Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses

LUKIC, DANIEL; Eberle, Jonas; Thormann, Jana; Holzschuh, Carolus; Ahrens, Dirk

doi:10.1002/ece3.7836

Cited by 10 publications

(13 citation statements)

References 117 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The correlation between divergent genital morphology and evolutionary entities was widely confirmed by integrative taxonomy studies (Ahrens & Ribera, 2009;Eberle et al, 2016), including even genomic data (Dietz et al, 2021). The here observed low congruence of MOTUs with morphospecies (match ratio: 0.57-0.67) was not unexpected since previous studies on tropical Sericini have showed similarly low match ratios Dalstein et al, 2019;Lukic et al, 2021). Some of them were subject to strong variation (between 0.14 and 1) depending on the different selected subclades being analyzed .…”

Section: Discussionsupporting

confidence: 81%

“…While results of COI barcoding have been so far mainly compared with morphospecies entities, the congruence of the outcome of different DNA‐based species delimitations has only rarely been analyzed in detail. Outcomes have often been characterized as “different” without quantifying the difference (Ahrens et al, 2016; Dalstein et al, 2019; Lukic et al, 2021). These differences are explored here in detail, exemplified by a case study of Sri Lankan Sericini chafers.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

Ranasinghe

Eberle

Thormann

et al. 2022

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species-rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology-based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over-splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio-based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.

show abstract

Section: Discussionsupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

Ranasinghe

Eberle

Thormann

et al. 2022

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

show abstract

“…All these results emphasize the importance of assessing species boundaries within an integrative framework, in which not only molecular data but also morphological, life history and ecological information are considered (e.g., Lukic et al, 2021).…”

Section: Phlyctinus Diversity and Phylogenetic Relationshipsmentioning

confidence: 84%

Late Cenozoic environmental changes drove the diversification of a weevil genus endemic to the Cape Floristic Region

et al. 2022

View full text Add to dashboard Cite

The Cape Floristic Region in the Republic of South Africa is a well-recognized hotspot of biodiversity. Although this region is mostly known for its high level of plant diversity and endemicity, it also hosts an understudied and likely diverse arthropod fauna. Here we investigate the evolutionary history and timing of diversification of the apterous weevil genus Phlyctinus (Curculionidae: Entiminae), which is endemic to the coastal area and adjacent mountain ranges of the Cape floristic region and generally associated with sunflower plants (Asteraceae). We use a diverse array of molecular analyses (phylogenetic inference, molecular species delimitation and dating analyses) to analyse a novel molecular dataset of 202 weevil specimens (including 170 Phlyctinus sampled in 60 sites), and sequenced for two mitochondrial and four nuclear gene fragments. Phylogenetic and dating analyses indicate that the genus started diversifying in the late Miocene, with contrasting diversification dynamics for the three inferred clades, which present disjunct distributions. Host plant records and the lack of relatedness of species living in sympatry indicate that the diversification of Phlyctinus was predominantly driven by allopatric (geographic) speciation. We hypothesize that the interplay between topography and recurring cycles of coastline-habitat fragmentation resulting from sea level oscillations spurred the diversification of the most speciose clade, whereas in the two remaining clades populations likely remained connected thus hampering allopatric speciation. Interestingly, this pattern echoes with the role of sea level oscillations as an important driver of the radiation of several lineages in the coastline ecosystems of the Cape Floristic Region.

show abstract

“…Considering disagreements between morphospecies registered in the sequence database and the estimated ESUs, anatomical morphology can help us to evaluate the species diversity with the species delimitation results ( Lukic et al, 2021 ). Five ESUs in our sites can be largely distinguished into four morphological patterns ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…2 ). In this study, we conservatively treat ESU 28 and ESU 29 as a single species because there are no morphological differences in genitalia or external appearance, and some species delimitation methods are known to oversplit ( Lukic et al, 2021 ). ESU 30 has also very similar external morphology to that of ESU 28 and ESU 29, but pattern of genitalia such as the digitiform gland was clearly different ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Species identification of introduced veronicellid slugs in Japan

Hirano

Kagawa

Fujimoto

et al. 2022

PeerJ

View full text Add to dashboard Cite

Reliable identification of species is important for protecting native ecosystems against the invasion of non-native species. DNA barcoding using molecular markers, such as the mitochondrial cytochrome oxidase subunit 1 (COI) gene, helps researchers distinguish species. In this study, we focused on introduced veronicellid slugs in the Ryukyu Islands and some greenhouses on mainland Japan. Some veronicellids are medium-to-high risk pest species for humans. Identifying veronicellid species by their external morphology is difficult and unreliable because there is substantial overlap between intraspecific variation and interspecific differentiation. Therefore, internal morphologies such as male genitalia have been the primary traits used to distinguish veronicellids. To identify introduced veronicellid slugs in Japan to the species level, we used morphological assessment of male genitalia and DNA barcoding of the standard COI gene fragment. We also conducted species-delimitation analyses based on the genetic data. The results showed that five evolutionarily significant units, corresponding to four nominal species inhabit the Ryukyu Islands, of which two species were also found in the greenhouses of mainland Japan, including the first record of Sarasinula plebeia in Japan. The presence of non-native slug species could increase the transmission of parasites in Japan.

show abstract

Excluding spatial sampling bias does not eliminate oversplitting in DNA‐based species delimitation analyses

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 10 publications

References 117 publications

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

Late Cenozoic environmental changes drove the diversification of a weevil genus endemic to the Cape Floristic Region

Species identification of introduced veronicellid slugs in Japan

Contact Info

Product

Resources

About