Rarity and Incomplete Sampling in DNA-Based Species Delimitation

Ahrens, Dirk; Fujisawa, Tomochika; Krammer, Hans-Joachim; Eberle, Jonas; Fabrizi, Silvia; Vogler, Alfried P.

doi:10.1093/sysbio/syw002

Cited by 156 publications

(171 citation statements)

References 67 publications

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“…In the case of GMYC and PTP, our findings corroborate the study of Ahrens et al. () highlighting that rarely sampled species are not problematic per se for tree‐based approaches to species delimitation. The impact of sampling pattern was most dramatic for haplowebs: this is because the sampling of only two sequences per species is equivalent to sampling a single diploid individual, the two haplotypes of which are automatically considered conspecific using the haploweb approach (unlike tree‐based or distance‐based approaches that may consider them as heterospecific).…”

Section: Resultssupporting

confidence: 89%

The hitchhiker's guide to single‐locus species delimitation

Dellicour

Flot

2018

Molecular Ecology Resources

153

116

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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.

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Section: Resultssupporting

confidence: 89%

The hitchhiker's guide to single‐locus species delimitation

Dellicour

Flot

2018

Molecular Ecology Resources

153

116

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“…This matches the result of a recent simulation study showing that single‐locus tree‐based, distance‐based and allele sharing‐based approaches give congruent species hypotheses when dealing with highly variable markers in species of small effective population size and low speciation rate (Dellicour and Flot ). Yet, several studies found that the ability of MMs to delimit species accurately declined as the mean or among‐species variance in effective population size (Ne) increased (Esselstyn et al , Fujisawa and Barraclough , Dellicour and Flot , Ahrens et al ). However, larger Ne was either found to result in over‐splitting or lumping depending on the method used, differences in Ne between the common ancestor and descendant species and most importantly on the relative change of speciation rate.…”

Section: Discussionmentioning

confidence: 99%

Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

et al. 2017

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Ecologists increasingly rely on molecular delimitation methods (MMs) to identify species boundaries, thereby potentially increasing the number of putative species because of the presence of morphologically cryptic species. It has been argued that cryptic species could challenge our understanding of what determine large‐scale biodiversity patterns which have traditionally been documented from morphology alone. Here, we used morphology and three MMs to derive four different sets of putative species among the European groundwater crustaceans. Then, we used regression models to compare the relative importance of spatial heterogeneity, productivity and historical climates, in shaping species richness and range size patterns across sets of putative species. We tested three predictions. First, MMs would yield many more putative species than morphology because groundwater is a constraining environment allowing little morphological changes. Second, for species richness, MMs would increase the importance of spatial heterogeneity because cryptic species are more likely along physical barriers separating ecologically similar regions than along resource gradients promoting ecologically‐based divergent selection. Third, for range size, MMs would increase the importance of historical climates because of reduced and asymmetrical fragmentation of large morphological species ranges at northern latitudes. MMs yielded twice more putative species than morphology and decreased by 10‐fold the average species range size. Yet, MMs strengthened the mid‐latitude ridge of high species richness and the Rapoport effect of increasing range size at higher latitudes. Species richness predictors did not vary between morphology and MMs but the latter increased the proportion of variance in range size explained by historical climates. These findings demonstrate that our knowledge of groundwater biodiversity determinants is robust to overlooked cryptic species because the latter are homogeneously distributed along environmental gradients. Yet, our findings call for incorporating multiple species delimitation methods into the analysis of large‐scale biodiversity patterns across a range of taxa and ecosystems.

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“…Congruence of morphological species units with mOTUs was quantified with the match ratio adapted from Ahrens et al. (); the match ratio is calculated as follows: 2 × N match /( N mOTU + N morph ), where N match is the number of putative species that are the same between the two methods of delimitation, and N mOTU and N morph refer to the total number of mOTUs at a given percentage distance threshold and total number of morphological species units, respectively.…”

Section: Methodsmentioning

confidence: 99%

Sorting specimen‐rich invertebrate samples with cost‐effective NGS barcodes: Validating a reverse workflow for specimen processing

Wang

Srivathsan

Foo

et al. 2018

Molecular Ecology Resources

104

168

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Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.

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Rarity and Incomplete Sampling in DNA-Based Species Delimitation

Cited by 156 publications

References 67 publications

The hitchhiker's guide to single‐locus species delimitation

The hitchhiker's guide to single‐locus species delimitation

Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

Sorting specimen‐rich invertebrate samples with cost‐effective NGS barcodes: Validating a reverse workflow for specimen processing

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