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Csabai Z, Čiamporová-Zaťovičová Z, Boda P, Čiampor F. 50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160922. [PMID: 36539085 DOI: 10.1016/j.scitotenv.2022.160922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The essential key to routine molecular species identification (DNA barcoding/metabarcoding) is the existence of an error-free DNA barcode reference library providing full coverage of all species. Published studies generally state the need to produce more barcodes, and control their quality, but unfortunately, the number of barcoded species is still low. However, to initiate real progress, we need to know where the gaps lie, how big they are and why they persist. Our aims were to draw and understand the current state of knowledge regarding species diversity, distribution, and barcode coverage, and offer solutions for improvement. In this study, we used two groups of aquatic insects, beetles and true bugs. We have compiled and critically evaluated an essentially complete and up-to-date European list, containing 1527 species. The list served as a basis for the barcode gap analyses in the Barcode-of-Life-Data-System (BOLD) conducted in three subsequent years (2020-2022). The overall barcode coverage of the pan-European fauna was around 50 % in both groups. The lowest coverage was in the Mediterranean, the Balkans and South-eastern Europe. The coverage in each country depended significantly on the local diversity, the number of rare, endemic species and the similarity of its fauna to that of the most active barcoding European countries. Gap analyses showed a very small increase in species coverage (<1 % in European aquatic beetles) despite an ~25 % increase in the number of barcodes. Hence, it is clear that future barcoding campaigns must prioritise quality over quantity. To visibly improve reference libraries, we need to increase the involvement of taxonomic experts and focus on targeted studies and underexplored but biodiversity-rich areas.
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Affiliation(s)
- Zoltán Csabai
- University of Pécs, Faculty of Sciences, Department of Hydrobiology, Ifjúság útja 6, H7624 Pécs, Hungary; Masaryk University, Faculty of Sciences, Department of Zoology and Botany, Kotlářská 2, 62500 Brno, Czech Republic; Balaton Limnological Research Institute, Klebelsberg Kuno utca 3, 8237 Tihany, Hungary.
| | - Zuzana Čiamporová-Zaťovičová
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Department of Biodiversity and Ecology, Dúbravská cesta 9, 84523 Bratislava, Slovakia; Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Pál Boda
- Centre for Ecological Research, Institute of Aquatic Ecology, Bem tér 18/c, H4026 Debrecen, Hungary.
| | - Fedor Čiampor
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Department of Biodiversity and Ecology, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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3
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Delocado ED, Freitag H. Two new species of Byrrhinus Motschulsky, 1858 (Coleoptera, Limnichidae, Limnichinae) from Negros, Philippines. Zookeys 2021; 1070:51-72. [PMID: 34819771 PMCID: PMC8599385 DOI: 10.3897/zookeys.1070.70531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/22/2021] [Indexed: 11/24/2022] Open
Abstract
Two new species of Limnichidae beetles, Byrrhinusnegrosensis sp. nov. and Byrrhinusvillarini sp. nov., are described from the Island of Negros in the Philippines. The adult specimens of the new species can be differentiated by patterns of body punctation, colour and orientation of elytral pubescence, posterolateral angle of pronotum, tarsomere length ratio and aedeagal form. Two clades, representing the two new species, were retrieved in the Maximum Likelihood gene tree using the 3'-end of the COI gene. Maximum genetic divergence within B.negrosensis sp. nov. and B.villarini sp. nov. were recorded to be 2.3% and 1.3%, respectively, while the mean interspecific divergence between the two new species was 19.7%. Morphological descriptions, digital photographs and COI sequences were provided for the two species. The state of knowledge of Byrrhinus is reviewed and an updated Philippine checklist is provided. By coupling morphological and molecular data, this paper provides the first additional new species of Philippine Byrrhinus in the last 28 years.
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Affiliation(s)
- Emmanuel D. Delocado
- Ateneo Biodiversity Research Laboratory, Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, 1108 PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
| | - Hendrik Freitag
- Ateneo Biodiversity Research Laboratory, Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, 1108 PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
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Okutaner AY, Sarikaya AD, Sarikaya Z, Zdikmen H. A geometric morphometric evaluation on three populations of endemic species, Dorcadion micans (Cerambycidae, Coleoptera) in Ankara Province from Turkey with a new subspecies description. Zootaxa 2021; 5004:167-180. [PMID: 34811313 DOI: 10.11646/zootaxa.5004.1.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Indexed: 11/04/2022]
Abstract
Due to some biological features, species belonging to genus Dorcadion Dalman, 1817 (Coleoptera: Cerambycidae) can be easily divided into isolated populations. This can be considered as an important factor of speciation process and allows the observation of various effects of biological evolution of taxa. These effects can be measured on morphological characters with some different approaches such as geometric morphometrics. This study aims to determine pronotum and elytra shape differences of the samples of three isolated localities of Turkey (Akyurt, Bala, and Beynam) detected in Ankara, and to contribute to taxonomic and evolutionary knowledge of Dorcadion micans Thomson (1867) by evaluating the analysis of outcomes. As a result, significant differences between populations were detected both in pronotum and elytra. Besides, common variations were observed in some morphological characters of the Bala and Beynam populations, unlike Akyurt population. Accordingly, the distinguishing characters are discussed, and the following new subspecies is described: Dorcadion micans majoripunctum ssp. nov. from Ankara province in Northern part of Central Anatolia.
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Affiliation(s)
- Atilay Yamur Okutaner
- Krehir Ahi Evran University, Faculty of Arts and Sciences, Department of Anthropology, 40200, Krehir, Turkey.
| | - Asli Doan Sarikaya
- Krehir Ahi Evran University, Faculty of Arts and Sciences, Department of Anthropology, 40200, Krehir, Turkey.
| | - Zkan Sarikaya
- Krehir Ahi Evran University, Faculty of Health Sciences, Department of Child Development, 40200, Krehir, Turkey.
| | - Hseyin Zdikmen
- Gazi University, Science Faculty, Department of Biology, 06500 Ankara, Turkey.
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Population genetics and geometric morphometrics of the freshwater snail Segmentina nitida reveal cryptic sympatric species of conservation value in Europe. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01369-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractSegmentina nitida Müller 1774 is a rare European freshwater snail of drainage ditches and marshland, which has seen a marked decrease in range (~ 80%) over the last 100 years in the UK. This has been attributed to over-dredging of drainage ditches for land management, conversion of grazing marshes to arable farmland, as well as eutrophication. Segmentina nitida is identified as a priority species in the UK Biodiversity Action Plan (UKBAP) that recommends further research to inform reintroduction and translocation for its conservation. We used nuclear markers (microsatellites and ITS2) and a mitochondrial (COI) marker to investigate population structure in S. nitida individuals sampled from Poland, Germany, Sweden, and the UK to identify differences within and between populations. Data based on 2D landmark-based geometric morphometrics of S. nitida shells was used to determine if phenotypic variation followed genetic differentiation. Two distinct genetic lineages of S. nitida were identified in ITS and COI phylogenies as well as cluster analysis of microsatellite markers, one of these lineages was present in eastern Europe (Poland, Sweden- Lineage 2), and one in western Europe (UK, Germany- Lineage 1), with lineages co-occurring in German populations. No genetic admixture was observed in German populations containing both lineages. These two lineages were also distinct in shape, with lineage 2 individuals having significantly wider shells and taller and wider apertures than those in Lineage 1. ~ 85% of shells assigned to the predicted lineage in a discriminant analysis of Procrustes shape coordinates. We infer that S. nitida includes at least one sympatric cryptic species. We discuss the implications of these findings on the conservation status of S. nitida in the UK and Europe.
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Brasero N, Ghisbain G, Lecocq T, Michez D, Valterová I, Biella P, Monfared A, Williams PH, Rasmont P, Martinet B. Resolving the species status of overlooked West‐Palaearctic bumblebees. ZOOL SCR 2021. [DOI: 10.1111/zsc.12486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nicolas Brasero
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Guillaume Ghisbain
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Thomas Lecocq
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
- Université de Lorraine, INRAE, URAFPA Nancy France
| | - Denis Michez
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Irena Valterová
- Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry Prague Czech Republic
- Faculty of Tropical AgriSciences Czech University of Life Sciences Prague Czech Republic
| | - Paolo Biella
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Milano Italy
| | - Alireza Monfared
- Department of Plant Protection, Faculty of Agriculture Yasouj University Yasouj Iran
| | | | - Pierre Rasmont
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Baptiste Martinet
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
- Evolutionary Biology & Ecology Université Libre de Bruxelles Bruxelles Belgium
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Neves JMM, Perez A, Fabré NN, Pereira RJ, Mott T. Integrative taxonomy reveals extreme morphological conservatism in sympatric
Mugil
species from the Tropical Southwestern Atlantic. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessika M. M. Neves
- Laboratório de Biologia Integrativa Instituto de Ciências Biológicas e da SaúdeUniversidade Federal de Alagoas Maceió Brazil
| | - Alfredo Perez
- Laboratório de Ecologia, Peixes e Pesca Instituto de Ciências Biológicas e da SaúdeUniversidade Federal de Alagoas Maceió Brazil
| | - Nidia Noemi Fabré
- Laboratório de Ecologia, Peixes e Pesca Instituto de Ciências Biológicas e da SaúdeUniversidade Federal de Alagoas Maceió Brazil
| | - Ricardo J. Pereira
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Tamí Mott
- Laboratório de Biologia Integrativa Instituto de Ciências Biológicas e da SaúdeUniversidade Federal de Alagoas Maceió Brazil
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Identifying Chagas disease vectors using elliptic Fourier descriptors of body contour: a case for the cryptic dimidiata complex. Parasit Vectors 2020; 13:332. [PMID: 32611375 PMCID: PMC7329423 DOI: 10.1186/s13071-020-04202-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/20/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Triatoma dimidiata (Reduviidae: Triatominae) is an important vector of Chagas disease in various countries in the Americas. Phylogenetic studies have defined three lineages in Mexico and part of Central America. While there is a marked genetic differentiation, methods for identifying them using morphometric analyses with landmarks have not yet been fully resolutive. Elliptical Fourier descriptors (EFDs), which mathematically describe the shape of any closed two-dimensional contours, could be a potentially useful alternative method. Our objective was to validate the use of EFDs for the identification of three lineages of this species complex. METHOD A total of 84 dorsal view images of individuals of the three lineages were used. Body contours were described with EFDs using between 5 and 30 harmonics. The number of obtained coefficients was reduced by a principal components analysis and the first axis scores were used as shape variables. A linear discriminant function analysis and an ordination plot of the discriminant analysis were performed using the shape variables. A confusion matrix of the ordination plot of the discriminant analysis was obtained to estimate the classification errors, the first five PC scores were statistically compared, and a neural network were then performed using the shape variables. RESULTS The first principal component explained 50% of the variability, regardless the number of harmonics used. The results of discriminant analysis get improved by increasing the number of harmonics and components considered. With 25 harmonics and 30 components, the identification of haplogroups was achieved with an overall efficiency greater than 97%. The ordering diagram showed the correct discrimination of haplogroups, with only one error of discrimination corroborated by the confusion matrix. When comparing the first five PC scores, significant differences were found among at least two haplogroups. The 30 multilayer perceptron neural networks were also efficient in identification, reaching 91% efficiency with the validation data. CONCLUSIONS The use of EFD is a simple and useful method for the identification of the main lineages of Triatoma dimidiata, with high values of correct identification.
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Abstract
The use of the "integrative approach" for classification of organisms since its formal establishment in 2005 has become a recurrent theme of zoosystematics. A bibliometric survey of the publications on integrative taxonomy of animals, which is aimed at exploring the most popular areas of research and characterizing the practical systematists' attitudes to this new approach, is presented. An analysis of 582 papers, which appeared between 2005 and 2017 in journals indexed by Scopus and the Web of Science Core Collection, has illustrated the gradual growth of the popularity of integrative taxonomy as well as some biases in the representation of higher taxa in "integrated" studies. It has been shown that the "integrative" papers have more chance of appearing in a top-ranking journal and gain relatively more citations as compared with non-integrative papers. The obtained results are discussed in the context of the "taxonomic impediment" problem thought to be a consequence of the institutional crisis of traditional taxonomy, which has been vividly debated over the past decades.
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Affiliation(s)
- Maxim V Vinarski
- Laboratory of Macroecology and Biogeography of Invertebrates, Saint-Petersburg State University, Saint-Petersburg, Russia
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10
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Duarte ME, de Mendonça RS, Skoracka A, Silva ES, Navia D. Integrative taxonomy of Abacarus mites (Eriophyidae) associated with hybrid sugarcane plants, including description of a new species. EXPERIMENTAL & APPLIED ACAROLOGY 2019; 78:373-401. [PMID: 31278610 DOI: 10.1007/s10493-019-00388-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
Phytophagous mites belonging to the Eriophyoidea are extremely diverse and highly host-specific. Their accurate morphological identification is hampered by their reduced size and simplified bodies and by the existence of cryptic species complexes. Previous studies have demonstrated the urgency of applying multisource methods to accurate taxonomic identification of eriophyoid mites, especially species belonging to the genus Abacarus. This genus comprises 65 species, of which 37 are associated with grasses and four with sugarcane Saccharum (Poaceae). Recently, Abacarus specimens very similar to Abacarus sacchari were collected from the sugarcane crop in Brazil; however, their taxonomic placement was uncertain. In this study, we used an integrative approach to determine whether A. aff. sacchari specimens belong to A. sacchari or constitute a cryptic species. Morphological data were combined with molecular phylogeny based on the nucleotide sequences of three markers, one mitochondrial (COI) and two nuclear (D2 region of 28S and ITS). Morphological differences were observed between A. aff. sacchari, A. sacchari and A. doctus. The phylogenetic relationships among these three taxa and the genetic distances separating them revealed an interspecific divergence. The results of the morphological and molecular methods were congruent and supported the existence of a new species: Abacarus neosacchari n. sp. Duarte and Navia, herein described. This species belongs to the Abacarus cryptic species complex associated with sugarcane in the Americas. The results of this study, presenting the occurrence of multiple Abacarus species associated with sugarcane, contribute to the knowledge on plants and mites diversity by adding up one more clue highlighting that plant hybridization can be an important mechanism contributing to the speciation of plant-feeding arthropods.
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Affiliation(s)
- Mércia Elias Duarte
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil
| | - Renata Santos de Mendonça
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, 70297-400, Brazil
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Edmilson Santos Silva
- Universidade Federal de Alagoas, Campus Arapiraca, Arapiraca, 57309-005, Brazil
- Universidade Federal de Alagoas, Centro de Ciências Agrárias (CECA), Alagoas, 57100-000, Brazil
| | - Denise Navia
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil.
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Guareschi S, Wood PJ. Taxonomic changes and non-native species: An overview of constraints and new challenges for macroinvertebrate-based indices calculation in river ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:40-46. [PMID: 30639717 DOI: 10.1016/j.scitotenv.2019.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Freshwater ecosystems face many threats in the form of reduced water quantity, poor water quality and the loss of biodiversity. As a result, aquatic biomonitoring tools are required to enable the evaluation of these critical changes. Currently, macroinvertebrate-based indices are globally the most widely used biomonitoring tools in fluvial ecosystems. However, very little is known about the potential effects of changes in taxonomic understanding (updating of classification and nomenclature) or the presence of new non-native species for biotic indices calculation. This is especially relevant given that errors, incorrect classification or exclusion of new/updated nomenclature may affect ecological status evaluations and have direct consequences for the management and conservation of freshwater systems. In this discussion paper the main constraints, challenges and implications of these issues are outlined and case studies from a range of European countries are discussed. However, similar challenges affect rivers and managers globally and will potentially be amplified further in the future. Bioassessment science needs to be open to improvements, and current tools and protocols need to be flexible so that they can be updated and revised rapidly to allow new scientific developments to be integrated. This discussion highlights specific examples and new ideas that may contribute to the future development of aquatic biomonitoring using macroinvertebrates and other faunal and floral groups in riverine ecosystems.
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Affiliation(s)
- Simone Guareschi
- Department of Ecology and Hydrology, Regional Campus of International Excellence "Campus Mare Nostrum" University of Murcia, 30100, Spain.
| | - Paul J Wood
- Geography and Environment, Centre for Hydrological and Ecosystem Science, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK
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Alitto RADS, Amaral ACZ, de Oliveira LD, Serrano H, Seger KR, Guilherme PDB, Domenico MD, Christensen AB, Lourenço LB, Tavares M, Borges M. Atlantic West Ophiothrix spp. in the scope of integrative taxonomy: Confirming the existence of Ophiothrix trindadensis Tommasi, 1970. PLoS One 2019; 14:e0210331. [PMID: 30673722 PMCID: PMC6343879 DOI: 10.1371/journal.pone.0210331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/20/2018] [Indexed: 11/20/2022] Open
Abstract
We re-describe and confirm the validity of Ophiothrix trindadensis Tommasi, 1970 (Echinodermata: Ophiuroidea). This is a native species from Brazil, however it lacked a type series deposited in scientific collections. The recognition of O. trindadensis was made possible using integrative taxonomy applied to many specimens from the type locality (Trindade Island) as well as from different locations along the Brazilian coast (Araçá Bay and Estuarine Complex of Paranaguá). Initially, 835 specimens were studied and divided into four candidate species (CS) inferred from external morphological characters. Afterwards, the CSs were compared using integrative taxonomy based on external morphology, arm microstructures morphology (arm ossicle), morphometry, and molecular studies (fragments of the mitochondrial genes 16S and COI). Analyses indicated CS1 and CS2 as O. trindadensis, and CS3 as O. angulata, both valid species. CS4 remains O. cf. angulata as more data, including their ecology and physiology, are needed to be definitively clarified. Our integrative investigation using specimens from the type locality overcame the lack of type specimens and increased the reliable identification of O. trindadensis and O. angulata.
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Affiliation(s)
- Renata Aparecida dos Santos Alitto
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Museu de Zoologia “Adão José Cardoso”, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | | | - Letícia Dias de Oliveira
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Museu de Zoologia “Adão José Cardoso”, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Helena Serrano
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Museu de Zoologia “Adão José Cardoso”, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Karin Regina Seger
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Departamento de Biologia Celular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | | | - Maikon Di Domenico
- Centro de Estudos do Mar, Universidade Federal do Paraná, Pontal do Paraná, Paraná, Brasil
| | | | - Luciana Bolsoni Lourenço
- Departamento de Biologia Celular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Marcos Tavares
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brasil
| | - Michela Borges
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Museu de Zoologia “Adão José Cardoso”, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
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Adams NE, Inoue K, Seidel RA, Lang BK, Berg DJ. Isolation drives increased diversification rates in freshwater amphipods. Mol Phylogenet Evol 2018; 127:746-757. [PMID: 29908996 DOI: 10.1016/j.ympev.2018.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 02/21/2018] [Accepted: 06/11/2018] [Indexed: 01/06/2023]
Abstract
Vicariance and dispersal events affect current biodiversity patterns in desert springs. Whether major diversification events are due to environmental changes leading to radiation or due to isolation resulting in relict species is largely unknown. We seek to understand whether the Gammarus pecos species complex underwent major diversification events due to environmental changes in the area leading either to radiation into novel habitats, or formation of relicts due to isolation. Specifically, we tested the hypothesis that Gammarus in the northern Chihuahuan Desert of New Mexico and Texas, USA are descendants of an ancient marine lineage now containing multiple undescribed species. We sequenced a nuclear (28S) and two mitochondrial (16S, COI) genes from gammarid amphipods representing 16 desert springs in the northern Chihuahuan Desert. We estimated phylogenetic relationships, divergence times, and diversification rates of the Gammarus pecos complex. Our results revealed that the region contained two evolutionarily independent lineages: a younger Freshwater Lineage that shared a most-recent-common-ancestor with an older Saline Lineage ∼66.3 MYA (95.6-42.4 MYA). Each spring system generally formed a monophyletic clade based on the concatenated dataset. Freshwater Lineage diversification rates were 2.0-9.8 times higher than rates of the Saline Lineage. A series of post-Cretaceous colonizations by ancestral Gammarus taxa was likely followed by isolation. Paleo-geological, hydrological, and climatic events in the Neogene-to-Quaternary periods (23.03 MYA - present) in western North America promoted allopatric speciation of both lineages. We suggest that Saline Lineage populations include two undescribed Gammarus species, while the Freshwater Lineage shows repetition of fine-scale genetic structure in all major clades suggesting incipient speciation. Such ongoing speciation suggests that this region will continue to be a biodiversity hotspot for amphipods and other freshwater taxa.
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Affiliation(s)
- Nicole E Adams
- Department of Biology, Miami University, Oxford, OH 45056, United States.
| | - Kentaro Inoue
- Department of Biology, Miami University, Oxford, OH 45056, United States
| | - Richard A Seidel
- Department of Biology, Miami University, Oxford, OH 45056, United States
| | - Brian K Lang
- New Mexico Department of Game and Fish, Santa Fe, NM 87507, United States
| | - David J Berg
- Department of Biology, Miami University, Hamilton, OH 45011, United States
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Pallarés S, Arribas P, Bilton DT, Millán A, Velasco J, Ribera I. The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles. Mol Ecol 2017; 26:5614-5628. [PMID: 28833872 DOI: 10.1111/mec.14334] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/31/2017] [Indexed: 12/24/2022]
Abstract
Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso- and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation-resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso- and hypersaline habitats.
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Affiliation(s)
- Susana Pallarés
- Department of Ecology and Hydrology, Facultad de Biología, University of Murcia, Murcia, Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group, IPNA-CSIC, Santa Cruz de Tenerife, Spain
| | - David T Bilton
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, Plymouth University, Plymouth, UK
| | - Andrés Millán
- Department of Ecology and Hydrology, Facultad de Biología, University of Murcia, Murcia, Spain
| | - Josefa Velasco
- Department of Ecology and Hydrology, Facultad de Biología, University of Murcia, Murcia, Spain
| | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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15
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Sheth BP, Thaker VS. DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation. Genome 2017; 60:618-628. [DOI: 10.1139/gen-2015-0167] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.
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Affiliation(s)
- Bhavisha P. Sheth
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Vrinda S. Thaker
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
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16
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Merényi Z, Varga T, Hubai AG, Pitlik P, Erős Á, Trappe JM, Bratek Z. Challenges in the delimitation of morphologically similar species: a case study of Tuber brumale agg. (Ascomycota, Pezizales). Mycol Prog 2017. [DOI: 10.1007/s11557-017-1296-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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17
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Pallarés S, Botella-Cruz M, Arribas P, Millán A, Velasco J. Aquatic insects in a multistress environment: cross-tolerance to salinity and desiccation. J Exp Biol 2017; 220:1277-1286. [DOI: 10.1242/jeb.152108] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/16/2017] [Indexed: 01/09/2023]
Abstract
Exposing organims to a particular stressor may enhance tolerance to a subsequent stress, when protective mechanisms against both stressors are shared. Such cross-tolerance is a common adaptive response in dynamic multivariate environments and often indicates potential co-evolution of stress traits. Many aquatic insects in inland saline waters from Mediterranean-climate regions are sequentially challenged with salinity and desiccation stress. Thus, cross-tolerance to these physiologically similar stressors could have been positively selected in insects of these regions. We used adults of the saline water beetles Enochrus jesusarribasi (Hydrophilidae) and Nebrioporus baeticus (Dytiscidae) to test cross-tolerance responses to desiccation and salinity. In independent laboratory experiments, we evaluated the effects of i) salinity stress on the subsequent resistance to desiccation and ii) desiccation stress (rapid and slow dehydration) on the subsequent tolerance to salinity. Survival, water loss and haemolymph osmolality were measured. Exposure to stressful salinity improved water control under subsequent desiccation stress in both species, with a clear cross-tolerance (enhanced performance) in N. baeticus. In contrast, general negative effects on performance were found under the inverse stress sequence. The rapid and slow dehydration produced different water loss and haemolymph osmolality dynamics that were reflected in different survival patterns. Our finding of cross-tolerance to salinity and desiccation in ecologically similar species from distant lineages, together with parallel responses between salinity and thermal stress previously found in several aquatic taxa, highlights the central role of adaption to salinity and co-occurring stressors in arid inland waters, having important implications for the species' persistence under climate change.
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Affiliation(s)
- Susana Pallarés
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - María Botella-Cruz
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Paula Arribas
- Department of Life Sciences, Natural History Museum London, London, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Spain
| | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Josefa Velasco
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
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18
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Breitman MF, Bonino MF, Sites JW, Avila LJ, Morando M. Morphological Variation, Niche Divergence, and Phylogeography of Lizards of the Liolaemus lineomaculatus Section (Liolaemini) from Southern Patagonia. HERPETOLOGICAL MONOGRAPHS 2015. [DOI: 10.1655/herpmonographs-d-14-00003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- M. Florencia Breitman
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Marcelo F. Bonino
- INIBIOMA (CONICET-UNCOMA), Laboratorio de Fotobiología, Centro Regional Universitario Bariloche, Quintral 1250, 8400, Bariloche, Río Negro, Argentina
| | - Jack W. Sites
- Brigham Young University, Life Sciences Building, Biology Department, Provo, UT 84602, USA
| | - Luciano J. Avila
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Mariana Morando
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
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19
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Katz AD, Giordano R, Soto-Adames FN. Operational criteria for cryptic species delimitation when evidence is limited, as exemplified by North AmericanEntomobrya(Collembola: Entomobryidae). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12220] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aron D. Katz
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
| | - Rosanna Giordano
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
| | - Felipe N. Soto-Adames
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
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20
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Tocchio LJ, Gurgel-Gonçalves R, Escobar LE, Peterson AT. Niche similarities among white-eared opossums (Mammalia, Didelphidae): Is ecological niche modelling relevant to setting species limits? ZOOL SCR 2014. [DOI: 10.1111/zsc.12082] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Luana J. Tocchio
- Laboratório de Parasitologia Médica e Biologia de Vetores; Faculdade de Medicina; Área de Patologia; Universidade de Brasília; Asa Norte CEP 70.910-900 Distrito Federal Brazil
| | - Rodrigo Gurgel-Gonçalves
- Laboratório de Parasitologia Médica e Biologia de Vetores; Faculdade de Medicina; Área de Patologia; Universidade de Brasília; Asa Norte CEP 70.910-900 Distrito Federal Brazil
| | - Luis E. Escobar
- Center for Global Health and Translational Science; State University of New York Upstate Medical University; Syracuse NY 13210 USA
- Facultad de Ecología y Recursos Naturales; Universidad Andres Bello; Av. República 440 Santiago Chile
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21
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Hidalgo-Galiana A, Sánchez-Fernández D, Bilton DT, Cieslak A, Ribera I. Thermal niche evolution and geographical range expansion in a species complex of western Mediterranean diving beetles. BMC Evol Biol 2014; 14:187. [PMID: 25205299 PMCID: PMC4180321 DOI: 10.1186/s12862-014-0187-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/11/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Species thermal requirements are one of the principal determinants of their ecology and biogeography, although our understanding of the interplay between these factors is limited by the paucity of integrative empirical studies. Here we use empirically collected thermal tolerance data in combination with molecular phylogenetics/phylogeography and ecological niche modelling to study the evolution of a clade of three western Mediterranean diving beetles, the Agabus brunneus complex. RESULTS The preferred mitochondrial DNA topology recovered A. ramblae (North Africa, east Iberia and Balearic islands) as paraphyletic, with A. brunneus (widespread in the southwestern Mediterranean) and A. rufulus (Corsica and Sardinia) nested within it, with an estimated origin between 0.60-0.25 Ma. All three species were, however, recovered as monophyletic using nuclear DNA markers. A Bayesian skyline plot suggested demographic expansion in the clade at the onset of the last glacial cycle. The species thermal tolerances differ significantly, with A. brunneus able to tolerate lower temperatures than the other taxa. The climatic niche of the three species also differs, with A. ramblae occupying more arid and seasonal areas, with a higher minimum temperature in the coldest month. The estimated potential distribution for both A. brunneus and A. ramblae was most restricted in the last interglacial, becoming increasingly wider through the last glacial and the Holocene. CONCLUSIONS The A. brunneus complex diversified in the late Pleistocene, most likely in south Iberia after colonization from Morocco. Insular forms did not differentiate substantially in morphology or ecology, but A. brunneus evolved a wider tolerance to cold, which appeared to have facilitated its geographic expansion. Both A. brunneus and A. ramblae expanded their ranges during the last glacial, although they have not occupied areas beyond their LGM potential distribution except for isolated populations of A. brunneus in France and England. On the islands and possibly Tunisia secondary contact between A. brunneus and A. ramblae or A. rufulus has resulted in introgression. Our work highlights the complex dynamics of speciation and range expansions within southern areas during the last glacial cycle, and points to the often neglected role of North Africa as a source of European biodiversity.
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Affiliation(s)
- Amparo Hidalgo-Galiana
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - David Sánchez-Fernández
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - David T Bilton
- />Marine Biology and Ecology Research Centre, Plymouth University, Drake Circus, PL4 8AA Plymouth, UK
| | - Alexandra Cieslak
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Ignacio Ribera
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
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22
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Andújar C, Arribas P, Ruiz C, Serrano J, Gómez-Zurita J. Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation ofMesocarabus(Coleoptera: Carabidae). Mol Ecol 2014; 23:4344-61. [DOI: 10.1111/mec.12793] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 11/30/2022]
Affiliation(s)
- C. Andújar
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
| | - P. Arribas
- Departamento de Ecología e Hidrología; Facultad de Biología; Universidad de Murcia; Murcia 30100 Spain
| | - C. Ruiz
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
- Departamento de Ciencias Naturales; Universidad Técnica Particular de Loja; San Cayetano Alto s/n C.P. 11 01 608 Loja Ecuador
| | - J. Serrano
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; Murcia 30100 Spain
| | - J. Gómez-Zurita
- Animal Biodiversity and Evolution; Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra); Pg. Marítim de la Barceloneta 37 Barcelona 08003 Spain
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23
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Arribas P, Andújar C, Abellán P, Velasco J, Millán A, Ribera I. Tempo and mode of the multiple origins of salinity tolerance in a water beetle lineage. Mol Ecol 2013; 23:360-73. [DOI: 10.1111/mec.12605] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/14/2013] [Accepted: 11/22/2013] [Indexed: 01/10/2023]
Affiliation(s)
- Paula Arribas
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Carmelo Andújar
- Departamento de Zoología y Antropología Física; Universidad de Murcia; Murcia 30100 Spain
| | - Pedro Abellán
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Josefa Velasco
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Andrés Millán
- Departamento de Ecología e Hidrología; Universidad de Murcia; Murcia 30100 Spain
| | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona 08003 Spain
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