浅尺度系统发生组学方法揭示了新热带隐性水生甲虫(鞘翅目:诺特科)同域世系间的重复分化模式

IF 4.7 1区 农林科学 Q1 ENTOMOLOGY Systematic Entomology Pub Date : 2024-06-20 DOI:10.1111/syen.12643
Stephen M. Baca, Grey T. Gustafson, Devon A. DeRaad, Alana Alexander, Paul M. Hime, Andrew E. Z. Short
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引用次数: 0

摘要

Notomicrus traili物种群(鞘翅目:Noteridae)是水生甲虫的一个品系,分布于整个南美洲,并延伸到墨西哥和西印度群岛。以前的研究揭示了这一群体中的物种复杂性,多个不同的支系分布重叠,N. traili 和密切相关的 Notomicrus gracilipes 的支系被认为是多系的。在这里,我们有针对性地捕获了超保守元素(UCE),以研究 N. traili 群内的关系和进化模式。首先,我们使用短线程全基因组测序技术对四个虎皮鹦鹉属设计了一个虎皮鹦鹉特异性 UCE 探针集(Noteridae 3.4Kv1),目标基因位点超过 3400 个。利用该探针集,我们从整个新热带地区的 44 个 traili 组标本的种群水平取样中获取了 UCE 数据,重点是圭亚那盾地区,那里有几个推定的 N. traili 组种群分布重叠。我们对所得到的数据矩阵进行了各种修剪和数据完整性处理,并采用并列最大似然法和聚合一致法重建了系统发生。我们恢复了稳健的系统发育估计,发现了 traili 群中几个系统发育上不同的支系,它们的分布有重叠。为了检验种群的遗传独特性,我们使用嵌合参考方法从 UCE 对齐中提取单核苷酸多态性(SNP)数据,绘制 UCE 富集读数,并使用主成分分析(PCA)和 STRUCTURE 检验遗传聚类模式。种群遗传结果与恢复的系统发育结构高度一致,揭示了在已识别的支系内高度共享的共祖关系,与支系间有限的共祖关系形成鲜明对比。我们发现的模式与 traili 类在新热带地区的反复分化和扩散一致,这突出表明了量身定制的 UCE 方法在促进浅尺度系统发育重建和种群遗传分析方面的有效性,它可以揭示鞘翅目昆虫系统地理学的新方面。
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A shallow‐scale phylogenomics approach reveals repeated patterns of diversification among sympatric lineages of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)
The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed to N. traili and the closely related Notomicrus gracilipes recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the N. traili group. First, we use short‐read whole‐genome sequencing of four noterid genera to design a noterid‐specific UCE probe set (Noteridae 3.4Kv1) targeting over 3400 unique loci. Using this probe set, we capture UCE data from population‐level sampling of 44 traili group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative N. traili group populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within the traili group that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments using a chimeric reference method to map UCE‐enriched reads and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co‐ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of the traili group in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow‐scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography.
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来源期刊
Systematic Entomology
Systematic Entomology 生物-进化生物学
CiteScore
10.50
自引率
8.30%
发文量
49
审稿时长
>12 weeks
期刊介绍: Systematic Entomology publishes original papers on insect systematics, phylogenetics and integrative taxonomy, with a preference for general interest papers of broad biological, evolutionary or zoogeographical relevance.
期刊最新文献
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