Stephen M. Baca, Grey T. Gustafson, Devon A. DeRaad, Alana Alexander, Paul M. Hime, Andrew E. Z. Short
{"title":"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","authors":"Stephen M. Baca, Grey T. Gustafson, Devon A. DeRaad, Alana Alexander, Paul M. Hime, Andrew E. Z. Short","doi":"10.1111/syen.12643","DOIUrl":null,"url":null,"abstract":"The <jats:italic>Notomicrus traili</jats:italic> 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 <jats:italic>N. traili</jats:italic> and the closely related <jats:italic>Notomicrus gracilipes</jats:italic> recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the <jats:italic>N. traili</jats:italic> 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 <jats:italic>traili</jats:italic> group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative <jats:italic>N. traili</jats:italic> 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 <jats:italic>traili</jats:italic> 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 <jats:italic>traili</jats:italic> 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.","PeriodicalId":22126,"journal":{"name":"Systematic Entomology","volume":null,"pages":null},"PeriodicalIF":4.7000,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A shallow‐scale phylogenomics approach reveals repeated patterns of diversification among sympatric lineages of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)\",\"authors\":\"Stephen M. Baca, Grey T. Gustafson, Devon A. DeRaad, Alana Alexander, Paul M. Hime, Andrew E. Z. Short\",\"doi\":\"10.1111/syen.12643\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The <jats:italic>Notomicrus traili</jats:italic> 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 <jats:italic>N. traili</jats:italic> and the closely related <jats:italic>Notomicrus gracilipes</jats:italic> recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the <jats:italic>N. traili</jats:italic> 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 <jats:italic>traili</jats:italic> group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative <jats:italic>N. traili</jats:italic> 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 <jats:italic>traili</jats:italic> 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 <jats:italic>traili</jats:italic> 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.\",\"PeriodicalId\":22126,\"journal\":{\"name\":\"Systematic Entomology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.7000,\"publicationDate\":\"2024-06-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Systematic Entomology\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1111/syen.12643\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"ENTOMOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Systematic Entomology","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1111/syen.12643","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"ENTOMOLOGY","Score":null,"Total":0}
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.
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.