University of Oulu

Hinojosa, JC, Koubínová, D, Szenteczki, MA, et al. A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol Ecol. 2019; 28: 3857– 3868.

A mirage of cryptic species : genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris

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Author: Hinojosa, Joan C.1; Koubínová, Darina2; Szenteczki, Mark A.3;
Organizations: 1Institut de Biologia Evolutiva (CSIC‐UPF), Barcelona, Spain
2Unit of Research and Collection, Museum of Natural History, Geneva, Switzerland
3Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
4Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETHZ, Zürich, Switzerland
5Department of Ecology and Genetics, University of Oulu, Oulu, Finland
Format: article
Version: accepted version
Access: open
Online Access: PDF Full Text (PDF, 1.2 MB)
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Language: English
Published: John Wiley & Sons, 2019
Publish Date: 2020-06-24


Mitochondrial DNA (mtDNA) sequencing has led to an unprecedented rise in the identification of cryptic species. However, it is widely acknowledged that nuclear DNA (nuDNA) sequence data are also necessary to properly define species boundaries. Next generation sequencing techniques provide a wealth of nuclear genomic data, which can be used to ascertain both the evolutionary history and taxonomic status of putative cryptic species. Here, we focus on the intriguing case of the butterfly Thymelicus sylvestris (Lepidoptera: Hesperiidae). We identified six deeply diverged mitochondrial lineages; three distributed all across Europe and found in sympatry, suggesting a potential case of cryptic species. We then sequenced these six lineages using double‐digest restriction‐site associated DNA sequencing (ddRADseq). Nuclear genomic loci contradicted mtDNA patterns and genotypes generally clustered according to geography, i.e., a pattern expected under the assumption of postglacial recolonization from different refugia. Further analyses indicated that this strong mtDNA/nuDNA discrepancy cannot be explained by incomplete lineage sorting, sex‐biased asymmetries, NUMTs, natural selection, introgression or Wolbachia‐mediated genetic sweeps. We suggest that this mitonuclear discordance was caused by long periods of geographic isolation followed by range expansions, homogenizing the nuclear but not the mitochondrial genome. These results highlight T. sylvestris as a potential case of multiple despeciation and/or lineage fusion events. We finally argue, since mtDNA and nuDNA do not necessarily follow the same mechanisms of evolution, their respective evolutionary history reflects complementary aspects of past demographic and biogeographic events.

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Series: Molecular ecology
ISSN: 0962-1083
ISSN-E: 1365-294X
ISSN-L: 0962-1083
Volume: 28
Issue: 17
Pages: 3857 - 3868
DOI: 10.1111/mec.15153
Type of Publication: A1 Journal article – refereed
Field of Science: 1184 Genetics, developmental biology, physiology
1181 Ecology, evolutionary biology
Funding: Financial support for this research was provided by project CGL2016‐76322‐P (AEI/FEDER, UE) and 2017‐SGR‐991 (Generalitat de Catalunya) to Roger Vila and by predoctoral fellowship BES‐2017‐080641 to Joan Carles Hinojosa. Nadir Alvarez was funded by project PP00P3_172899 from the Swiss National Science Foundation. Computational resources for certain analyses were supplied by the Ministry of Education, Youth and Sports of the Czech Republic under the Projects CESNET (Project No. LM2015042) and CERIT‐Scientific Cloud (Project No. LM2015085) provided within the program Projects of Large Research, Development and Innovations Infrastructures.
Copyright information: © 2019 John Wiley & Sons Ltd. This is the peer reviewed version of the following article: Hinojosa, JC, Koubínová, D, Szenteczki, MA, et al. A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol Ecol. 2019; 28: 3857– 3868, which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.