University of Oulu

Joshi, M., Espeland, M., Dincă, V., Vila, R., Tahami, M. S., Dietz, L., Mayer, C., Martin, S., Dapporto, L., & Mutanen, M. (2022). Delimiting continuity: Comparison of target enrichment and double digest restriction‐site associated DNA sequencing for delineating admixing parapatric Melitaea butterflies. Systematic Entomology, 47(4), 637–654.

Delimiting continuity : comparison of target enrichment and double digest restriction-site associated DNA sequencing for delineating admixing parapatric Melitaea butterflies

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Author: Joshi, Mukta1; Espeland, Marianne2; Dincă, Vlad1;
Organizations: 1Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
2Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig, Bonn, Germany
3Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
4ZEN Lab, Dipartimento di Biologia, dell' Università di Firenze, Sesto Fiorentino, Italy
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2.4 MB)
Persistent link:
Language: English
Published: John Wiley & Sons, 2022
Publish Date: 2022-12-20


Parapatrically distributed taxa pose a challenge for species delimitation due to the presence of gene flow and inherent arbitrariness of exactly defining the species boundaries in such systems. We tackled the problem of species delimitation in a parapatric species pair of Melitaea butterflies using two popular genomic methods—double digest restriction-site associated DNA sequencing (ddRAD) and target enrichment. We compared newly generated target enrichment dataset with 1733 loci to the already available ddRAD data from a previous study on the same set of specimens using a suite of phylogenetic, population genetic, and species delimitation methods. We recovered consistent phylogenetic relationships across the datasets, both demonstrating the presence of a genetically distinct Balkan lineage and paraphyly of Melitaea athalia with respect to Melitaea celadussa. Population genetic STRUCTURE analyses supported the presence of two species when using ddRAD data, but three species when using target enrichment, while a Bayes factor delimitation analysis found both two and three species scenarios equally decisive in both datasets. As the results obtained from both methods were largely congruent, we discuss some practical considerations and benefits of target enrichment over RAD sequencing. We conclude that the choice of method of genomic data collection does not influence the results of phylogenetic analyses at alpha taxonomic level, given a sufficient number of loci. Finally, we recommend a solution for delineating species in parapatric scenarios by proposing that parapatric taxa be consistently classified as subspecies or complete species, but not both, to promote taxonomic stability.

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Series: Systematic entomology
ISSN: 0307-6970
ISSN-E: 1365-3113
ISSN-L: 0307-6970
Volume: 47
Issue: 4
Pages: 637 - 654
DOI: 10.1111/syen.12557
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
Funding: Academy of Finland, Grant/Award Numbers: 314702, 328895; MCIN/AEI, Grant/Award Number: PID2019-107078GB-I00
Academy of Finland Grant Number: 314702
Detailed Information: 314702 (Academy of Finland Funding decision)
328895 (Academy of Finland Funding decision)
Dataset Reference: Raw target enrichment sequencing data is archived on the NCBI Sequence Read Archive under BioProject ID PRJNA802033. Raw ddRAD data are available under BioProject ID PRJNA638526.
Copyright information: © 2022 The Authors. This is an open access article under the terms of theCreative Commons AttributionLicense, which permits use, distribution and reproduction in any medium,provided the original work is properly cited.