Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma)
Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma)
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DOI：
10.3389/fevo.2021.678110
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发表时间：
2021-07
期刊：
影响因子：
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通讯作者：
A. Leaché;Hayden R. Davis;S. Singhal;M. Fujita;Megan E. Lahti;K. Zamudio
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作者：
A. Leaché;Hayden R. Davis;S. Singhal;M. Fujita;Megan E. Lahti;K. Zamudio
生物多样性的系统基因组学研究有助于检测细微尺度的种群遗传结构以及物种和种群的人口历史。然而，确定种群间测量的遗传差异是否反映物种水平的分化仍然是物种划界的核心挑战。一种可能的解决方案是比较假定的新物种与其他密切相关物种之间的遗传差异，有时被称为基于参考的分类法。要被描述为一个新物种，一个种群至少应该和其他物种一样分化。在这里，我们使用系统发育学数据(ddRADseq数据)建立了一个基于参考的角蜥蜴(Phrynosoma；17种)分类，为划分大短角蜥蜴物种复合体(P.hernandesi)的物种提供了一个框架。以前对这个物种复合体的物种划分研究产生了相互矛盾的结果，形态数据表明，Hernandesi由5个物种组成，而线粒体DNA支持从1到10+个物种。为了帮助解决这一冲突，我们首先使用SNP数据估计了Hernandesi和近亲的时间校准物种树。这些结果支持P.hernandesi的Parparly；我们建议识别两个种，以促进与种单系一致的分类学。有强有力的证据表明，Hernandesi内有三个种群，人口模型和混合分析表明，这些种群不是生殖隔离的，这与之前的形态分析一致，表明杂交可能是常见的。最后，我们通过量化所有18个金线虫物种的遗传分化水平来表征种群-物种边界。Hernandesi西部和南部种群的遗传分化程度未能超过其他Phrynosoma物种，但北部种群的估计种群规模相对较小，导致它看起来是一个相对分化的物种。这些比较突出了将以参考为基础的物种划界方法付诸实践的困难。然而，以参考为基础的方法为一致评估具有相似生活史和生态特征的生物体分支内的生物多样性提供了一个有希望的框架。
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.