1
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Wei X, Zhu J, Hoffmann AA, Jia J, Xiao M, Duan F, Zhang Y, Zhong H, Ge J, Yu W, Zhang L, Jiang W. Wolbachia infection status and molecular diversity in the species of tribe Tagiadini Mabille, 1878 (Lepidoptera: Hesperiidae) collected in China. Ecol Evol 2024; 14:e11279. [PMID: 38633519 PMCID: PMC11021859 DOI: 10.1002/ece3.11279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Wolbachia, one of the most ubiquitous heritable symbionts in lepidopteran insects, can cause mitochondrial introgression in related host species. We recently found mito-nuclear discordance in the Lepidopteran tribe Tagiadini Mabille 1878 from which Wolbachia has not been reported. In this study, we found that 13 of the 46 species of Tagiadini species tested were positive for Wolbachia. Overall, 14% (15/110) of Tagiadini specimens were infected with Wolbachia and nine new STs were found from 15 isolates. A co-phylogenetic comparison, divergence time estimation and Wolbachia recombination analysis revealed that mito-nuclear discordance in Tagiadini species is not mediated by Wolbachia, but Wolbachia acquisition in Tagiadini appears to have occurred mainly through horizontal transmission rather than codivergence.
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Affiliation(s)
- Xiaoying Wei
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | | | - Ary A. Hoffmann
- School of BioSciences, Bio21 InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Jiqin Jia
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Mengqi Xiao
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Feiyu Duan
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yimin Zhang
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Huimin Zhong
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Jingyan Ge
- Shanghai No. 3 Girl's High SchoolShanghaiChina
| | - Weidong Yu
- College of Continuing EducationShanghai Normal UniversityShanghaiChina
| | - Lei Zhang
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Weibin Jiang
- College of Life SciencesShanghai Normal UniversityShanghaiChina
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2
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Lukhtanov VA. Polytypic species concept and subspecies in the genomic era. Proc Natl Acad Sci U S A 2024; 121:e2317038121. [PMID: 38377202 PMCID: PMC10907253 DOI: 10.1073/pnas.2317038121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg199034, Russia
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3
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Ivanov V, Lee KM, Mutanen M. ddRAD Sequencing and DNA Barcoding. Methods Mol Biol 2024; 2744:213-221. [PMID: 38683321 DOI: 10.1007/978-1-0716-3581-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.
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Affiliation(s)
- Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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4
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Chan KO, Mulcahy DG, Anuar S. The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex). Syst Biol 2023; 72:1209-1219. [PMID: 37478480 DOI: 10.1093/sysbio/syad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/19/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiates the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
| | - Daniel G Mulcahy
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Shahrul Anuar
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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5
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MacGuigan DJ, Mount GG, Watkins-Colwell GJ, Near TJ, Lambert MR. Genomic Data Clarify Aquarana Systematics and Reveal Isolation-by-Distance Dominates Phylogeography of the Wide-Ranging Frog Rana clamitans. ICHTHYOLOGY & HERPETOLOGY 2022. [DOI: 10.1643/h2021129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel J. MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260;
| | | | - Gregory J. Watkins-Colwell
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Thomas J. Near
- Division of Vertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511; (GJWC) gregory.
| | - Max R. Lambert
- Science Division, Habitat Program, Washington Department of Fish & Wildlife, Olympia, Washington 98501;
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6
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Polic D, Yıldırım Y, Lee KM, Franzén M, Mutanen M, Vila R, Forsman A. Linking large-scale genetic structure of three Argynnini butterfly species to geography and environment. Mol Ecol 2022; 31:4381-4401. [PMID: 35841126 PMCID: PMC9544544 DOI: 10.1111/mec.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022]
Abstract
Understanding which factors and processes are associated with genetic differentiation within and among species remains a major goal in evolutionary biology. To explore differences and similarities in genetic structure and its association with geographical and climatic factors in sympatric sister species, we conducted a large‐scale (>32° latitude and >36° longitude) comparative phylogeographical study on three Argynnini butterfly species (Speyeria aglaja, Fabriciana adippe and F. niobe) that have similar life histories, but differ in ecological generalism and dispersal abilities. Analyses of nuclear (ddRAD‐sequencing derived SNP markers) and mitochondrial (COI sequences) data revealed differences between species in genetic structure and how genetic differentiation was associated with climatic factors (temperature, solar radiation, precipitation, wind speed). Geographical proximity accounted for much of the variation in nuclear and mitochondrial structure and evolutionary relationships in F. adippe and F. niobe, but only explained the pattern observed in the nuclear data in S. aglaja, for which mitonuclear discordance was documented. In all species, Iberian and Balkan individuals formed genetic clusters, suggesting isolation in glacial refugia and limited postglacial expansion. Solar radiation and precipitation were associated with the genetic structure on a regional scale in all species, but the specific combinations of environmental and geographical factors linked to variation within species were unique, pointing to species‐specific responses to common environments. Our findings show that the species share similar colonization histories, and that the same ecological factors, such as niche breadth and dispersal capacity, covary with genetic differentiation within these species to some extent, thereby highlighting the importance of comparative phylogeographical studies in sympatric sister species.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Markus Franzén
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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7
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Solovyev VI, Dubatolov VV, Vavilova VY, Kosterin OE. Estimating range disjunction time of the Palearctic Admirals (Limenitis L.) with COI and histone H1 genes. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Pronounced mito-nuclear discordance and various Wolbachia infections in the water ringlet Erebia pronoe have resulted in a complex phylogeographic structure. Sci Rep 2022; 12:5175. [PMID: 35338196 PMCID: PMC8956704 DOI: 10.1038/s41598-022-08885-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 03/08/2022] [Indexed: 11/28/2022] Open
Abstract
Several morphological and mitochondrial lineages of the alpine ringlet butterfly species Erebia pronoe have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1α, RPS5) gene sequences and compared them with sequences from the sister species Erebia melas. Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with Wolbachia strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the E. pronoe-melas complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in E. melas and E. pronoe glottis can be explained by different ages of Wolbachia infections with different Wolbachia strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of E. pronoe glottis in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.
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9
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Hinojosa JC, Dapporto L, Pitteloud C, Koubínová D, Hernández-Roldán J, Vicente JC, Alvarez N, Vila R. Hybridization fuelled diversification in Spialia butterflies. Mol Ecol 2022; 31:2951-2967. [PMID: 35263484 PMCID: PMC9310813 DOI: 10.1111/mec.16426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/17/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022]
Abstract
The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double‐digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes.
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Affiliation(s)
- Joan C Hinojosa
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Leonardo Dapporto
- ZEN lab, Biology Department, Università degli Studi di Firenze, 50019, Sesto Fiorentino, Italy
| | - Camille Pitteloud
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Darina Koubínová
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Juan Hernández-Roldán
- Departamento de Biología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Calle Darwin 2, 28049, Madrid, Spain
| | - Juan Carlos Vicente
- Asociación Española para la Protección de las Mariposas y su Medio (ZERYNTHIA), Madrid, Spain
| | - Nadir Alvarez
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Boulevard d'Ivoy 4, 1205, Geneva, Switzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
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10
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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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11
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Silva-Brandão KL, Cirino M, Magaldi LDM, Gueratto PE, Mattos RG, Freitas AVL. Subspecies limits and hidden Wolbachia diversity in Actinote pellenea butterflies. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1965669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Karina L. Silva-Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Candido Rondom, 400, Campinas, 13083-875, São Paulo, Brazil
| | - Mariana Cirino
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Candido Rondom, 400, Campinas, 13083-875, São Paulo, Brazil
| | - Luiza De Moraes Magaldi
- Programa de Pós-graduação em Ecologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Instituto de Biologia, Departamento de Biologia Animal, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Campinas, 13083-862, São Paulo, Brazil
| | - Patrícia Eyng Gueratto
- Programa de Pós-graduação em Ecologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Instituto de Biologia, Departamento de Biologia Animal, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Campinas, 13083-862, São Paulo, Brazil
| | - Ricardo Gabriel Mattos
- Programa de Pós-graduação em Ecologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - André V. L. Freitas
- Instituto de Biologia, Departamento de Biologia Animal, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Campinas, 13083-862, São Paulo, Brazil
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12
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Arif S, Gerth M, Hone-Millard WG, Nunes MDS, Dapporto L, Shreeve TG. Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles. Mol Ecol 2021; 30:5196-5213. [PMID: 34402109 DOI: 10.1111/mec.16126] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022]
Abstract
The paradigm of isolation in southern refugia during glacial periods followed by expansions during interglacials, producing limited genetic differentiation in northern areas, dominates European phylogeography. However, the existence of complex structured populations in formerly glaciated areas, and islands connected to mainland areas during glacial maxima, call for alternative explanations. We reconstructed the mtDNA phylogeography of the widespread Polyommatus Icarus butterfly with an emphasis on the formerly glaciated and connected British Isles. We found distinct geographical structuring of CO1 haplogroups, with an ancient lineage restricted to the marginal European areas, including Northern Scotland and Outer Hebrides. Population genomic analyses, using ddRADSeq genomic markers, also reveal substantial genetic structuring within Britain. However, there is negligble mito-nuclear concordance consistent with independent demographic histories of mitochondrial versus nuclear DNA. While mtDNA-Wolbachia associations in northern Britain could account for the geographic structuring of mtDNA across most of the British Isles, for nuclear DNA markers (derived from ddRADseq data) butterflies from France cluster between northern and southern British populations - an observation consistent with a scenario of multiple recolonisation. Taken together our results suggest that contemporary mtDNA structuring in the British Isles (and potentially elsewhere in Europe) largely results from Wolbachia infections, however, nuclear genomic structuring suggests a history of at least two distinct colonisations. This two-stage colonisation scenario has previously been put forth to explain genetic diversity and structuring in other British flora and fauna. Additionally, we also present preliminary evidence for potential Wolbachia-induced feminization in the Outer Hebrides.
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Affiliation(s)
- Saad Arif
- Centre for Functional Genomics, Oxford Brookes University, Oxford, UK.,Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Michael Gerth
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | | | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Leonardo Dapporto
- ZEN Laboratory, Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Timothy G Shreeve
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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13
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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14
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Pazhenkova EA, Lukhtanov VA. Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria. Mol Ecol 2021; 30:4819-4832. [PMID: 34288183 DOI: 10.1111/mec.16085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
Introgressive hybridization is more common in nature than previously thought, and its role and creative power in evolution is hotly discussed but not completely understood. Introgression occurs more frequently in sympatry between recently diverged taxa, or when the speciation process has not yet been completed. However, there are relatively few documented cases of hybridization that erodes reproductive barriers between distantly related species. Here, we use whole genome and mitochondrial data to examine how introgression from a distant congener affects pattern of genetic differentiation in the Levant fritillary butterfly Melitaea acentria. We show that this local taxon has evolved as a peripatric geographic isolate of the widespread Melitaea persea, and that there has been significant unidirectional gene flow from the sympatric, nonclosely related Melitaea didyma to M. acentria. We found direct evidence of ongoing sporadic hybridization between M. didyma and M. acentria, which are separated by at least 5 million years of independent evolution. Elevated differentiation and lower level of introgression on the sex Z chromosome compared to autosomes suggest that the Z chromosome has accumulated loci acting as intrinsic postzygotic barriers. Our results show that introgression from M. didyma has been an additional source of nucleotide diversity in the M. acentria population, providing material for drift and selection.
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Affiliation(s)
- Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia.,Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
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15
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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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16
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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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17
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Cerca J, Maurstad MF, Rochette NC, Rivera‐Colón AG, Rayamajhi N, Catchen JM, Struck TH. Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- José Cerca
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
- Department of Natural History NTNU University MuseumNorwegian University of Science and Technology Trondheim Norway
| | - Marius F. Maurstad
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
- Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| | - Nicolas C. Rochette
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Angel G. Rivera‐Colón
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Niraj Rayamajhi
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Torsten H. Struck
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
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18
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Lopez-Vaamonde C, Kirichenko N, Cama A, Doorenweerd C, Godfray HCJ, Guiguet A, Gomboc S, Huemer P, Landry JF, Laštůvka A, Laštůvka Z, Lee KM, Lees DC, Mutanen M, van Nieukerken EJ, Segerer AH, Triberti P, Wieser C, Rougerie R. Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.626752] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named species recognized, many of which are difficult to identify using morphology only. Here we explore the use of DNA barcodes as a tool for identification and species discovery in European gracillariids. We present a barcode library including 6,791 COI sequences representing 242 of the 263 (92%) resident species. Our results indicate high congruence between morphology and barcodes with 91.3% (221/242) of European species forming monophyletic clades that can be identified accurately using barcodes alone. The remaining 8.7% represent cases of non-monophyly making their identification uncertain using barcodes. Species discrimination based on the Barcode Index Number system (BIN) was successful for 93% of species with 7% of species sharing BINs. We discovered as many as 21 undescribed candidate species, of which six were confirmed from an integrative approach; the other 15 require additional material and study to confirm preliminary evidence. Most of these new candidate species are found in mountainous regions of Mediterranean countries, the South-Eastern Alps and the Balkans, with nine candidate species found only on islands. In addition, 13 species were classified as deep conspecific lineages, comprising a total of 27 BINs with no intraspecific morphological differences found, and no known ecological differentiation. Double-digest restriction-site associated DNA sequencing (ddRAD) analysis showed strong mitonuclear discrepancy in four out of five species studied. This discordance is not explained by Wolbachia-mediated genetic sweeps. Finally, 26 species were classified as “unassessed species splits” containing 71 BINs and some involving geographical isolation or ecological specialization that will require further study to test whether they represent new cryptic species.
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19
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Vanhove M, Pina‐Martins F, Coelho AC, Branquinho C, Costa A, Batista D, Príncipe A, Sousa P, Henriques A, Marques I, Belkadi B, Knowles LL, Paulo OS. Using gradient Forest to predict climate response and adaptation in Cork oak. J Evol Biol 2021; 34:910-923. [DOI: 10.1111/jeb.13765] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Mathieu Vanhove
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Francisco Pina‐Martins
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Ana Cristina Coelho
- Centro de Electrónica, Optoelectronica e Telecomunicações Universidade do Algarve Faro Portugal
| | - Cristina Branquinho
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária Oeiras Portugal
- CENSE ‐ Center for Environmental and Sustainability Research NOVA University of Lisbon Caparica Portugal
| | - Dora Batista
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | - Adriana Príncipe
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Paulo Sousa
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - André Henriques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Isabel Marques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Forest Research Centre Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | | | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Octávio S. Paulo
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
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20
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Sucháčková Bartoňová A, Konvička M, Marešová J, Wiemers M, Ignatev N, Wahlberg N, Schmitt T, Faltýnek Fric Z. Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies. Sci Rep 2021; 11:3019. [PMID: 33542272 PMCID: PMC7862691 DOI: 10.1038/s41598-021-82433-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host's mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.
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Affiliation(s)
- Alena Sucháčková Bartoňová
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Martin Konvička
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jana Marešová
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Martin Wiemers
- Senckenberg German Entomological Institute, Müncheberg, Germany
| | - Nikolai Ignatev
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Thomas Schmitt
- Senckenberg German Entomological Institute, Müncheberg, Germany
- Faculty of Natural Sciences I, Institute of Biology, Zoology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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21
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Ivanov V, Marusik Y, Pétillon J, Mutanen M. Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae). Sci Rep 2021; 11:2177. [PMID: 33500478 PMCID: PMC7838170 DOI: 10.1038/s41598-021-81788-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.
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Affiliation(s)
- Vladislav Ivanov
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Yuri Marusik
- grid.493323.c0000 0004 0399 5314Institute for Biological Problems of the North, RAS, Magadan, Russia ,grid.412219.d0000 0001 2284 638XDepartment of Zoology and Entomology, University of the Free State, Bloemfontein, 9300 South Africa
| | - Julien Pétillon
- grid.410368.80000 0001 2191 9284UMR CNRS ECOBIO, Université de Rennes 1, Rennes, France
| | - Marko Mutanen
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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22
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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23
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Schär S, Menchetti M, Schifani E, Hinojosa JC, Platania L, Dapporto L, Vila R. Integrative biodiversity inventory of ants from a Sicilian archipelago reveals high diversity on young volcanic islands (Hymenoptera: Formicidae). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00442-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Ståhls G, Meier R, Sandrock C, Hauser M, Šašić Zorić L, Laiho E, Aracil A, Doderović J, Badenhorst R, Unadirekkul P, Mohd Adom NAB, Wein L, Richards C, Tomberlin JK, Rojo S, Veselić S, Parviainen T. The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species. BMC Evol Biol 2020; 20:60. [PMID: 32448128 PMCID: PMC7247124 DOI: 10.1186/s12862-020-01627-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/13/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species. RESULTS Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N = 1), Oriental (N = 4), and the Eastern Palearctic (N = 4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes. CONCLUSIONS Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.
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Affiliation(s)
- Gunilla Ståhls
- Finnish Museum of Natural History Luomus, Zoology unit, University of Helsinki, PO Box 17, FI-00014, Helsinki, Finland.
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Block S3 #05-01, 14 Science Dr 4, Singapore, 117543, Singapore
| | - Christoph Sandrock
- Department of Livestock Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, 5070, Frick, Switzerland
| | - Martin Hauser
- California Department of Food and Agriculture, Plant Pest Diagnostics Branch, 3294 Meadowview Road, Sacramento, California, 95832-1448, USA
| | | | - Elina Laiho
- Finnish Museum of Natural History Luomus, Zoology unit, University of Helsinki, PO Box 17, FI-00014, Helsinki, Finland
| | - Andrea Aracil
- Department of Environmental Sciences & Natural Resources, University of Alicante, PO Box 99, E-03080, Alicante, Spain
| | - Jovana Doderović
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, 2100, Serbia
| | | | - Phira Unadirekkul
- Department of Biological Sciences, National University of Singapore, Block S3 #05-01, 14 Science Dr 4, Singapore, 117543, Singapore
| | - Nur Arina Binte Mohd Adom
- Department of Biological Sciences, National University of Singapore, Block S3 #05-01, 14 Science Dr 4, Singapore, 117543, Singapore
| | - Leo Wein
- Protenga, 302 Ang Mo Kio Ave 3, #01-1840 560302, Singapore, Singapore
| | | | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, TAMU 2475, College Station, TX, 77843-2475, USA
| | - Santos Rojo
- Department of Environmental Sciences & Natural Resources, University of Alicante, PO Box 99, E-03080, Alicante, Spain
| | - Sanja Veselić
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, 2100, Serbia
| | - Tuure Parviainen
- VTT Technical Research Centre of Finland Ltd, TT2 Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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25
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Scalercio S, Cini A, Menchetti M, Vodă R, Bonelli S, Bordoni A, Casacci LP, Dincă V, Balletto E, Vila R, Dapporto L. How long is 3 km for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula. J Anim Ecol 2020; 89:2013-2026. [PMID: 32207150 DOI: 10.1111/1365-2656.13196] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/21/2020] [Indexed: 11/28/2022]
Abstract
Populations inhabiting Mediterranean islands often show contrasting genetic lineages, even on islands that were connected to the mainland during glacial maxima. This pattern is generated by forces acting in historical and contemporary times. Understanding these phenomena requires comparative studies integrating genetic structure, functional traits and dispersal constraints. Using as a model the butterfly species living across the Messina strait (3 km wide) separating Sicily from the Italian Peninsula, we aimed to unravel the mechanisms limiting the dispersal of matrilines and generating genetic differentiation across a narrow sea strait. We analysed the mitochondrial COI gene of 84 butterfly species out of 90 documented in Sicily and compared them with populations from the neighbouring southern Italian Peninsula (1,398 sequences) and from the entire Palaearctic region (8,093 sequences). For each species, we regressed 13 functional traits and 2 ecological constraints to dispersal (winds experienced at the strait and climatic suitability) against genetic differentiation between Sicily and Italian Peninsula to understand the factors limiting dispersal. More than a third of the species showed different haplogroups across the strait and most of them also represented endemic haplogroups for this island. One fifth of Sicilian populations (and 32.3% of endemic lineages) had their closest relatives in distant areas, instead of the neighbouring Italian Peninsula, which suggests high relictuality. Haplotype diversity was significantly explained by the length of the flight period, an intrinsic phenology trait, while genetic differentiation was explained by both intrinsic traits (wingspan and degree of generalism) and contemporary local constraints (winds experienced at the strait and climatic suitability). A relatively narrow sea strait can produce considerable differentiation among butterfly matrilines and this phenomenon showed a largely deterministic fingerprint. Because of unfavourable winds, populations of the less dispersive Sicilian butterflies tended to differentiate into endemic variants or to maintain relict populations. Understanding these phenomena required the integration of DNA sequences, species traits and physical constraints for a large taxon at continental scale. Future studies may reveal if the patterns here shown for mitochondrial DNA are also reflected in the nuclear genome or, alternatively, are the product of limited female dispersal.
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Affiliation(s)
- Stefano Scalercio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Foreste e Legno, Contrada Li Rocchi, Rende, Italy
| | - Alessandro Cini
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy.,Centre for Biodiversity and Environment Research, University College London, London, UK
| | - Mattia Menchetti
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Raluca Vodă
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Simona Bonelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Adele Bordoni
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Luca Pietro Casacci
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy.,Muzeum i Instytut Zoologii, Polskiej Akademii Nauk, Warsaw, Poland
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Emilio Balletto
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leonardo Dapporto
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
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Local adaptation fuels cryptic speciation in terrestrial annelids. Mol Phylogenet Evol 2020; 146:106767. [PMID: 32081763 DOI: 10.1016/j.ympev.2020.106767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/13/2020] [Indexed: 11/23/2022]
Abstract
Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as it is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between 17 populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.
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Dincă V, Lee KM, Vila R, Mutanen M. The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly. Proc Biol Sci 2019; 286:20191311. [PMID: 31530141 PMCID: PMC6784721 DOI: 10.1098/rspb.2019.1311] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise FST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.
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Affiliation(s)
- Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37, 08003 Barcelona, Spain
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
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