1
|
Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
Collapse
Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
| |
Collapse
|
2
|
Klesser R, Blick T, Fritze MA, Marten A, Hemauer M, Kastner L, Höfer H, Jäger G, Husemann M. Ice cage: new records and cryptic, isolated lineages in wingless snow flies (Diptera, Limoniidae: Chionea spp.) in German lower mountain ranges. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:15. [PMID: 38478046 PMCID: PMC10937758 DOI: 10.1007/s00114-024-01900-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
In Earth's history warm and cold periods have alternated. Especially, during the Pleistocene, the alternation between these different climatic conditions has led to frequent range expansions and retractions of many species: while thermophilic species dispersed during warm periods, cold adapted species retracted to cold refugia and vice versa. After the last Pleistocene cycle many cold adapted taxa found refuges in relict habitats in mountain ranges. One example for such a cold adapted relict is the flightless snow fly Chionea araneoides (Dalman, 1816). It can be found in lower mountain ranges of Central Europe exclusively in stone runs and stony accumulations which provide cold microclimates. Imagines develop only in winter. They have strongly restricted ranges and hence experienced strong isolation predicting that local populations may show local adaptation and hence also genetic differentiation. We investigated this for several middle mountain ranges of Germany using the COI barcoding gene. Our analyses revealed two distinct lineages, one in the Bavarian Forest and a second one in all other more northern locations up to Scandinavia. These lineages likely go back to post-Pleistocene isolation and should be studied in more detail in the future, also to confirm the taxonomic status of both lineages. Further, we confirmed former records of the species for Germany and report new records for the federal states of Saxony, Lower Saxony, Saxony-Anhalt and Thuringia. Finally, we provide the first evidence of two types of males for the species, a small and a larger male type.
Collapse
Affiliation(s)
- Robert Klesser
- Leibniz Institut zur Analyse des Biodiversitätswandels, ztm, Zoologisches Museum Hamburg Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
- Naturkundemuseum Leipzig, Lortzingstraße 3, D-04105, Leipzig, Germany.
| | - Theo Blick
- Private researcher, Heidloh 8, D-95503, Hummeltal, Germany
| | - Michael-Andreas Fritze
- Arbeitsgruppe für Tierökologie und Planung GmbH, Johann-Strauß-Str. 22, 70794, Filderstadt, Germany
| | - Andreas Marten
- Harz National Park, Lindenallee 35, D-38855, Wernigerode, Germany
| | - Michael Hemauer
- Private researcher, Wallbergstraße 20, D-81539, Munich, Germany
| | - Laura Kastner
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
| | - Hubert Höfer
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
| | - Gero Jäger
- Private researcher, Fuldatalstraße 55, D-34125, Kassel, Germany
| | - Martin Husemann
- Leibniz Institut zur Analyse des Biodiversitätswandels, ztm, Zoologisches Museum Hamburg Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
| |
Collapse
|
3
|
Jiang Y, Yang J, Folk RA, Zhao J, Liu J, He Z, Peng H, Yang S, Xiang C, Yu X. Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes. BMC PLANT BIOLOGY 2024; 24:181. [PMID: 38468197 PMCID: PMC10926627 DOI: 10.1186/s12870-024-04882-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group. RESULTS Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters. CONCLUSION This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.
Collapse
Affiliation(s)
- Yinzi Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, 39762, MS, USA
| | - Jianli Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, Yunnan, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhengshan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Shixiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Chunlei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xiangqin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| |
Collapse
|
4
|
Rodrigues BL, da Silva Costa G, Godoy RE, Pereira Júnior AM, Cella W, Ferreira GEM, de Medeiros JF, Shimabukuro PHF. Molecular and morphometric study of Brazilian populations of Psychodopygus davisi. MEDICAL AND VETERINARY ENTOMOLOGY 2024; 38:83-98. [PMID: 37867259 DOI: 10.1111/mve.12701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023]
Abstract
In this study, we analysed the molecular and morphometric differences of several populations of the putative sand fly vector Psychodopygus davisi (Root, 1934) (Diptera, Psychodidae, Phlebotominae) in Brazil. We amplified the 658 base pair fragments of the DNA barcoding region-cytochrome c oxidase subunit 1 (COI) gene-for 57 specimens of P. davisi and three specimens of Psychodopygus claustrei (Abonnenc, Léger & Fauran, 1979). We merged our data with public sequences of the same species available from GenBank. Then, the combined dataset-87 sequences and 20 localities-was analysed using population structure analysis and different species delimitation approaches. Geometric morphometry of wings was performed for 155 specimens of P. davisi populations from the North, Midwest and Southeast Brazilian regions, analysing the differences in centroid sizes and canonical variates. Molecular analysis indicated high intraspecific genetic distance values for P. davisi (maximum p distance = 5.52%). All algorithms identified P. davisi and P. claustrei as distinct molecular taxonomic units, despite the low interspecific distance (p distance to the nearest neighbour = 4.79%). P. davisi sequences were split into four genetic clusters by population structure analysis and at least five genetic lineages using intermediate scenarios of the species delimitation algorithms. The species validation analysis of BPP strongly supported the five-species model in our dataset. We found high genetic diversity in this taxon, which is in agreement with its wide geographic distribution in Brazil. Furthermore, the wing analysis showed that specimens from the Southeast Region of Brazil are different from those in the North and the Midwest. The evolutionary patterns of P. davisi populations in Brazil suggest the presence of candidate species, which need to be validated in future studies using a more comprehensive approach with both genomic data and morphological characters.
Collapse
Affiliation(s)
- Bruno Leite Rodrigues
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP), São Paulo, Brazil
| | - Glaucilene da Silva Costa
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório Central de Saúde Pública do Estado de Rondônia, LACEN-RO, Porto Velho, Brazil
| | | | | | - Wilsandrei Cella
- Programa de Pós Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense, Paraná, Brazil
- Universidade do Estado do Amazonas (UEA), Tefé, Brazil
| | - Gabriel Eduardo Melim Ferreira
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Epidemiologia Genética, Fiocruz Rondônia, Porto Velho, Brazil
| | - Jansen Fernandes de Medeiros
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Entomologia, Fiocruz Rondônia, Porto Velho, Brazil
| | - Paloma Helena Fernandes Shimabukuro
- Grupo de Estudos em Leishmanioses, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
- Coleção de Flebotomíneos (Fiocruz/COLFLEB), Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
| |
Collapse
|
5
|
Saran C, Genç HY. Genetic diversity of diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae) populations in Türkiye. Mol Biol Rep 2024; 51:146. [PMID: 38236331 DOI: 10.1007/s11033-023-08928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/10/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae), is an important worldwide pest of plants belonging to the Brassicaceae family. In this study, we investigated genetic diversity of DBM populations in Brassicaceae production areas in Türkiye using the partial mtDNA CO1 gene region. METHODS We determined 43 samples from 11 different populations for haplotype variations using the partial mitochondrial DNA sequences a 684 bp fragment of the CO1 gene. RESULTS The results indicated that, the average haplotype diversity (Hd) was determined as 0.962 and nucleotide diversity (π) was determined as 0.557%. In neutrality tests, negative values were obtained in Tajima's D and Fu' Fs tests (Fu' Fs=-0.40, Tajima's D=-0.01). Tajima's D test was not found significant (p > 0.05). Fst value among DBM population estimates ranged from 0 to 0.631. Barcode gap distance was determined as 1.6%, but the intraspecies of genetic distance were found to be 0.15%. CONCLUSION In conclusion, the presented study provided detailed and fundamental information about the genetic diversity of DBM populations in Türkiye. Further studies are needed to develop alternative pest management strategies for DBM populations integrating genetic approaches.
Collapse
Affiliation(s)
- Ceren Saran
- Faculty of Agriculture, Department of Agricultural Biotechnology, Çanakkale Onsekiz Mart University, Çanakkale, 17100, Turkey
| | - Hanife Yandayan Genç
- Faculty of Agriculture, Department of Agricultural Biotechnology, Çanakkale Onsekiz Mart University, Çanakkale, 17100, Turkey.
| |
Collapse
|
6
|
Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [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: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
Collapse
Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| |
Collapse
|
7
|
Kaiser S, Stransky B, Jennings RM, Kihara TC, Brix S. Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench. Zootaxa 2023; 5293:401-434. [PMID: 37518475 DOI: 10.11646/zootaxa.5293.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Indexed: 08/01/2023]
Abstract
Hadal trenches are perceived as a unique deep-sea ecosystem with fundamentally different communities compared to the nearby abyss. So far, however, scarce information exists about how populations are genetically linked within a trench and about mechanisms for species divergence. The present study presents the morphological and molecular-genetic characterization and description of a new nannoniscid species within the genus Austroniscus Vanhöffen, 1914 obtained from abyssal and hadal depths of the Puerto Rico Trench, NW Atlantic. Samples were collected as part of the Vema-TRANSIT expedition onboard RV Sonne in January 2015. Because of the large depth differences between sampling locations (4,552-8,338 m), we expected to find different species within the genus inhabiting abyssal and hadal sites. Initial morphological examination using traditional light microscopy and Confocal Laser Scanning Microscopy was paired with subsequent molecular analysis based on mtDNA (COI and 16S). Contrary to our assumptions, combined morphological and molecular species delimitation analyses (sGMYC, mPTP, ABGD) revealed the presence of only one species spanning the abyssal and hadal seafloor of the Puerto Rico Trench. In addition, comparison with type material could show that this species belongs to a new species, Austroniscus brandtae n. sp., which is described herein. Incongruence between some species delimitation methods suggesting the presence of multiple species is interpreted as strong genetic population structuring within the trench, which is also supported by the analysis of the haplotype networks. The geographic and bathymetric distribution of Austroniscus species is discussed. The species described herein represents the first in the genus Austroniscus from the Atlantic Ocean and the deepest record of the genus to date, and hence significantly expanding previously known limits of its geographic and bathymetric range.
Collapse
Affiliation(s)
- Stefanie Kaiser
- University of Łódź; Faculty of Biology and Environmental Protection; Department of Invertebrate Zoology and Hydrobiology; Banacha St. 12/16; Łódź; 90-237; Poland; Senckenberg Research Institute; Department of Marine Zoology; Section Crustacea; Senckenberganlage 25; 60325 Frankfurt; Germany.
| | - Bente Stransky
- Museum of Nature; Leibniz Institute for the Analysis of Biodiversity Change (LIB); Centre for Taxonomy and Morphology; Martin- Luther-King-Platz 3; 20146 Hamburg; Germany.
| | - Robert M Jennings
- Temple University; Biology Department; 1900 North 12th Street; Philadelphia; PA 19122; USA.
| | - Terue Cristina Kihara
- Integrated Environmental Solutions UG-INES; c/o DZMB; Südstrand 44; 26382 Wilhelmshaven; Germany.
| | - Saskia Brix
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Martin-Luther-King-Platz 3; 20146 Hamburg; Germany.
| |
Collapse
|
8
|
Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [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: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
Collapse
Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| |
Collapse
|
9
|
Esquivel DA, Pereira MJR, Stuhler JD, Rossoni DM, Velazco PM, Bianchi FM. Multiples lines of evidence unveil cryptic diversity in the Lophostoma brasiliense (Chiroptera: Phyllostomidae) complex. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2110172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Diego A. Esquivel
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, 91501-970, Brazil
- Fundación Kurupira, Bogotá, D.C, Colombia
| | - Maria Joáo Ramos Pereira
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, 91501-970, Brazil
- Centre for Environmental and Marine Studies, Universidade de Aveiro, Aveiro, 3810-193, Portugal
| | - John D. Stuhler
- Department of Natural Resources Management, Texas Tech University, Lubbock, 79409, USA
| | - Daniela M. Rossoni
- Department of Biological Science, Florida State University, Tallahassee, 32306-1058, USA
- Field Museum of Natural History, Negaunee Integrative Research Center, Chicago, 60605, USA
| | - Paúl M. Velazco
- American Museum of Natural History, Department of Mammalogy, New York, 10024-5193, USA
- Department of Biology, Arcadia University, Glenside, 19038, USA
| | - Filipe Michels Bianchi
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, 91501-970, Brazil
| |
Collapse
|
10
|
Zhou LY, Zhan ZH, Zhu XL, Wan X. Multilocus phylogeny and species delimitation suggest synonymies of two Lucanus Scopoli, 1763 (Coleoptera, Lucanidae) species names. Zookeys 2022; 1135:139-155. [PMID: 36761796 PMCID: PMC9836572 DOI: 10.3897/zookeys.1135.89257] [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: 06/20/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
Phylogenetic relationsships of four nominal Lucanus Scopoli, 1763 species, L.swinhoei Parry, 1874, L.continentalis Zilioli, 1998, L.liuyei Huang & Chen, 2010, and L.wuyishanensis Schenk, 1999, are assessed based on mitochondrial (16S rDNA, COI) and nuclear (28S rDNA, Wingless) genes. The genetic distance is 0.0072 between L.swinhoei and L.continentalis, and 0.0094 between L.wuyishanensis and L.liuyei. Three species-delimitation approaches (ABGD, PTP, and GMYC) consistently showed L.swinhoei + L.continentalis and L.wuyishanensis + L.liuyei as two MOTUs. A new synonymy, L.liuyei = L.wuyishanensis, is proposed. Synonymy of L.swinhoei over L.continentalis is confirmed.
Collapse
Affiliation(s)
- Li Yang Zhou
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
| | - Zhi Hong Zhan
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, 111 Jiulong Rd., Hefei, 230601, China
| | - Xue Li Zhu
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
| | - Xia Wan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
| |
Collapse
|
11
|
Guo B, Kong L. Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda). Genes (Basel) 2022; 13:genes13122273. [PMID: 36553540 PMCID: PMC9778293 DOI: 10.3390/genes13122273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.
Collapse
Affiliation(s)
- Bingyu Guo
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
- Correspondence:
| |
Collapse
|
12
|
Daniels SR, Busschau T, Gullacksen G, Marais H, Gouws G, Barnes A. Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
AbstractWe examined the systematics of a ubiquitously distributed southern African freshwater crab, Potamonautes sidneyi s.l. species complex. Specimens were subjected to DNA sequence analyses of two mitochondrial loci (16S rRNA + COI). We applied three species delimitations methods (ASAP, bGMYC and bPTP) to test their utility in delineating species boundaries in Potamonautes and three additional Afrotropical genera (Liberonautes, Nesonautes and Seychellum). The combined mtDNA dataset retrieved five clades. Clade 1 comprised of P. barbarai, clade 2 comprised of specimens from the interior of the Great Karoo Basin, sister to P. sidneyi s.s. in clade 3. Clade 4 was confined to Eswatini and the Mpumalanga Province of South Africa, and sister to clade 5 that comprised P. danielsi. The three species delimitation methods either over- or underestimated the number of species. Phylogenetically, specimens from the Great Karoo Basin (clade 2) were equidistant to P. sidneyi s.s. and P. perlatus, while the Eswatini and Mpumalanga specimens (clade 4) were sister to P. danielsi. Clades 2 and 4 are herein described as P. karooensis sp. nov. and P. valles sp. nov., respectively.
Collapse
Affiliation(s)
- Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | - Theo Busschau
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | | | - Hannes Marais
- Mpumalanga Tourism and Parks Agency, Aquatic Unit , Lydenburg, 1120 , South Africa
| | - Gavin Gouws
- National Research Foundation - South African Institute for Aquatic Biodiversity , Private Bag 1015, Makhanda, 6140 , South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| |
Collapse
|
13
|
OTU Delimitation with Earthworm DNA Barcodes: A Comparison of Methods. DIVERSITY 2022. [DOI: 10.3390/d14100866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although DNA barcodes-based operational taxonomic units (OTUs) are increasingly used in earthworm research, the relative efficiency of the different methods available to delimit them has not yet been tested on a comprehensive dataset. For this study, we used three datasets containing 651, 2304 and 4773 COI barcodes of earthworms from French Guiana, respectively, to compare five of these methods: two phylogenetic methods—namely Poisson Tree Processes (PTP) and General Mixed Yule Coalescence (GMYC)—and three distance matrix methods—namely Refined Single Linkage (RESL, used for assigning Barcode Index Numbers in the Barcode of Life Data systems), Automatic Barcode Gap Discovery (ABGD), and Assemble Species by Automatic Partitioning (ASAP). We found that phylogenetic approaches are less suitable for delineating OTUs from DNA barcodes in earthworms, especially for large sets of sequences. The computation times are unreasonable, they often fail to converge, and they also show a strong tendency to oversplit species. Among distance-based methods, RESL also has a clear tendency to oversplitting, while ABGD and ASAP are less prone to mismatches and have short computation times. ASAP requires less a priori knowledge for model parameterisation than AGBD, provides efficient graphical outputs, and has a much lower tendency to generate mismatches.
Collapse
|
14
|
Sonet G, Smitz N, Vangestel C, Samyn Y. DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy. PLoS One 2022; 17:e0270321. [PMID: 36215236 PMCID: PMC9550079 DOI: 10.1371/journal.pone.0270321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5' end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.
Collapse
Affiliation(s)
- Gontran Sonet
- Joint Experimental Molecular Unit—JEMU, Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- * E-mail:
| | - Nathalie Smitz
- Joint Experimental Molecular Unit—JEMU, Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Carl Vangestel
- Joint Experimental Molecular Unit—JEMU, Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Yves Samyn
- Recent Invertebrates Collections, Scientific Heritage Service, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| |
Collapse
|
15
|
Wilson TC, Rossetto M, Bain D, Yap JS, Wilson PD, Stimpson ML, Weston PH, Croft L. A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity. AMERICAN JOURNAL OF BOTANY 2022; 109:1652-1671. [PMID: 36164832 PMCID: PMC9828017 DOI: 10.1002/ajb2.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. METHODS To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution. RESULTS Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. CONCLUSIONS The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.
Collapse
Affiliation(s)
- Trevor C. Wilson
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - David Bain
- Ecosystems and Threatened Species, Biodiversity Conservation and ScienceNSW Department of Planning and EnvironmentWollongongAustralia
| | - Jia‐Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Peter D. Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical ScienceThe Royal Botanic Garden SydneyAustralia
| | - Margaret L. Stimpson
- Botany, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Peter H. Weston
- Plant Discovery and Evolution, Australian Institute of Botanical ScienceRoyal Botanic Gardens and Domain TrustSydneyAustralia
| | - Larry Croft
- Centre of Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelong3125VictoriaAustralia
| |
Collapse
|
16
|
FREYHOF JÖRG, KAYA CÜNEYT, GEIGER MATTHIASF. A practical approach to revise the Oxynoemacheilus bergianus species group (Teleostei: Nemacheilidae). Zootaxa 2022; 5128:151-194. [DOI: 10.11646/zootaxa.5128.2.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 11/04/2022]
Abstract
The Oxynoemacheilus bergianus species group is revised based on tree topology (ML, NJ, MP), distance (K2P and ASAP) and Poisson tree process analyses of DNA barcode data tested against morphometric and morphological characters including colour patterns. The O. bergianus species group is distinguished from other Oxynoemacheilus groups based on morphological characters: its constituent species have a slender caudal peduncle, a suborbital flap in the male, a mottled or blotched colour pattern, and lack bold, black spots on the caudal-fin base. It is also supported as a monophyletic unit in our molecular analysis.
The O. bergianus group includes 10 molecular clades following congruently well-supported NJ, MP and ML based entities. Species described as O. bergianus, O. banarescui, O. erdali, O. fatsaensis, O. samanticus, and O. simavicus from Turkey, O. lenkoranensis from Azerbaijan, and O. longipinnis and O. parvinae from Iran belong to this species group. The group includes also four unnamed molecular clades. We were unable to detect external differences between any of the molecular clades in colour pattern or any morphometric or morphological characters examined. In the 10 molecular clades in the O. bergianus species group, the intraclade K2P distance ranges from 0.0–1.8% while the distances between molecular clades ranges from 0.6–5.9%. To resolve the species diversity of this group, we also analysed the intraspecific and interspecific variability in the K2P distance of DNA barcode data from 53 other Oxynoemacheilus species. Here, the intraspecific variability ranges from 0.0–2.4% while the interspecific K2P distance ranges from 1.2–20.8%. In the O. bergianus species group, only four groups are detected by the mPTP species delimitation approach distinguished by a K2P distance of 2.9% or more. We treat these four groups as valid species, corresponding to O. banarescui, O. bergianus, O. fatsaensis, and O. simavicus. Oxynoemacheilus samanticus from the Kızılırmak and Seyhan drainages, O. lenkoranensis from the Caspian basin, O. erdali from the Euphrates, and O. longipinnis and O. parvinae from the Tigris drainage are treated as synonyms of O. bergianus. Fishes from an unnamed molecular clade from the upper Tigris, and from a second unnamed clade from the upper Euphrates, are both identified as O. bergianus. Oxynoemacheilus bergianus might be a junior synonym of O. bergi from the Kura. The distribution range of O. simavicus, described from the Simav drainage in the Marmara basin, is expanded to the east and two molecularly differentiated population groups occur in the Sakarya drainage, the Büyük Melen River and potentially in other adjacent coastal streams. Oxynoemacheilus fatsaensis, described from the coastal stream Elekçi in northern Anatolia, is also widespread in the Yeşilırmak drainage. Morphological characters proposed to distinguish O. fatsaensis from the other species of the O. bergianus group could not be confirmed by our data on fishes from the Yeşilırmak. This study also discusses the theoretical background, our reasons for conducting this revision in the way we did, and what the alternatives would be.
Collapse
|
17
|
Ferrão M, de Souza RA, Colatreli OP, Hanken J, Lima AP. Hidden in the litter: cryptic diversity of the leaf-litter toad Rhinella castaneotica– proboscidea complex revealed through integrative taxonomy, with description of a new species from south-western Amazonia. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2039317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Romildo Augusto de Souza
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Olavo Pinhatti Colatreli
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Albertina Pimentel Lima
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| |
Collapse
|
18
|
Catzim VV, Elías-Gutiérrez M, Pérez-Lachaud G. Contribution to the lady beetle fauna of the Yucatan Peninsula and integrative taxonomy for species delimitation. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2017060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Vannesa V. Catzim
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
| | - Manuel Elías-Gutiérrez
- Departamento de Ecología y Sistemática Acuática, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
| | - Gabriela Pérez-Lachaud
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Avenida Centenario Km 5.5, Chetumal, 77014, Quintana Roo, México
| |
Collapse
|
19
|
Fassio G, Bouchet P, Oliverio M, Strong EE. Re-evaluating the case for poecilogony in the gastropod Planaxis sulcatus (Cerithioidea, Planaxidae). BMC Ecol Evol 2022; 22:13. [PMID: 35130841 PMCID: PMC8822645 DOI: 10.1186/s12862-022-01961-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background Planaxis sulcatus has been touted as a textbook example of poecilogony, with members of this wide-ranging Indo-Pacific marine gastropod said to produce free-swimming veligers as well as brooded juveniles. A recent paper by Wiggering et al. (BMC Evol Biol 20:76, 2020) assessed a mitochondrial gene phylogeny based on partial COI and 16S rRNA sequences for 31 individuals supplemented by observations from the brood pouch of 64 mostly unsequenced individuals. ABGD and bGYMC supported three reciprocally monophyletic clades, with two distributed in the Indo-Pacific, and one restricted to the northern Indian Ocean and Red Sea. Given an apparent lack of correlation between clade membership and morphological differentiation or mode of development, the reported 3.08% maximum K2P model-corrected genetic divergence in COI among all specimens was concluded to represent population structuring. Hence, the hypothesis that phylogenetic structure is evidence of cryptic species was rejected and P. sulcatus was concluded to represent a case of geographic poecilogony. Results Our goal was to reassess the case for poecilogony in Planaxis sulcatus with a larger molecular dataset and expanded geographic coverage. We sequenced an additional 55 individuals and included published and unpublished sequence data from other sources, including from Wiggering et al. Our dataset comprised 108 individuals (88 COI, 81 16S rRNA) and included nine countries unrepresented in the previous study. The expanded molecular dataset yielded a maximum K2P model-corrected genetic divergence among all sequenced specimens of 12.09%. The value of 3.08% erroneously reported by Wiggering et al. is the prior maximal distance value that yields a single-species partition in ABGD, and not the maximum K2P intraspecific divergence that can be calculated for the dataset. The bGMYC analysis recognized between two and six subdivisions, while the best-scoring ASAP partitions recognized two, four, or five subdivisions, not all of which were robustly supported in Bayesian and maximum likelihood phylogenetic analyses of the concatenated and single gene datasets. These hypotheses yielded maximum intra-clade genetic distances in COI of 2.56–6.19%, which are more consistent with hypothesized species-level thresholds for marine caenogastropods. Conclusions Based on our analyses of a more comprehensive dataset, we conclude that the evidence marshalled by Wiggering et al. in support of Planaxis sulcatus comprising a single widespread, highly variable species with geographic poecilogony is unconvincing and requires further investigation in an integrative taxonomic framework. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01961-7.
Collapse
|
20
|
Majoros SE, Adamowicz SJ. Phylogenetic signal of sub-arctic beetle communities. Ecol Evol 2022; 12:e8520. [PMID: 35222946 PMCID: PMC8848465 DOI: 10.1002/ece3.8520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022] Open
Abstract
Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.
Collapse
|
21
|
Using Species Groups to Approach the Large and Taxonomically Unresolved Freshwater Fish Family Nemacheilidae (Teleostei: Cypriniformes). BIOLOGY 2022; 11:biology11020175. [PMID: 35205042 PMCID: PMC8869502 DOI: 10.3390/biology11020175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 11/17/2022]
Abstract
Large animal families with unresolved taxonomy are notoriously difficult to handle with respect to their biodiversity, systematics, and evolutionary history. We approach a large and taxonomically unresolved family of freshwater fishes (Nemacheilidae, >600 species) by proposing, on the basis of morphologic data, a species group within the family and study its phylogeny with conclusions regarding its diversity, taxonomy, and biogeographic history. Phylogenetic analyses of two mitochondrial and three nuclear genes of 139 specimens, representing about 46 species (17 candidate species from the proposed species-group, plus 29 comparative species), revealed that the proposed species group does not form a distinct monophyletic lineage, but that the candidate and comparative species mixed in three different lineages. However, the results revealed more than 20% of undescribed species within the ingroup and showed that species do not cluster according to the presently recognised genera. At least one of the genetic clades shows signs of an eastward range expansion during the second half of Miocene from north India via Myanmar into Laos, western China, and western Thailand. We conclude that the approach of picking monophyletic lineages to study biodiversity, systematics, and evolutionary history helps to open the door to large animal families.
Collapse
|
22
|
Li F, Xu X, Zhang Z, Liu F, Yang Z, Li D. Multilocus species delimitation and phylogeny of the genus
Calommata
(Araneae, Atypidae) in southern China. ZOOL SCR 2022. [DOI: 10.1111/zsc.12525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Fan Li
- Centre for Behavioral Ecology & Evolution College of Life Sciences Hubei University Wuhan China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Xin Xu
- Centre for Behavioral Ecology & Evolution College of Life Sciences Hubei University Wuhan China
- College of Life Sciences Hunan Normal University Changsha China
| | - Zengtao Zhang
- Centre for Behavioral Ecology & Evolution College of Life Sciences Hubei University Wuhan China
| | - Fengxiang Liu
- Centre for Behavioral Ecology & Evolution College of Life Sciences Hubei University Wuhan China
| | - Zizhong Yang
- National‐Local Joint Engineering Research Center of Entomoceutics Dali University Dali China
| | - Daiqin Li
- Department of Biological Sciences National University of Singapore Singapore Singapore
| |
Collapse
|
23
|
OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
24
|
OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
25
|
Dong X, Yi W, Zheng C, Zhu X, Wang S, Xue H, Ye Z, Bu W. Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data. ZOOL SCR 2021. [DOI: 10.1111/zsc.12523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenbo Yi
- Department of Biology Xinzhou Teachers University Xinzhou China
| | - Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Shujing Wang
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Huaijun Xue
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| |
Collapse
|
26
|
Podnar M, Grbac I, Tvrtković N, Hörweg C, Haring E. Hidden diversity, ancient divergences, and tentative Pleistocene microrefugia of European scorpions (Euscorpiidae: Euscorpiinae) in the eastern Adriatic region. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Irena Grbac
- Croatian Natural History Museum Zagreb Croatia
| | | | | | - Elisabeth Haring
- Natural History Museum Vienna Vienna Austria
- Faculty of Life Science Department of Evolutionary Biology University of Vienna Vienna Austria
| |
Collapse
|
27
|
Chou MH, Tseng WZ, Sang YD, Morgan B, De Vivo M, Kuan YH, Wang LJ, Chen WY, Huang JP. Incipient speciation and its impact on taxonomic decision: a case study using a sky island sister-species pair of stag beetles (Lucanidae: Lucanus). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab105] [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
Species delimitation can be difficult when the divergence between focal taxa is in the incipient stage of speciation, because conflicting results are expected among different data sets, and the species limits can differ depending on the species concept applied. We studied speciation history and investigated the impact on taxonomic decision-making when using different types of data in a Taiwanese endemic sister-species pair of stag beetles, Lucanus miwai and Lucanus yulaoensis, from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3%; however, L. miwai might not be monophyletic. The result of our multispecies coalescent-based species delimitation using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of the genealogical divergence index (gdi) corresponded to the ambiguous zone of species delimitation. We also showed that post-divergence gene flow is unlikely. Our study demonstrates challenges in the delineation of incipient species, but shows the importance of understanding the speciation history and adopting integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions.
Collapse
Affiliation(s)
- Ming-Hsun Chou
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Zhe Tseng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yao-De Sang
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Liang-Jong Wang
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Wei-Yun Chen
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
28
|
Muster C, Spelda J, Rulik B, Thormann J, von der Mark L, Astrin JJ. The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions. Ecol Evol 2021; 11:13815-13829. [PMID: 34707820 PMCID: PMC8525104 DOI: 10.1002/ece3.8088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.
Collapse
Affiliation(s)
- Christoph Muster
- Zoologisches Institut und MuseumUniversität GreifswaldGreifswaldGermany
| | - Jörg Spelda
- SNSB‐Zoologische Staatssammlung MünchenMunichGermany
| | - Björn Rulik
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | - Jana Thormann
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | | | | |
Collapse
|
29
|
Roslin T, Somervuo P, Pentinsaari M, Hebert PDN, Agda J, Ahlroth P, Anttonen P, Aspi J, Blagoev G, Blanco S, Chan D, Clayhills T, deWaard J, deWaard S, Elliot T, Elo R, Haapala S, Helve E, Ilmonen J, Hirvonen P, Ho C, Itämies J, Ivanov V, Jakovlev J, Juslén A, Jussila R, Kahanpää J, Kaila L, Jari-PekkaKaitila, Kakko A, Kakko I, Karhu A, Karjalainen S, Kjaerandsen J, Koskinen J, Laasonen EM, Laasonen L, Laine E, Lampila P, Levesque-Beaudin V, Lu L, Lähteenaro M, Majuri P, Malmberg S, Manjunath R, Martikainen P, Mattila J, McKeown J, Metsälä P, Miklasevskaja M, Miller M, Miskie R, Muinonen A, Veli-MattiMukkala, Naik S, Nikolova N, Nupponen K, Ovaskainen O, Österblad I, Paasivirta L, Pajunen T, Parkko P, Paukkunen J, Penttinen R, Perez K, Pohjoismäki J, Prosser S, Raekunnas M, Rahulan M, Rannisto M, Ratnasingham S, Raukko P, Rinne A, Rintala T, Miranda Romo S, Salmela J, Salokannel J, Savolainen R, Schulman L, Sihvonen P, Soliman D, Sones J, Steinke C, Ståhls G, Tabell J, Tiusanen M, Várkonyi G, Vesterinen EJ, Viitanen E, Vikberg V, Viitasaari M, Vilen J, Warne C, Wei C, Winqvist K, Zakharov E, Mutanen M. A molecular-based identification resource for the arthropods of Finland. Mol Ecol Resour 2021; 22:803-822. [PMID: 34562055 DOI: 10.1111/1755-0998.13510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.
Collapse
Affiliation(s)
- Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Petri Ahlroth
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Perttu Anttonen
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Santiago Blanco
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Jeremy deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Stephanie deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler Elliot
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Riikka Elo
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Jari Ilmonen
- Metsähallitus, Parks & Wildlife Finland, Vantaa, Finland
| | | | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Aino Juslén
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Jere Kahanpää
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Iiro Kakko
- Forssa Museum of Natural History, Forssa, Finland
| | | | | | - Jostein Kjaerandsen
- The Arctic University Museum of Norway, UiT -The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Janne Koskinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | | | | | | | | | | | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meri Lähteenaro
- Division of Systematics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Entomology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Meredith Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadia Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Timo Pajunen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Juho Paukkunen
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ritva Penttinen
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sean Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meeri Rannisto
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | - Jukka Salmela
- Regional Museum of Lapland, Arktikum, Rovaniemi, Finland.,Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Riitta Savolainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Leif Schulman
- Finnish Environment Institute (SYKE), Helsinki, Finland.,Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Pasi Sihvonen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Dina Soliman
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gunilla Ståhls
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Mikko Tiusanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Gergely Várkonyi
- Biodiversity Centre, Finnish Environment Institute SYKE, Kuhmo, Finland
| | - Eero J Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biology, University of Turku, Turku, Finland
| | | | | | | | | | - Connor Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Evgeny Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| |
Collapse
|
30
|
Lin X, Jiang K, Liu W, Liu W, Bu W, Wang X, Mo L. Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956. Ecol Evol 2021; 11:12161-12172. [PMID: 34522368 PMCID: PMC8427567 DOI: 10.1002/ece3.7979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.
Collapse
Affiliation(s)
- Xiao‐Long Lin
- College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal DiversityTianjin Normal UniversityTianjinChina
| | - Wei Liu
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Jun Bu
- College of Life SciencesNankai UniversityTianjinChina
| | - Xin‐Hua Wang
- College of Life SciencesNankai UniversityTianjinChina
| | - Lidong Mo
- Crowther LabInstitute of Integrative BiologyETH Zurich (Swiss Federal Institute of Technology)ZurichSwitzerland
| |
Collapse
|
31
|
Salnitska M, Solodovnikov A. DNA barcode sheds light on species boundaries in the common morphologically variable rove beetle Quedius umbrinus-complex that puzzled taxonomists for more than a century (Coleoptera, Staphylinidae). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1943559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Maria Salnitska
- X-BIO Institute, University of Tyumen, 6 Volodarskogo Str, Tyumen, 625003, Russian Federation
| | - Alexey Solodovnikov
- Zoological Museum, Natural History Museum of Denmark at the University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark
- Zoological Institute, Russian Academy of Science, 1 Universitetskaya Emb, St. Petersburg, 199034, Russian Federation
| |
Collapse
|
32
|
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]
|
33
|
Hofman S, Grego J, Rysiewska A, Osikowski A, Falniowski A. Two new species of the Balkan genus Paladilhiopsis Pavlović, 1913 (Caenogastropoda, Moitessieriidae). Zookeys 2021; 1046:157-176. [PMID: 34239339 PMCID: PMC8238927 DOI: 10.3897/zookeys.1046.64489] [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: 02/16/2021] [Accepted: 03/19/2021] [Indexed: 11/12/2022] Open
Abstract
The Balkan Peninsula is inhabited by the worldwide most diverse subterranean gastropod fauna. This fauna is still poorly studied, since its habitats are not easily accessible, and its sampled populations are mostly not rich in specimens' numbers. Often only empty shells are known, but the shell is hardly useful, not only in phylogeny reconstruction, but even in species determination. The exclusively obligatory subterranean family Moitessieriidae is especially poorly studied. Representatives of the genus Paladilhiopsis Pavlović, 1913 (Moitessieriidae) collected at three localities, distributed in Croatia and Bosnia & Herzegovina, were studied. The pigmentation of their shells and soft parts, as well as the female and male reproductive organs in one taxon, are presented. The partial sequences of the molecular markers mitochondrial cytochrome oxidase subunit I (COI) and nuclear histone 3 (H3) were used to infer their systematic status and phylogenetic relationships. Two species new to science are described. For one of them, also studied anatomically, 15 specimens were sequenced for COI, and all show the same haplotype.
Collapse
Affiliation(s)
- Sebastian Hofman
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387, Kraków, Poland
| | - Jozef Grego
- Horná Mičiná 219, SK-97401, Banská Bystrica, Slovakia
| | - Aleksandra Rysiewska
- Department of Malacology, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387, Kraków, Poland
| | - Artur Osikowski
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059, Kraków, Poland
| | - Andrzej Falniowski
- Department of Malacology, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387, Kraków, Poland
| |
Collapse
|
34
|
Bustamante DE, Calderon MS, Leiva S, Mendoza JE, Arce M, Oliva M. Three new species of Trichoderma in the Harzianum and Longibrachiatum lineages from Peruvian cacao crop soils based on an integrative approach. Mycologia 2021; 113:1056-1072. [PMID: 34128770 DOI: 10.1080/00275514.2021.1917243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The hyperdiverse genus Trichoderma is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (acl1, act, rpb2, and tef1) to delimit species of two lineages of Trichoderma. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, T.awajun, sp. nov., T. jaklitschii, sp. nov., and T. peruvianum, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in Trichoderma.
Collapse
Affiliation(s)
- Danilo E Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru.,Facultad de Ingeniería Civil y Ambiental, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Martha S Calderon
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru.,Facultad de Ingeniería Civil y Ambiental, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Santos Leiva
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Jani E Mendoza
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Marielita Arce
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Manuel Oliva
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| |
Collapse
|
35
|
Levicoy D, Rosenfeld S, Cárdenas L. Divergence time and species delimitation of microbivalves in the Southern Ocean: the case of Kidderia species. Polar Biol 2021; 44:1365-1377. [PMID: 34092908 PMCID: PMC8169414 DOI: 10.1007/s00300-021-02885-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/18/2022]
Abstract
The systematics of Subantarctic and Antarctic near-shore marine benthic invertebrates requires major revision and highlights the necessity to incorporate additional sources of information in the specimen identification chart in the Southern Ocean (SO). In this study, we aim to improve our understanding of the biodiversity of Kidderia (Dall 1876) through molecular and morphological comparisons of Antarctic and Subantarctic taxa. The microbivalves of the genus Kidderia are small brooding organisms that inhabit intertidal and shallow subtidal rocky ecosystems. This genus represents an interesting model to test the vicariance and dispersal hypothesis in the biogeography of the SO. However, the description of Kidderia species relies on a few morphological characters and biogeographic records that raise questions about the true diversity in the group. Here we will define the specimens collected with genetic tools, delimiting their respective boundaries across provinces of the SO, validating the presence of two species of Kidderia. Through the revision of taxonomic issues and species delimitation, it was possible to report that the Antarctic species is Kidderia subquadrata and the species recorded in the Subantarctic islands Diego Ramirez, South Georgia and the Kerguelen Archipelago is Kidderia minuta. The divergence time estimation suggests the origin and diversification of Kidderia lineages are related to historical vicariant processes probably associated with the separation of the continental landmasses close to the late Eocene.
Collapse
Affiliation(s)
- Daniela Levicoy
- Centro FONDAP- IDEAL, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Chile
| | - Sebastián Rosenfeld
- Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras #3425, Ñuñoa, Santiago Chile.,Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Avenida Bulnes 01890, Punta Arenas, Chile.,Instituto de Ecología y Biodiversidad, Las Palmeras 3425, Ñuñoa, Santiago Chile.,Centro de Investigación Gaia-Antártica, Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas, Chile
| | - Leyla Cárdenas
- Centro FONDAP- IDEAL, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Chile
| |
Collapse
|
36
|
Brunke AJ, Pentinsaari M, Klimaszewski J. Integrative taxonomy of Nearctic and Palaearctic Aleocharinae: new species, synonymies, and records (Coleoptera, Staphylinidae). Zookeys 2021; 1041:27-99. [PMID: 34140825 PMCID: PMC8184736 DOI: 10.3897/zookeys.1041.64460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/29/2021] [Indexed: 11/27/2022] Open
Abstract
A long tradition of separate Nearctic and Palaearctic taxonomic studies of the diverse aleocharine rove beetles (Coleoptera: Staphylinidae) has obscured the recognition of Holarctic species and detection of adventive species in both regions. Recently, integrated study of the two regions through detailed morphological comparisons and development of an authoritatively identified DNA barcode reference library has revealed the degree to which these two aleocharine faunas are interconnected, both naturally and through human activity. Here this approach is adopted to recognize new species, reveal Holarctic species, and recognize adventive species in both North America and Europe. The following new species are described: Isoglossatriangularis Klimaszewski, Brunke & Pentinsaari, sp. nov. from British Columbia; Gnypetaimpressicollis Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario, Maryland and North Carolina; Aloconotapseudogregaria Klimaszewski, Brunke & Pentinsaari, sp. nov., from Ontario and Virginia; and Philhygrapseudolaevicollis Klimaszewski, Brunke & Pentinsaari, sp. nov. from eastern Canada. Dasygnypetavelata and Philhygraangusticauda are revealed to be Holarctic species, resulting in the following synonymies: Dasygnypetavelata (Erichson, 1839) = Gnypetaminuta Klimaszewski & Webster, 2008, syn. nov. and Philhygraangusticauda (Bernhauer, 1909) = Atheta (Philhygra) pinegensis Muona, 1983, syn. nov. The Nearctic species Hylotaochracea (and genus Hylota), Thecturotatenuissima, and Trichiusarobustula are newly reported from the Palaearctic region as adventive, resulting in the following synonymies: Hylotaochracea Casey, 1906 = Stichoglossa (Dexiogyia) forticornis Strand, 1939, syn. nov.; Thecturotatenuissima Casey, 1893 = Athetamarchii Dodero, 1922, syn. nov.; and Trichiusarobustula Casey, 1893 = T.immigrata Lohse, 1984, syn. nov. The Palaearctic species Amarocharaforticornis, Anomognathuscuspidatus, Oligotapumilio, and Parocyusarubicunda are newly confirmed from the Nearctic region as adventive, resulting in the following synonymies: Parocyusarubicunda (Erichson, 1837) = Chiloporaamericana Casey, 1906, syn. nov. and Anomognathuscuspidatus (Erichson, 1839) = Thecturaamericana Casey, 1893, syn. nov. The genus Dasygnypeta, sensu nov. is newly reported from North America, Paradilacra is newly reported from eastern North America, and Haploglossa is newly reported from Canada, resulting in the following synonymy: Paradilacradensissima (Bernhauer, 1909) = Gnypetasaccharina Klimaszewski & Webster, 2008, syn. nov. Native Cypheawallisi is newly reported from across Canada and C.curtula is removed from the Nearctic fauna. The status of both Gyrophaenaaffinis and Homalotaplana is uncertain but these species are no longer considered to be adventive in North America. Three new combinations are proposed: Dasygnypetabaranowskii (Klimaszewski, 2020) and D.nigrella (LeConte, 1863) (both from Gnypeta) and Mocytascopula (Casey, 1893) (from Acrotona). Dolosota Casey, 1910, syn. nov. (type species Eurypronotascopula Casey), currently a subgenus of Acrotona, is therefore synonymized with Mocyta Mulsant & Rey, 1874. Additionally, four new Canadian records and 18 new provincial and state records are reported.
Collapse
Affiliation(s)
- Adam J Brunke
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada Canadian National Collection of Insects, Arachnids and Nematodes Ottawa Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, 50 Stone Road East, University of Guelph, Guelph, Ontario, N1G 2W1, Canada University of Guelph Guelph Canada
| | - Jan Klimaszewski
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, PO Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec Sainte-Foy, Québec Canada
| |
Collapse
|
37
|
Heylen OCG, Debortoli N, Marescaux J, Olofsson JK. A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:819. [PMID: 33924227 PMCID: PMC8074783 DOI: 10.3390/plants10040819] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/30/2021] [Accepted: 04/18/2021] [Indexed: 05/29/2023]
Abstract
The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.
Collapse
Affiliation(s)
| | | | | | - Jill K. Olofsson
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, bygning 7, DK-1353 Copenhagen, Denmark;
| |
Collapse
|
38
|
|
39
|
Magoga G, Fontaneto D, Montagna M. Factors affecting the efficiency of molecular species delimitation in a species-rich insect family. Mol Ecol Resour 2021; 21:1475-1489. [PMID: 33565247 DOI: 10.1111/1755-0998.13352] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: (i) the number of haplotypes per species (as a proxy for genetic diversity), (ii) the geographic distance among conspecific collection localities (as a proxy of sampling width), (iii) the difficulty related to morphological identification of species, and (iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.
Collapse
Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Ricerca Sulle Acque (IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy.,BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici, Italy
| |
Collapse
|
40
|
Yuan JJ, Chen D, Wan X. A multilocus assessment reveals two new synonymies for East Asian Cyclommatus stag beetles (Coleoptera, Lucanidae). Zookeys 2021; 1021:65-79. [PMID: 33727883 PMCID: PMC7943532 DOI: 10.3897/zookeys.1021.58832] [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: 09/26/2020] [Accepted: 01/31/2021] [Indexed: 11/12/2022] Open
Abstract
Cyclommatus scutellaris Möllenkamp, 1912, Cyclommatus elsae Kriesche, 1921 and Cyclommatus tamdaoensis Fujita, 2010 are East Asian stag beetle species with long-debated taxonomic relationships due to high intraspecific morphological variability. In this study, we applied multilocus phylogenetic analyses to reassess their relationships. Two mitochondrial genes (16S rDNA, COI) and two nuclear genes (28S rDNA, Wingless) were used to reconstruct the phylogeny through the Bayesian inference (BI) and Maximum Likelihood (ML) methods. Both topologies supported two clades: the clade C. scutellaris was sister to the clade (C. elsae + C. tamdaoensis) with the subclade C. tamdaoensis embedded in the subclade C. elsae. The Kimura 2-parameter (K2P) genetic distance analysis yielded a low mean value (≤0.035) among the three taxa, which was well below the minimum mean value between other Cyclommatus species (≥0.122). We also compared the accuracy and efficiency of two approaches, GMYC and ABGD, in delimitating the three lineages. The result shows that ABGD is a better approach than GMYC. Our molecular data recognizes the three species as different populations of a single species, ranging from Taiwan Island to the continent. Therefore, we propose two new junior synonyms for C. scutellaris: C. tamdaoensis, syn. nov. and C. elsae syn. nov.
Collapse
Affiliation(s)
- Jiao Jiao Yuan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
| | - Dan Chen
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
| | - Xia Wan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
| |
Collapse
|
41
|
Gonçalves LT, Bianchi FM, Deprá M, Calegaro-Marques C. Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda. Genome 2021; 64:705-717. [PMID: 33460338 DOI: 10.1139/gen-2020-0140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.
Collapse
Affiliation(s)
- Leonardo Tresoldi Gonçalves
- Laboratório de Helmintologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Filipe Michels Bianchi
- Laboratório de Entomologia Sistemática, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Laboratório de Drosophila, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cláudia Calegaro-Marques
- Laboratório de Helmintologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| |
Collapse
|
42
|
Lin X, Mo L, Bu W, Wang X. The first comprehensive DNA barcode reference library of Chinese
Tanytarsus
(Diptera: Chironomidae) for environmental DNA metabarcoding. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xiao‐Long Lin
- College of Life Sciences Nankai University Tianjin China
- Department of Natural History NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | - Lidong Mo
- Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland
| | - Wen‐Jun Bu
- College of Life Sciences Nankai University Tianjin China
| | - Xin‐Hua Wang
- College of Life Sciences Nankai University Tianjin China
| |
Collapse
|
43
|
Tineo D, Bustamante DE, Calderon MS, Mendoza JE, Huaman E, Oliva M. An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru. PLoS One 2020; 15:e0242469. [PMID: 33301452 PMCID: PMC7728213 DOI: 10.1371/journal.pone.0242469] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/01/2020] [Indexed: 12/30/2022] Open
Abstract
The assignment of accurate species names is crucial, especially for those with confirmed agronomic potential such as highland papayas. The use of additional methodologies and data sets is recommended to establish well-supported boundaries among species of Vasconcellea. Accordingly, six chloroplast (trnL-trnF, rpl20-rps12, psbA-trnH intergenic spacers, matK and rbcL genes) and nuclear (ITS) markers were used to delimit species in the genus Vasconcellea using phylogeny and four DNA-based methods. Our results demonstrated congruence among different methodologies applied in this integrative study (i.e., morphology, multilocus phylogeny, genetic distance, coalescence methods). Genetic distance (ABGD, SPN), a coalescence method (BPP), and the multilocus phylogeny supported 22–25 different species of Vasconcellea, including the following five new species from northern Peru: V. badilloi sp. nov., V. carvalhoae sp. nov., V. chachapoyensis sp. nov., V. pentalobis sp. nov., and V. peruviensis sp. nov. Genetic markers that gave better resolution for distinguishing species were ITS and trnL-trnF. Phylogenetic diversity and DNA-species delimitation methods could be used to discover taxa within traditionally defined species.
Collapse
Affiliation(s)
- Daniel Tineo
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Danilo E. Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
- * E-mail:
| | - Martha S. Calderon
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Jani E. Mendoza
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Eyner Huaman
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Manuel Oliva
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| |
Collapse
|
44
|
Puillandre N, Brouillet S, Achaz G. ASAP: assemble species by automatic partitioning. Mol Ecol Resour 2020; 21:609-620. [PMID: 33058550 DOI: 10.1111/1755-0998.13281] [Citation(s) in RCA: 375] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
Collapse
Affiliation(s)
- Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sophie Brouillet
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,SMILE Group, CIRB, UMR 7241, Collège de France, CNRS, INSERM, Paris, France.,Éco-anthropologie, Muséum National d'Histoire Naturelle, CNRS UMR 7206, Université de Paris, Paris, France
| |
Collapse
|
45
|
DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau. BMC Evol Biol 2020; 20:151. [PMID: 33183225 PMCID: PMC7663858 DOI: 10.1186/s12862-020-01718-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/04/2020] [Indexed: 01/12/2023] Open
Abstract
Background The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions. Conclusions The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.
Collapse
|
46
|
Wu RW, Liu XJ, Ouyang S, Wu XP. Comparative Analyses of the Complete Mitochondrial Genomes of Three Lamprotula (Bivalvia: Unionidae) Species: Insight into the Shortcomings of Mitochondrial DNA for Recently Diverged Species Delimitation. MALACOLOGIA 2020. [DOI: 10.4002/040.063.0106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Rui-Wen Wu
- School of Life Sciences, Nanchang University, Nanchang 330031, People's Republic of China
| | - Xiong-Jun Liu
- School of Resource, Environment and Chemical Engineering, Nanchang University, Nanchang 330031, People's Republic of China
| | - Shan Ouyang
- School of Life Sciences, Nanchang University, Nanchang 330031, People's Republic of China
| | - Xiao-Ping Wu
- School of Life Sciences, Nanchang University, Nanchang 330031, People's Republic of China
| |
Collapse
|
47
|
Gu J, Jiang B, Wang H, Wei T, Lin L, Huang Y, Huang J. Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence. PLoS One 2020; 15:e0237882. [PMID: 32845927 PMCID: PMC7449498 DOI: 10.1371/journal.pone.0237882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.
Collapse
Affiliation(s)
- Jingxiao Gu
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
| | - Bing Jiang
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
| | - Haojie Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People’s Republic of China
| | - Tao Wei
- Tanxi Street Agency, Liunan Subdistrict, Liuzhou, Guangxi, People’s Republic of China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, People’s Republic of China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, People’s Republic of China
| | - Jianhua Huang
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
| |
Collapse
|
48
|
Wiggering B, Neiber MT, Gebauer K, Glaubrecht M. One species, two developmental modes: a case of geographic poecilogony in marine gastropods. BMC Evol Biol 2020; 20:76. [PMID: 32591013 PMCID: PMC7318368 DOI: 10.1186/s12862-020-01644-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
Background Poecilogony, the presence of two developmental modes in the same animal species, is a rare phenomenon. Few cases of poecilogony have been suggested for marine invertebrates including molluscs and even less stood extensive testing, mostly revealing a species pair with differing developmental modes. We studied a textbook example of poecilogony in the viviparous snail Planaxis sulcatus (Gastropoda: Planaxidae), for the first time throughout its entire distribution range. Results In the Western Indian Ocean and Red Sea this intertidal species is observed to have large, shelled juveniles, whereas in the Indo-West Pacific planktotrophic veliger larvae are released from a subhaemocoelic brood pouch. We uncovered a shift in developmental modes across its range: from west to east successively earlier developmental stages are released. Furthermore, genetic data based on mitochondrial DNA suggests to recognize P. sulcatus as a single species rather than a group of cryptic species. A reconstruction of the ancestral area of P. sulcatus based on molecular data outlines the Western Indian Ocean and the Indo-West Pacific as area of origin. Conclusion The findings supporting Planaxis sulcatus as a single widespread species and the geographical shift from one reproductive mode to another suggest for this species to truly represent a case of geographic poecilogony, i.e. differing developmental modes between populations of the same species. Furthermore, the results of our ancestral range estimation imply the release of planktotrophic larvae as the ancestral developmental mode.
Collapse
Affiliation(s)
- Benedikt Wiggering
- Department of Animal Diversity, Center of Natural History (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
| | - Marco T Neiber
- Department of Animal Diversity, Center of Natural History (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Katharina Gebauer
- Department of Animal Diversity, Center of Natural History (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Matthias Glaubrecht
- Department of Animal Diversity, Center of Natural History (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| |
Collapse
|
49
|
Mignotte A, Garros C, Gardès L, Balenghien T, Duhayon M, Rakotoarivony I, Tabourin L, Poujol L, Mathieu B, Ibañez-Justicia A, Deniz A, Cvetkovikj A, Purse BV, Ramilo DW, Stougiou D, Werner D, Pudar D, Petrić D, Veronesi E, Jacobs F, Kampen H, Pereira da Fonseca I, Lucientes J, Navarro J, de la Puente JM, Stefanovska J, Searle KR, Khallaayoune K, Culverwell CL, Larska M, Bourquia M, Goffredo M, Bisia M, England M, Robin M, Quaglia M, Miranda-Chueca MÁ, Bødker R, Estrada-Peña R, Carpenter S, Tchakarova S, Boutsini S, Sviland S, Schäfer SM, Ozoliņa Z, Segliņa Z, Vatansever Z, Huber K. The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level. Parasit Vectors 2020; 13:265. [PMID: 32434592 PMCID: PMC7238629 DOI: 10.1186/s13071-020-04114-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/29/2020] [Indexed: 11/27/2022] Open
Abstract
Background Culicoides obsoletus is an abundant and widely distributed Holarctic biting midge species, involved in the transmission of bluetongue virus (BTV) and Schmallenberg virus (SBV) to wild and domestic ruminants. Females of this vector species are often reported jointly with two morphologically very close species, C. scoticus and C. montanus, forming the Obsoletus/Scoticus Complex. Recently, cryptic diversity within C. obsoletus was reported in geographically distant sites. Clear delineation of species and characterization of genetic variability is mandatory to revise their taxonomic status and assess the vector role of each taxonomic entity. Our objectives were to characterize and map the cryptic diversity within the Obsoletus/Scoticus Complex. Methods Portion of the cox1 mitochondrial gene of 3763 individuals belonging to the Obsoletus/Scoticus Complex was sequenced. Populations from 20 countries along a Palaearctic Mediterranean transect covering Scandinavia to Canary islands (North to South) and Canary islands to Turkey (West to East) were included. Genetic diversity based on cox1 barcoding was supported by 16S rDNA mitochondrial gene sequences and a gene coding for ribosomal 28S rDNA. Species delimitation using a multi-marker methodology was used to revise the current taxonomic scheme of the Obsoletus/Scoticus Complex. Results Our analysis showed the existence of three phylogenetic clades (C. obsoletus clade O2, C. obsoletus clade dark and one not yet named and identified) within C. obsoletus. These analyses also revealed two intra-specific clades within C. scoticus and raised questions about the taxonomic status of C. montanus. Conclusions To our knowledge, our study provides the first genetic characterization of the Obsoletus/Scoticus Complex on a large geographical scale and allows a revision of the current taxonomic classification for an important group of vector species of livestock viruses in the Palaearctic region.![]()
Collapse
Affiliation(s)
- Antoine Mignotte
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France. .,Cirad, UMR ASTRE, 34398, Montpellier, France.
| | - Claire Garros
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France. .,Cirad, UMR ASTRE, 34398, Montpellier, France.
| | - Laetitia Gardès
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France.,Cirad, UMR ASTRE, 97170, Petit-Bourg, Guadeloupe, France
| | - Thomas Balenghien
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France.,Cirad, UMR ASTRE, 34398, Montpellier, France.,Institut Agronomique et Vétérinaire Hassan II, Unité Parasitologie et Maladies Parasitaires, 10100, Rabat, Morocco
| | - Maxime Duhayon
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France.,Cirad, UMR ASTRE, 34398, Montpellier, France
| | - Ignace Rakotoarivony
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France.,Cirad, UMR ASTRE, 34398, Montpellier, France
| | - Laura Tabourin
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France.,Cirad, UMR ASTRE, 34398, Montpellier, France
| | - Léa Poujol
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France.,Cirad, UMR ASTRE, 34398, Montpellier, France
| | - Bruno Mathieu
- Institute of Parasitology and Tropical Pathology of Strasbourg, Université de Strasbourg, DIHP UR 7292, 67000, Strasbourg, France
| | - Adolfo Ibañez-Justicia
- Centre for Monitoring of Vectors, National Reference Centre, Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Ahmet Deniz
- Veterinary Control Central Research Institute, Ankara, Turkey
| | - Aleksandar Cvetkovikj
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Republic of North Macedonia
| | - Bethan V Purse
- Centre for Ecology, Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| | - David W Ramilo
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Despoina Stougiou
- Department of Parasitology-Parasitic Diseases, Entomology & Bee Health, Veterinary Centre of Athens, Athens, Greece
| | - Doreen Werner
- Leibniz-Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Dubravka Pudar
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Dušan Petrić
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Eva Veronesi
- National Centre for Vector Entomology, Institute of Parasitology, University of Zürich, Zürich, Switzerland
| | - Frans Jacobs
- Centre for Monitoring of Vectors, National Reference Centre, Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Isabel Pereira da Fonseca
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Javier Lucientes
- Department of Animal Pathology, AgriFood Institute of Aragón (IA2) Veterinary Faculty, 50013, Zaragoza, Spain
| | - Javier Navarro
- Departamento de Microbiología, Laboratorio de Producción y Sanidad Animal de Granada, Junta de Andalucía, Granada, Spain
| | - Josue Martinez de la Puente
- Doñana Biological Station, CSIC, Sevilla, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Jovana Stefanovska
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Republic of North Macedonia
| | - Kate R Searle
- Centre for Ecology & Hydrology, Edinburgh, OX10 8BB, UK
| | - Khalid Khallaayoune
- Institut Agronomique et Vétérinaire Hassan II, Unité Parasitologie et Maladies Parasitaires, 10100, Rabat, Morocco
| | - C Lorna Culverwell
- Department of Virology, University of Helsinki, Medicum, Haartmaninkatu 3, Helsinki, 00014, Finland
| | | | - Maria Bourquia
- Cirad, UMR ASTRE, 34398, Montpellier, France.,Institut Agronomique et Vétérinaire Hassan II, Unité Parasitologie et Maladies Parasitaires, 10100, Rabat, Morocco
| | - Maria Goffredo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', Campo Boario, 64100, Teramo, Italy
| | - Marina Bisia
- Department of Parasitology-Parasitic Diseases, Entomology & Bee Health, Veterinary Centre of Athens, Athens, Greece
| | | | - Matthew Robin
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Leahurst, Chester High Road, Neston, Cheshire, CH64 7TE, UK
| | - Michela Quaglia
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', Campo Boario, 64100, Teramo, Italy
| | - Miguel Ángel Miranda-Chueca
- Applied Zoology and Animal Conservation Research Group, University of the Balearic Islands UIB, Palma, Spain
| | - René Bødker
- University of Copenhagen, Copenhagen, Denmark
| | - Rosa Estrada-Peña
- Department of Animal Pathology, AgriFood Institute of Aragón (IA2) Veterinary Faculty, 50013, Zaragoza, Spain
| | | | - Simona Tchakarova
- National Diagnostic and Research Veterinary Medical Institute, Sofia, Bulgaria
| | - Sofia Boutsini
- Department of Parasitology-Parasitic Diseases, Entomology & Bee Health, Veterinary Centre of Athens, Athens, Greece
| | | | - Stefanie M Schäfer
- Centre for Ecology, Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| | - Zanda Ozoliņa
- Institute of Food safety, Animal Health and Environment 'BIOR', Riga, Latvia
| | - Zanda Segliņa
- Institute of Food safety, Animal Health and Environment 'BIOR', Riga, Latvia
| | - Zati Vatansever
- Veterinary Control Central Research Institute, Ankara, Turkey
| | - Karine Huber
- ASTRE, Univ Montpellier, Cirad, INRAE, Montpellier, France
| |
Collapse
|
50
|
Hundsdoerfer AK, Lee KM, Kitching IJ, Mutanen M. Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths. Genome Biol Evol 2020; 11:2136-2150. [PMID: 31143925 PMCID: PMC6685492 DOI: 10.1093/gbe/evz113] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of “when do nondiscrete entities become distinct, mutually exclusive evolutionary units”? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.
Collapse
Affiliation(s)
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ian J Kitching
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Finland
| |
Collapse
|