Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil.
Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP 09972-270, Brazil.
Syst Biol. 2018 Jul 1;67(4):700-718. doi: 10.1093/sysbio/syy004.
Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective population sizes and branch lengths, and the resulting estimation errors are still poorly understood in wild populations. In this study, we used an integrative approach, including sequence capture of ultra-conserved elements (UCEs), mtDNA Sanger sequencing and morphological data to investigate species limits and phylogenetic relationships in face of gene flow in an Amazonian endemic species (Myrmoborus lugubris: Aves). We used commonly implemented species tree and model-based approaches to understand the potential effects of gene flow in phylogenetic reconstructions. The genetic structure observed was congruent with the four recognized subspecies of M. lugubris. Morphological and UCEs data supported the presence of a wide hybrid zone between M. l. femininus from the Madeira river and M. l. lugubris from the Middle and lower Amazon river, which were recovered as sister taxa by species tree methods. When fitting gene flow into simulated demographic models with different topologies, the best-fit model indicated these two taxa as non-sister lineages, a finding that is in agreement with the results of mitochondrial and morphological analyses. Our results demonstrated that failing to account for gene flow when estimating phylogenies at shallow divergence levels can generate topological uncertainty, which can nevertheless be statistically well supported, and that model testing approaches using simulated data can be useful tools to test alternative phylogenetic hypotheses.
在群体成为独立的进化谱系之前，微观进化过程的影响往往会产生多样化的复杂情景，这可能会影响系统发育重建。在物种树估计中不考虑基因流会直接影响拓扑结构、有效种群大小和分支长度，而在野生种群中，这些由此产生的估计误差仍然知之甚少。在这项研究中，我们使用了一种综合方法，包括超保守元件（UCEs）的序列捕获、mtDNA Sanger 测序和形态学数据，以研究在亚马逊特有物种（Myrmoborus lugubris：鸟类）面临基因流时的物种界限和系统发育关系。我们使用了常用的物种树和基于模型的方法来了解基因流对系统发育重建的潜在影响。观察到的遗传结构与公认的 M. lugubris 的四个亚种一致。形态学和 UCEs 数据支持在 Madeira 河的 M. l. femininus 和 Middle 和 lower Amazon 河的 M. l. lugubris 之间存在广泛的杂交区，物种树方法将这两个亚种归为姐妹分类群。当将基因流拟合到具有不同拓扑结构的模拟人口统计模型中时，最佳拟合模型表明这两个分类群不是姐妹谱系，这一发现与线粒体和形态学分析的结果一致。我们的结果表明，在估计浅分歧水平的系统发育时，如果不考虑基因流，可能会产生拓扑不确定性，但这些不确定性在统计学上是可以得到很好支持的，并且使用模拟数据进行模型检验的方法可以成为测试替代系统发育假设的有用工具。
