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Iwasa-Arai T, Siqueira SGL, Sobral-Souza T, Leite FPP, Andrade SCS. Continent-island boundary and environment-shaped evolution in the marine amphipod Ampithoe marcuzzii complex (Crustacea: Eumalacostraca: Ampithoidae). Sci Rep 2024; 14:608. [PMID: 38182880 PMCID: PMC10770051 DOI: 10.1038/s41598-023-51049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024] Open
Abstract
Marine amphipods are crustaceans that lack a larval phase and consequently have low dispersion rates. Despite that, these crustaceans present a remarkable ability to be transported by rafting on natural floating substrata, especially macroalgae, where they find shelter, food and a mating ground. The species Ampithoe marcuzzii is widely distributed throughout the western Atlantic Ocean. Here, it was used as a model to study seascape genomics and phylogeography in invertebrates with low dispersion capacities. We anticipated that the lineages would present isolation-by-distance patterns. However, surface currents and other abiotic variables could facilitate connectivity among distant sites. Based on mitochondrial and nuclear genes, SNPs, and environmental associations, we observed the presence of a species complex within A. marcuzzii, separating mainland and insular populations. Each species showed an independent evolutionary history, with a strong latitudinal population structure and evidence of isolation-by-distance and isolation-by-environment, characterizing the 'continent' species. Historical expansion and environmental variables were observed associated with the southeastern population, and ecological niche modeling corroborated the region as a paleorefuge. Conversely, populations from 'islands' presented complicated evolutionary histories, with closer localities genetically isolated and distant localities connected. These findings indicate that insular populations with low dispersion capacity might be more susceptible to spatial connectivity by floating substrata and to changes in surface currents. In contrast, mainland populations might be more vulnerable to local climate changes due to lack of gene flow.
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Affiliation(s)
- Tammy Iwasa-Arai
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Silvana G L Siqueira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Fosca P P Leite
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Baptista L, Fassio G, Gofas S, Oliverio M, P Ávila S, M Santos A. Evaluating the taxonomic status of the large sized Tricolia Risso, 1826 in the Northeast Atlantic and Mediterranean Sea. Mol Phylogenet Evol 2023:107857. [PMID: 37315708 DOI: 10.1016/j.ympev.2023.107857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
Despite a long history of taxonomic studies on the genus Tricolia Risso, 1826, there is a shortfall on thorough systematic molecular reviews of the taxon from the NE Atlantic and Mediterranean coasts. Aiming to assess the genetic distinctness among morphospecies and the taxonomic status of currently accepted large sized species in these areas, we conducted a molecular phylogenetic analysis of the genus based on one mitochondrial (cox1) and two nuclear (28S and ITS2) markers. Seven Tricolia species were consistently retrieved in the analyses, including a new genetic lineage in the NE Atlantic designated as Tricolia sp. 1. Molecular analyses revealed that only one species, T. azorica, occurs in the NE Atlantic archipelagos. The sister taxa T. pullus (Mediterranean) and T. picta (NE Atlantic) should be classified as distinct species, instead of subspecies of the T. pullus group (sensu Gofas 1982). Tricolia miniata is also a complex of species in the Mediterranean and future studies across the distribution range are necessary to clarify its status.
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Affiliation(s)
- Lara Baptista
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801 Ponta Delgada, Açores, Portugal; MPB-Marine Palaeontology and Biogeography Lab, University of the Azores, Rua da Mãe de Deus, 9501-801 Ponta Delgada, Açores, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, R. Mãe de Deus 13A, 9500-321 Ponta Delgada, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal.
| | - Giulia Fassio
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, Viale dell'Università 32, I-00185, Rome, Italy and NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| | - Serge Gofas
- Departamento de Biología Animal, Facultad de Ciencias, Universidad de MálagaE-29071 Málaga, Spain; Muséum National d'Histoire Naturelle, Paris, France
| | - Marco Oliverio
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, Viale dell'Università 32, I-00185, Rome, Italy and NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| | - Sérgio P Ávila
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801 Ponta Delgada, Açores, Portugal; MPB-Marine Palaeontology and Biogeography Lab, University of the Azores, Rua da Mãe de Deus, 9501-801 Ponta Delgada, Açores, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, R. Mãe de Deus 13A, 9500-321 Ponta Delgada, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal; Departamento de Biologia, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal
| | - António M Santos
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, no. 7, 4485-661 Vairão, Portugal
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Hupało K, Copilaș-Ciocianu D, Leese F, Weiss M. Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude. Cladistics 2023; 39:129-143. [PMID: 36576962 DOI: 10.1111/cla.12520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022] Open
Abstract
DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito-nuclear discordance. Therefore, reports of putative species based solely on mitochondrial DNA should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or where divergence within the same morphospecies is high. Freshwater amphipods are particularly interesting in this context because numerous putative cryptic species have been reported. Here, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within Echinogammarus sicilianus. We used an integrative approach combining DNA barcoding with mate selection observations, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Within a relatively small sampling area, we detected twelve COI MOTUs (divergence = 1.8-20.3%), co-occurring in syntopy at two-thirds of the investigated sites. We found that pair formation was random and there was extensive nuclear gene flow among the ten MOTUs co-occurring within the same river stretch. The four most common MOTUs were also indistinguishable with respect to functional morphology. Therefore, the evidence best fits the hypothesis of a single, yet genetically diverse, species within the main river system. The only two MOTUs sampled outside the focal area were genetically distinct at the nuclear level and may represent distinct species. Our study reveals that COI-based species delimitation can significantly overestimate species diversity, highlighting the importance of integrative taxonomy for species validation, especially in hyperdiverse complexes with syntopically occurring mitochondrial MOTUs.
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Affiliation(s)
- Kamil Hupało
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
| | - Denis Copilaș-Ciocianu
- Nature Research Centre, Laboratory of Evolutionary Ecology of Hydrobionts, Akademijos 2, Vilnius, 08412, Lithuania
| | - Florian Leese
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 2, Essen, 45141, Germany
| | - Martina Weiss
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 2, Essen, 45141, Germany
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Revealing the diversity of the green Eulalia (Annelida, Phyllodocidae) species complex along the European coast, with description of three new species. ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-022-00597-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Teixeira MAL, Bakken T, Vieira PE, Langeneck J, Sampieri BR, Kasapidis P, Ravara A, Nygren A, Costa FO. The curious and intricate case of the European Hediste diversicolor (Annelida, Nereididae) species complex, with description of two new species. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2116124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Marcos A. L. Teixeira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Torkild Bakken
- Norwegian University of Science and Technology, NTNU University Museum, Trondheim, NO-7491, Norway
| | - Pedro E. Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Joachim Langeneck
- Dipartimento di Biologia, Università di Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Bruno R. Sampieri
- Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas – IB/UNICAMP, Rua Charles Darwin, Bloco N, Cidade Universitária, Campinas, SP, Brasil
| | - Panagiotis Kasapidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Anávyssos, Greece
| | - AscensÃO Ravara
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal
| | - Arne Nygren
- Institutionen for marina vetenskaper, Göteborgs Universitet, Tjärnö, Strömstad, Sweden
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
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Teixeira MAL, Langeneck J, Vieira PE, Hernández JC, Sampieri BR, Kasapidis P, Mucciolo S, Bakken T, Ravara A, Nygren A, Costa FO. Reappraisal of the hyperdiverse. INVERTEBR SYST 2022. [DOI: 10.1071/is21084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D
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Baptista L, Berning B, Curto M, Waeschenbach A, Meimberg H, Santos AM, Ávila SP. Morphospecies and molecular diversity of ‘lace corals’: the genus Reteporella (Bryozoa: Cheilostomatida) in the central North Atlantic Azores Archipelago. BMC Ecol Evol 2022; 22:128. [PMCID: PMC9635095 DOI: 10.1186/s12862-022-02080-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background As in most bryozoans, taxonomy and systematics of species in the genus Reteporella Busk, 1884 (family Phidoloporidae) has hitherto almost exclusively been based on morphological characters. From the central North Atlantic Azores Archipelago, nine Reteporella species have historically been reported, none of which have as yet been revised. Aiming to characterise the diversity and biogeographic distribution of Azorean Reteporella species, phylogenetic reconstructions were conducted on a dataset of 103 Azorean Reteporella specimens, based on the markers cytochrome C oxidase subunit 1, small and large ribosomal RNA subunits. Morphological identification was based on scanning electron microscopy and complemented the molecular inferences. Results Our results reveal two genetically distinct Azorean Reteporella clades, paraphyletic to eastern Atlantic and Mediterranean taxa. Moreover, an overall concordance between morphological and molecular species can be shown, and the actual bryozoan diversity in the Azores is greater than previously acknowledged as the dataset comprises three historically reported species and four putative new taxa, all of which are likely to be endemic. The inclusion of Mediterranean Reteporella specimens also revealed new species in the Adriatic and Ligurian Sea, whilst the inclusion of additional phidoloporid taxa hints at the non-monophyly of the genus Reteporella. Conclusion Being the first detailed genetic study on the genus Reteporella, the high divergence levels inferred within the genus Reteporella and family Phidoloporidae calls for the need of further revision. Nevertheless, the overall concordance between morphospecies and COI data suggest the potential adequacy of a 3% cut-off to distinguish Reteporella species. The discovery of new species in the remote Azores Archipelago as well as in the well-studied Mediterranean Sea indicates a general underestimation of bryozoan diversity. This study constitutes yet another example of the importance of integrative taxonomical approaches on understudied taxa, contributing to cataloguing genetic and morphological diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02080-z.
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Affiliation(s)
- Lara Baptista
- grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, 9501-801 Pólo dos Açores, Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal ,grid.7338.f0000 0001 2096 9474MPB-Marine Palaeontology and Biogeography Lab, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal ,grid.5173.00000 0001 2298 5320University of Natural Resources and Life Sciences (BOKU), Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Vienna, Austria
| | - Björn Berning
- grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, 9501-801 Pólo dos Açores, Ponta Delgada, Açores, Portugal ,grid.7338.f0000 0001 2096 9474MPB-Marine Palaeontology and Biogeography Lab, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal ,Oberösterreichische Landes-Kultur GmbH, Geowissenschaftliche Sammlungen, 4060 Leonding, Austria
| | - Manuel Curto
- grid.5173.00000 0001 2298 5320University of Natural Resources and Life Sciences (BOKU), Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Vienna, Austria ,grid.9983.b0000 0001 2181 4263MARE, Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Harald Meimberg
- grid.5173.00000 0001 2298 5320University of Natural Resources and Life Sciences (BOKU), Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Vienna, Austria
| | - António M. Santos
- grid.5808.50000 0001 1503 7226Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal ,grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Sérgio P. Ávila
- grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, 9501-801 Pólo dos Açores, Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal ,grid.7338.f0000 0001 2096 9474MPB-Marine Palaeontology and Biogeography Lab, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal ,grid.7338.f0000 0001 2096 9474Departamento de Biologia, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal
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Disentangling the Taxonomic Status of Caprella penantis sensu stricto (Amphipoda: Caprellidae) Using an Integrative Approach. Life (Basel) 2022; 12:life12020155. [PMID: 35207443 PMCID: PMC8878143 DOI: 10.3390/life12020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/21/2022] Open
Abstract
Despite its importance in intertidal and shallow-water marine ecosystems, Caprella penantis continues to be one of the most taxonomically challenging amphipods in the world. A recent molecular study focusing on C. penantis sensu stricto pointed out the existence of three highly divergent lineages, indicating the possible existence of a process of ongoing speciation and, thus, casting doubt on the taxonomic status of this species. In the present study, we used an integrative approach to continue to shed light on the taxonomy and distribution of this caprellid. To this end, we combined morphological and genetic data (COI and 18S) and included, for the first time, populations from its type locality. Our analyses provide strong evidence of the existence of potentially three distinct species, genetically and geographically restricted, within C. penantis sensu stricto, with the distribution of the true C. penantis sensu stricto restricted to the UK (type locality), the northern coast of the Iberian Peninsula, and the Azores. Results show the co-occurrence of two of these species in a locality of northern Portugal and indicate the existence of distinct evolutionary and diversification patterns along the eastern Atlantic region. Overall, our study highlights the use of an integrative approach to properly assess species boundaries and unravel hidden biodiversity in amphipods.
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Teixeira MAL, Vieira PE, Ravara A, Costa FO, Nygren A. From 13 to 22 in a second stroke: revisiting the European Eumida sanguinea (Phyllodocidae: Annelida) species complex. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Eumida sanguinea is a recognized polychaete species complex which, in previous studies, has been reported to have additional undescribed diversity. We detected nine additional lineages by analysing DNA sequence data (mitochondrial: COI, 16S rRNA and nuclear loci: ITS region and 28S rRNA) of E. sanguinea morphotype populations from a broader sampling effort in European marine waters. Traditional morphological features failed to provide consistent differences or unique characters that could be used to distinguish these Eumida species. However, by complementing DNA data with morphometrics, geographic range, colour and pigmentation patterns, we revealed five new species. Two of these undescribed species derived from the previously signalled Eumida lineages S21 and GB22, which are here named as E. schanderi sp. nov. and E. fenwicki sp. nov., respectively. Three other species are based on newly discovered lineages, namely E. fauchaldi sp. nov., E. langenecki sp. nov. and E. pleijeli sp. nov. From the six new lineages remaining, three are represented by fewer than two well-preserved specimens, which prevented further comprehensive analysis. The last three lineages were only distinct when using mitochondrial markers. Integrative taxonomy is essential to elucidate evolutionary phenomena and eventually allow informed use of species complexes exhibiting stasis in biomonitoring or other ecological studies.
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Affiliation(s)
- Marcos A L Teixeira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Ascensão Ravara
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Arne Nygren
- Institutionen for marina vetenskaper, Göteborgs Universitet, Tjärnö, Strömstad, Sweden
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Radulovici AE, Vieira PE, Duarte S, Teixeira MAL, Borges LMS, Deagle BE, Majaneva S, Redmond N, Schultz JA, Costa FO. Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.67862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.
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Miao X, Xiao J, Fan S, Zang Y, Zhang X, Wang Z. Assessing Herbivorous Impacts of Apohale sp. on the Ulva prolifera Green Tide in China. FRONTIERS IN PLANT SCIENCE 2021; 12:795560. [PMID: 34975983 PMCID: PMC8715085 DOI: 10.3389/fpls.2021.795560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/19/2021] [Indexed: 06/03/2023]
Abstract
An epiphytic gammarid species, Apohyale sp. , was abundant in the floating Ulva prolifera (U. prolifera), which forms large-scale green tides in the Yellow Sea (YSGT). Field observation and laboratory experiments were subsequently conducted to study the species identity, abundance, and grazing effects on the floating algal biomass. The abundance of Apohyale sp. showed great spatial variation and varied from 0.03 to 1.47 inds g-1 in the YSGT. In average, each gram of Apohyale sp. body mass can consume 0.43 and 0.60 g algal mass of U. prolifera per day, and the grazing rates varied among the algae cultured with different nutritional seawaters. It was estimated that grazing of Apohale sp. could efficiently reduce ~0.4 and 16.6% of the algal growth rates in Rudong and Qingdao, respectively. The U. prolifera fragments resulting from gnawing of Apohyale sp. had a higher growth rate and similar photosynthetic activities compared to the floating algae, indicating probably positive feedback on the floating algal biomass. This research corroborated the significant impact of Apohyale sp. on the floating algal mass of YSGT through the top-down control. However, further research is needed to understand the population dynamics of these primary predators and hence their correlation with the expansion or decline of YSGT, especially under the complex food webs in the southern Yellow Sea.
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Affiliation(s)
- Xiaoxiang Miao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Jie Xiao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Shiliang Fan
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Zongling Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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12
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Desiderato A, Mamos T, Rewicz T, Burzynski A, Mucciolo S. First Glimpse at the Diverse Aquaporins of Amphipod Crustaceans. Cells 2021; 10:3417. [PMID: 34943925 PMCID: PMC8699810 DOI: 10.3390/cells10123417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/31/2022] Open
Abstract
The importance of aquaporins (AQPs) in the transport of water and solutes through cell membranes is well recognized despite being relatively new. To date, despite their abundance, diversity, and presence in disparate environments, amphipods have only been mentioned in studies about the AQPs of other animals and have never been further investigated. In this work, we aimed to recover from public data available AQPs of these crustaceans and reconstruct phylogenetic affinities. We first performed BLAST searches with several queries of diverse taxa against different NCBI databases. Then, we selected the clades of AQPs retrieving the amphipod superfamily Gammaroidea as monophyletic and ran phylogenetic analyses to assess their performances. Our results show how most of the AQPs of amphipods are similar to those of other crustaceans, despite the Prip-like displayed different paralogs, and report for the first time a putative Aqp8-like for arthropods. We also found that the candidate genes of Prip-like, Bib-like, Aqp12-like, and Glp-like help solve deeper relationships in phylogenies of amphipods while leaving uncertainties in shallower parts. With our findings, we hope to increase attention to the study of amphipods as models for AQP functioning and evolution.
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Affiliation(s)
- Andrea Desiderato
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Banacha 12/16, 90-237 Łódź, Poland; (T.M.); (T.R.); (S.M.)
| | - Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Banacha 12/16, 90-237 Łódź, Poland; (T.M.); (T.R.); (S.M.)
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Banacha 12/16, 90-237 Łódź, Poland; (T.M.); (T.R.); (S.M.)
| | - Artur Burzynski
- Department of Genetics and Marine Biotechnology, Polish Academy of Sciences, Institute of Oceanology, Powstańców Warszawy 55, 81-712 Sopot, Poland;
| | - Serena Mucciolo
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Banacha 12/16, 90-237 Łódź, Poland; (T.M.); (T.R.); (S.M.)
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13
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Jażdżewska AM, Tandberg AHS, Horton T, Brix S. Global gap-analysis of amphipod barcode library. PeerJ 2021; 9:e12352. [PMID: 34760373 PMCID: PMC8572522 DOI: 10.7717/peerj.12352] [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: 06/22/2021] [Accepted: 09/29/2021] [Indexed: 12/02/2022] Open
Abstract
In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called 'gold-standard' gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as "white gaps". Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.
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Affiliation(s)
- Anna Maria Jażdżewska
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | - Tammy Horton
- National Oceanography Centre, Southampton, United Kingdom
| | - Saskia Brix
- Department for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Hamburg, Germany
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14
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Borges LMS, Treneman NC, Haga T, Shipway JR, Raupach MJ, Altermark B, Carlton JT. Out of taxonomic crypsis: A new trans-arctic cryptic species pair corroborated by phylogenetics and molecular evidence. Mol Phylogenet Evol 2021; 166:107312. [PMID: 34530118 DOI: 10.1016/j.ympev.2021.107312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/06/2021] [Accepted: 09/09/2021] [Indexed: 01/17/2023]
Abstract
Cryptic species are a common phenomenon in cosmopolitan marine species. The use of molecular tools has often uncovered cryptic species occupying a fraction of the geographic range of the original morphospecies. Shipworms (Teredinidae) are marine bivalves, living in drift and fixed wood, many of which have a conserved morphology across cosmopolitan distributions. Herein novel and GenBank mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S rRNA) DNA sequences are employed to produce a phylogeny of the Teredinidae and delimit a cryptic species pair in the Psiloteredo megotara complex. The anatomy, biogeography, and ecology of P. megotara, Psiloteredo sp. and Nototeredo edax are compared based on private and historic museum collections and a thorough literature review. Morphological and anatomical characters of P. megotara from the North Atlantic and Psiloteredo sp. from Japan were morphologically indistinguishable, and differ in pallet architecture and soft tissue anatomy from N. edax. The two Psiloteredo species were then delimited as genetically distinct species using four molecular-based methods. Consequently, the Northwest Pacific species, Psiloteredo pentagonalis, first synonymized with N. edax and then with P. megotara, is resurrected. Nototeredo edax, P. megotara and P. pentagonalis are redescribed based upon morphological and molecular characters. Phylogenetic analysis further revealed cryptic species complexes within the cosmopolitan species Bankia carinata and possibly additional cryptic lineages within the cosmopolitan Lyrodus pedicellatus.
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Affiliation(s)
- Luísa M S Borges
- L(3) Scientific Solutions, Runder Berg 7e, 21502 Geesthacht, Germany.
| | - Nancy C Treneman
- Oregon Institute of Marine Biology, P.O. Box 5389, Charleston, OR 97420, USA.
| | - Takuma Haga
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan.
| | - J Reuben Shipway
- Institute of Marine Sciences, University of Portsmouth, Ferry Rd, Portsmouth, UK. & Microbiology Department, University of Massachusetts, Amherst, MA, USA.
| | - Michael J Raupach
- Sektion Hemiptera, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany.
| | - Bjørn Altermark
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, PB 6050 Langnes, 9037 Tromsø, Norway.
| | - James T Carlton
- Ocean & Coastal Studies Program, Williams College-Mystic Seaport, Mystic, CT 06355, USA.
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15
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Paz-Ríos CE, Pech D, Carrera-Parra LF, Simões N. Biodiversity and biogeographic affinity of benthic amphipods from the Yucatan Shelf: an analysis across the warm Northwest Atlantic ecoregions. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1947920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Carlos E. Paz-Ríos
- Laboratorio de Biodiversidad Marina y Cambio Climatico (BIOMARCCA), El Colegio de la Frontera Sur, Lerma, Campeche, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climatico (BIOMARCCA), El Colegio de la Frontera Sur, Lerma, Campeche, Mexico
| | - Luis F. Carrera-Parra
- Departamento de Sistematica y Ecologia Acuatica, El Colegio de la Frontera Sur, Chetumal, Quintana Roo, Mexico
| | - Nuno Simões
- Laboratorio Nacional de Resiliencia Costera, Puerto de Abrigo, Sisal, Yucatan, Mexico
- Unidad Academica Sisal, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, Puerto de Abrigo, Sisal, Yucatan, Mexico
- International Chair for Ocean and Coastal Studies, Harte Research Institute, Texas A&M University, Corpus Christi, Texas, USA
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16
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Vieira PE, Lavrador AS, Parente MI, Parretti P, Costa AC, Costa FO, Duarte S. Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Pedro E. Vieira
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Ana S. Lavrador
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Manuela I. Parente
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Paola Parretti
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
- MARE – Marine and Environmental Sciences Centre Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI) Edifício Madeira Tecnopolo Funchal Portugal
| | - Ana C. Costa
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory University of Azores Ponta Delgada Portugal
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) Department of Biology University of Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) University of Minho Braga Portugal
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17
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Phylogeography and genetic diversity of the commercially-collected Caribbean blue-legged hermit crab (Clibanarius tricolor). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01348-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Sampieri BR, Vieira PE, Teixeira MAL, Seixas VC, Pagliosa PR, Amaral ACZ, Costa FO. Molecular diversity within the genus Laeonereis (Annelida, Nereididae) along the west Atlantic coast: paving the way for integrative taxonomy. PeerJ 2021; 9:e11364. [PMID: 34123584 PMCID: PMC8164838 DOI: 10.7717/peerj.11364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/07/2021] [Indexed: 11/20/2022] Open
Abstract
The polychaete genus Laeonereis (Annelida, Nereididae) occurs over a broad geographic range and extends nearly across the entire Atlantic coast of America, from the USA to Uruguay. Despite the research efforts to clarify its diversity and systematics, mostly by morphological and ecological evidence, there is still uncertainty, mainly concerning the species Laeonereis culveri, which constitutes an old and notorious case of taxonomic ambiguity. Here, we revised the molecular diversity and distribution of Laeonereis species based on a multi-locus approach, including DNA sequence analyses of partial segments of the cytochrome c oxidase subunit I (COI), 16S rRNA, and 28S rRNA genes. We examined Laeonereis specimens collected from 26 sites along the American Atlantic coast from Massachusetts (USA) to Mar del Plata (Argentina). Although no comprehensive morphological examination was performed between different populations, the COI barcodes revealed seven highly divergent MOTUs, with a mean K2P genetic distance of 16.9% (from 6.8% to 21.9%), which was confirmed through four clustering algorithms. All MOTUs were geographically segregated, except for MOTUs 6 and 7 from southeastern Brazil, which presented partially overlapping ranges between Rio de Janeiro and São Paulo coast. Sequence data obtained from 16S rRNA and 28S rRNA markers supported the same MOTU delimitation and geographic segregation as those of COI, providing further evidence for the existence of seven deeply divergent lineages within the genus. The extent of genetic divergence between MOTUs observed in our study fits comfortably within the range reported for species of polychaetes, including Nereididae, thus providing a strong indication that they might constitute separate species. These results may therefore pave the way for integrative taxonomic studies, aiming to clarify the taxonomic status of the Laeonereis MOTUs herein reported.
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Affiliation(s)
- Bruno R Sampieri
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Museu de Zoologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
| | - Pedro E Vieira
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
| | - Marcos A L Teixeira
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
| | - Victor C Seixas
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo R Pagliosa
- Laboratório de Biodiversidade e Conservação Marinha, Universidade Federal de Santa Catarina, Florianopólis, Santa Catarina, Brazil
| | | | - Filipe O Costa
- Centro de Biologia Molecular e Ambiental, Universidade do Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), Universidade do Minho, Braga, Portugal
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19
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Fontes JT, Vieira PE, Ekrem T, Soares P, Costa FO. BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries. Mol Ecol Resour 2020; 21:573-583. [PMID: 33000878 DOI: 10.1111/1755-0998.13262] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 01/12/2023]
Abstract
Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R-based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.
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Affiliation(s)
- João T Fontes
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Pedro E Vieira
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Pedro Soares
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Filipe O Costa
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
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20
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Teixeira MAL, Vieira PE, Pleijel F, Sampieri BR, Ravara A, Costa FO, Nygren A. Molecular and morphometric analyses identify new lineages within a large
Eumida
(Annelida) species complex. ZOOL SCR 2019. [DOI: 10.1111/zsc.12397] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marcos A. L. Teixeira
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
| | - Pedro E. Vieira
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
| | - Fredrik Pleijel
- Institutionen for marina vetenskaper Göteborgs Universitet Tjärnö Strömstad Sweden
| | - Bruno R. Sampieri
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
- Museu de Zoologia Instituto de Biologia Universidade Estadual de Campinas – IB/UNICAMP Campinas Brazil
| | - Ascensão Ravara
- Departamento de Biologia CESAM – Centro de Estudos do Ambiente e do Mar Universidade de Aveiro Aveiro Portugal
| | - Filipe O. Costa
- Departamento de Biologia CBMA Centre of Molecular and Environmental Biology Universidade do Minho Braga Portugal
- Institute of Science and Innovation for Bio‐Sustainability (IB‐S) Universidade do Minho Braga Portugal
| | - Arne Nygren
- Institutionen for marina vetenskaper Göteborgs Universitet Tjärnö Strömstad Sweden
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