Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.
Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA.
Heredity (Edinb). 2023 Jan;130(1):14-21. doi: 10.1038/s41437-022-00571-9. Epub 2022 Nov 5.
Discordance between different genomic regions, often identified through multilocus sequencing of selected markers, presents particular difficulties in identifying historical processes which drive species diversity and boundaries. Mechanisms causing discordance, such as incomplete lineage sorting or introgression due to interspecific hybridization, are better identified based on population-level genomic datasets. In the toads of the Rhinella granulosa species group, patterns of mito-nuclear discordance and potential hybridization have been reported by several studies. However, these patterns were proposed based on few loci, such that alternative mechanisms behind gene-tree heterogeneity cannot be ruled out. Using genome-wide ddRADseq loci from a subset of species within this clade, we found only partial concordance between currently recognized species-level taxon boundaries and patterns of genetic structure. While most taxa within the R. granulosa group correspond to clades, genetic clustering analyses sometimes grouped distinct taxonomic units into a single cluster. Moreover, levels of admixture between inferred clusters were limited and restricted to a single taxon pair which is best explained by incomplete lineage sorting as opposed to introgressive hybridization, according to D-statistics results. These findings contradict previous assertions of widespread cryptic diversity and gene flow within the R. granulosa clade. Lastly, our analyses suggest that diversification events within the Rhinella granulosa group mostly dated back to the early Pliocene, being generally younger than species divergences in other closely related clades that present high levels of cross-species gene flow. This finding uniquely contradicts common assertions that this young clade of toads exhibits interspecific hybridization.
不同基因组区域之间的不协调性,通常通过选择标记的多基因序列来识别,这给识别驱动物种多样性和边界的历史进程带来了特殊的困难。导致不协调性的机制,如由于种间杂交导致的不完全谱系分选或基因渗入,基于群体水平的基因组数据集可以更好地识别。在 Rhinella granulosa 物种群的蟾蜍中,已有多项研究报道了线粒体-核不协调性和潜在杂交的模式。然而,这些模式是基于少数基因座提出的,因此不能排除基因树异质性背后的替代机制。使用该分支内一些物种的全基因组 ddRADseq 基因座,我们发现目前公认的种级分类群边界与遗传结构模式之间只有部分一致性。虽然 R. granulosa 组内的大多数分类群与分支相对应,但遗传聚类分析有时会将不同的分类单元归入单个聚类。此外,推断出的聚类之间的混合程度有限,仅限于一个单一种对,根据 D 统计结果,这最好用不完全谱系分选而不是基因渗入来解释。这些发现与之前关于 R. granulosa 分支内广泛存在隐多样性和基因流动的说法相矛盾。最后,我们的分析表明,Rhinella granulosa 组内的多样化事件主要可以追溯到上新世早期,通常比其他具有高种间基因流动的密切相关分支中的物种分歧要年轻。这一发现与普遍认为这个年轻的蟾蜍分支存在种间杂交的说法相矛盾。