Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.

中文翻译：

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系统发育不一致是由响尾蛇 （Viperidae： Crotalus 和 Sistrurus） 内部物种快速多样化过程中的广泛渗入和不完整谱系分选驱动的


系统发育基因组学使我们能够揭示进化过程随时间变化的历史信号，并估计解释这些信号的系统发育网络。从全基因组数据中获得的见解使我们能够进一步确定整个基因组的杂交、渗入和祖先多态性对系统发育信号的贡献。在这里，我们关注这些过程如何导致响尾蛇（Crotalus 属和 Sistrurus属）之间的系统发育不一致，该组基于各种分子数据集和分析方法存在许多相互冲突的系统发育假设。我们使用从几乎所有已知物种采样的转录组生成的基因组数据来解决响尾蛇系统发育的不稳定性。这些基因组数据，使用合并和基于网络的方法进行分析，揭示了许多快速物种形成的例子，其中单个基因树与物种树发生冲突。此外，响尾蛇的进化历史以不完全的物种形成和频繁的杂交为主，这两者都可能影响了过去对系统发育的解释。我们提出了一个新的框架，其中只有根据全基因组数据和基于网络的分析方法才能理解该群体的进化关系。我们的数据表明，像在响尾蛇中看到的网络辐射只能在系统发育背景下理解，因此在我们试图了解其他快速辐射物种的进化历史时，需要类似的方法。