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Tahami MS, Dincă V, Lee KM, Vila R, Joshi M, Heikkilä M, Dapporto L, Schmid S, Huemer P, Mutanen M. Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies. Genes (Basel) 2021; 12:genes12122009. [PMID: 34946956 PMCID: PMC8700966 DOI: 10.3390/genes12122009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celadussa at the contact zone, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate genetic make-up of European M. athalia populations with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia-celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.
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Affiliation(s)
- Mohadeseh Sadat Tahami
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
- Correspondence:
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC—Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37, 08003 Barcelona, Spain;
| | - Mukta Joshi
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
| | - Maria Heikkilä
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland;
| | - Leonardo Dapporto
- Numerical and Experimental Zoology Laboratory (ZEN Lab), Dipartimento di Biologia, Dell’ Università di Firenze, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy;
| | - Sarah Schmid
- Departement de Biologie Computationnelle, Faculte de Biologie et Medecine, Universite de Lausanne, 1015 Lausanne, Switzerland;
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Krajnc-Str. 1, A-6060 Hall, Austria;
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland; (V.D.); (K.M.L.); (M.J.); (M.M.)
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2
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Scalercio S, Infusino M, Huemer P, Mutanen M. Pruning the Barcode Index Numbers tree: Morphological and genetic evidence clarifies species boundaries in the
Eupithecia conterminata
complex (Lepidoptera: Geometridae) in Europe. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Stefano Scalercio
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria Centro di Ricerca Foreste e Legno Rende Italy
| | - Marco Infusino
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria Centro di Ricerca Foreste e Legno Rende Italy
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H. Naturwissenschaftliche Sammlungen Hall Austria
| | - Marko Mutanen
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
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3
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Delocado ED, Freitag H. Two new species of Byrrhinus Motschulsky, 1858 (Coleoptera, Limnichidae, Limnichinae) from Negros, Philippines. Zookeys 2021; 1070:51-72. [PMID: 34819771 PMCID: PMC8599385 DOI: 10.3897/zookeys.1070.70531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/22/2021] [Indexed: 11/24/2022] Open
Abstract
Two new species of Limnichidae beetles, Byrrhinusnegrosensis sp. nov. and Byrrhinusvillarini sp. nov., are described from the Island of Negros in the Philippines. The adult specimens of the new species can be differentiated by patterns of body punctation, colour and orientation of elytral pubescence, posterolateral angle of pronotum, tarsomere length ratio and aedeagal form. Two clades, representing the two new species, were retrieved in the Maximum Likelihood gene tree using the 3'-end of the COI gene. Maximum genetic divergence within B.negrosensis sp. nov. and B.villarini sp. nov. were recorded to be 2.3% and 1.3%, respectively, while the mean interspecific divergence between the two new species was 19.7%. Morphological descriptions, digital photographs and COI sequences were provided for the two species. The state of knowledge of Byrrhinus is reviewed and an updated Philippine checklist is provided. By coupling morphological and molecular data, this paper provides the first additional new species of Philippine Byrrhinus in the last 28 years.
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Affiliation(s)
- Emmanuel D. Delocado
- Ateneo Biodiversity Research Laboratory, Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, 1108 PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
| | - Hendrik Freitag
- Ateneo Biodiversity Research Laboratory, Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, 1108 PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
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Ebdon S, Laetsch DR, Dapporto L, Hayward A, Ritchie MG, Dincӑ V, Vila R, Lohse K. The Pleistocene species pump past its prime: Evidence from European butterfly sister species. Mol Ecol 2021; 30:3575-3589. [PMID: 33991396 DOI: 10.1111/mec.15981] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
The Pleistocene glacial cycles had a profound impact on the ranges and genetic make-up of organisms. While it is clear that the contact zones that have been described for many sister taxa are secondary and have formed in the current interglacial, it is unclear when the taxa involved began to diverge. Previous estimates based on small numbers of loci are unreliable given the stochasticity of genetic drift and the contrasting effects of incomplete lineage sorting and gene flow on gene divergence. Here, we use genome-wide transcriptome data to estimate divergence for 18 sister species pairs of European butterflies showing either sympatric or contact zone distributions. We find that in most cases, species divergence predates the mid-Pleistocene transition or even the entire Pleistocene period. We also show that although post-divergence gene flow is restricted to contact zone pairs, they are not systematically younger than sympatric pairs. This suggests that contact zones are not limited to the initial stages of the speciation process, but can involve notably old taxa. Finally, we show that mitochondrial divergence and nuclear divergence are only weakly correlated and mitochondrial divergence is higher for contact zone pairs.
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Affiliation(s)
- Sam Ebdon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Leonardo Dapporto
- ZEN Laboratory, Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Cornwall, UK
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, UK
| | - Vlad Dincӑ
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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5
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D'Ercole J, Dincă V, Opler PA, Kondla N, Schmidt C, Phillips JD, Robbins R, Burns JM, Miller SE, Grishin N, Zakharov EV, DeWaard JR, Ratnasingham S, Hebert PDN. A DNA barcode library for the butterflies of North America. PeerJ 2021; 9:e11157. [PMID: 33976967 PMCID: PMC8061581 DOI: 10.7717/peerj.11157] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.
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Affiliation(s)
- Jacopo D'Ercole
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Paul A Opler
- Colorado State University, Fort Collins, CO, United States of America
| | | | - Christian Schmidt
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food, Guelph, Ontario, Canada
| | - Jarrett D Phillips
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.,School of Computer Science, University of Guelph, Guelph, Ontario, Canada
| | - Robert Robbins
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - John M Burns
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Scott E Miller
- Department of Entomology, Smithsonian Institution, Washington DC, United States of America
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States of America.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States of America
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jeremy R DeWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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6
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Maggioni D, Assandri G, Ramazzotti F, Magnani D, Pellegrino I, Valsecchi E, Galimberti A. Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1896795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- D. Maggioni
- Department of Environmental and Earth Sciences (DISAT), University of Milano - Bicocca, Milan, Italy
- Marine Research and High Education (MaRHE) Center, University of Milano - Bicocca, Faafu Magoodhoo, Maldives
| | - G. Assandri
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Italy
| | - F. Ramazzotti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - D. Magnani
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - I. Pellegrino
- Department of Sciences and Technological Innovation (DISIT), University of Eastern Piedmont, Alessandria, Italy
| | - E. Valsecchi
- Department of Environmental and Earth Sciences (DISAT), University of Milano - Bicocca, Milan, Italy
| | - A. Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
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7
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Dincă V, Dapporto L, Somervuo P, Vodă R, Cuvelier S, Gascoigne-Pees M, Huemer P, Mutanen M, Hebert PDN, Vila R. High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity. Commun Biol 2021; 4:315. [PMID: 33750912 PMCID: PMC7943782 DOI: 10.1038/s42003-021-01834-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 02/11/2021] [Indexed: 11/09/2022] Open
Abstract
The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.
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Affiliation(s)
- Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu, 90014, Oulu, Finland.
- Institut de Biologia Evolutiva (CSIC-UPF), 03008, Barcelona, Spain.
| | - Leonardo Dapporto
- ZEN lab, Dipartimento di Biologia, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, FI-00014, Helsinki, Finland
| | | | - Sylvain Cuvelier
- VVE Workgroup Butterflies, Diamantstraat 4, 8900, Ieper, Belgium
| | | | - Peter Huemer
- Naturwissenschaftliche Sammlungen, Sammlungs- und Forschungszentrum, Tiroler Landesmuseen, 6060, Hall in Tirol, Austria
| | - Marko Mutanen
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu, 90014, Oulu, Finland
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), 03008, Barcelona, Spain
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8
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Hinojosa JC, Dapporto L, Brockmann E, Dincă V, Tikhonov V, Grishin N, Lukhtanov VA, Vila R. Overlooked cryptic diversity in Muschampia (Lepidoptera: Hesperiidae) adds two species to the European butterfly fauna. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa171] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Cryptic species represent a challenge for documenting global biodiversity. Even in well-studied groups, such as European butterflies, the application of integrative approaches has allowed the recognition of an unexpected number of cryptic taxa. Here, we combine the analysis of mitochondrial (cytochrome c oxidase I, COI) and nuclear (internal transcribed spacer 2, ITS2) markers with geometric morphometrics of the male genitalia to study diversity within the butterfly Muschampia proto. The nuclear marker reveals three well-supported and deeply diverged lineages, which are also detected based on mitochondrial DNA, although the latter recovers one of them as paraphyletic with poor support. These lineages also present distinct male genital characters, which allow blind assignment of > 97% of specimens when applying a jackknife procedure. We conclude that M. proto comprises three cryptic species that started to differentiate ~2 Mya: M. proto, distributed in northern Africa, the Iberian Peninsula and southern France; Muschampia alta comb. & stat. nov., occurring in southern Italy and the Balkan Peninsula; and Muschampia proteides, present in the easternmost part of Europe, the Near East and Iran. This discovery adds two new species to the European butterfly fauna and highlights the necessity to continue investigating potential cryptic diversity.
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Affiliation(s)
- Joan C Hinojosa
- Institut de Biologia Evolutive (CSIC-UPF), Passeig de la Barceloneta 37-49, Barcelona, Spain
| | - Leonardo Dapporto
- ZEN lab, Dipartimento di Biologia, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | | | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Valentin Tikhonov
- North Caucasus Federal University, Ulitsa Pushkina 1, Stavropol, Russia
| | - Nick Grishin
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, USA
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, St. Petersburg, Russia
| | - Roger Vila
- Institut de Biologia Evolutive (CSIC-UPF), Passeig de la Barceloneta 37-49, Barcelona, Spain
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