Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)

IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Phylogenetics and Evolution Pub Date : 2024-06-13 DOI:10.1016/j.ympev.2024.108129
Sara González-Delgado , Paula C. Rodríguez-Flores , Gonzalo Giribet
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Abstract

Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.

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测试双壳类动物(软体动物门:双壳类)中用于系统发育推断的超保守元素(UCE)。
双壳类动物是重要的渔业资源和文物。利用形态学和分子特征进行双壳类动物系统发育的传统由来已久,许多具有重要商业价值的物种都有基因组资源。然而,双壳类家族之间的关系一直不稳定,有丝分裂基因组学与基于桑格扩增子测序或系统转录组学的结果之间存在重大冲突。在这里,我们设计并测试了双壳纲的超保守元素探针集,目的是使用数百个位点,而无需对昂贵且复杂的全基因组或转录组进行测序分析,并将双壳纲系统发生学应用于博物馆标本。我们的探针集成功捕获了 1,513 个 UCE,总长度为 263,800 bp,每个 UCE 的平均长度为 174.59 ± 3.44(从 28 到 842 bp 不等)。利用不同的数据矩阵和系统发育推断方法,在双壳纲和多纳科内对该 UCE 探针集进行了系统发育测试,结果表明在多个分类水平上都取得了良好的效果。此外,我们的探针集还能捕捉到 1900 年前采集的博物馆标本中的大量 UCE。总之,这是双壳类系统发生学的一个新颖而有用的资源。
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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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