Introgression across narrow contact zones shapes the genomic landscape of phylogenetic variation in an African bird clade

IF 6.1 1区 生物学 Q1 EVOLUTIONARY BIOLOGY
Loïs Rancilhac, Stacey G de Souza, Sifiso M Lukhele, Matteo Sebastianelli, Bridget O Ogolowa, Michaella Moysi, Christos Nikiforou, Tsyon Asfaw, Colleen T Downs, Alan Brelsford, Bridgett M vonHoldt, Alexander N G Kirschel
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引用次数: 0

Abstract

Genomic analyses of hybrid zones provide excellent opportunities to investigate the consequences of introgression in nature. In combination with phylogenomics analyses, hybrid zone studies may illuminate the role of ancient and contemporary gene flow in shaping variation of phylogenetic signals across the genome, but this avenue has not been explored yet. We combined phylogenomic and geographic cline analyses in a Pogoniulus tinkerbird clade to determine whether contemporary introgression through hybrid zones contributes to gene-tree heterogeneity across the species ranges. We found diverse phylogenetic signals across the genome with the most common topologies supporting monophyly among taxa connected by secondary contact zones. Remarkably, these systematic conflicts were also recovered when selecting only individuals from each taxon's core range. Using analyses of derived allele sharing and “recombination aware” phylogenomics, we found that introgression shapes gene-tree heterogeneity, and the species tree most likely supports monophyletic red-fronted tinkerbirds, as recovered in previous reconstructions based on mitochondrial DNA. Furthermore, by fitting geographic clines across two secondary contact zones, we found that introgression rates were lower in genomic regions supporting the putative species tree compared to those supporting the two taxa in contact as monophyletic. This demonstrates that introgression through narrow contact zones shapes gene-tree heterogeneity even in allopatric populations. Finally, we did not find evidence that mitochondria-interacting nuclear genes acted as barrier loci. Our results show that species can withstand important amounts of introgression while maintaining their phenotypic integrity and ecological separation, raising questions regarding the genomic architecture of adaptation and barriers to gene flow.
跨越狭窄接触带的渗入形成了非洲鸟类进化进化的基因组景观
杂交带的基因组分析为研究自然中基因渗入的后果提供了极好的机会。结合系统基因组学分析,杂交区研究可能阐明古代和现代基因流在形成基因组系统发育信号变异中的作用,但这一途径尚未被探索。我们结合了Pogoniulus修补鸟进化枝的系统基因组学和地理渐变分析,以确定通过杂交带的当代渗入是否有助于物种范围内基因树的异质性。我们发现整个基因组具有不同的系统发育信号,最常见的拓扑结构支持由次级接触带连接的类群之间的单系性。值得注意的是,当只从每个分类单元的核心范围中选择个体时,这些系统冲突也被恢复了。通过对衍生等位基因共享和“重组意识”系统基因组学的分析,我们发现基因导入形成了基因树的异质性,并且物种树很可能支持单系红毛修补鸟,正如之前基于线粒体DNA重建所恢复的那样。此外,通过拟合两个次级接触带的地理曲线,我们发现在支持假定物种树的基因组区域,与支持两个接触类群为单系的基因组区域相比,渗入率更低。这表明,即使在异域种群中,通过狭窄接触区的渗入也会形成基因树异质性。最后,我们没有发现线粒体相互作用的核基因作为屏障位点的证据。我们的研究结果表明,物种可以承受大量的基因渗入,同时保持其表型完整性和生态分离,这就提出了关于适应基因组结构和基因流动障碍的问题。
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来源期刊
Systematic Biology
Systematic Biology 生物-进化生物学
CiteScore
13.00
自引率
7.70%
发文量
70
审稿时长
6-12 weeks
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.
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