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Lukhtanov VA, Dantchenko AV. Cryptic Taxa Revealed through Combined Analysis of Chromosomes and DNA Barcodes: The Polyommatus ripartii Species Complex in Armenia and NW Iran. INSECTS 2024; 15:545. [PMID: 39057277 PMCID: PMC11277131 DOI: 10.3390/insects15070545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77-79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73-75), P. demavendi antonius, subsp. nov. (n = 71-73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29-34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Alexander V. Dantchenko
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
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Lo YY, Cheng RC, Lin CP. Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan. PLoS One 2024; 19:e0301776. [PMID: 38722906 PMCID: PMC11081396 DOI: 10.1371/journal.pone.0301776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 05/13/2024] Open
Abstract
An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.
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Affiliation(s)
- Ying-Yuan Lo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Wild Animals Division, Biodiversity Research Institute, Nantou, Taiwan
| | - Ren-Chung Cheng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Research Center for Global Change Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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3
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Sgarlata GM, Rasolondraibe E, Salmona J, Le Pors B, Ralantoharijaona T, Rakotonanahary A, Jan F, Manzi S, Iribar A, Zaonarivelo JR, Volasoa Andriaholinirina N, Rasoloharijaona S, Chikhi L. The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species. Mol Phylogenet Evol 2024; 193:107997. [PMID: 38128795 DOI: 10.1016/j.ympev.2023.107997] [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] [Received: 02/10/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.
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Affiliation(s)
| | - Emmanuel Rasolondraibe
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Jordi Salmona
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Barbara Le Pors
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Tantely Ralantoharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Ando Rakotonanahary
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Fabien Jan
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Amaia Iribar
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - John Rigobert Zaonarivelo
- Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, 201 Antsiranana, Madagascar.
| | | | - Solofonirina Rasoloharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
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4
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Dähn O, Werner D, Mathieu B, Kampen H. Large-Scale Cytochrome C Oxidase Subunit I Gene Data Analysis for the Development of a Multiplex Polymerase Chain Reaction Test Capable of Identifying Biting Midge Vector Species and Haplotypes (Diptera: Ceratopogonidae) of the Culicoides Subgenus Avaritia Fox, 1955. Genes (Basel) 2024; 15:323. [PMID: 38540382 PMCID: PMC10969821 DOI: 10.3390/genes15030323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
The emergence of culicoid-transmitted bluetongue and Schmallenberg viruses in several European countries demonstrated the ability of indigenous biting midge species to transmit pathogens. Entomologic research programs identified members of the Obsoletus Group (Culicoides subgenus Avaritia) as keyplayers in disease epidemiology in Europe. However, morphological identification of potential vectors is challenging due to the recent discovery of new genetic variants (haplotypes) of C. obsoletus sensu stricto (s.s.), forming distinct clades. In this study, 4422 GenBank entries of the mitochondrial cytochrome c oxidase subunit I (COI) gene of subgenus Avaritia members of the genus Culicoides were analyzed to develop a conventional multiplex PCR, capable of detecting all vector species and clades of the Western Palearctic in this subgenus. Numerous GenBank entries incorrectly assigned to a species were identified, analyzed and reassigned. The results suggest that the three C. obsoletus clades represent independent species, whereas C. montanus should rather be regarded as a genetic variant of C. obsoletus s.s. Based on these findings, specific primers were designed and validated with DNA material from field-caught biting midges which achieved very high diagnostic sensitivity (100%) when compared to an established reference PCR (82.6%).
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Affiliation(s)
- Oliver Dähn
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany
| | - Bruno Mathieu
- Institutes of Bacteriology and Parasitology, Medical Faculty, University of Strasbourg, UR 3073 PHAVI, 67000 Strasbourg, France
| | - Helge Kampen
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany
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5
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Miralles A, Puillandre N, Vences M. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy. Methods Mol Biol 2024; 2744:77-104. [PMID: 38683312 DOI: 10.1007/978-1-0716-3581-0_4] [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
Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.
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Affiliation(s)
- Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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6
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Ahrens D. Species Diagnosis and DNA Taxonomy. Methods Mol Biol 2024; 2744:33-52. [PMID: 38683310 DOI: 10.1007/978-1-0716-3581-0_2] [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
The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.
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Affiliation(s)
- Dirk Ahrens
- Museum A. Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.
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7
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Shapoval NA, Kir’yanov AV, Krupitsky AV, Yakovlev RV, Romanovich AE, Zhang J, Cong Q, Grishin NV, Kovalenko MG, Shapoval GN. Phylogeography of Two Enigmatic Sulphur Butterflies, Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897 (Lepidoptera, Pieridae), with Relations to Wolbachia Infection. INSECTS 2023; 14:943. [PMID: 38132616 PMCID: PMC10743618 DOI: 10.3390/insects14120943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
The genus Colias Fabricius, 1807 includes numerous taxa and forms with uncertain status and taxonomic position. Among such taxa are Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897, interpreted in the literature either as conspecific forms, as subspecies of different but morphologically somewhat similar Colias species or as distinct species-level taxa. Based on mitochondrial and nuclear DNA markers, we reconstructed a phylogeographic pattern of the taxa in question. We recover and include in our analysis DNA barcodes of the century-old type specimens, the lectotype of C. tamerlana deposited in the Natural History Museum (Museum für Naturkunde), Berlin, Germany (ZMHU) and the paralectotype of C. tamerlana and the lectotype of C. mongola deposited in the Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (ZISP). Our analysis grouped all specimens within four (HP_I-HP_IV) deeply divergent but geographically poorly structured clades which did not support nonconspecifity of C. mongola-C. tamerlana. We also show that all studied females of the widely distributed haplogroup HP_II were infected with a single Wolbachia strain belonging to the supergroup B, while the males of this haplogroup, as well as all other investigated specimens of both sexes, were not infected. Our data highlight the relevance of large-scale sampling dataset analysis and the need for testing for Wolbachia infection to avoid erroneous phylogenetic reconstructions and species misidentification.
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Affiliation(s)
- Nazar A. Shapoval
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 St. Petersburg, Russia
| | - Alexander V. Kir’yanov
- Photonics Department, Centro de Investigaciones en Optica, Lomas del Bosque 115, Leon 37150, Mexico;
| | - Anatoly V. Krupitsky
- Department of Entomology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, GSP-1, korp. 12, 119991 Moscow, Russia;
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Pr. 33, 119071 Moscow, Russia
| | - Roman V. Yakovlev
- Department of Ecology, Altai State University, Lenina Pr. 61, 656049 Barnaul, Russia;
- Institute of Biology, Tomsk State University, Lenina Pr. 36, 634050 Tomsk, Russia
| | - Anna E. Romanovich
- Resource Center for Development of Molecular and Cellular Technologies, St. Petersburg State University, Universitetskaya Nab., 7/9, 199034 St. Petersburg, Russia;
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Department of Biochemistry, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
- Eugene McDermott Center For Human Growth & Development, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Eugene McDermott Center For Human Growth & Development, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Department of Biochemistry, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Margarita G. Kovalenko
- Research and Methodological Department of Entomology, All-Russian Plant Quarantine Center, Pogranichnaya 32, 140150 Bykovo, Russia;
| | - Galina N. Shapoval
- Department of Ecology, Altai State University, Lenina Pr. 61, 656049 Barnaul, Russia;
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da Silva FL, Pinho LC, Stur E, Nihei SS, Ekrem T. DNA barcodes provide insights into the diversity and biogeography of the non-biting midge Polypedilum (Diptera, Chironomidae) in South America. Ecol Evol 2023; 13:e10602. [PMID: 37841227 PMCID: PMC10568203 DOI: 10.1002/ece3.10602] [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: 02/08/2023] [Revised: 08/04/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
South America, particularly within its tropical belt, is renowned for its unparalleled high levels of species richness, surpassing other major biomes. Certain neotropical areas harbor fragmented knowledge of insect diversity and face imminent threats from biodiversity loss and climate change. Hence, there is an urgent need for rapid estimation methods to complement slower traditional taxonomic approaches. A variety of algorithms for delimiting species through single-locus DNA barcodes have been developed and applied for rapid species diversity estimates across diverse taxa. However, tree-based and distance-based methods may yield different group assignments, leading to potential overestimation or underestimation of putative species. Here, we investigate the performance of different DNA-based species delimitation approaches to rapidly estimate the diversity of Polypedilum (Chironomidae, Diptera) in South America. Additionally, we test the hypothesis that significant differences exist in the community structure of Polypedilum fauna between South America and its neighboring regions, particularly the Nearctic. Our analysis encompasses a dataset of 1492 specimens from 598 locations worldwide, with a specific focus on South America. Within this region, we analyzed a subset of 247 specimens reported from 37 locations. Using various methods including the Barcode Index Number (BIN), Bayesian Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), single-rate Poisson tree processes (sPTP), and generalized mixed Yule coalescent (sGMYC), we identify molecular operational taxonomic units (MOTUs) ranging from 267 to 520. Our results indicate that the sGMYC method is the most suitable for estimating putative species in our dataset, resulting in the identification of 75 species in the Neotropical region, particularly in South America. Notably, this region exhibited higher species richness in comparison to the Palearctic and Oriental realms. Additionally, our findings suggest potential differences in species composition of Polypedilum fauna between the Neotropical and the adjacent Nearctic realms, highlighting high levels of endemism and species richness in the first. These results support our hypothesis that there are substantial differences exist in species composition between the Polypedilum fauna in South America and the neighboring regions.
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Affiliation(s)
- Fabio Laurindo da Silva
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Present address:
Laboratory of Aquatic Insect Biodiversity and Ecology, Department of Zoology, Institute of BiosciencesUniversity of São PauloSão PauloBrazil
| | - Luiz Carlos Pinho
- Laboratory of Systematic of Diptera, Department of Ecology and ZoologyFederal University of Santa CatarinaFlorianópolisBrazil
| | - Elisabeth Stur
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Silvio Shigueo Nihei
- Laboratory of Systematic and Biogeography of Insecta, Department of Zoology, Institute of BiosciencesUniversity of São PauloSão PauloBrazil
| | - Torbjørn Ekrem
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
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9
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Liao CQ, Hirowatari T, Yagi S, Wang M, Wang X, Huang GH. The fauna of the family Adelidae (Insecta, Lepidoptera, Adeloidea) from China. Zootaxa 2023; 5348:1-152. [PMID: 38221502 DOI: 10.11646/zootaxa.5348.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Indexed: 01/16/2024]
Abstract
Ninety-eight species of the family Adelidae, belonging to three genera in two subfamilies, were recorded and described in China, with illustrations of the adults and their genitalia. Keys to subfamilies, genera and species are also provided. Twenty-four new species are described, nine species are newly recorded from China, and four new combinations are made. Ecological photos and DNA barcodes of some species are provided, and the phylogenetic analysis based on cytochrome c oxidase subunit I (COI) sequences are conducted. The new taxa are as follows: Nemophora pseudalbiantennella Liao, Hirowatari & Huang, sp. nov., N. badagongshana Liao, Hirowatari & Huang, sp. nov., N. longlabiae Liao, Hirowatari & Huang, sp. nov., N. quadrata Liao, Hirowatari & Huang, sp. nov., N. basalistriata Liao, Hirowatari & Huang, sp. nov., N. digitata Liao, Hirowatari & Huang, sp. nov., N. duplicifascia Liao, Hirowatari & Huang, sp. nov., N. hunanensis Liao, Hirowatari & Huang, sp. nov., N. purpurata Liao, Hirowatari & Huang, sp. nov., N. arcuatifasciata Liao, Hirowatari & Huang, sp. nov., N. caeruliantenna Liao, Hirowatari & Huang, sp. nov., N. xizangensis Liao, Hirowatari & Huang, sp. nov., N. caerulea Liao, Hirowatari & Huang, sp. nov., N. songgangensis Liao, Hirowatari & Huang, sp. nov., N. conjugata Liao, Hirowatari & Huang, sp. nov., N. latilobula Liao, Hirowatari & Huang, sp. nov., N. longispina Liao, Hirowatari & Huang, sp. nov., N. ganziensis Liao, Hirowatari & Huang, sp. nov., N. jiajinshana Liao, Hirowatari & Huang, sp. nov., N. litangensis Liao, Hirowatari & Huang, sp. nov., N. tianpingshana Liao, Hirowatari & Huang, sp. nov., N. triangulifascia Liao, Hirowatari & Huang, sp. nov., N. yajiagengensis Liao, Hirowatari & Huang, sp. nov., and N. bispina Liao, Hirowatari & Huang, sp. nov. The newly recorded taxa from China are: Nematopogon distinctus Yasuda, 1957, Adela nobilis Christoph, 1882, A. praepilosa Hirowatari, 1997, Nemophora albiantennella Issiki, 1930, N. chionites (Meyrick, 1907), N. smaragdaspis (Meyrick, 1924), N. trimetrella Stringer, 1930, N. optima (Butler, 1878), and N. bifasciatella Issikii, 1930. The new combinations are N. servata (Meyrick, 1925) com. nov., N. diplophragma (Meyrick, 1938) com. nov., N. chionella (Caradja, 1935) com. nov., and N. chrysocharis (Caradja, 1938) com. nov.
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Affiliation(s)
- Cheng-Qing Liao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha; Hunan; 410128 P. R. China; Leafminer Group; School of Life Sciences; Gannan Normal University; Ganzhou; Jiangxi; 341000 P. R. China.
| | - Toshiya Hirowatari
- Entomological Laboratory; Faculty of Agriculture; Kyushu University; 744 Motooka; Nishi-ku; Fukuoka; 819-0395 Japan.
| | - Sadahisa Yagi
- Entomological Laboratory; Faculty of Agriculture; Kyushu University; 744 Motooka; Nishi-ku; Fukuoka; 819-0395 Japan.
| | - Min Wang
- Department of Entomology; South China Agricultural University; Guangzhou; Guangdong 510642; P. R. China.
| | - Xing Wang
- College of Science; Qiongtai Normal University; Haikou; Hainan 571100; P. R. China.
| | - Guo-Hua Huang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha; Hunan; 410128 P. R. China.
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10
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Posada-López L, Rodrigues BL, Velez ID, Uribe S. Improving the COI DNA barcoding library for Neotropical phlebotomine sand flies (Diptera: Psychodidae). Parasit Vectors 2023; 16:198. [PMID: 37308979 DOI: 10.1186/s13071-023-05807-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/10/2023] [Indexed: 06/14/2023] Open
Abstract
Sand fly species are traditionally identified using morphological traits, though this method is hampered by the presence of cryptic species. DNA barcoding is a widely used tool in the case of insects of medical importance, where it is necessary to know quickly which species are present in a transmission area. Here, we assess the usefulness of mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding as a practical tool for species identification, correct assignment of isomorphic females, and to evaluate the detection of cryptic diversity that occurs in the same species. A fragment of the COI gene was used to generate 156 new barcode sequences for sand flies from different countries of the Neotropical region, mainly Colombia, which had been identified morphologically as 43 species. The sequencing of the COI gene allowed the detection of cryptic diversity within species and correctly associated isomorphic females with males identified by morphology. The maximum intraspecific genetic distances ranged from 0 to 8.32% and 0 to 8.92% using uncorrected p distances and the Kimura 2-parameter (K2P) model, respectively. The minimum interspecific distance (nearest neighbor) for each species ranged from 1.5 to 14.14% and 1.51 to 15.7% using p and K2P distances, respectively. Three species had more than 3% maximum intraspecific distance: Psychodopygus panamensis, Micropygomyia cayennensis cayennensis, and Pintomyia evansi. They also were split into at least two molecular operational taxonomic units (MOTUs) each, using different species delimitation algorithms. Regarding interspecific genetic distances, the species of the genera Nyssomyia and Trichophoromyia generated values lower than 3% (except Nyssomyia ylephiletor and Ny. trapidoi). However, the maximum intraspecific distances did not exceed these values, indicating the presence of a barcode gap despite their proximity. Also, nine sand fly species were DNA barcoded for the first time: Evandromyia georgii, Lutzomyia sherlocki, Ny. ylephiletor, Ny. yuilli pajoti, Psathyromyia punctigeniculata, Sciopemyia preclara, Trichopygomyia triramula, Trichophoromyia howardi, and Th. velezbernali. The COI DNA barcode analysis enabled the correct delimitation of several Neotropical sand fly species from South and Central America and raised questions about the presence of cryptic species for some taxa, which should be further assessed.
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Affiliation(s)
- Laura Posada-López
- PECET (Programa de Estudio y Control de Enfermedades Tropicales), Universidad de Antioquia, Medellín, Colombia.
- Programa de Pós-graduação em Saúde Pública, Faculdade de Saúde Pública (FSP/USP), São Paulo, SP, Brasil.
| | - Bruno Leite Rodrigues
- Programa de Pós-graduação em Saúde Pública, Faculdade de Saúde Pública (FSP/USP), São Paulo, SP, Brasil
| | - Ivan Dario Velez
- PECET (Programa de Estudio y Control de Enfermedades Tropicales), Universidad de Antioquia, Medellín, Colombia
| | - Sandra Uribe
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Campus, Medellín, Colombia
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11
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de Araújo L, Ramos LI, Vieira MMDR, Oliveira AVD, Portela-Castro ALDB, Borin-Carvalho LA, Fernandes CA. Cytogenetic and Molecular Characterization of Eigenmannia aff. desantanai (Gymnotiformes: Sternopygidae): A First Report of System of Sex Chromosomes ZW 1W 2/ZZ in Gymnotiformes. Zebrafish 2023; 20:77-85. [PMID: 36930749 DOI: 10.1089/zeb.2022.0059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Gymnotiformes a monophyletic group of fish endemic to the Neotropics, represent an important component of the freshwater ichthyofauna that presents relevant taxonomic problems. Thus, in view of the morphological complexity involving Eigenmannia (Gymnotiformes) fish species, this study aimed to characterize Eigenmannia aff. desantanai of the upper Paraguay River basin through cytogenetic and molecular analyses, to help in the correct identification and delimitation of species. This study reports a multiple sex system of the type ZW1W2/ZZ, with 2n = 31 for females and 2n = 30 for males. A single pair of chromosomes carrying the nucleolar organizing regions (NORs) was detected. The heterochromatin was colocated in NOR sites and mainly located in the centromeric regions of chromosomes. Besides that, individual sequences COI from the specimens of E. aff. desantanai were obtained, totalizing three haplotypes. The distance p between the haplotypes in E. aff. desantanai, ranged from 0.2% to 7.1%. Species delimitation tests indicated the existence of two possible operational taxonomic units of E. aff. desantanai. Thus, this study reports a new multiple sex system in Gymnotiformes and these specimens previously identified as E. aff. desantanai may belong to two distinct species.
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Affiliation(s)
- Laís de Araújo
- Programa de Pós-Graduação em Genética e Melhoramento, Centro de Ciências Agrárias (CCA) da Universidade Estadual de Maringá, Maringá, Brazil
| | - Laura Ivana Ramos
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Centro de Ciências Biológicas (CCB) da Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Alessandra Valéria de Oliveira
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Centro de Ciências Biológicas (CCB) da Universidade Estadual de Maringá, Maringá, Brazil.,Programa de Pós-Graduação em Biotecnologia Ambiental, Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Centro de Ciências Biológicas (CCB) da Universidade Estadual de Maringá, Maringá, Brazil.,Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá (UEM), Av. Colombo, 5790, 87020-900, Maringá, Brazil
| | - Ana Luiza de Brito Portela-Castro
- Programa de Pós-Graduação em Biotecnologia Ambiental, Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Centro de Ciências Biológicas (CCB) da Universidade Estadual de Maringá, Maringá, Brazil.,Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá (UEM), Av. Colombo, 5790, 87020-900, Maringá, Brazil
| | - Luciana Andreia Borin-Carvalho
- Programa de Pós-Graduação em Genética e Melhoramento, Centro de Ciências Agrárias (CCA) da Universidade Estadual de Maringá, Maringá, Brazil.,Programa de Pós-Graduação em Biotecnologia Ambiental, Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Centro de Ciências Biológicas (CCB) da Universidade Estadual de Maringá, Maringá, Brazil
| | - Carlos Alexandre Fernandes
- Programa de Pós-Graduação em Biotecnologia Ambiental, Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Centro de Ciências Biológicas (CCB) da Universidade Estadual de Maringá, Maringá, Brazil.,Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá (UEM), Av. Colombo, 5790, 87020-900, Maringá, Brazil.,Programa de Pós-Graduação em Biologia Comparada, Centro de Ciências Biológicas (CCB) da Universidade Estadual de Maringá, Maringá, Brazil
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12
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Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
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Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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13
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Song C, Wang L, Lei T, Qi X. New Color-Patterned Species of Microtendipes Kieffer, 1913 (Diptera: Chironomidae) and a Deep Intraspecific Divergence of Species by DNA Barcodes. INSECTS 2023; 14:227. [PMID: 36975912 PMCID: PMC10054112 DOI: 10.3390/insects14030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The genus Microtendipes Kieffer (Diptera: Chironomidae) has a nearly worldwide distribution, comprising more than 60 species, which are further divided into two species groups based on larval stage. However, species delimitation and identification among the adults of this genus are controversial and uncertain. For instance, previous studies have provided many synonymies based on conspecific color pattern variations in Microtendipes species. Here, we used DNA barcode data to address Microtendipes species delimitation as well as to test whether color pattern variations can be diagnostic characters for interspecific identification. The 151 DNA barcodes used, 51 of which were contributed by our laboratory, represent 21 morphospecies. Species with specific color patterns could be accurately separated based on DNA barcodes. Consequently, the color patterns of adult males could be important diagnostic characters. The average intraspecific and interspecific sequence divergences were 2.8% and 12.5%, respectively, and several species exhibited deep intraspecific divergences higher than 5%. Molecular operational taxonomic units (OTUs) ranged from 21 to 73, based on methods including phylogenetic trees, the assemble species by automatic partitioning method, the Poisson tree process (PTP), and the general mixed Yule-coalescent (GMYC) method. As a result of these analyses, five new species were recognized (M. baishanzuensis sp. nov., M. bimaculatus sp. nov., M. nigrithorax sp. nov., M. robustus sp. nov., and M. wuyiensis sp. nov.).
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Affiliation(s)
- Chao Song
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
| | - Le Wang
- Nanjing Institute of Environmental Sciences under Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
| | - Xin Qi
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
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14
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Escobar D, Pérez F, Ortiz B, Fontecha G. PCR-RFLP assays for the identification of Anopheles (Diptera: Culicidae) species circulating in Honduras. Malar J 2023; 22:57. [PMID: 36805673 PMCID: PMC9938605 DOI: 10.1186/s12936-023-04494-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/13/2023] [Indexed: 02/20/2023] Open
Abstract
BACKGROUND Vector populations are a key target for malaria control and elimination. In Honduras, there are at least 12 reported anopheline species, however, the definitive number of species remains uncertain. Due to the inherent limitations of morphological identification of Anopheles species, molecular approaches have been developed to provide accurate identification and robust surveillance of local malaria vectors. The aim of this study was to design and assess three PCR-RFLP assays to identify anopheline species known to presently occur in Honduras. METHODS Mosquitoes captured between 2018 and 2022 in seven malaria-endemic and non-endemic departments in Honduras were analysed. The ITS2 ribosomal region and three restriction enzyme-based assays were evaluated in silico and experimentally. RESULTS A total of 132 sequences from 12 anopheline species were analysed. The ITS2 marker showed length polymorphisms that generated products between 388 and 592 bp and no relevant intraspecies polymorphisms were found. Furthermore, the three PCR-RFLP assays were able to differentiate 11 species with sufficient precision and resolution. CONCLUSION The ITS2 region was shown to be a useful molecular marker for identifying local Anopheles species. In addition, the PCR-RFLP assays evaluated here proved to be capable of discriminating most of the anopheline species present in Honduras. These methods provide alternatives to improve entomological surveillance of Anopheles in Honduras and other Mesoamerican countries.
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Affiliation(s)
- Denis Escobar
- grid.10601.360000 0001 2297 2829Microbiology Research Institute, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Fernando Pérez
- grid.10601.360000 0001 2297 2829Microbiology Research Institute, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Bryan Ortiz
- grid.10601.360000 0001 2297 2829Microbiology Research Institute, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Gustavo Fontecha
- Microbiology Research Institute, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras.
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15
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Schütte A, Stüben PE, Astrin JJ. Molecular Weevil Identification Project: A thoroughly curated barcode release of 1300 Western Palearctic weevil species (Coleoptera, Curculionoidea). Biodivers Data J 2023; 11:e96438. [PMID: 38357418 PMCID: PMC10865102 DOI: 10.3897/bdj.11.e96438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/08/2022] [Indexed: 01/25/2023] Open
Abstract
The Molecular Weevil Identification project (MWI) studies the systematics of Western Palearctic weevils (superfamily Curculionoidea) in an integrative taxonomic approach of DNA barcoding, morphology and ecology. This barcode release provides almost 3600 curated CO1 sequences linked to morphological vouchers in about 1300 weevil species. The dataset is presented in statistical distance tables and as a Neighbour-Joining tree. Bayesian Inference trees are computed for the subfamilies Cryptorhynchinae, Apioninae and Ceutorhynchinae. Altogether, 18 unresolved taxonomic issues are discussed. A new barcode primer set is presented. Finally, we establish group-specific genetic distances for many weevil genera to serve as a tool in species delineation. These values are statistically based on distances between "good species" and their congeners. With this morphologically calibrated approach, we could resolve most alpha-taxonomic questions within the MWI project.
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Affiliation(s)
- André Schütte
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn Germany
| | - Peter E Stüben
- Curculio Institute, Mönchengladbach, Germany Curculio Institute Mönchengladbach Germany
| | - Jonas J Astrin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn Germany
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16
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Kvist S, Earl I, Kink E, Oceguera-Figueroa A, Trontelj P. Phylogenetic relationships and species delimitation in Haemopis (Annelida: Hirudinea: Haemopidae). Mol Phylogenet Evol 2023; 178:107648. [PMID: 36283573 DOI: 10.1016/j.ympev.2022.107648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022]
Abstract
The Holarctic leech genus Haemopis currently includes 11 species, all of which are macrophagous, as opposed to their more infamous bloodfeeding counterparts among hirudiniform leeches. In spite of their ecological importance as fish food and predators of freshwater invertebrates, there is a paucity of data regarding morphology and genetic variation that might guide future identification efforts for members of the genus. The lack of detailed descriptions of distinguishing morphological features, coupled with the absence of a robust phylogenetic hypothesis for the genus, have conspired to prevent meaningful inferences on the natural history of the group. In an attempt to remedy this, we present new genetic (using COI, 12S rDNA, 28S rDNA and 18S rDNA) data for the majority of the known species diversity within the genus in order to both infer a phylogenetic hypothesis and to introduce authoritative DNA barcodes for the newly collected species. The potential of these barcodes is increased through rigorous morphological investigations of the specimens, with comparisons to the original literature. Our resulting phylogenetic hypothesis is agnostic as to the geographic origin of the genus, with equal probability afforded to both a Nearctic and Palearctic origin. Beyond this, we show that there is a strong tendency towards a barcoding gap within the genus, but that a distinct gap is lacking due to the relatively high genetic variation found within H. marmorata. Taken together, our results shed light on species delimitation within, and evolutionary history of, this often-neglected group of leeches.
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Affiliation(s)
- Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 2B4, Canada.
| | - Ismay Earl
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 2B4, Canada
| | - Ester Kink
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
| | - Alejandro Oceguera-Figueroa
- Laboratorio de Helmintología, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Peter Trontelj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
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17
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Olds CG, Berta‐Thompson JW, Loucks JJ, Levy RA, Wilson AW. Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11508. [PMID: 36818783 PMCID: PMC9934593 DOI: 10.1002/aps3.11508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
PREMISE Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once. METHODS We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens. RESULTS The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs. DISCUSSION The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.
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Affiliation(s)
- C. Gary Olds
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
- The Department of Integrative BiologyUniversity of Colorado DenverDenverColoradoUSA
| | | | - Justin J. Loucks
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
| | - Richard A. Levy
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
| | - Andrew W. Wilson
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
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18
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Kilian IC, Espeland M, Mey W, Wowor D, Hadiaty RK, von Rintelen T, Herder F. DNA barcoding unveils a high diversity of caddisflies (Trichoptera) in the Mount Halimun Salak National Park (West Java; Indonesia). PeerJ 2022; 10:e14182. [PMID: 36530410 PMCID: PMC9753737 DOI: 10.7717/peerj.14182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/14/2022] [Indexed: 12/14/2022] Open
Abstract
Background Trichoptera are one of the most diverse groups of freshwater insects worldwide and one of the main bioindicators for freshwater quality. However, in many areas, caddisflies remain understudied due to lack of taxonomic expertise. Meanwhile, globally increasing anthropogenic stress on freshwater streams also threatens Trichoptera diversity. Methods To assess the Trichoptera diversity of the area within and around the Mount Halimun Salak National Park (MHSNP or Taman Nasional Gunung Halimun Salak) in West Java (Indonesia), we conducted a molecular-morphological study on Trichoptera diversity using larvae from a benthic survey and adults from hand-netting. In addition to morphological identification, we applied four different molecular taxon delimitation approaches (Generalized Mixed Yule Coalescent, Bayesian Poisson Tree Processes, Automatic Barcode Gap Discovery and Assemble Species by Automatic Partitioning) based on DNA barcoding of Cytochrome-C-Oxidase I (COI). Results The molecular delimitation detected 72 to 81 Operational Taxonomic Units (OTU). Only five OTUs could be identified to species level by comparing sequences against the BOLD database using BLAST, and four more to the genus level. Adults and larvae could be successfully associated in 18 cases across six families. The high diversity of Trichoptera in this area highlights their potential as bioindicators for water quality assessment. Conclusions This study provides an example of how molecular approaches can benefit the exploration of hidden diversity in unexplored areas and can be a valuable tool to link life stages. However, our study also highlights the need to improve DNA barcode reference libraries of Trichoptera for the Oriental region.
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Affiliation(s)
- Isabel C. Kilian
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Marianne Espeland
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Wolfram Mey
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Daisy Wowor
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, Indonesia
| | - Renny K. Hadiaty
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, Indonesia
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Fabian Herder
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
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Timm VF, Gonçalves LT, Valente V, Deprá M. The efficiency of the COI gene as a DNA barcode and an overview of Orthoptera (Caelifera and Ensifera) sequences in the BOLD System. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2022-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Orthoptera, among the oldest and most numerous insect lineages, is an excellent model for evolutionary studies but has numerous taxonomic problems. To mitigate these issues, the cytochrome c oxidase subunit I (COI), standardized with the DNA barcode for Metazoa, is increasingly used for specimen identification and species delimitation. We tested the performance of COI as a DNA barcode in Orthoptera, using two analyses based on intra- and interspecific distances, barcode gap and Probability of Correct Identification (PCI); and estimated species richness through Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP). We filtered all sequences of Orthoptera available in Barcode of Life Data System (BOLD) and used 11,605 COI sequences, covering 1,132 species, 226 genera, and 18 families. The overall average PCI was 73.86%. For 82.2% of genera the barcode gap boxplots were classified as good or intermediate, indicating that COI can be effective as a DNA barcode in Orthoptera, although with varying efficiency depending on the need for more information. ABGD and ASAP inferred species richness similar to labels informed by BOLD for the suborders Caelifera and Ensifera. The representation of Orthoptera in the BOLD database and the results of these analyses are discussed.
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Affiliation(s)
- Vítor Falchi Timm
- Universidade Federal do Rio Grande do Sul, 28124, Departamento de Genética, Porto Alegre, RS, Brazil
| | | | - V.l.S. Valente
- Universidade Federal do Rio Grande do Sul, 28124, Departamento de Genética, Porto Alegre, RS, Brazil,
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20
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Chaiphongpachara T, Changbunjong T, Sumruayphol S, Laojun S, Suwandittakul N, Kuntawong K. Geometric morphometrics versus DNA barcoding for the identification of malaria vectors Anopheles dirus and An. baimaii in the Thai-Cambodia border. Sci Rep 2022; 12:13236. [PMID: 35918453 PMCID: PMC9345986 DOI: 10.1038/s41598-022-17646-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Anopheles (Cellia) dirus Peyton & Harrison and Anopheles baimaii Sallum & Peyton are sibling species within the Dirus complex belonging to the Leucosphyrus group, and have been incriminated as primary vectors of malaria in Thailand. In the present study, DNA barcoding and geometric morphometrics were used to distinguish between An. dirus and An. baimaii in the international border areas, Trat Province, eastern Thailand. Our results revealed that DNA barcoding based on the cytochrome c oxidase subunit I gene could not be used to distinguish An. dirus from An. baimaii. The overlapping values between intra- and interspecific genetic divergence indicated no barcoding gap present for An. dirus and An. baimaii (ranging from 0 to 0.99%). However, the results of the geometric morphometric analysis based on the wing shape clearly distinguished An. dirus and An. baimaii, with 92.42% of specimens assigned to the correct species. We concluded that geometric morphometrics is an effective tool for the correct species identification of these two malaria vectors. Our findings could be used to make entomological surveillance information more accurate, leading to further effective mosquito control planning in Thailand and other countries in Southeast Asia.
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Affiliation(s)
- Tanawat Chaiphongpachara
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand.
| | - Tanasak Changbunjong
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand.,The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Suchada Sumruayphol
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Sedthapong Laojun
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Nantana Suwandittakul
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Kewarin Kuntawong
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
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21
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Toro-Delgado E, Hernández-Roldán J, Dincă V, Vicente JC, Shaw MR, Quicke DL, Vodă R, Albrecht M, Fernández-Triana J, Vidiella B, Valverde S, Dapporto L, Hebert PDN, Talavera G, Vila R. Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The study of ecological interactions between plants, phytophagous insects and their natural enemies is an essential but challenging component for understanding ecosystem dynamics. Molecular methods such as DNA barcoding can help elucidate these interactions. In this study, we employed DNA barcoding to establish hostplant and parasitoid interactions with hesperiid butterflies, using a complete reference library for Hesperiidae of continental Europe and north-western Africa (53 species, 100% of those recorded) based on 2934 sequences from 38 countries. A total of 233 hostplant and parasitoid interactions are presented, some recovered by DNA barcoding larval remains or parasitoid cocoons. Combining DNA barcode results with other lines of evidence allowed 94% species-level identification for Hesperiidae, but success was lower for parasitoids, in part due to unresolved taxonomy. Potential cases of cryptic diversity, both in Hesperiidae and Microgastrinae, are discussed. We briefly analyse the resulting interaction networks. Future DNA barcoding initiatives in this region should focus attention on north-western Africa and on parasitoids, because in these cases barcode reference libraries and taxonomy are less well developed.
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Affiliation(s)
| | - Juan Hernández-Roldán
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid , c/ Darwin, 2, ES - 28049 Madrid , Spain
| | - Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu , 90014 Oulu , Finland
- Research Institute of the University of Bucharest (ICUB), University of Bucharest , Bucharest , Romania
| | | | - Mark R Shaw
- National Museums of Scotland , Edinburgh , UK
| | - Donald Lj Quicke
- Department of Biology, Faculty of Life Sciences, Chulalongkorn University , Bangkok , Thailand
| | | | | | | | - Blai Vidiella
- Centre de Recerca Matemàtica , Edifici C , Campus de Bellaterra, Barcelona , Spain
| | - Sergi Valverde
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- European Centre for Living Technology , Venice , Italy
| | - Leonardo Dapporto
- Dipartimento di Biologia, University of Florence , 50019 Sesto Fiorentino , Italy
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph , Guelph, ON N1G 2W1 , Canada
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona , Passeig del Migdia s/n, 08038 Barcelona , Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
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22
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Ricarte A, Nedeljković Z, Aguado-Aranda P, Marcos-García MÁ. Assessing the Diversity and Systematics of Brachyopini Hoverflies (Diptera: Syrphidae) in the Iberian Peninsula, Including the Descriptions of Two New Species. INSECTS 2022; 13:insects13070648. [PMID: 35886824 PMCID: PMC9319642 DOI: 10.3390/insects13070648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Hoverflies are a diverse family of insects (6000+ species) providing multiple ecosystem services and direct benefits to society, for example, in pollination and pest control. The extent to which hoverflies can benefit society depends on how well their basics are known, i.e., taxonomy (classification), biology and ecology. Small and inconspicuous hoverflies such as those of the genera Chrysogaster, Melanogaster, Lejogaster, Orthonevra and Riponnensia (tribe Brachyopini) do not usually catch the attention of the general public neither of scientists, and their classification is often poorly known at least in areas of their range. So, the aim of the present work is to gain knowledge in the classification of hoverflies by studying the species of the five genera above-mentioned in the Iberian Peninsula, which has one of the highest biodiversity levels in Europe. We discovered and described two new species from Spain, promoted a subspecies to species and proposed other nomenclatural acts to stabilise these hoverflies’ classification in Europe. Our results are reinforced with DNA analysis to locate the studied species in a wider systematic framework within the Brachyopini. Abstract Five genera of Brachyopini, Chrysogaster Meigen, 1800, Melanogaster Rondani, 1857, Lejogaster Rondani, 1857, Orthonevra Macquart, 1829 and Riponnensia Maibach et al. 1994a are here revised from the Iberian region. Two new species, Melanogaster baetica Ricarte and Nedeljković, sp. n. and Orthonevra arcana Ricarte and Nedeljković sp. n., are described from Spain, and a third species, Chrysogaster coerulea Strobl in Czerny and Strobl, 1909 stat. n., is reinstated as valid and redescribed. A lectotype is designated for Orthonevra plumbago (Loew, 1840). The holotype of Orthonevra incisa (Loew, 1843) and the lectotype of O. plumbago are described in detail and illustrated. Melanogaster baetica sp. n. is similar to Melanogaster parumplicata (Loew, 1840) in male genitalia morphology, while O. arcana sp. n. is similar to O. incisa in the entirely-pollinose sternum I and the conspicuous incision on the posterior margin of tergum V in female. The first Iberian record of Chrysogaster rondanii Maibach and Goeldlin de Tiefenau, 1995 is provided, whilst Melanogaster aerosa is removed from the Iberian checklist of Syrphidae. Identification keys are presented to the five Brachyopini genera and 18 species now reported from the Iberian Peninsula (Chrysogaster, 6 spp.; Lejogaster, 2 spp.; Melanogaster, 3 spp.; Orthonevra, 5 spp.; Riponnensia, 2 spp.). COI (Cytochrome c oxidase subunit I) barcodes of the two new species plus C. coerulea, Chrysogaster solstitialis (Fallén, 1817), Orthonevra nobilis (Fallén, 1817) and Orthonevra frontalis (Loew, 1843) were successfully obtained from Spanish specimens. A COI-based tree was produced to locate these taxa in a wider systematic framework within the tribe.
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23
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Zamani A, Dal Pos D, Fric ZF, Orfinger AB, Scherz MD, Bartoňová AS, Gante HF. The future of zoological taxonomy is integrative, not minimalist. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2063964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Zamani
- Zoological Museum, Biodiversity Unit, University of Turku, 20500 Turku, Finland
| | - Davide Dal Pos
- Department of Biology, University of Central Florida, 4110 Libra dr. Rm 442, Orlando, FL 32816, USA
| | - Zdenek Faltýnek Fric
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Alexander B. Orfinger
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Center for Water Resources, Florida A&M University, Tallahassee, FL 32301, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Alena Sucháčková Bartoňová
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Hugo F. Gante
- cE3c—Center for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
- Department of Biology, KU Leuven, Section Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 32 box 2439, Leuven, B-3000, Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 17, Tervuren, 3080, Belgium
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24
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Bian X, Garner BH, Liu H, Vogler AP. The SITE-100 Project: Site-Based Biodiversity Genomics for Species Discovery, Community Ecology, and a Global Tree-of-Life. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.787560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most insect communities are composed of evolutionarily diverse lineages, but detailed phylogenetic analyses of whole communities are lacking, in particular in species-rich tropical faunas. Likewise, our knowledge of the Tree-of-Life to document evolutionary diversity of organisms remains highly incomplete and especially requires the inclusion of unstudied lineages from species-rich ecosystems. Here we present the SITE-100 program, which is an attempt at building the Tree-of-Life from whole-community sampling of high-biodiversity sites around the globe. Combining the local site-based sets into a global tree produces an increasingly comprehensive estimate of organismal phylogeny, while also re-tracing evolutionary history of lineages constituting the local community. Local sets are collected in bulk in standardized passive traps and imaged with large-scale high-resolution cameras, which is followed by a parataxonomy step for the preliminary separation of morphospecies and selection of specimens for phylogenetic analysis. Selected specimens are used for individual DNA extraction and sequencing, usually to sequence mitochondrial genomes. All remaining specimens are bulk extracted and subjected to metabarcoding. Phylogenetic analysis on the mitogenomes produces a reference tree to which short barcode sequences are added in a secondary analysis using phylogenetic placement methods or backbone constrained tree searches. However, the approach may be hampered because (1) mitogenomes are limited in phylogenetic informativeness, and (2) site-based sampling may produce poor taxon coverage which causes challenges for phylogenetic inference. To mitigate these problems, we first assemble nuclear shotgun data from taxonomically chosen lineages to resolve the base of the tree, and add site-based mitogenome and DNA barcode data in three hierarchical steps. We posit that site-based sampling, though not meeting the criterion of “taxon-completeness,” has great merits given preliminary studies showing representativeness and evenness of taxa sampled. We therefore argue in favor of site-based sampling as an unorthodox but logistically efficient way to construct large phylogenetic trees.
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25
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Phillips JD, Gillis DJ, Hanner RH. Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.859099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.
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26
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Identifying the Genetic Distance Threshold for Entiminae (Coleoptera: Curculionidae) Species Delimitation via COI Barcodes. INSECTS 2022; 13:insects13030261. [PMID: 35323559 PMCID: PMC8953793 DOI: 10.3390/insects13030261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/27/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023]
Abstract
The subfamily Entiminae is the largest group in the family Curculionidae, and it has long represented a challenge in traditional and molecular classification. Here, we analyzed intra- and interspecific genetic distances of 621 public COI barcode sequences (658bp) from 39 genera and 110 species of Entiminae, to determine parameters most congruent in retaining established species. We found that the mean intraspecific genetic distance (3.07%) was much smaller than the mean interspecific one (21.96%), but there is a wide range of overlap between intra- and interspecific genetic distances (0.77−18.01%), indicating that there is no consistent, universal barcoding gap. Specifically, DNA barcoding gap analysis for morphospecies revealed that 102 of 110 morphospecies had barcoding gaps, and 9.18% was the optimum threshold of genetic distances for 97 species delimitation. We further confirmed this threshold with barcodes from 27 morphologically identified specimens (including 21 newly reported barcodes) sequenced from five genera and seven species. We also identified thresholds to delimit congeneric species within 14 selected genera (species > 2), which varied from 7.42% (Trichalophus) to 13.48% (Barypeithes). We herein present optimal parameters for species identification in the Entiminae. Our study suggests that despite no universal genetic distance threshold value in subfamily Entiminae, 9.18% is optimal for most species. We recommend a wider sampling of geographic populations to better account for intraspecific distance variation, and that genetic distance thresholds for species delimitation should be refined at the genus level.
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27
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Martinsson S, Malmberg K, Bakken T, Korshunova T, Martynov A, Lundin K. Species delimitation and phylogeny of
Doto
(Nudibranchia: Dotidae) from the Northeast Atlantic, with a discussion on food specialization. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Svante Martinsson
- Systematics and Biodiversity Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | | | - Torkild Bakken
- NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | | | | | - Kennet Lundin
- Gothenburg Natural History Museum Gothenburg Sweden
- Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden
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28
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Singh OP, Sindhania A, Sharma G, Mishra S, Sharma SK, Singh PK, Das MK. Are members of the Anopheles fluviatilis complex conspecific? Acta Trop 2021. [DOI: https://doi.org/10.1016/j.actatropica.2021.106149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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29
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Singh OP, Sindhania A, Sharma G, Mishra S, Sharma SK, Singh PK, Das MK. Are members of the Anopheles fluviatilis complex conspecific? Acta Trop 2021. [DOI: https:/doi.org/10.1016/j.actatropica.2021.106149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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30
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Tan D, Parus A, Dunbar M, Espeland M, Willmott KR. Cytochrome c oxidase subunit I barcode species delineation methods imply critically underestimated diversity in ‘common’ Hermeuptychia butterflies (Lepidoptera: Nymphalidae: Satyrinae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
DNA ‘barcoding’ has contributed greatly to resolving species limits in rapidly diverging tropical insect groups. Here, we explored species diversity in the widespread, cryptic Neotropical butterfly genus Hermeuptychia by generating 601 new sequences of the cytochrome c oxidase I (COI) barcode, tripling available information. Our dataset focused in particular on Ecuador, a biogeographically pivotal country, with additional sequences from Brazil, Costa Rica, French Guiana, Guatemala, Mexico, Panama and Peru. We examined the performance of two phylogeny-based approaches for objectively delineating species, Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP), as well as a clustering-based approach, Automatic Barcode Gap Discovery (ABGD), on the combined dataset, including our data and 302 published sequences. In general, GMYC and PTP tended to cluster or split likely species as assessed from morphology, depending on model settings, whereas ABGD was less sensitive and produced a more plausible classification. Numerous sequences formed well-supported clades, putative species, that were unrepresented in previously published datasets. The average diversity across all methods was 45 species, in contrast to the 11 species recognized in the current taxonomy. The resulting COI dataset, in combination with ongoing genomic and morphological research, should significantly clarify our understanding of Hermeuptychia species diversity.
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Affiliation(s)
- Denise Tan
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Anamaria Parus
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Michelle Dunbar
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Marianne Espeland
- Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer allee, Bonn, Germany
| | - Keith R Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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31
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Uhlir C, Schwentner M, Meland K, Kongsrud JA, Glenner H, Brandt A, Thiel R, Svavarsson J, Lörz AN, Brix S. Adding pieces to the puzzle: insights into diversity and distribution patterns of Cumacea (Crustacea: Peracarida) from the deep North Atlantic to the Arctic Ocean. PeerJ 2021; 9:e12379. [PMID: 34824910 PMCID: PMC8590803 DOI: 10.7717/peerj.12379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
The Nordic Seas have one of the highest water-mass diversities in the world, yet large knowledge gaps exist in biodiversity structure and biogeographical distribution patterns of the deep macrobenthic fauna. This study focuses on the marine bottom-dwelling peracarid crustacean taxon Cumacea from northern waters, using a combined approach of morphological and molecular techniques to present one of the first insights into genetic variability of this taxon. In total, 947 specimens were assigned to 77 morphologically differing species, representing all seven known families from the North Atlantic. A total of 131 specimens were studied genetically (16S rRNA) and divided into 53 putative species by species delimitation methods (GMYC and ABGD). In most cases, morphological and molecular-genetic delimitation was fully congruent, highlighting the overall success and high quality of both approaches. Differences were due to eight instances resulting in either ecologically driven morphological diversification of species or morphologically cryptic species, uncovering hidden diversity. An interspecific genetic distance of at least 8% was observed with a clear barcoding gap for molecular delimitation of cumacean species. Combining these findings with data from public databases and specimens collected during different international expeditions revealed a change in the composition of taxa from a Northern Atlantic-boreal to an Arctic community. The Greenland-Iceland-Scotland-Ridge (GIS-Ridge) acts as a geographical barrier and/or predominate water masses correspond well with cumacean taxa dominance. A closer investigation on species level revealed occurrences across multiple ecoregions or patchy distributions within defined ecoregions.
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Affiliation(s)
- Carolin Uhlir
- Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany.,German Center for Marine Biodiversity Research (DZMB), Senckenberg Research Institute, Hamburg, Germany
| | - Martin Schwentner
- Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany.,Natural History Museum Vienna, Vienna, Austria
| | - Kenneth Meland
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jon Anders Kongsrud
- Department of Natural History, University Museum of Bergen (ZMBN), Bergen, Norway
| | - Henrik Glenner
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Centre of Macroecology, Evolution and Climate (CMEC), Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ralf Thiel
- Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany
| | - Jörundur Svavarsson
- Faculty of Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Anne-Nina Lörz
- Institute for Marine Ecosystems and Fisheries Science, Center for Earth System Research and Sustainability (CEN), Universität Hamburg, Hamburg, Germany
| | - Saskia Brix
- German Center for Marine Biodiversity Research (DZMB), Senckenberg Research Institute, Hamburg, Germany
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32
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Tolley KA, Telford NS, Taft JM, Bates MF, Conradie W, Makhubo BG, Alexander GJ. Taxonomic inflation due to inadequate sampling: are girdled lizards (Cordylus minor species complex) from the Great Karoo one and the same? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Great Karoo and Namaqualand of South Africa are home to a species complex of morphologically conserved lizards that occur in allopatry (Karoo: Cordylus aridus, Cordylus cloetei, Cordylus minor; Namaqualand: Cordylus imkeae). However, there are negligible morphological differences and a lack of obvious physical or climatic barriers, particularly among the three Karoo species. We hypothesized that poor geographic coverage in previous studies and lack of an explicit species concept has caused taxonomic inflation. We therefore tested species boundaries by examining multiple criteria: multi-gene phylogenetics, niche distribution modelling and re-examination of diagnostic morphological features with a larger sample size. We found that C. aridus, C. cloetei and C. minor lack diagnosable differences for both genetics and morphology. Distribution modelling, ranging from present day to the last interglacial period, show connectivity has been maintained especially during cooler periods. Conversely, C. imkeae is morphologically diagnosable, genetically distinct and lacks connectivity with the other taxa. By evaluating multiple operational criteria, we conclude that the C. minor species complex comprises only two species, C. minor (with C. aridus and C. cloetei as junior synonyms) and C. imkeae, demonstrating that species defined from inadequate data and lack of an explicit species concept can lead to taxonomic inflation.
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Affiliation(s)
- Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicolas S Telford
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
| | - Jody M Taft
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael F Bates
- Division of Herpetology, Department of Animal and Plant Systematics, National Museum, Bloemfontein, South Africa
- Department of Zoology & Entomology, University of the Free State, Bloemfontein, South Africa
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), Gqeberha, South Africa
- Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Buyisile G Makhubo
- Division of Herpetology, Department of Animal and Plant Systematics, National Museum, Bloemfontein, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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33
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Singh OP, Sindhania A, Sharma G, Mishra S, Sharma SK, Singh PK, Das MK. Are members of the Anopheles fluviatilis complex conspecific? Acta Trop 2021; 224:106149. [PMID: 34599889 DOI: 10.1016/j.actatropica.2021.106149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 02/05/2023]
Abstract
Anopheles fluviatilis sensu lato, a primary malaria vector in India, has been identified to be comprised of four cryptic species, provisionally designated as species S, T, U and V. However, Kumar et al. (Mol Ecol Resour, 2013;13:354-61) considered all of the then known three members of this species complex (S, T and U) conspecific. The specific status of species S and T was refuted based on the lack of sufficient barcode gap in mitochondrial-CO1 and the perceived presence of heterozygotes in populations as detected through one of the two species-specific PCR assays employed for the cryptic species identification. The existence of species U was refuted claiming that earlier investigations have already refuted their existence. Here we discuss problems associated with the CO1-based barcode approach for delimitation of cryptic species, the perceived heterozygosity between species S and T based on a species-specific PCR assay, and interpretation of published reports. We demonstrated that fixed differences do exist in the ITS2-rDNA sequence of species S and T with no evidence of heterozygotes in sympatric populations and, that the observed heterozygosity by Kumar et al. in the ITS2-based species diagnostic PCR is due to the high mispriming tendency of the T-specific primer with species S. We infer that mitochondrial DNA-based 'barcoding gap', an arbitrary threshold recommended for species delimitation, alone, is inadequate to delimit the members of An. fluviatilis complex.
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Affiliation(s)
- Om P Singh
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India.
| | - Ankita Sindhania
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India
| | - Gunjan Sharma
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India
| | - Shobhna Mishra
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, 110077, India
| | - Surya K Sharma
- National Institute of Malaria Research, Field Unit, Sector-5, Rourkela 769 002, Orissa, India
| | - Piyoosh K Singh
- National Institute of Malaria Research, Field Unit, T. B. Sanitorium complex, Itki, Ranchi, 835301
| | - Manoj K Das
- National Institute of Malaria Research, Field Unit, T. B. Sanitorium complex, Itki, Ranchi, 835301
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Lawley JW, Gamero-Mora E, Maronna MM, Chiaverano LM, Stampar SN, Hopcroft RR, Collins AG, Morandini AC. The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa). PeerJ 2021; 9:e11954. [PMID: 34589293 PMCID: PMC8435205 DOI: 10.7717/peerj.11954] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.
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Affiliation(s)
- Jonathan W. Lawley
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- School of Environment and Science, Coastal and Marine Research Centre, Australian Rivers Institute, Griffith University, Gold Coast, Queensland, Australia
| | - Edgar Gamero-Mora
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Maximiliano M. Maronna
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Luciano M. Chiaverano
- Instituto Nacional de Investigación y Desarrollo Pesquero, Mar del Plata, Buenos Aires, Argentina
| | - Sérgio N. Stampar
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras, Universidade Estadual Paulista, Assis, São Paulo, Brazil
| | - Russell R. Hopcroft
- College of Fisheries and Ocean Sciences, University of Alaska—Fairbanks, Fairbanks, Alaska, United States
| | - Allen G. Collins
- National Systematics Laboratory of the National Oceanic and Atmospheric Administration Fisheries Service, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States
| | - André C. Morandini
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
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35
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Makhov IA, Gorodilova YYU, Lukhtanov VA. Sympatric occurrence of deeply diverged mitochondrial DNA lineages in Siberian geometrid moths (Lepidoptera: Geometridae): cryptic speciation, mitochondrial introgression, secondary admixture or effect of Wolbachia? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The divergent sympatric mitochondrial lineages within traditionally recognized species present a challenge regularly faced by taxonomists and evolutionary biologists. We encountered this problem when studying the Siberian geometrid moths, Alcis deversata and Thalera chlorosaria. Within each of these species we found two deeply diverged mitochondrial lineages that demonstrated a level of genetic differentiation exceeding the standard interspecific DNA barcode threshold. Using analyses of nuclear genes, morphology, ecological preferences and Wolbachia endosymbionts, we tested five hypotheses that might explain the mitochondrial pattern observed: cryptic speciation, ancestral polymorphism, interspecific mitochondrial introgression, secondary admixture of allopatrically evolved populations and an effect of intracellular Wolbachia endosymbionts. We demonstrate that in A. deversata and Th. chlorosaria the mitochondrial differences are not correlated with differences in nuclear genes, morphology, ecology and Wolbachia infection status, thus not supporting the hypothesis of cryptic species and an effect of Wolbachia. Mitochondrial introgression can lead to a situation in which one species has both its own mitochondrial lineage and the lineage obtained from another species. We found this situation in the species pair Alcis repandata and Alcis extinctaria. We conclude that the mitochondrial heterogeneity in A. deversata and Th. chlorosaria is most likely to be attributable to the secondary admixture of allopatrically evolved populations.
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Affiliation(s)
- Ilia A Makhov
- Department of Entomology, Saint Petersburg State University, Universitetskaya Embankment 7/9, 199034 Saint Petersburg, Russia
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, 199034 Saint Petersburg, Russia
| | - Yelizaveta Y U Gorodilova
- Biological Faculty, Saint Petersburg State University, Botanicheskaya Street 17, Stary Peterhof, Saint Petersburg 198504, Russia
| | - Vladimir A Lukhtanov
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, 199034 Saint Petersburg, Russia
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36
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Gao Y, Zhang Y, Dietrich CH, Duan Y. Phylogenetic analyses and species delimitation of Nephotettix Matsumura (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini) in China based on molecular data. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Carugati L, Melis R, Cariani A, Cau A, Crobe V, Ferrari A, Follesa MC, Geraci ML, Iglésias SP, Pesci P, Tinti F, Cannas R. Combined COI barcode‐based methods to avoid mislabelling of threatened species of deep‐sea skates. Anim Conserv 2021. [DOI: 10.1111/acv.12716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Carugati
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - R. Melis
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - A. Cariani
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - A. Cau
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - V. Crobe
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - A. Ferrari
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - M. C. Follesa
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - M. L. Geraci
- Department of Biological Geological and Environmental Sciences (BiGeA) – Marine biology and fisheries laboratory University of Bologna Fano (PU) Italy
- Institute for Biological Resources and Marine Biotechnologies (IRBIM) National Research Council (CNR) Mazara del Vallo (TP) Italy
| | - S. P. Iglésias
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d’Histoire naturelleCNRSSorbonne UniversitéEPHEUniversité des AntillesStation Marine de Concarneau Concarneau France
| | - P. Pesci
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | - F. Tinti
- Department of Biological, Geological and Environmental Sciences (BiGeA) University of Bologna Bologna Italy
| | - R. Cannas
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
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Crobe V, Ferrari A, Hanner R, Leslie RW, Steinke D, Tinti F, Cariani A. Molecular Taxonomy and Diversification of Atlantic Skates (Chondrichthyes, Rajiformes): Adding More Pieces to the Puzzle of Their Evolutionary History. Life (Basel) 2021; 11:life11070596. [PMID: 34206388 PMCID: PMC8303890 DOI: 10.3390/life11070596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 11/16/2022] Open
Abstract
Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, hampers accurate species identification. Here, 432 individual skate samples collected from four major ocean areas of the Atlantic were barcoded and taxonomically analysed. A BOLD project ELASMO ATL was implemented with the aim of establishing a new fully available and well curated barcode library containing both biological and molecular information. The evolutionary histories of the 38 skate taxa were estimated with two concatenated mitochondrial markers (COI and NADH2) through Maximum Likelihood and Bayesian inference. New evolutionary lineages within the genus Raja were discovered off Angola, where paleogeographic history coupled with oceanographic discontinuities could have contributed to the establishment of isolated refugia, playing a fundamental role among skates' speciation events. These data successfully resolved many taxonomic ambiguities, identified cryptic diversity within valid species and demonstrated a highly cohesive monophyletic clustering among the order, laying the background for further inference of evolutionary patterns suitable for addressing management and conservation issues.
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Affiliation(s)
- Valentina Crobe
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
- Correspondence: (V.C.); (F.T.)
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
| | - Robert Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Robin W. Leslie
- Department of Agriculture, Forestry and Fisheries (DAFF), Branch Fisheries Management, Cape Town 8018, South Africa;
- Department of Ichthyology and Fisheries Science (DIFS), Rhodes University, Grahamstown 6139, South Africa
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
- Correspondence: (V.C.); (F.T.)
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 240126 Bologna, Italy; (A.F.); (A.C.)
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39
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He JJ, Jin DT, Wang YS, Che YL, Wang ZQ. Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae). Zookeys 2021; 1036:121-151. [PMID: 34040483 PMCID: PMC8128847 DOI: 10.3897/zookeys.1036.63232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/01/2021] [Indexed: 11/19/2022] Open
Abstract
Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M.angusta and M.mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margatteadeltodonta J-J He & Z-Q Wang, sp. nov., Margatteacuspidata J-J He & Z-Q Wang, sp. nov., Margatteacaudata J-J He & Z-Q Wang, sp. nov., Margatteaparatransversa J-J He & Z-Q Wang, sp. nov., Margatteadisparilis J-J He & Z-Q Wang, sp. nov., Margatteatransversa J-J He & Z-Q Wang, sp. nov., and Margatteabicruris J-J He & Z-Q Wang, sp. nov.
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Affiliation(s)
- Jia-Jun He
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Du-Ting Jin
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Yi-Shu Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Yan-Li Che
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Zong-Qing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
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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: 10] [Impact Index Per Article: 3.3] [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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Abad-Franch F, Monteiro FA, Pavan MG, Patterson JS, Bargues MD, Zuriaga MÁ, Aguilar M, Beard CB, Mas-Coma S, Miles MA. Under pressure: phenotypic divergence and convergence associated with microhabitat adaptations in Triatominae. Parasit Vectors 2021; 14:195. [PMID: 33832518 PMCID: PMC8034103 DOI: 10.1186/s13071-021-04647-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background Triatomine bugs, the vectors of Chagas disease, associate with vertebrate hosts in highly diverse ecotopes. It has been proposed that occupation of new microhabitats may trigger selection for distinct phenotypic variants in these blood-sucking bugs. Although understanding phenotypic variation is key to the study of adaptive evolution and central to phenotype-based taxonomy, the drivers of phenotypic change and diversity in triatomines remain poorly understood. Methods/results We combined a detailed phenotypic appraisal (including morphology and morphometrics) with mitochondrial cytb and nuclear ITS2 DNA sequence analyses to study Rhodnius ecuadoriensis populations from across the species’ range. We found three major, naked-eye phenotypic variants. Southern-Andean bugs primarily from vertebrate-nest microhabitats (Ecuador/Peru) are typical, light-colored, small bugs with short heads/wings. Northern-Andean bugs from wet-forest palms (Ecuador) are dark, large bugs with long heads/wings. Finally, northern-lowland bugs primarily from dry-forest palms (Ecuador) are light-colored and medium-sized. Wing and (size-free) head shapes are similar across Ecuadorian populations, regardless of habitat or phenotype, but distinct in Peruvian bugs. Bayesian phylogenetic and multispecies-coalescent DNA sequence analyses strongly suggest that Ecuadorian and Peruvian populations are two independently evolving lineages, with little within-lineage phylogeographic structuring or differentiation. Conclusions We report sharp naked-eye phenotypic divergence of genetically similar Ecuadorian R. ecuadoriensis (nest-dwelling southern-Andean vs palm-dwelling northern bugs; and palm-dwelling Andean vs lowland), and sharp naked-eye phenotypic similarity of typical, yet genetically distinct, southern-Andean bugs primarily from vertebrate-nest (but not palm) microhabitats. This remarkable phenotypic diversity within a single nominal species likely stems from microhabitat adaptations possibly involving predator-driven selection (yielding substrate-matching camouflage coloration) and a shift from palm-crown to vertebrate-nest microhabitats (yielding smaller bodies and shorter and stouter heads). These findings shed new light on the origins of phenotypic diversity in triatomines, warn against excess reliance on phenotype-based triatomine-bug taxonomy, and confirm the Triatominae as an informative model system for the study of phenotypic change under ecological pressure. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04647-z.
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Affiliation(s)
- Fernando Abad-Franch
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil. .,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Fernando A Monteiro
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil. .,Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, USA.
| | - Márcio G Pavan
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
| | - James S Patterson
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - M Dolores Bargues
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - M Ángeles Zuriaga
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - Marcelo Aguilar
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador.,Instituto Juan César García, Quito, Ecuador
| | - Charles B Beard
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, USA
| | - Santiago Mas-Coma
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - Michael A Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Rodrigues BL, Baton LA, Shimabukuro PHF. Single-locus DNA barcoding and species delimitation of the sandfly subgenus Evandromyia (Aldamyia). MEDICAL AND VETERINARY ENTOMOLOGY 2020; 34:420-431. [PMID: 32590879 DOI: 10.1111/mve.12458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Sandfly specimens from the subgenus Evandromyia (Aldamyia) Galati, 2003 (Diptera: Psychodidae: Phlebotominae) were collected between 2012 and 2019 from nine localities in seven Brazilian states, morphologically-identified, and then DNA barcoded by sequencing the mitochondrial cytochrome c oxidase subunit I (coi) gene. Forty-four new barcode sequences generated from 10 morphospecies were combined with 49 previously published sequences from the same subgenus and analysed using sequence-similarity methods (best-match criteria) to assess their ability at specimen identification, while four different species delimitation methods (ABGD, GMYC, PTP and TCS) were used to infer molecular operational taxonomic units (MOTUs). Overall, seven of the 11 morphospecies analysed were congruent with both the well-supported clades identified by phylogenetic analysis and the MOTUs inferred by species delimitation, while the remaining four morphospecies - E. carmelinoi, E. evandroi, E. lenti and E. piperiformis - were merged into a single well-supported clade/MOTU. Although E. carmelinoi, E. evandroi and E. lenti were indistinguishable using coi DNA barcodes, E. piperiformis did form a distinct phylogenetic cluster and could be correctly identified using best-match criteria. Despite their apparent morphological differences, we propose on the basis of the molecular similarity of their DNA barcodes that these latter four morphospecies should be considered members of a recently-diverged species complex.
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Affiliation(s)
- B L Rodrigues
- Grupo de Estudos em Leishmanioses, Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - L A Baton
- 50 Rowntree Way Saffron Walden, Essex, CB11 4DL, U.K
| | - P H F Shimabukuro
- Grupo de Estudos em Leishmanioses, Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
- Coleção de Flebotomíneos (FIOCRUZ/COLFLEB), Instituto René Rachou-Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
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43
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Sindhania A, Das MK, Sharma G, Surendran SN, Kaushal BR, Lohani HP, Singh OP. Molecular forms of Anopheles subpictus and Anopheles sundaicus in the Indian subcontinent. Malar J 2020; 19:417. [PMID: 33213479 PMCID: PMC7678295 DOI: 10.1186/s12936-020-03492-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/11/2020] [Indexed: 11/28/2022] Open
Abstract
Background Anopheles subpictus and Anopheles sundaicus are closely related species, each comprising several sibling species. Ambiguities exist in the classification of these two nominal species and the specific status of members of these species complexes. Identifying fixed molecular forms and mapping their spatial distribution will help in resolving the taxonomic ambiguities and understanding their relative epidemiological significance. Methods DNA sequencing of Internal Transcribed Spacer-2 (ITS2), 28S-rDNA (D1-to-D3 domains) and cytochrome oxidase-II (COII) of morphologically identified specimens of two nominal species, An. subpictus sensu lato (s.l.) and An. sundaicus s.l., collected from the Indian subcontinent, was performed and subjected to genetic distance and molecular phylogenetic analyses. Results Molecular characterization of mosquitoes for rDNA revealed the presence of two molecular forms of An. sundaicus s.l. and three molecular forms of An. subpictus s.l. (provisionally designated as Form A, B and C) in the Indian subcontinent. Phylogenetic analyses revealed two distinct clades: (i) subpictus clade, with a single molecular form of An. subpictus (Form A) prevalent in mainland India and Sri Lanka, and (ii) sundaicus clade, comprising of members of Sundaicus Complex, two molecular forms of An. subpictus s.l. (Form B and C), prevalent in coastal areas or islands in Indian subcontinent, and molecular forms of An. subpictus s.l. reported from Thailand and Indonesia. Based on the number of float-ridges on eggs, all An. subpictus molecular Form B were classified as Species B whereas majority (80%) of the molecular Form A were classified as sibling species C. Fixed intragenomic sequence variation in ITS2 with the presence of two haplotypes was found in molecular Form A throughout its distribution. Conclusion A total of three molecular forms of An. subpictus s.l. and two molecular forms of An. sundaicus s.l. were recorded in the Indian subcontinent. Phylogenetically, two forms of An. subpictus s.l. (Form B and C) prevalent in coastal areas or islands in the Indian subcontinent and molecular forms reported from Southeast Asia are members of Sundaicus Complex. Molecular Form A of An. subpictus is distantly related to all other forms and deserve a distinct specific status.
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Affiliation(s)
- Ankita Sindhania
- National Institute of Malaria Research, Sector 8 Dwarka, New Delhi, 110077, India
| | - Manoj K Das
- National Institute of Malaria Research, Field Unit, Itki, Ranchi, 835301, India
| | - Gunjan Sharma
- National Institute of Malaria Research, Sector 8 Dwarka, New Delhi, 110077, India
| | | | - B R Kaushal
- Department of Zoology, Kumaun University, Nainital, India
| | | | - Om P Singh
- National Institute of Malaria Research, Sector 8 Dwarka, New Delhi, 110077, India.
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44
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Kundu S, Kumar H, Tyagi K, Chandra K, Kumar V. DNA barcoding of selected short-horned grasshoppers (Orthoptera: Acrididae) from Indian Himalayan region. Mitochondrial DNA B Resour 2020; 5:3618-3623. [PMID: 33367033 PMCID: PMC7594861 DOI: 10.1080/23802359.2020.1830725] [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: 06/04/2020] [Accepted: 09/25/2020] [Indexed: 12/03/2022] Open
Abstract
In the context of Indian zoogeography, the DNA barcode data of short-horned grasshoppers (family Acrididae) are limited in global databases. Hence, the present study was aimed to collect selected Acridid species from the Indian Himalayan regions and generate DNA barcode data to enrich the global database. The estimated K2P genetic distances, Bayesian analysis (BA) topology and multiple species delimitation methods (ABGD, bPTP, and GMYC) clearly discriminate all the studied species. Based on high genetic distance (7.5%), multiple clades, and more than one molecular operational taxonomic unit, the present study elucidates the allopatric speciation and presence of possible cryptic diversity of Oxya japonica within India, China, and Russia. The present study suggests the collection of multiple specimens from different geographical locations and the generation of more DNA barcode data would facilitate the actual diversity of this insect group.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hirdesh Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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Alström P, van Linschooten J, Donald PF, Sundev G, Mohammadi Z, Ghorbani F, Shafaeipour A, van den Berg A, Robb M, Aliabadian M, Wei C, Lei F, Oxelman B, Olsson U. Multiple species delimitation approaches applied to the avian lark genus Alaudala. Mol Phylogenet Evol 2020; 154:106994. [PMID: 33250446 DOI: 10.1016/j.ympev.2020.106994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.
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Affiliation(s)
- Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Jip van Linschooten
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Paul F Donald
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society, P.O. Box 537, Ulaanbaatar 210646a, Ulaanbaatar, Mongolia
| | - Zeinolabedin Mohammadi
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Fatemeh Ghorbani
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Arya Shafaeipour
- Department of Biology, Faculty of Science, Yasouj University, Yasouj, Iran
| | - Arnoud van den Berg
- The Sound Approach, c/o Duinlustparkweg 98, 2082 EG Santpoort-Zuid, the Netherlands
| | - Magnus Robb
- The Sound Approach, c/o Rua Dr Pedro Almeida Lima 6, 2710-122 Sintra, Portugal
| | - Mansour Aliabadian
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Chentao Wei
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bengt Oxelman
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
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Candia-Ramírez DT, Francke OF. Another stripe on the tiger makes no difference? Unexpected diversity in the widespread tiger tarantula Davus pentaloris (Araneae: Theraphosidae: Theraphosinae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Integrative taxonomy is relevant for the discovery and delimitation of cryptic species by incorporating different sources of evidence to construct rigorous species hypotheses. The genus Davus was recently revised and it was found that Davus pentaloris presents high morphological variation across its widespread distribution. However, tarantulas usually present low dispersal capabilities that occasionally result in local endemism. In order to evaluate species boundaries within this taxon, we examine the morphological variation and, additionally, employ four strategies based on mtDNA data (COI): two distance-based [automatic barcode gap discovery (ABGD) and Neighbor-Joining (NJ)] and two tree-based methods [general mixed Yule coalescent (GMYC) and Bayesian Poisson tree process (bPTP)]. Available morphological evidence recovers 13 putative morphospecies, but the different methods based on molecular data recover a variable number of candidate species (16–18). Based on the congruence across all analyses and the available morphological data, we recognize 13 clearly diagnosable species, 12 of them new to science. We conclude that the underestimation of the diversity in D. pentaloris was mainly caused by deficient practices in taxonomy, rather than by the presence of cryptic diversity. Although COI is a functional barcoding marker and it gives reliable results in our study, we recommend combining multiple sources of evidence and strategies to construct better species delimitation hypotheses.
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Affiliation(s)
- Daniela T Candia-Ramírez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510 Coyoacán, Mexico City, Mexico
- Colección Nacional de Arácnidos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
| | - Oscar F Francke
- Colección Nacional de Arácnidos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
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47
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Lukhtanov VA, Dantchenko AV, Khakimov FR, Sharafutdinov D, Pazhenkova EA. Karyotype evolution and flexible (conventional versus inverted) meiosis in insects with holocentric chromosomes: a case study based on Polyommatus butterflies. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Polyommatus butterflies have holocentric chromosomes, which are characterized by kinetic activity distributed along the entire chromosome length, and the highest range of haploid chromosome numbers (n) known within a single eukaryotic genus (from n = 10 to n = 226). Previous analyses have shown that these numbers most likely evolved gradually from an ancestral karyotype, in accordance with the Brownian motion model of chromosome change accumulation. Here we studied chromosome sets within a monophyletic group of previously non-karyotyped Polyommatus species. We demonstrate that these species have a limited interspecific chromosome number variation from n = 16 to n = 25, which is consistent with the Brownian motion model prediction. We also found intra- and interpopulation variation in the chromosome numbers. These findings support the model of karyotype evolution through the gradual accumulation of neutral or weakly underdominant rearrangements that can persist in the heterozygous state within a population. For Polyommatus poseidonides we report the phenomenon of flexible meiosis in which the chromosome multivalents are able to undergo either conventional or inverted meiosis within the same individual. We hypothesise that the ability to invert the order of the meiotic events may be adaptive and can facilitate proper chromosome segregation in chromosomal heterozygotes, thus promoting rapid karyotype evolution.
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Affiliation(s)
- Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexander V Dantchenko
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Fayzali R Khakimov
- Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of the Republic of Tajikistan, Dushanbe, Tajikistan
| | - Damir Sharafutdinov
- Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of the Republic of Tajikistan, Dushanbe, Tajikistan
| | - Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia
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Bohmann K, Mirarab S, Bafna V, Gilbert MTP. Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification. Mol Ecol 2020; 29:2521-2534. [PMID: 32542933 PMCID: PMC7496323 DOI: 10.1111/mec.15507] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023]
Abstract
Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based "genome skimming" alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its "DNA-mark") for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such "DNA-marks," it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.
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Affiliation(s)
- Kristine Bohmann
- Section for Evolutionary GenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Siavash Mirarab
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan DiegoCAUSA
| | - Vineet Bafna
- Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoCAUSA
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary HologenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- NTNU University MuseumTrondheimNorway
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49
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Huang W, Xie X, Huo L, Liang X, Wang X, Chen X. An integrative DNA barcoding framework of ladybird beetles (Coleoptera: Coccinellidae). Sci Rep 2020; 10:10063. [PMID: 32572078 PMCID: PMC7308296 DOI: 10.1038/s41598-020-66874-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
Even though ladybirds are well known as economically important biological control agents, an integrative framework of DNA barcoding research was not available for the family so far. We designed and present a set of efficient mini-barcoding primers to recover full DNA barcoding sequences for Coccinellidae, even for specimens collected 40 years ago. Based on these mini-barcoding primers, we obtained 104 full DNA barcode sequences for 104 species of Coccinellidae, in which 101 barcodes were newly reported for the first time. We also downloaded 870 COI barcode sequences (658 bp) from GenBank and BOLD database, belonging to 108 species within 46 genera, to assess the optimum genetic distance threshold and compare four methods of species delimitation (GMYC, bPTP, BIN and ABGD) to determine the most accurate approach for the family. The results suggested the existence of a 'barcode gap' and that 3% is likely an appropriate genetic distance threshold to delimit species of Coccinellidae using DNA barcodes. Species delimitation analyses confirm ABGD as an accurate and efficient approach, more suitable than the other three methods. Our research provides an integrative framework for DNA barcoding and descriptions of new taxa in Coccinellidae. Our results enrich DNA barcoding public reference libraries, including data for Chinese coccinellids. This will facilitate taxonomic identification and biodiversity monitoring of ladybirds using metabarcoding.
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Affiliation(s)
- Weidong Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm; Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China
| | - Xiufeng Xie
- Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, 510507, China
| | - Lizhi Huo
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, 510405, China
| | - Xinyue Liang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm; Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China
| | - Xingmin Wang
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China
| | - Xiaosheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm; Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510640, China.
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China.
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50
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Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N. A complete time-calibrated multi-gene phylogeny of the European butterflies. Zookeys 2020; 938:97-124. [PMID: 32550787 PMCID: PMC7289901 DOI: 10.3897/zookeys.938.50878] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/03/2020] [Indexed: 11/12/2022] Open
Abstract
With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.
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Affiliation(s)
- Martin Wiemers
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Straße 90, 15374, Müncheberg, Germany UFZ - Helmholtz Centre for Environmental Research Halle Germany.,UFZ - Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120, Halle, Germany Senckenberg Deutsches Entomologisches Institut Müncheberg Germany
| | - Nicolas Chazot
- Department of Biology, Lund University, 22362, Lund, Sweden Lund University Lund Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden University of Gothenburg Gothenburg Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Christopher W Wheat
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden Stockholm University Stockholm Sweden
| | - Oliver Schweiger
- UFZ - Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120, Halle, Germany Senckenberg Deutsches Entomologisches Institut Müncheberg Germany
| | - Niklas Wahlberg
- Department of Biology, Lund University, 22362, Lund, Sweden Lund University Lund Sweden
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