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Nam K, Nègre N, Saldamando Benjumea CI. Two host-plant strains in the fall armyworm. INSECT SCIENCE 2024. [PMID: 38437152 DOI: 10.1111/1744-7917.13346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 03/06/2024]
Abstract
The fall armyworm (Spodoptera frugiperda) is one of the major pest insects damaging diverse crops including cotton, corn, rice, and sorghum. Fall armyworms have been identified as two morphologically indistinguishable strains, the corn strain, and the rice strain, named after their preferred host-plants. Although initially recognized as host-plant strains, there has been an ongoing debate regarding whether the corn and rice strains should be considered as such. In this article, we present arguments based on recent population genomics studies supporting that these two strains should be considered to be host-plant strains. Furthermore, host-plant adaptation appears to be a driving evolutionary force responsible for incipient speciation in the fall armyworm.
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Affiliation(s)
- Kiwoong Nam
- DGIMI, Université de Montpellier, INRAE, Montpellier, France
| | - Nicolas Nègre
- DGIMI, Université de Montpellier, INRAE, Montpellier, France
| | - Clara Ines Saldamando Benjumea
- Grupo de Biotecnología-Vegetal UNALMED-CIB, Laboratorio de Ecología y Evolución de Insectos 16-223, Facultad de Ciencias, Departamento de Biociencias, Universidad Nacional de Colombia, Medellín, Colombia
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2
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Balke M, Neven K, Villastrigo A, Ospina-Torres R, Prieto C, Gutierrez Rubiano N, Lotta I, Dueñas LF, Hendrich L. Eastern Colombian Páramo Liodessus Guignot, 1939 diving beetles are genetically structured, but show signs of hybridization, with description of new species and subspecies (Coleoptera, Dytiscidae). Zookeys 2023; 1143:165-187. [DOI: 10.3897/zookeys.1143.97461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/16/2022] [Indexed: 02/04/2023] Open
Abstract
We studied Liodessus diving beetles from six eastern Colombian Páramo areas, as well as from the Altiplano. We discovered a highly characteristic new species, based on male genital morphology, Liodessus santarositasp. nov., in the Páramo de Guantiva-Rusia. Specimens from the Altiplano around Bogotá, and the Páramos of Almorzadero, Chingaza, Matarredonda, Rabanal y Rio Bogotá and Sumapaz form one clade of genetically similar populations based on mitochondrial Cox1 sequence data. The individuals of this clade are sub-structured according to their geographic distribution. The populations differ from each other mainly in terms of body size and coloration and, at most, subtly in their genital morphology. In two cases, we find putative hybrid populations between Altiplano and Páramo areas. We suggest that the different Páramo populations are in an early phase of speciation, and perhaps already genetically isolated in some cases. They are here assigned subspecies status to highlight these ongoing processes pending more comprehensive geographic sampling and use of genomic data. We refer to this clade as the Liodessus bogotensis complex, containing Liodessus b. bogotensis Guignot, 1953; Liodessus b. almorzaderossp. nov.; Liodessus b. chingazassp. nov.; Liodessus b. lacunaviridis Balke et al., 2021, stat. nov.; Liodessus b. matarredondassp. nov., and Liodessus b. sumapazssp. nov.
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Zhang C, Mao B, Wang H, Dai L, Huang Y, Chen Z, Huang J. The Complete Mitogenomes of Three Grasshopper Species with Special Notes on the Phylogenetic Positions of Some Related Genera. INSECTS 2023; 14:85. [PMID: 36662013 PMCID: PMC9865218 DOI: 10.3390/insects14010085] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Clarifying phylogenetic position and reconstructing robust phylogeny of groups using various evidences are an eternal theme for taxonomy and systematics. In this study, the complete mitogenomes of Longzhouacris mirabilis, Ranacris albicornis, and Conophyma zhaosuensis were sequenced using next-generation sequencing (NGS), and the characteristics of the mitogenomes are presented briefly. The mitogenomes of the three species are all circular molecules with total lengths of 16,164 bp, 15,720 bp, and 16,190 bp, respectively. The gene structures and orders, as well as the characteristics of the mitogenomes, are similar to those of other published mitogenomes in Caelifera. The phylogeny of the main subfamilies of Acrididae with prosternal process was reconstructed using a selected dataset of mitogenome sequences under maximum likelihood (ML) and Bayesian inference (BI) frameworks. The results showed that the genus Emeiacris consistently fell into the subfamily Melanoplinae rather than Oxyinae, and the genus Choroedocus had the closest relationship with Shirackiacris of the subfamily Eyprepocnemidinae in both phylogenetic trees deduced from mitogenome protein coding genes (PCGs). This finding is entirely consistent with the morphological characters, which indicate that Emeiacris belongs to Melanoplinae and Choroedocus belongs to Eyprepocnemidinae. In addition, the genera Conophymacris and Xiangelilacris, as well as Ranacris and Menglacris, are two pairs of the closest relatives, but their phylogenetic positions need further study to clarify.
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Affiliation(s)
- Chulin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha 410004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China
- Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Benyong Mao
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Hanqiang Wang
- Shanghai Entomological Museum, Chinese Academy of Sciences, Shanghai 200032, China
| | - Li Dai
- Shanghai Entomological Museum, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Zhilin Chen
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China
| | - Jianhua Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha 410004, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China
- Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
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Forni G, Cussigh A, Brock PD, Jones BR, Nicolini F, Martelossi J, Luchetti A, Mantovani B. Taxonomic revision of the Australian stick insect genus Candovia (Phasmida: Necrosciinae): insight from molecular systematics and species-delimitation approaches. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The Phasmida genus Candovia comprises nine traditionally recognized species, all endemic to Australia. In this study, Candovia diversity is explored through molecular species-delimitation analyses using the COIFol gene fragment and phylogenetic inferences leveraging seven additional mitochondrial and nuclear loci. Molecular results were integrated with morphological observations, leading us to confirm the already described species and to the delineation of several new taxa and of the new genus Paracandovia. New Candovia species from various parts of Queensland and New South Wales are described and illustrated (C. alata sp. nov., C. byfieldensis sp. nov., C. dalgleishae sp. nov., C. eungellensis sp. nov., C. karasi sp. nov., C. koensi sp. nov. andC. wollumbinensis sp. nov.). New combinations are proposed and species removed from synonymy with the erection of the new genus Paracandovia (P. cercata stat. rev., comb. nov., P. longipes stat. rev., comb. nov., P. pallida comb. nov., P. peridromes comb. nov., P. tenera stat. rev., comb. nov.). Phylogenetic analyses suggest that the egg capitulum may have independently evolved multiple times throughout the evolutionary history of these insects. Furthermore, two newly described species represent the first taxa with fully developed wings in this previously considered apterous clade.
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Affiliation(s)
- Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
- Department of Agricultural and Environmental Sciences, University of Milan , Milano , Italy
| | - Alex Cussigh
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
- Department of Agricultural and Environmental Sciences, University of Milan , Milano , Italy
| | - Paul D Brock
- The Natural History Museum , Cromwell Road, London , UK
| | - Braxton R Jones
- School of Life and Environmental Sciences, The University of Sydney , Sydney NSW 2006 , Australia
| | - Filippo Nicolini
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Jacopo Martelossi
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
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Hlebec D, Sivec I, Podnar M, Kučinić M. DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera). PeerJ 2022; 10:e13213. [PMID: 35469200 PMCID: PMC9034701 DOI: 10.7717/peerj.13213] [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: 12/27/2021] [Accepted: 03/12/2022] [Indexed: 01/12/2023] Open
Abstract
Background The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy. Methods A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies. Results Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.
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Affiliation(s)
- Dora Hlebec
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia,Zoological Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany,Croatian Biospeleological Society, Zagreb, Croatia
| | - Ignac Sivec
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | | | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Laurito M, Ayala AM, Arias-Builes DL, Almirón WR. Improving the DNA Barcode Library of Mosquito Species With New Identifications and Discoveries in North-Central Argentina. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:173-183. [PMID: 34661674 DOI: 10.1093/jme/tjab160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 06/13/2023]
Abstract
The family Culicidae is represented by 244 species in Argentina, many of them with epidemiological importance. DNA barcodes are effective tools for identifying mosquito species, for knowing genetic variability, and for establishing phylogenetic relationships. This work aims to explore mosquito diversity employing different species delimitation approaches and to establish formally a DNA barcode library for the Argentinian mosquito fauna. Barcode fragments of 80 specimens of Argentinian mosquitoes of 28 species of the genera Aedeomyia Theobald (Diptera: Culicidae), Anopheles Meigen (Diptera: Culicidae), Coquillettidia Dyar (Diptera: Culicidae), Culex L. (Diptera: Culicidae), Haemagogus Williston (Diptera: Culicidae), Mansonia Blanchard (Diptera: Culicidae), Nyssorhynchus Blanchard (Diptera: Culicidae), Ochlerotatus Lynch-Arribálzaga (Diptera: Culicidae), Psorophora Robinneau-Desvoidy (Diptera: Culicidae) and Uranotaenia Lynch-Arribálzaga (Diptera: Culicidae) were sequenced. Another 82 sequences were obtained from public databases to establish the phylogenetic relationships using Maximum Likelihood and Bayesian Inference, and the species boundaries based on three approaches (ABGD, GMYC, and mPTP). Sixteen of the 28 species sequenced were recovered as monophyletic, of which 12 were also recognized as molecular operational taxonomic units according to the three methodologies. The disparity between morphology and barcode-based identifications could be explained by synonymy, species complexes occurrence, hybridization, incomplete lineage sorting, or the effect of the geographical scale of sampling. Twenty of the 28 sequenced species are new barcodes for Argentina and 11 are the first for science. This increases from 31 to 52 (12.7 to 21.31%) and from six to 10 (28.57 to 47.62%) the number of species and genera, respectively, with barcode sequences in Argentina. New species records are provided.
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Affiliation(s)
- M Laurito
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Avenida Velez Sarsfield 299, X5000JJC, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Avenida Velez Sarsfield 1611, X5016GCA, Córdoba, Argentina
| | - A M Ayala
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Avenida Velez Sarsfield 299, X5000JJC, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Instituto de Diversidad y Ecología Animal (IDEA), Avenida Velez Sarsfield 299, X5000JJC, Córdoba, Argentina
| | - D L Arias-Builes
- Centro de Investigación e Innovación Tecnológica (CENIIT), CONICET, Universidad Nacional de La Rioja. Gdor. Luis Vernet and Apostol Felipe, La Rioja, Argentina
| | - W R Almirón
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Avenida Velez Sarsfield 299, X5000JJC, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Avenida Velez Sarsfield 1611, X5016GCA, Córdoba, Argentina
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Davies OK, Dorey JB, Stevens MI, Gardner MG, Bradford TM, Schwarz MP. Unparalleled mitochondrial heteroplasmy and Wolbachia co-infection in the non-model bee, Amphylaeus morosus. CURRENT RESEARCH IN INSECT SCIENCE 2022; 2:100036. [PMID: 36003268 PMCID: PMC9387454 DOI: 10.1016/j.cris.2022.100036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]
Abstract
Mitochondrial heteroplasmy is the occurrence of more than one type of mitochondrial DNA within a single individual. Although generally reported to occur in a small subset of individuals within a species, there are some instances of widespread heteroplasmy across entire populations. Amphylaeus morosus is an Australian native bee species in the diverse and cosmopolitan bee family Colletidae. This species has an extensive geographical range along the eastern Australian coast, from southern Queensland to western Victoria, covering approximately 2,000 km. Seventy individuals were collected from five localities across this geographical range and sequenced using Sanger sequencing for the mitochondrial cytochrome c oxidase subunit I (COI) gene. These data indicate that every individual had the same consistent heteroplasmic sites but no other nucleotide variation, suggesting two conserved and widespread heteroplasmic mitogenomes. Ion Torrent shotgun sequencing revealed that heteroplasmy occurred across multiple mitochondrial protein-coding genes and is unlikely explained by transposition of mitochondrial genes into the nuclear genome (NUMTs). DNA sequence data also demonstrated a consistent co-infection of Wolbachia across the A. morosus distribution with every individual infected with both bacterial strains. Our data are consistent with the presence of two mitogenomes within all individuals examined in this species and suggest a major divergence from standard patterns of mitochondrial inheritance. Because the host's mitogenome and the Wolbachia genome are genetically linked through maternal inheritance, we propose three possible hypotheses that could explain maintenance of the widespread and conserved co-occurring bacterial and mitochondrial genomes in this species.
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Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R. ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 2021; 19:217. [PMID: 34587965 PMCID: PMC8479912 DOI: 10.1186/s12915-021-01141-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. RESULTS We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. CONCLUSIONS We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Johnathan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany.
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Meregalli M, Borovec R, Cervella P, Santovito A, Toševski I, Ottati S, Nakládal O. The Namaini, a new weevil tribe with six new genera from South Africa (Coleoptera: Curculionidae: Entiminae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Based on a phylogenetic analysis of a large number of mainly undescribed edaphic Entiminae from South Africa, a new tribe of entimine weevils is described, which includes six new genera. Taxa included in Namaini trib. nov. are clustered into seven clades that are used to delimit the following genera: Nama, type genus of the tribe, plus the new genera Cederbergia gen. nov., Cervellaea gen. nov., Namaquania gen. nov., Pentamerica gen. nov., Springbokia gen. nov. and Yamalaka gen. nov. A key to the genera is given and four new species are described.
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Affiliation(s)
- Massimo Meregalli
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina, Torino, Italy
| | - Roman Borovec
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Department of Forest Protection and Entomology, Kamýcká, Praha 6-Suchdol, Czech Republic
| | - Piero Cervella
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina, Torino, Italy
| | - Alfredo Santovito
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina, Torino, Italy
| | - Ivo Toševski
- Institute for Plant Protection and Environment, Banatska, Zemun, Serbia
| | - Sara Ottati
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini, Grugliasco (TO), Italy
| | - Oto Nakládal
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Department of Forest Protection and Entomology, Kamýcká, Praha 6-Suchdol, Czech Republic
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Chakraborty C, Sharma AR, Sharma G, Bhattacharya M, Patra BC, Sarkar BK, Banerjee S, Banerjee K, Lee SS. Understanding the molecular evolution of tiger diversity through DNA barcoding marker ND4 and NADH dehydrogenase complex using computational biology. Genes Genomics 2021; 43:759-773. [PMID: 33884571 DOI: 10.1007/s13258-021-01089-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Currently, Tigers (the top predator of an ecosystem) are on the list of endangered species. Thus the need is to understand the tiger's population genomics to design their conservation strategies. OBJECTIVE We analyzed the molecular evolution of tiger diversity using NADH dehydrogenase subunit 4 (ND4), a significant electron transport chain component. METHODS We have analyzed nucleotide composition and distribution pattern of ND genes, molecular evolution, evolutionary conservation pattern and conserved blocks of NADH, phylogenomics of ND4, and estimating species divergence, etc., using different bioinformatics tools and software, and MATLAB programming and computing environment. RESULTS The nucleotide composition and distribution pattern of ND genes in the tiger genome demonstrated an increase in the number of adenine (A) and a lower trend of A+T content in some place of the distribution analysis. However, the observed distributions were not significant (P > 0.05). Evolutionary conservation analysis showed three highly align blocks (186 to 198, 406 to 416, and 527 to 545). On mapping the molecular evolution of ND4 among model species (n = 30), we observed its presence in a broader range of species. ND4 based molecular evolution of tiger diversity and time divergence for a tiger (20 different other species) shows that genus Panthera originated more or less at a similar time. CONCLUSIONS The nucleotide composition and nucleotide distribution pattern of tiger ND genes showed the evolutionary pattern and origin of tiger and Panthera lineage concerning the molecular clock, which will help to understand their adaptive evolution.
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Affiliation(s)
- Chiranjib Chakraborty
- Institute For Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, Republic of Korea. .,Department of Biotechnology, Adamas University, North, 24 Parganas, Kolkata, West Bengal, 700126, India.
| | - Ashish Ranjan Sharma
- Institute For Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, Republic of Korea
| | - Garima Sharma
- Department of Biomedical Science & Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Manojit Bhattacharya
- Institute For Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, Republic of Korea
| | - Bidhan C Patra
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal, India
| | - Bimal Kumar Sarkar
- Department of Physics, Adamas University, North, 24 Parganas, Kolkata, West Bengal, 700126, India
| | - Saptarshi Banerjee
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Kankana Banerjee
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Sang-Soo Lee
- Institute For Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, Republic of Korea. .,Institute for Skeletal Aging and Orthopedic Surgery, Hallym University Hospital-College of Medicine, Chuncheon-si, Gangwon-do, 24252, Republic of Korea.
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11
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Freitag H, de Vries R, Paterno M, Maestri S, Delledonne M, Thompson CG, Lamed H, Lambert R, Fox MF, Gonzalez MC, Delocado ED, Sabordo MR, Pangantihon CV, Njunjić I. Hydraena (s.str.) dinarica, new species (Coleoptera: Hydraenidae) along with further records of Hydraena spp. from Durmitor National Park, Montenegro and comments on the DNA barcoding problem with the genus. Biodivers Data J 2021; 9:e59892. [PMID: 33519262 PMCID: PMC7815695 DOI: 10.3897/bdj.9.e59892] [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: 10/24/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022] Open
Abstract
Background Long-palped Water Beetles were collected during a taxon expedition in Montenegro which involved citizen scientists, students and taxonomists. The material was collected from springs, brooks, fens and the Tara River, at altitudes between 600 m and 1450 m above sea level, using fine-meshed hand-nets and by manual checking of submerged substrates. The morphological species delimitation was supplemented and congruent with mtDNA sequences mainly obtained in the field using the newly-developed MinION-based ONTrack pipeline. New information The new species Hydraenadinarica Freitag & de Vries, sp. n. from Durmitor Mt. is described, illustrated and compared in detail to closely-related congeners of the H.saga d'Orchymont, 1930/H.emarginata Rey, 1885 species complex. Five additional species and female specimens of two unidentified morphospecies of the genus were also recorded in the vicinity of Durmitor National Park. New records and the first DNA barcodes for Hydraenabiltoni Jäch & Díaz, 2012 (endemic to Montenegro) and H.morio Kiesenwetter, 1849 are provided. Further records of H.nigrita Germar, 1824, H.minutissima Stephens, 1829, H.subintegra Ganglbauer, 1901 and females of two unidentified morphospecies are commented upon. The resulting inter- and intraspecific genetic distances and some observations of low or zero sequence divergence between recently-diverged species of Hydraena Kugelann, 1794 are briefly discussed.
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Affiliation(s)
- Hendrik Freitag
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Rick de Vries
- Amstelveenseweg 980B, Amsterdam, Netherlands Amstelveenseweg 980B Amsterdam Netherlands
| | - Marta Paterno
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, Verona, Italy University of Verona, Department of Biotechnology, Strada Le Grazie 15 Verona Italy
| | - Simone Maestri
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, Verona, Italy University of Verona, Department of Biotechnology, Strada Le Grazie 15 Verona Italy
| | - Massimo Delledonne
- University of Verona, Department of Biotechnology, Strada Le Grazie 15, Verona, Italy University of Verona, Department of Biotechnology, Strada Le Grazie 15 Verona Italy
| | - Cameron G Thompson
- Oxford Brookes University, Department of Health and Life Sciences, Oxford, United Kingdom Oxford Brookes University, Department of Health and Life Sciences Oxford United Kingdom
| | - Helena Lamed
- 39 av Melbourne, Mont-Royal, Quebec, Canada 39 av Melbourne, Mont-Royal Quebec Canada
| | - Rebekah Lambert
- 340 N. Adams Street, Eugene, Oregon, United States of America 340 N. Adams Street Eugene, Oregon United States of America
| | - Michael F Fox
- 340 N. Adams Street, Eugene, Oregon, United States of America 340 N. Adams Street Eugene, Oregon United States of America
| | - Mariela C Gonzalez
- Taxon Expeditions, Rembrandtstraat 20, Leiden, Netherlands Taxon Expeditions, Rembrandtstraat 20 Leiden Netherlands
| | - Emmanuel D Delocado
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Marc R Sabordo
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Clister V Pangantihon
- Ateneo de Manila University, Quezon City, Philippines Ateneo de Manila University Quezon City Philippines
| | - Iva Njunjić
- Taxon Expeditions, Rembrandtstraat 20, Leiden, Netherlands Taxon Expeditions, Rembrandtstraat 20 Leiden Netherlands.,Naturalis Biodiversity Center, Darwinweg 2, Leiden, Netherlands Naturalis Biodiversity Center, Darwinweg 2 Leiden Netherlands
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12
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Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, Jr FČ. Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae). Zookeys 2021; 1003:31-55. [PMID: 33384561 PMCID: PMC7752891 DOI: 10.3897/zookeys.1003.55541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/17/2020] [Indexed: 11/17/2022] Open
Abstract
Ancyronyxlianlabangorumsp. nov. (Coleoptera, Elmidae), a new spider riffle beetle from the Kelabit Highlands (Sarawak, northern Borneo), is described. Illustrations of the habitus and diagnostic characters of the new species and the similar, polymorphic A.pulcherrimus Kodada et al. are presented. Differences to closely related species, based on COI nucleotide sequences and morphological characters, are discussed. Ancyronyxpulcherrimus is here recorded from Sarawak for the first time, based on DNA barcoding.
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Affiliation(s)
- Ján Kodada
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina B-1, SK-842 15, Bratislava, Slovakia Comenius University Bratislava Slovakia
| | - Manfred A Jäch
- Naturhistorisches Museum Wien, Burgring 7, A-1010, Wien, Austria Naturhistorisches Museum Wien Vienna Austria
| | - Hendrik Freitag
- Ateneo de Manila University, Biology Department, School of Science and Engineering, Loyola Heights, Quezon City, 1108, Philippines Ateneo de Manila University Quezon Philippines.,Universiti Brunei Darussalam, Environmental and Life Sciences, Faculty of Science, Jalan Tungku Link, Gadong, BE1410, Brunei Universiti Brunei Darussalam Gadong Brunei.,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, 10115, Germany Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Zuzana Čiamporová-Zaťovičová
- Zoology Lab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523, Bratislava, Slovakia Plant Science and Biodiversity Centre, Slovak Academy of Sciences Bratislava Slovakia
| | - Katarína Goffová
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina B-1, SK-842 15, Bratislava, Slovakia Comenius University Bratislava Slovakia
| | - Dávid Selnekovič
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina B-1, SK-842 15, Bratislava, Slovakia Comenius University Bratislava Slovakia
| | - Fedor Čiampor Jr
- Zoology Lab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523, Bratislava, Slovakia Plant Science and Biodiversity Centre, Slovak Academy of Sciences Bratislava Slovakia
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Hendrich L, Watts CH, Balke M. The “minute diving beetles” of southern Australia – taxonomic revision of Gibbidessus Watts, 1978, with description of six new species (Coleoptera, Dytiscidae, Bidessini). Zookeys 2020; 975:11-49. [PMID: 33117063 PMCID: PMC7572521 DOI: 10.3897/zookeys.975.55456] [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: 06/15/2020] [Accepted: 09/08/2020] [Indexed: 11/20/2022] Open
Abstract
Morphology and mitochondrial DNA sequence data are used to reassess the taxonomy of Australian diving beetles previously assigned to the genera Uvarus Guignot, 1939 and Gibbidessus Watts, 1978. Gibbidessus was described as a monotypic genus for Gibbidessuschipi Watts, 1978. The genus is significantly extended here. Based on molecular systematic evidence, Uvaruspictipes (Lea, 1899) is transferred to Gibbidessus. Gibbidessuschipi and Gibbidessuspictipescomb. nov. are redescribed, and six new species are described: Gibbiddessusatomussp. nov. (SW Australia, Northcliffe area) [the smallest epigean diving beetle in Australia], G.davidisp. nov. (SW Australia), G.drikdrikensissp. nov. (Victoria), G.kangarooensissp. nov. (SA Kangaroo Island), G.pederzaniisp. nov. (SW Australia, Nannup area), and G. rottnestensissp. nov. (SW Australia). Species are delineated using characters such as male genital structure and beetle size, shape and colour pattern. Mitochondrial Cox1 data for 27 individuals, representing five species, were generated, and revealed clusters congruent with the morphological evidence. Gibbidessus occur in southern Australia, with the centre of diversification in the isolated peat- and wetlands of SW Australia. All species occur in very shallow water of seasonal, exposed or half-shaded wetlands and flooded meadows.
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Bhunjun CS, Dong Y, Jayawardena RS, Jeewon R, Phukhamsakda C, Bundhun D, Hyde KD, Sheng J. A polyphasic approach to delineate species in Bipolaris. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00446-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Xiao L, Zhang S, Long C, Guo Q, Xu J, Dai X, Wang J. Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications. Genes (Basel) 2019; 10:E992. [PMID: 31805706 PMCID: PMC6947639 DOI: 10.3390/genes10120992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/16/2022] Open
Abstract
A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.
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Affiliation(s)
- Lifang Xiao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jianguo Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
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16
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Hendrich L, Shaverdo H, Hájek J, Balke M. Taxonomic revision of Australian Copelatus Erichson, 1832 (Coleoptera, Dytiscidae, Copelatinae). Zookeys 2019; 889:81-152. [PMID: 31777439 PMCID: PMC6872603 DOI: 10.3897/zookeys.889.39090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/24/2019] [Indexed: 11/12/2022] Open
Abstract
The genus Copelatus in Australia is revised and nine species are recognised. One new species, Copelatus martinbaehri sp. nov., is described from Papua New Guinea (Central Province) and Cape York Peninsula (Iron Range NP and Mt Tozer). Copelatus divisus Watts, 1978, syn. nov., is considered a junior synonym of C. portior Guignot, 1956, described from New Guinea. Species delimitation is based on the morphological characters and Cox1 data. All species are (re)described, and their important species characters (median lobes, parameres, habitus and colour patterns) are illustrated. A key to all nine species is provided. The known distribution and habitat preferences of each species are outlined briefly. In Australia, all nine species are distributed in the northern half of the continent. Four species are also reported from New Guinea: in addition to C. martinbaehri sp. nov., we record C. clarki Sharp, 1882 for the first time from southern New Guinea, and consider literature records of C. irregularis W.J. Macleay, 1871 and C. marginatus Sharp, 1882 from New Guinea as doubtful. Copelatus portior is widely distributed in Australasia, while C. tenebrosus is widely distributed in the Indomalayan and Australasian realms. All Australian Copelatus are confirmed to be lentic, found in a large variety of stagnant water, mainly in lowland areas up to 250 m.
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Affiliation(s)
- Lars Hendrich
- SNSB-Zoologische Staatssammlung, Münchhausenstrasse 21, D-81247 München, GermanySNSB-Zoologische StaatssammlungMünchenGermany
| | - Helena Shaverdo
- Naturhistorisches Museum, Burgring 7, 1010 Vienna, AustriaNaturhistorisches MuseumViennaAustria
| | - Jiří Hájek
- Department of Entomology, National Museum, Cirkusová 1740, CZ-193 00 Praha 9, Horní Počernice, Czech RepublicDepartment of Entomology, National MuseumPrahaCzech Republic
| | - Michael Balke
- SNSB-Zoologische Staatssammlung, Münchhausenstrasse 21, D-81247 München, GermanySNSB-Zoologische StaatssammlungMünchenGermany
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17
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Scicchitano V, Dedeine F, Mantovani B, Luchetti A. Molecular systematics, biogeography, and colony fusion in the European dry-wood termites Kalotermes spp. (Blattodea, Termitoidae, Kalotermitidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2018; 108:523-531. [PMID: 29070094 DOI: 10.1017/s0007485317001080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
European dry-wood termites belong to the genus Kalotermes (Kalotermitidae), one of the two termite genera in Europe. Until the recent description of two new species, Kalotermes italicus in Italy and Kalotermes phoenicae in the eastern Mediterranean area, Kalotermes flavicollis was the only taxon known in this region. The presence of additional entities, suggested by morphological and physiological variation observed in K. flavicollis, was supported by molecular studies revealing four distinct genetic lineages: lineage A, K. flavicollis sensu strictu, from the Aegean area to Italy; lineage B, in Tuscany; lineage SC, in Sardinia and Corsica; lineage SF, in southern France. Lineages A and B may form mixed colonies, suggesting hybridization. To draw a more detailed picture of Kalotermes evolution and biogeography in Europe, we analyzed samples from previously unsampled areas, such as Spain and southern Italy, by means of the highly informative cox1/trnL/cox2 mitochondrial DNA marker. Overall, phylogenetic analyses confirmed previously identified lineages and taxa, but widened the distribution of the lineage SC to the mainland and of the lineage SF to Spain and Portugal. Results further provided evidence for the synonymy between lineage B and K. italicus. Species delimitation analysis suggested that the three K. flavicollis lineages, as well as K. italicus, can be separate taxa. Data also suggest a possible interspecific hybridization between K. italicus and both K. flavicollis lineages A and SC.
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Affiliation(s)
- V Scicchitano
- Dipartimento di Scienze Biologiche,Geologiche e Ambientali - Università di Bologna,via Selmi 3, 40126 Bologna,Italy
| | - F Dedeine
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université François-Rabelais de Tours,Parc Grandmont, 37200 Tours,France
| | - B Mantovani
- Dipartimento di Scienze Biologiche,Geologiche e Ambientali - Università di Bologna,via Selmi 3, 40126 Bologna,Italy
| | - A Luchetti
- Dipartimento di Scienze Biologiche,Geologiche e Ambientali - Università di Bologna,via Selmi 3, 40126 Bologna,Italy
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Stokkan M, Jurado-Rivera JA, Oromí P, Juan C, Jaume D, Pons J. Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda). Mol Phylogenet Evol 2018; 127:988-999. [PMID: 30004011 DOI: 10.1016/j.ympev.2018.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 11/29/2022]
Abstract
The amphi-Atlantic distributions exhibited by many thalassoid stygobiont (obligate subterranean) crustaceans have been explained by fragmentation by plate tectonics of ancestral shallow water marine populations. The amphipod stygobiont genus Pseudoniphargus is distributed across the Mediterranean region but also in the North Atlantic archipelagos of Bermuda, Azores, Madeira and the Canaries. We used species delimitation methods and mitogenome phylogenetic analyses to clarify the species diversity and evolutionary relationships within the genus and timing their diversification. Analyses included samples from the Iberian Peninsula, northern Morocco, the Balearic, Canarian, Azores and Madeira archipelagoes plus Bermuda. In most instances, morphological and molecular-based species delimitation analyses yielded consistent results. Notwithstanding, in a few cases either incipient speciation with no involvement of detectable morphological divergence or species crypticism were the most plausible explanations for the disagreement found between morphological and molecular species delimitations. Phylogenetic analyses based on a robust calibrated mitochondrial tree suggested that Pseudoniphargus lineages have a younger age than for other thalassoid amphipods displaying a disjunct distribution embracing both sides of the Atlantic Ocean. A major split within the family was estimated to occur at the Paleocene, when a lineage from Northern Iberian Peninsula diverged from the rest of pseudoniphargids. Species diversification in the peri-Mediterranean area was deduced to occur in early Miocene to Tortonian times, while in the Atlantic islands it started in the Pliocene. Our results show that the current distribution pattern of Pseudoniphargus resulted from a complex admix of relatively ancient vicariance events and several episodes of long- distance dispersal.
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Affiliation(s)
- Morten Stokkan
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain
| | - José A Jurado-Rivera
- Dept. of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7'5, Palma 07122, Balearic Islands, Spain
| | - Pedro Oromí
- Dept. of Animal Biology, Edaphology and Geology, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, s/n. Campus de Anchieta, Ap. correos 456, La Laguna 38200, Tenerife, Spain
| | - Carlos Juan
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain; Dept. of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7'5, Palma 07122, Balearic Islands, Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, Esporles, 07190 Balearic Islands, Spain.
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Freitag H, Kodada J. A taxonomic review of the genus AncyronyxErichson, 1847 from Sulawesi (Insecta: Coleoptera: Elmidae). J NAT HIST 2017. [DOI: 10.1080/00222933.2017.1285447] [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]
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20
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Hawlitschek O, Morinière J, Lehmann GUC, Lehmann AW, Kropf M, Dunz A, Glaw F, Detcharoen M, Schmidt S, Hausmann A, Szucsich NU, Caetano-Wyler SA, Haszprunar G. DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland. Mol Ecol Resour 2016; 17:1037-1053. [PMID: 27863033 DOI: 10.1111/1755-0998.12638] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 12/21/2022]
Abstract
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.
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Affiliation(s)
- O Hawlitschek
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37, 08003, Barcelona, Spain
| | - J Morinière
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - G U C Lehmann
- Department of Biology, Behavioural Physiology, Humboldt University Berlin, Invalidenstr. 43, 10115, Berlin, Germany
| | - A W Lehmann
- Orthoptera Working Group Brandenburg and Berlin, Friedensallee 37, 14532, Stahnsdorf, Germany
| | - M Kropf
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Gregor Mendel-Str. 33, 1180, Vienna, Austria
| | - A Dunz
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - F Glaw
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - M Detcharoen
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - S Schmidt
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - A Hausmann
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - N U Szucsich
- 3rd Zoological Dep., Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - S A Caetano-Wyler
- Université de Genève, Département de Génétique et Evolution, Quai Ernest Ansermet 30, 1211, Geneva 4, Switzerland
| | - G Haszprunar
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Department Biology II and GeoBio-Center of Ludwig-Maximilians-Universität München, Groβhaderner Str. 2, 82152, Planegg-Martinsried, Germany
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21
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Lyra GDM, Gurgel CFD, Costa EDS, de Jesus PB, Oliveira MC, Oliveira EC, Davis CC, Nunes JMDC. Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using molecular and morphological data. JOURNAL OF PHYCOLOGY 2016; 52:997-1017. [PMID: 27485203 DOI: 10.1111/jpy.12456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
Species in the genus Gracilaria that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the Gracilaria domingensis complex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and rbcL). We additionally applied six single-marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the G. domingensis complex includes seven distinct species, each of which are not all most closely related: G. cervicornis; a ressurected G. ferox; G. apiculata subsp. apiculata; a new species, Gracilaria baiana sp. nov.; G. intermedia subsp. intermedia; G. venezuelensis; and G. domingensis sensu stricto, which includes the later heterotypic synonym, G. yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae.
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Affiliation(s)
- Goia de M Lyra
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Feira de Santana, Bahia, 44031-460, Brazil
| | - C Frederico D Gurgel
- The Environment Institute, Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, DX 650-418, Adelaide, South Australia, 5005, Australia
- Department of Environment, Water and Natural Resources, State Herbarium of South Austrália, PO Box 2732, Kent Town, South Australia, 5071, Austrália
- Departamento de Botânica, CCB, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, São Paulo, 05508-090, Brazil
| | - Emmanuelle da S Costa
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, São Paulo, 05508-090, Brazil
| | - Priscila B de Jesus
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Feira de Santana, Bahia, 44031-460, Brazil
| | - Mariana C Oliveira
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, São Paulo, 05508-090, Brazil
| | - Eurico C Oliveira
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, São Paulo, 05508-090, Brazil
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - José Marcos de Castro Nunes
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s/n, Salvador, Bahia, 40170-115, Brazil
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Sikes DS, Bowser M, Morton JM, Bickford C, Meierotto S, Hildebrandt K. Building a DNA barcode library of Alaska's non-marine arthropods. Genome 2016; 60:248-259. [PMID: 28106469 DOI: 10.1139/gen-2015-0203] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska - i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.
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Affiliation(s)
- Derek S Sikes
- a University of Alaska Museum, Fairbanks, AK 99775-6960, USA
| | - Matthew Bowser
- b U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge, P.O. Box 2139, Soldotna, AK 99669, USA
| | - John M Morton
- b U.S. Fish and Wildlife Service, Kenai National Wildlife Refuge, P.O. Box 2139, Soldotna, AK 99669, USA
| | - Casey Bickford
- a University of Alaska Museum, Fairbanks, AK 99775-6960, USA
| | - Sarah Meierotto
- a University of Alaska Museum, Fairbanks, AK 99775-6960, USA.,c University of Kentucky, S-225 Ag. Sci. N, Lexington, KY 40546-0091, USA
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Meusel F, Schwentner M. Molecular and morphological delimitation of Australian Triops species (Crustacea: Branchiopoda: Notostraca)—large diversity and little morphological differentiation. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0306-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Islands in the desert: Species delimitation and evolutionary history of Pseudotetracha tiger beetles (Coleoptera: Cicindelidae: Megacephalini) from Australian salt lakes. Mol Phylogenet Evol 2016; 101:279-285. [DOI: 10.1016/j.ympev.2016.05.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 05/09/2016] [Accepted: 05/16/2016] [Indexed: 11/19/2022]
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Pentinsaari M, Vos R, Mutanen M. Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles. Mol Ecol Resour 2016; 17:393-404. [DOI: 10.1111/1755-0998.12557] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Mikko Pentinsaari
- Department of Genetics and Physiology; University of Oulu; PO Box 3000 Oulu FI-90014 Finland
| | - Rutger Vos
- Naturalis Biodiversity Center; Darwinweg 4 2333 CR Leiden the Netherlands
| | - Marko Mutanen
- Department of Genetics and Physiology; University of Oulu; PO Box 3000 Oulu FI-90014 Finland
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. Zookeys 2016; 592:121-41. [PMID: 27408547 PMCID: PMC4926639 DOI: 10.3897/zookeys.592.8316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/23/2016] [Indexed: 12/23/2022] Open
Abstract
As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | | | - Jérome Morinière
- Taxonomic coordinator – Barcoding Fauna Bavarica, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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Vasconcelos R, Montero-Mendieta S, Simó-Riudalbas M, Sindaco R, Santos X, Fasola M, Llorente G, Razzetti E, Carranza S. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago. PLoS One 2016; 11:e0149985. [PMID: 26930572 PMCID: PMC4772999 DOI: 10.1371/journal.pone.0149985] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.
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Affiliation(s)
- Raquel Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | - Santiago Montero-Mendieta
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | - Marc Simó-Riudalbas
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Xavier Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Mauro Fasola
- Dipartimento Scienze della Terra e dell'Ambiente, Università degli studi di Pavia, Pavia, Italy
| | - Gustavo Llorente
- Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Edoardo Razzetti
- Museo di Storia Naturale, Università degli studi di Pavia, Pavia, Italy
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-UPF, Consejo Superior de Investigaciones Científicas- Universitat Pompeu Fabra), Barcelona, Spain
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Thormann B, Ahrens D, Marín Armijos D, Peters MK, Wagner T, Wägele JW. Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding. PLoS One 2016; 11:e0148268. [PMID: 26849826 PMCID: PMC4744027 DOI: 10.1371/journal.pone.0148268] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 01/16/2016] [Indexed: 12/15/2022] Open
Abstract
Background Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates. Methodology/Principal Findings Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284–289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469–481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation. Conclusions/Significance Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.
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Affiliation(s)
- Birthe Thormann
- Zoological Research Museum Alexander Koenig, Bonn, Germany
- * E-mail:
| | - Dirk Ahrens
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Diego Marín Armijos
- Museo de Colecciones Biológicas MUTPL, Departamento de Ciencias Naturales, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Marcell K. Peters
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thomas Wagner
- Abteilung Biologie, Institut für Integrierte Naturwissenschaften, Universität Koblenz–Landau, Koblenz, Germany
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Balke M, Ruthensteiner B, Warikar EL, Neven K, Hendrich L. Two new species of Limbodessus diving beetles from New Guinea - short verbal descriptions flanked by online content (digital photography, μCT scans, drawings and DNA sequence data). Biodivers Data J 2016:e7096. [PMID: 26752969 PMCID: PMC4700388 DOI: 10.3897/bdj.3.e7096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/18/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND To date only one species of Limbodessus diving beetles has been reported from the Island of New Guinea, L. compactus (Clark, 1862), which is widerspread in the Australian region. NEW INFORMATION We describe two new species of microendemic New Guinea Limbodessus and use a compact descriptive format flanked by enriched online content in wiki powered species pages. Limbodessus baliem sp.n. is described from ca. 1,600 m altitude in the Baliem Valley of Papua and Limbodessus alexanderi sp.n. from >3,000 m altitude north of Sugapa, Papua. Based on our analysis, we also transfer three species from other genera to Limbodessus Guignot, 1939, with the following changes: Limbodessus deflectus (Ordish, 1966), new combination; Limbodessus leveri (J. Balfour-Browne, 1944), new combination; and Limbodessus plicatus (Sharp, 1882), new combination.
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Lin X, Stur E, Ekrem T. Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes. PLoS One 2015; 10:e0138993. [PMID: 26406595 PMCID: PMC4583400 DOI: 10.1371/journal.pone.0138993] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/07/2015] [Indexed: 01/08/2023] Open
Abstract
DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120-242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4-5% threshold is appropriate to delineate species of Tanytarsus non-biting midges.
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Affiliation(s)
- Xiaolong Lin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Elisabeth Stur
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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Schwarzfeld MD, Sperling FAH. Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae). Mol Phylogenet Evol 2015; 93:234-48. [PMID: 26265257 DOI: 10.1016/j.ympev.2015.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 07/31/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
Abstract
DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus.
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Affiliation(s)
- Marla D Schwarzfeld
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Dumas P, Barbut J, Le Ru B, Silvain JF, Clamens AL, d’Alençon E, Kergoat GJ. Phylogenetic molecular species delimitations unravel potential new species in the pest genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae). PLoS One 2015; 10:e0122407. [PMID: 25853412 PMCID: PMC4390195 DOI: 10.1371/journal.pone.0122407] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/20/2015] [Indexed: 02/03/2023] Open
Abstract
Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities.
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Affiliation(s)
- Pascaline Dumas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jérôme Barbut
- Direction des collections—USM 602, Muséum National d’Histoire Naturelle, Paris, France
| | - Bruno Le Ru
- IRD/CNRS, Laboratoire Evolution Génomes Spéciation, Avenue de la terrasse, Gif-sur-Yvette, France and Université Paris-Sud 11, Orsay, France
- Unité de Recherche IRD 072, African Insect Science for Food and Health (icipe), Nairobi, Kenya
| | - Jean-François Silvain
- IRD/CNRS, Laboratoire Evolution Génomes Spéciation, Avenue de la terrasse, Gif-sur-Yvette, France and Université Paris-Sud 11, Orsay, France
| | - Anne-Laure Clamens
- INRA—UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Emmanuelle d’Alençon
- UM2—UMR 1333 DGIMI, Université Montpellier 2, Montpellier, France
- INRA—UMR 1333 DGIMI, Université Montpellier 2, Montpellier, France
| | - Gael J. Kergoat
- INRA—UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), Montferrier-sur-Lez, France
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Kekkonen M, Mutanen M, Kaila L, Nieminen M, Hebert PDN. Delineating species with DNA barcodes: a case of taxon dependent method performance in moths. PLoS One 2015; 10:e0122481. [PMID: 25849083 PMCID: PMC4406103 DOI: 10.1371/journal.pone.0122481] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/22/2015] [Indexed: 11/26/2022] Open
Abstract
The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.
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Affiliation(s)
- Mari Kekkonen
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Oulu, Finland
| | - Lauri Kaila
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
| | - Marko Nieminen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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Li Y, Gunter N, Pang H, Bocak L. DNA-based species delimitation separates highly divergent populations within morphologically coherent clades of poorly dispersing beetles. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yun Li
- The Museum of Biology; Sun Yat-sen University; Guangzhou 510275 Guangdong China
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 771 46 Olomouc Czech Republic
| | - Nicole Gunter
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 771 46 Olomouc Czech Republic
| | - Hong Pang
- The Museum of Biology; Sun Yat-sen University; Guangzhou 510275 Guangdong China
| | - Ladislav Bocak
- Department of Zoology; Faculty of Science; Palacky University; 17. listopadu 50 771 46 Olomouc Czech Republic
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Meier R, Wong W, Srivathsan A, Foo M. $1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics 2015; 32:100-110. [DOI: 10.1111/cla.12115] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2015] [Indexed: 12/01/2022] Open
Affiliation(s)
- Rudolf Meier
- Lee Kong Chian Natural History Museum; National University of Singapore; 6 Science Drive 2 Singapore 117546 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
- University Scholars Programme; National University of Singapore, University Town; 18 College Avenue East Singapore 138593 Singapore
| | - Winghing Wong
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Amrita Srivathsan
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Maosheng Foo
- Lee Kong Chian Natural History Museum; National University of Singapore; 6 Science Drive 2 Singapore 117546 Singapore
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Hendrich L, Morinière J, Haszprunar G, Hebert PDN, Hausmann A, Köhler F, Balke M. A comprehensive
DNA
barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD. Mol Ecol Resour 2014; 15:795-818. [DOI: 10.1111/1755-0998.12354] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/23/2014] [Accepted: 11/26/2014] [Indexed: 02/03/2023]
Affiliation(s)
- Lars Hendrich
- Bavarian State Collection of Zoology (SNSB – ZSM) Münchhausenstrasse 21 81247 München Germany
| | - Jérôme Morinière
- Bavarian State Collection of Zoology (SNSB – ZSM) Münchhausenstrasse 21 81247 München Germany
| | - Gerhard Haszprunar
- Bavarian State Collection of Zoology (SNSB – ZSM) Münchhausenstrasse 21 81247 München Germany
- Department of Biology II and GeoBioCenter Ludwig‐Maximilians‐University Richard‐Wagner‐Straβe 10 80333 München Germany
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario (BIO) University of Guelph Guelph ON N1G 2W1 Canada
| | - Axel Hausmann
- Bavarian State Collection of Zoology (SNSB – ZSM) Münchhausenstrasse 21 81247 München Germany
- Department of Biology II and GeoBioCenter Ludwig‐Maximilians‐University Richard‐Wagner‐Straβe 10 80333 München Germany
| | - Frank Köhler
- Coleopterological Science Office – Frank Köhler Strombergstrasse 22a 53332 Bornheim Germany
| | - Michael Balke
- Bavarian State Collection of Zoology (SNSB – ZSM) Münchhausenstrasse 21 81247 München Germany
- Department of Biology II and GeoBioCenter Ludwig‐Maximilians‐University Richard‐Wagner‐Straβe 10 80333 München Germany
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Dávalos LM, Russell AL. Sex-biased dispersal produces high error rates in mitochondrial distance-based and tree-based species delimitation. J Mammal 2014. [DOI: 10.1644/14-mamm-a-107] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Huemer P, Karsholt O, Mutanen M. DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). Zookeys 2014:91-111. [PMID: 24843272 PMCID: PMC4023261 DOI: 10.3897/zookeys.404.7234] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/07/2014] [Indexed: 11/20/2022] Open
Abstract
We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera, Gelechiidae), based on data from 44 European species (including 4 subspecies). Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c oxidase 1) gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy of these taxa has to be re-assessed in the future. We investigated one such deep split in Caryocolum amaurella (Hering, 1924) and found it in congruence with yet unrecognized diagnostic morphological characters and specific host-plants. The integrative species delineation leads to the description of Caryocolum crypticumsp. n. from northern Italy, Switzerland and Greece. The new species and the hitherto intermixed closest relative C. amaurella are described in detail and adults and genitalia of both species are illustrated and a lectotype of C. amaurella is designated; a diagnostic comparison of the closely related C. iranicum Huemer, 1989, is added.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebgsges.m.b.H., Naturwissenschaftliche Sammlungen, Feldstr. 11a, A-6020 Innsbruck, Austria
| | - Ole Karsholt
- Zoological Museum, Natural History Museum of Denmark, Universitetsparken 15, DK-2100 Copenhagen
| | - Marko Mutanen
- Biodiversity Unit, Department of Biology, University of Oulu, Oulu, Finland
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Geiger MF, Herder F, Monaghan MT, Almada V, Barbieri R, Bariche M, Berrebi P, Bohlen J, Casal-Lopez M, Delmastro GB, Denys GPJ, Dettai A, Doadrio I, Kalogianni E, Kärst H, Kottelat M, Kovačić M, Laporte M, Lorenzoni M, Marčić Z, Özuluğ M, Perdices A, Perea S, Persat H, Porcelotti S, Puzzi C, Robalo J, Šanda R, Schneider M, Šlechtová V, Stoumboudi M, Walter S, Freyhof J. Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes. Mol Ecol Resour 2014; 14:1210-21. [DOI: 10.1111/1755-0998.12257] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/15/2014] [Accepted: 03/19/2014] [Indexed: 11/29/2022]
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Contreras Gutiérrez MA, Vivero RJ, Vélez ID, Porter CH, Uribe S. DNA barcoding for the identification of sand fly species (Diptera, Psychodidae, Phlebotominae) in Colombia. PLoS One 2014; 9:e85496. [PMID: 24454877 PMCID: PMC3893204 DOI: 10.1371/journal.pone.0085496] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/25/2013] [Indexed: 12/03/2022] Open
Abstract
Sand flies include a group of insects that are of medical importance and that vary in geographic distribution, ecology, and pathogen transmission. Approximately 163 species of sand flies have been reported in Colombia. Surveillance of the presence of sand fly species and the actualization of species distribution are important for predicting risks for and monitoring the expansion of diseases which sand flies can transmit. Currently, the identification of phlebotomine sand flies is based on morphological characters. However, morphological identification requires considerable skills and taxonomic expertise. In addition, significant morphological similarity between some species, especially among females, may cause difficulties during the identification process. DNA-based approaches have become increasingly useful and promising tools for estimating sand fly diversity and for ensuring the rapid and accurate identification of species. A partial sequence of the mitochondrial cytochrome oxidase gene subunit I (COI) is currently being used to differentiate species in different animal taxa, including insects, and it is referred as a barcoding sequence. The present study explored the utility of the DNA barcode approach for the identification of phlebotomine sand flies in Colombia. We sequenced 700 bp of the COI gene from 36 species collected from different geographic localities. The COI barcode sequence divergence within a single species was <2% in most cases, whereas this divergence ranged from 9% to 26.6% among different species. These results indicated that the barcoding gene correctly discriminated among the previously morphologically identified species with an efficacy of nearly 100%. Analyses of the generated sequences indicated that the observed species groupings were consistent with the morphological identifications. In conclusion, the barcoding gene was useful for species discrimination in sand flies from Colombia.
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Affiliation(s)
| | - Rafael J. Vivero
- Program of Study and Control of Tropical Diseases, University of Antioquia, Medellin, Colombia
| | - Iván D. Vélez
- Program of Study and Control of Tropical Diseases, University of Antioquia, Medellin, Colombia
| | - Charles H. Porter
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, United States of America
| | - Sandra Uribe
- Molecular Systematics Group, National University of Colombia, Medellin, Colombia
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41
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Huang J, Zhang A, Mao S, Huang Y. DNA barcoding and species boundary delimitation of selected species of Chinese Acridoidea (Orthoptera: Caelifera). PLoS One 2013; 8:e82400. [PMID: 24376533 PMCID: PMC3869712 DOI: 10.1371/journal.pone.0082400] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/22/2013] [Indexed: 11/26/2022] Open
Abstract
We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. "Best match (BM)", "best close match (BCM)", "all species barcodes (ASB)" and "back-propagation neural networks (BP-based method)" were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species.
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Affiliation(s)
- Jianhua Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, People's Republic of China
- College of Life Sciences, Guangxi Normal University, Guilin, People's Republic of China
| | - Aibing Zhang
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
| | - Shaoli Mao
- College of Life Sciences, Shaanxi Normal University, Xi'an, People's Republic of China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, People's Republic of China
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42
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Lees DC, Kawahara AY, Rougerie R, Ohshima I, Kawakita A, Bouteleux O, De Prins J, Lopez-Vaamonde C. DNA barcoding reveals a largely unknown fauna of Gracillariidae leaf-mining moths in the Neotropics. Mol Ecol Resour 2013; 14:286-96. [DOI: 10.1111/1755-0998.12178] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/15/2013] [Accepted: 09/18/2013] [Indexed: 01/15/2023]
Affiliation(s)
- D. C. Lees
- Department of Zoology; Cambridge University; Cambridge CB2 3EJ UK
| | - A. Y. Kawahara
- Florida Museum of Natural History; University of Florida; Gainesville FL 32611 USA
| | - R. Rougerie
- INRA; UR633 Zoologie Forestière; Orléans F-45075 France
| | - I. Ohshima
- Department of Life and Environmental Sciences; Kyoto Prefectural University; Kyoto Japan
| | - A. Kawakita
- Center for Ecological Research; Kyoto University; Kyoto Japan
| | - O. Bouteleux
- INRA; UR633 Zoologie Forestière; Orléans F-45075 France
| | - J. De Prins
- Entomology Section; Royal Museum for Central Africa; Leuvensesteenweg 13 Tervuren B-3080 Belgium
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43
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Jörger KM, Schrödl M. How to describe a cryptic species? Practical challenges of molecular taxonomy. Front Zool 2013; 10:59. [PMID: 24073641 PMCID: PMC4015967 DOI: 10.1186/1742-9994-10-59] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/03/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. RESULTS The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated. CONCLUSIONS To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.
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Affiliation(s)
- Katharina M Jörger
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Michael Schrödl
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Hawlitschek O, Nagy ZT, Berger J, Glaw F. Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles. PLoS One 2013; 8:e73368. [PMID: 24069192 PMCID: PMC3772021 DOI: 10.1371/journal.pone.0073368] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/23/2013] [Indexed: 12/21/2022] Open
Abstract
In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.
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Affiliation(s)
| | - Zoltán T. Nagy
- Royal Belgian Institute of Natural Sciences, JEMU, Brussels, Belgium
| | | | - Frank Glaw
- Zoologische Staatssammlung München, Munich, Germany
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Baselga A, Gómez-Rodríguez C, Novoa F, Vogler AP. Rare failures of DNA barcodes [corrected] to separate morphologically distinct species in a biodiversity survey of Iberian leaf beetles. PLoS One 2013; 8:e74854. [PMID: 24040352 PMCID: PMC3764165 DOI: 10.1371/journal.pone.0074854] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 08/06/2013] [Indexed: 11/19/2022] Open
Abstract
During a survey of genetic and species diversity patterns of leaf beetle (Coleoptera: Chrysomelidae) assemblages across the Iberian Peninsula we found a broad congruence between morphologically delimited species and variation in the cytochrome oxidase (cox1) gene. However, one species pair each in the genera Longitarsus Berthold and Pachybrachis Chevrolat was inseparable using molecular methods, whereas diagnostic morphological characters (including male or female genitalia) unequivocally separated the named species. Parsimony haplotype networks and maximum likelihood trees built from cox1 showed high genetic structure within each species pair, but no correlation with the morphological types and neither with geographic distributions. This contrasted with all analysed congeneric species, which were recovered as monophyletic. A limited number of specimens were sequenced for the nuclear 18S rRNA gene, which showed no or very limited variation within the species pair and no separation of morphological types. These results suggest that processes of lineage sorting for either group are lagging behind the clear morphological and presumably reproductive separation. In the Iberian chrysomelids, incongruence between DNA-based and morphological delimitations is a rare exception, but the discovery of these species pairs may be useful as an evolutionary model for studying the process of speciation in this ecological and geographical setting. In addition, the study of biodiversity patterns based on DNA requires an evolutionary understanding of these incongruences and their potential causes.
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Affiliation(s)
- Andrés Baselga
- Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
- * E-mail:
| | - Carola Gómez-Rodríguez
- Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Francisco Novoa
- Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alfried P. Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- Division of Biology, Imperial College London, Ascot, United Kingdom
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46
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Rajaei Sh H, Struwe JF, Raupach MJ, Ahrens D, Wägele JW. Integration of cytochromecoxidase I barcodes and geometric morphometrics to delimit species in the genusGnopharmia(Lepidoptera: Geometridae, Ennominae). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Hossein Rajaei Sh
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160; 53113; Bonn; Germany
| | - Jan-Frederic Struwe
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160; 53113; Bonn; Germany
| | - Michael J. Raupach
- Deutsches Zentrum für Marine Biodiversitätsforschung; Senckenberg am Meer; Südstrand 44; 26382; Wilhelmshaven; Germany
| | - Dirk Ahrens
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160; 53113; Bonn; Germany
| | - J. Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160; 53113; Bonn; Germany
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47
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Papadopoulou A, Cardoso A, Gómez-Zurita J. Diversity and diversification of Eumolpinae (Coleoptera: Chrysomelidae) in New Caledonia. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna Papadopoulou
- Animal Biodiversity and Evolution; Institute of Evolutionary Biology (CSIC-UPF); Passeig Marítim de la Barceloneta 37 08003 Barcelona Spain
| | - Anabela Cardoso
- Animal Biodiversity and Evolution; Institute of Evolutionary Biology (CSIC-UPF); Passeig Marítim de la Barceloneta 37 08003 Barcelona Spain
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution; Institute of Evolutionary Biology (CSIC-UPF); Passeig Marítim de la Barceloneta 37 08003 Barcelona Spain
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48
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Hendrich L, Balke M. Revision of Australian Matini diving beetles based on morphological and molecular data (Coleoptera, Dytiscidae, Matinae), with description of a new species. Zookeys 2013:41-64. [PMID: 23794866 PMCID: PMC3677404 DOI: 10.3897/zookeys.293.4472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/04/2013] [Indexed: 11/20/2022] Open
Abstract
Morphological characters and mitochondrial DNA sequence data were used to revise the Australian diving beetles in the genera Allomatus Mouchamps, 1964 and Batrachomatus Clark, 1863. As a result of these studies Allomatussyn. n. is synonymised with Batrachomatus, and Allomatus nannup Watts, 1978 from SW Australia and Allomatus wilsoni Mouchamps, 1964 from SE Victoria are transferred to Batrachomatus. The four Australian Matini species knownso far are re-described, and Batrachomatus larsonisp. n. from the Windsor Tableland in NE Queensland is described. After more than 40 years Batrachomatus wilsoni has been re-discovered in two rivers in Victoria. We delineate the species using traditionally employed morphological structures such as in the male genitalia and body size, shape and colour pattern, as well as mitochondrial cox1 sequence data for 20 individuals. Important species characters (median lobes, parameres and colour patterns) were illustrated. We provide an identification key and outline distribution and habitat preferences of each species. All Australian Matini are lotic, inhabiting permanent and intermittent streams, creeks and rivers.
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Affiliation(s)
- Lars Hendrich
- Zoologische Staatssammlung, Münchhausenstraße 21, D-81247 München, Germany
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49
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Corse E, Rampal J, Cuoc C, Pech N, Perez Y, Gilles A. Phylogenetic analysis of Thecosomata Blainville, 1824 (holoplanktonic opisthobranchia) using morphological and molecular data. PLoS One 2013; 8:e59439. [PMID: 23593138 PMCID: PMC3625178 DOI: 10.1371/journal.pone.0059439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/14/2013] [Indexed: 11/18/2022] Open
Abstract
Thecosomata is a marine zooplankton group, which played an important role in the carbonate cycle in oceans due to their shell composition. So far, there is important discrepancy between the previous morphological-based taxonomies, and subsequently the evolutionary history of Thecosomata. In this study, the remarkable planktonic sampling of TARA Oceans expedition associated with a set of various other missions allowed us to assess the phylogenetic relationships of Thecosomata using morphological and molecular data (28 S and COI genes). The two gene trees showed incongruities (e.g. Hyalocylis, Cavolinia), and high congruence between morphological and 28S trees (e.g. monophyly of Euthecosomata). The monophyly of straight shell species led us to reviving the Orthoconcha, and the split of Limacinidae led us to the revival of Embolus inflata replacing Limacina inflata. The results also jeopardized the Euthecosomata families that are based on plesiomorphic character state as in the case for Creseidae which was not a monophyletic group. Divergence times were also estimated, and suggested that the evolutionary history of Thecosomata was characterized by four major diversifying events. By bringing the knowledge of palaeontology, we propose a new evolutionary scenario for which macro-evolution implying morphological innovations were rhythmed by climatic changes and associated species turn-over that spread from the Eocene to Miocene, and were shaped principally by predation and shell buoyancy.
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Affiliation(s)
- Emmanuel Corse
- IMBE (UMR CNRS 7263, IRD 237) Evolution Génome Environnement, Aix-Marseille Université, Marseille, France.
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Riedel A, Sagata K, Suhardjono YR, Tänzler R, Balke M. Integrative taxonomy on the fast track - towards more sustainability in biodiversity research. Front Zool 2013; 10:15. [PMID: 23537182 PMCID: PMC3626550 DOI: 10.1186/1742-9994-10-15] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/28/2013] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND A so called "taxonomic impediment" has been recognized as a major obstacle to biodiversity research for the past two decades. Numerous remedies were then proposed. However, neither significant progress in terms of formal species descriptions, nor a minimum standard for descriptions have been achieved so far. Here, we analyze the problems of traditional taxonomy which often produces keys and descriptions of limited practical value. We suggest that phylogenetics and phenetics had a subtle and so far unnoticed effect on taxonomy leading to inflated species descriptions. DISCUSSION The term "turbo-taxonomy" was recently coined for an approach combining cox1 sequences, concise morphological descriptions by an expert taxonomist, and high-resolution digital imaging to streamline the formal description of larger numbers of new species. We propose a further development of this approach which, together with open access web-publication and automated pushing of content from journal into a wiki, may create the most efficient and sustainable way to conduct taxonomy in the future. On demand, highly concise descriptions can be gradually updated or modified in the fully versioned wiki-framework we use. This means that the visibility of additional data is not compromised, while the original species description -the first version- remains preserved in the wiki, and of course in the journal version. A DNA sequence database with an identification engine replaces an identification key, helps to avoid synonyms and has the potential to detect grossly incorrect generic placements. We demonstrate the functionality of a species-description pipeline by naming 101 new species of hyperdiverse New Guinea Trigonopterus weevils in the open-access journal ZooKeys. SUMMARY Fast track taxonomy will not only increase speed, but also sustainability of global species inventories. It will be of great practical value to all the other disciplines that depend on a usable taxonomy and will change our perception of global biodiversity. While this approach is certainly not suitable for all taxa alike, it is the tool that will help to tackle many hyperdiverse groups and pave the road for more sustainable comparative studies, e.g. in community ecology, phylogeography and large scale biogeographic studies.
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Affiliation(s)
- Alexander Riedel
- Museum of Natural History Karlsruhe (SMNK), Erbprinzenstr, Karlsruhe, 13, D-76133, Germany
| | - Katayo Sagata
- Papua New Guinea Institute for Biological Research (PNG-IBR), Goroka, Papua New Guinea
| | - Yayuk R Suhardjono
- Zoological Museum, Cibinong Science Center - LIPI, Jl. Raya, Jakarta- Bogor, Indonesia
| | - Rene Tänzler
- Zoological State Collection, Münchhausenstr, Munich, 21, D-81247, Germany
| | - Michael Balke
- Zoological State Collection, Münchhausenstr, Munich, 21, D-81247, Germany
- GeoBioCenter, Ludwig-Maximilians-University, Munich, Germany
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