A shallow‐scale phylogenomics approach reveals repeated patterns of diversification among sympatric lineages of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

• Published in: Systematic entomology Vol. 50; no. 1; pp. 82 - 101
• Main Authors: Baca, Stephen M., Gustafson, Grey T., DeRaad, Devon A., Alexander, Alana, Hime, Paul M., Short, Andrew E. Z.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.01.2025; Wiley Subscription Services, Inc
• Subjects: ancestry; Caribbean; Coleoptera; entomology; Gene polymorphism; Genetic analysis; Genetic diversity; Mexico; Neotropical biogeography; Neotropics; Noteridae; Notomicrus traili; Phylogenetics; Phylogeny; phylogeography; polyphyly; Population genetics; Single-nucleotide polymorphism; South America; species; species group; statistical analysis; Sympatric populations; sympatry; systematics; ultraconserved elements; Whole genome sequencing; Mexico; West Indies; South America; Caribbean
• ISSN: 0307-6970; 1365-3113
• DOI: 10.1111/syen.12643

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. The shallow‐scale phylogeography of the Neotropical Notomicrus traili complex is reconstructed using a robust UCE dataset captured with a tailored, noterid‐specific probe set. Phylogenomic and population genetic approaches recover several cryptic, genetically distinct lineages with overlapping spatial distributions and repeated geographic structuring. A repeated pattern of diversification and subsequent dispersal within the traili complex suggests that diversification is dispersal‐mediated and/or that some regions are conducive to lineage survival following dispersal.