The hitchhiker's guide to single‐locus species delimitation

Abstract

Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive "hitchhiker's guide" highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance-based (ABGD, "automatic barcode gap discovery"), allele sharing-based (haplowebs) and tree-based approaches (GMYC, "generalized mixed Yule-coalescent" and PTP, "Poisson tree processes") to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree-based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one-size-fit-all approach to single-locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.

Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the Northeast Pacific Ocean, and implications for conservation

“…ABGD has been reported to over-lump speciose datasets with high speciation rates (Dellicour and Flot, 2018). ABGD's conservatism and GMYC overestimates have also been shown on reef brittle stars (Boissin et al, 2017), while both studies indicated that PTP methods show a small advantage as the most stable, suggesting the presence of additional cryptic species but without over-splitting taxa.…”

“…Summarising, despite the differences in the number of delimited species, overall the methods recovered a broadly similar number of SSH. Congruence among different delimitation methods is a strong indication that the delimitation is correct, allowing the designation of cryptic species and rectification of taxonomic problems (Dellicour and Flot, 2018), always when possible taking into account the morphology.…”

Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the northeast Pacific Ocean and implications for conservation

“…Overall, these data show that the brittle star biodiversity in the deep sea is still greatly underestimated, while supporting the use of DNA barcoding as an effective and time-efficient method of species delimitation to complement morphological studies. Although we do not wish to suggest that single mitochondrial locus data should be used on their own to draw taxonomic conclusions, in much the same way as using single morphological characters is discouraged (DeSalle, 2006;Hofmann et al, 2019), we do argue that single gene barcoding could be the first step in identifying previously overlooked species, while also providing a guide in cases where morphological identification is difficult. It was only recently that a transcriptome-based analysis of Ophiuroidea (O'Hara et al, 2014) instigated a major reevaluation of morphology-based classifications (Smith et al, 1995), proving that there is still a lot to be discovered and reevaluated within this group.…”

“…For the mtDNA COI analyses genomic DNA was extracted from arm tissue in individuals larger than 1-2 mm or from whole individuals when smaller than 1-2 mm. DNA extractions were carried out using 30 µL Chelex (InstaGene Matrix, Bio-Rad) according to the protocol of Estoup et al (1996) and directly used as a DNA template for polymerase chain reaction (PCR). All DNA samples were stored at −20 • C. In the cases where the whole individual was used, 20-25 µL of the supernatant was first separated from the ophiuroid's voucher specimen, while the individual, which was generally intact, was transferred to 96 % ethanol and stored as a voucher for morphological identifications.…”

Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

“…Despite being cofounded by various problems, single-gene methods still predominate in the literature, often with sample sizes 48 that do not capture intraspecific haplotype variability, an issue scarcely parameterized (Phillips et al, 2019). Additionally, single-locus delimitation methods fall under several broad categories, 50 yet each suffers from limitations not easily overcome (Dellicour & Flot, 2018).…”