蝇谱系，有人认为它是隐性物种的复杂组合。树空间分析表明，具有更高系统发育分辨率的基因是在相似的选择压力下进化的，并且对种内基因流更具弹性，这使得这些基因组区域更有可能用于识别果实蝇组谱系。我们的研究结果有助于建立最重要的实蝇物种组之间的关系，同时也带来了进一步的数据，表明果实蝇组谱系甚至实蝇属的其他谱系的分化受到种间基因流的强烈影响。
