Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles

IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Phylogenetics and Evolution Pub Date : 2024-06-16 DOI:10.1016/j.ympev.2024.108130
Miranda B. Sherlock , Jeffrey W. Streicher , David J. Gower , Simon T. Maddock , Ronald A. Nussbaum , Oommen V. Oommen , Ana Serra Silva , Julia J. Day , Mark Wilkinson
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Abstract

Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands. These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.

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基因组 SNP 解决了塞舌尔群岛古老两栖动物岛屿辐射的系统发育问题
对于海洋岛屿来说,塞舌尔群岛的花岗岩质地非常罕见,这里有多个特有的两栖动物品系。其中包括一个古老的(可能约 6000 万年前)八种凯西拉类,它们中的大多数出现在多个岛屿上。这些无尾类有着复杂的分类历史,其物种间的系统发育关系一直难以解决。双位 RAD 测序(ddRADseq)已被广泛应用于系统地理学,并越来越多地应用于系统发育学,但其在解决远古分化方面的实用性还不太成熟。为了解决这个问题,我们应用 ddRADseq 生成了一个全基因组 SNP 面板,用于塞舌尔群岛无尾类的系统发生学分析。基于 129,154 个 SNPs,我们解决了深层和浅层分裂问题,并获得了强有力的支持。我们的研究结果证明了全基因组 SNP 在多个分类水平上的进化推断能力,并支持最近提出的 Grandisonia Taylor, 1968 与 Hypogeophis Peters, 1879 的同义。我们揭示了 Hypogeophis 的三个支系(大体型、中体型和短体型),并确定了体型矮小、体格粗壮和尖嘴表型的单一起源。
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来源期刊
Molecular Phylogenetics and Evolution
Molecular Phylogenetics and Evolution 生物-进化生物学
CiteScore
7.50
自引率
7.30%
发文量
249
审稿时长
7.5 months
期刊介绍: Molecular Phylogenetics and Evolution is dedicated to bringing Darwin''s dream within grasp - to "have fairly true genealogical trees of each great kingdom of Nature." The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution, further the development of phylogenetically more accurate taxonomic classifications, and ultimately bring a unified classification for all the ramifying lines of life. Phylogeographic studies will be considered for publication if they offer EXCEPTIONAL theoretical or empirical advances.
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