Dezhi Zhang, Huishang She, Shangyu Wang, Haitao Wang, Shi Li, Yalin Cheng, Gang Song, Chenxi Jia, Yanhua Qu, Frank E Rheindt, Urban Olsson, Per Alström, Fumin Lei
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Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which – in combination – support the following tree topology: (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. 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引用次数: 0
摘要
不同的基因组区域可能反映出相互冲突的系统发生拓扑结构,这主要是由于不完全的品系分类和/或基因流动造成的。要重建真正的物种树并探索系统发生冲突的潜在原因,基因组数据是必要的。在此,我们基于41种鸟类的全基因组重测序数据,研究了4种Emberiza(鸟类:Emberizidae)的系统发生关系,并讨论了Emberiza godlewskii(戈德勒夫斯基鹀)线粒体非单系的潜在原因。基于整个线粒体基因组和约 39 千碱基的非重组 W 染色体的分析表明,E. godlewskii 的北部和南部种群分别与 E. cioides 和 E. cia 是姊妹关系。与此相反,常染色体和 Z 染色体序列数据以及人口推断分析的系统发生信号反映了 E. godlewskii 的单系性,它们共同支持以下树拓结构:((E. godlewskii, E. cia), E. cioides), E. jankowskii)。利用 D 统计法,我们在不同品系之间检测到多个基因流事件,表明该支系内部存在普遍的内向杂交。cioides 的姊妹系或未取样的线粒体 + W 染色体的 E. cioides 系向北部 E. godlewskii 的引入可能解释了全基因组数据估计的物种树与 mtDNA/W 树拓扑之间的系统发生冲突。这些结果强调了利用基因组数据进行系统发育重建和物种划分的重要性。
Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae)
Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which – in combination – support the following tree topology: (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
期刊介绍:
Systematic Biology is the bimonthly journal of the Society of Systematic Biologists. Papers for the journal are original contributions to the theory, principles, and methods of systematics as well as phylogeny, evolution, morphology, biogeography, paleontology, genetics, and the classification of all living things. A Points of View section offers a forum for discussion, while book reviews and announcements of general interest are also featured.