Exploring species boundaries with multiple genetic loci using empirical data from non‐biting midges

Elisabeth Stur,Xiao‐Long Lin,Torbjørn Ekrem

doi:10.1111/zsc.12280

Elisabeth Stur, Xiao‐Long Lin + Show 1 more

Open Access

https://doi.org/10.1111/zsc.12280

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Abstract

Over the past decade, molecular approaches to species delimitation have seen rapid development. However, species delimitation based on a single locus, for example, DNA barcodes, can lead to inaccurate results in cases of recent speciation and incomplete lineage sorting. Here, we compare the performance of Automatic Barcode Gap Discovery (ABGD), Bayesian Poisson tree processes (PTP), networks, generalized mixed Yule coalescent (GMYC) and Bayesian phylogenetics and phylogeography (BPP) models to delineate cryptic species previously detected by DNA barcodes within Tanytarsus (Diptera: Chironomidae) non‐biting midges. We compare the results from analyses of one mitochondrial (cytochrome c oxidase subunit I [COI]) and three nuclear (alanyl‐tRNA synthetase 1 [AATS1], carbamoyl phosphate synthetase 1 [CAD1] and 6‐phosphogluconate dehydrogenase [PGD]) protein‐coding genes. Our results show that species delimitation based on multiple nuclear DNA markers is largely concordant with morphological variation and delimitations using a single locus, for example, the COI barcode. However, ABGD, GMYC, PTP and network models led to conflicting results based on a single locus and delineate species differently than morphology. Results from BPP analyses on multiple loci correspond best with current morphological species concept. In total, 10 lineages of the Tanytarsus curticornis species complex were uncovered. Excluding a Norwegian population of Tanytarsus brundini which might have undergone recent hybridization, this suggests six hitherto unrecognized species new to science. Five distinct species are well supported in the Tanytarsus heusdensis species complex, including two species new to science.

Highlights

Accurate assessment of species boundaries is critical for our understanding of biological diversity and speciation (Pimm et al, 2014)
In the T. heusdensis species complex, species delimitations based on the AATS1, CAD1 and PGD nuclear markers appear more reliable than those using the mitochondrial c oxidase subunit I (COI) gene
The five mitochondrial DNA lineages we previously identified in the T. heusdensis species complex (Lin et al, 2015) are recognized in the analyses based on nuclear markers

Summary

Introduction

Accurate assessment of species boundaries is critical for our understanding of biological diversity and speciation (Pimm et al, 2014). Genealogical concordance among multiple loci can provide convincing evidence for species boundaries and validate the presence of genetically distinctive but morphologically cryptic lineages. This has been explored in several insect taxa. Fossen, Ekrem, Nilsson, and Bergsten (2016) found evidence of genetically distinct lineages in closely related northern European water scavenger beetles using multiple loci, and Low et al (2016) delineated taxonomic boundaries in the largest species complex of black flies using multiple genes, morphological and chromosomal data. Within the Chironomidae, several potential cryptic species have been detected by DNA barcodes and subsequently confirmed by nuclear DNA markers and careful analyses of morphological characters (e.g., Anderson, Stur, & Ekrem, 2013)

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