Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale datasets and coalescent modelling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridisation. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least four operational taxonomic units (OTUs) across four species which diverged 183-278 kya. ABC modelling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.

中文翻译：

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博物馆皮肤能够识别与细胞核不一致相关的基因渗入


对密切相关物种的基因组和种群的采样增加表明，物种形成期间和之后的遗传交换水平比之前认为的要高。这种交换的一个明显表现是强烈的细胞核不一致，其中线粒体DNA（mtDNA）与核基因的差异比预期更多（或更少），这是由于mtDNA和核DNA（nDNA）在群体大小和突变率方面的差异而造成的。考虑到基因组规模的数据集和合并模型，我们现在可以自信地识别强烈不一致的案例，并专门针对历史或最近的基因渗入作为原因进行测试。通过群体抽样，结合历史博物馆标本和最近收集的组织中的外显子捕获数据，我们展示了基因组工具如何解决岩袋鼠 (Petrogale) 短尾猴群复杂的进化历史。特别是，应用人口和系统发育学方法，我们可以评估人口统计过程在驱动复杂进化模式中的作用，并评估古代基因渗入和杂交的作用。我们发现所描述的物种被很好地支持为 nDNA 基因的单系类群，但不支持 mtDNA，细胞核不一致涉及四个物种中至少四个操作分类单元 (OTU)，其分歧为 183-278 kya。 nDNA 基因树的 ABC 建模支持某些具有细胞核不一致的分类单元对在物种形成期间或之后的基因渗入。鉴于所涉及物种之间体型的巨大差异，基因流动的证据令人惊讶。已鉴定出基因渗入的异质模式，但似乎与物种之间的染色体差异无关。 这些和之前的结果表明，季风热带地区过去的动态气候可能促进了相关物种之间的网状分布。