1
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Zaharias P, Kantor YI, Fedosov AE, Puillandre N. Coupling DNA barcodes and exon-capture to resolve the phylogeny of Turridae (Gastropoda, Conoidea). Mol Phylogenet Evol 2024; 191:107969. [PMID: 38007006 DOI: 10.1016/j.ympev.2023.107969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Taxon sampling in most phylogenomic studies is often based on known taxa and/or morphospecies, thus ignoring undescribed diversity and/or cryptic lineages. The family Turridae is a group of venomous snails within the hyperdiverse superfamily Conoidea that includes many undescribed and cryptic species. Therefore 'traditional' taxon sampling could constitute a strong risk of undersampling or oversampling Turridae lineages. To minimize potential biases, we establish a robust sampling strategy, from species delimitation to phylogenomics. More than 3,000 cox-1 "barcode" sequences were used to propose 201 primary species hypotheses, nearly half of them corresponding to species potentially new to science, including several cryptic species. A 110-taxa exon-capture tree, including species representatives of the diversity uncovered with the cox-1 dataset, was build using up to 4,178 loci. Our results show the polyphyly of the genus Gemmula, that is split into up to 10 separate lineages, of which half would not have been detected if the sampling strategy was based only on described species. Our results strongly suggest that the use of blind, exploratory and intensive barcode sampling is necessary to avoid sampling biases in phylogenomic studies.
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Affiliation(s)
- Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France.
| | - Yuri I Kantor
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Alexander E Fedosov
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France
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2
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Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, González-Solís J. Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds. Mol Phylogenet Evol 2023; 179:107671. [PMID: 36442764 DOI: 10.1016/j.ympev.2022.107671] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
| | - Jose M Herranz
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, Madrid, Spain; Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Josephine R Paris
- Department of Health, Life and Environmental Sciences, University of l'Aquila, Coppito, Italy; Department of Biosciences, University of Exeter, Exeter, UK
| | - James R Whiting
- Department of Biosciences, University of Exeter, Exeter, UK; Department of Biological Sciences, Faculty of Sciences, University of Calgary, Calgary, Canada
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
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3
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do Espirito Santo BS, Rossi MF, Constanza Ovando XM, D'ávila S. Assessing Species Boundaries in the Freshwater Snail Family Physidae Using Coalescent-Based Delimitation Methods. MALACOLOGIA 2022. [DOI: 10.4002/040.065.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Bianca Sartini do Espirito Santo
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Mariana Fonseca Rossi
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Ximena Maria Constanza Ovando
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Sthefane D'ávila
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
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4
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Campbell EO, MacDonald ZG, Gage EV, Gage RV, Sperling FAH. Genomics and ecological modelling clarify species integrity in a confusing group of butterflies. Mol Ecol 2022; 31:2400-2417. [PMID: 35212068 DOI: 10.1111/mec.16407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/30/2022]
Abstract
Recent advances in both genomics and ecological modelling present new, multidisciplinary opportunities for resolving species boundaries and understanding the mechanisms that maintain their integrity in regions of contact. Here, we use a combination of high-throughput DNA sequencing and ecological niche modelling to resolve species boundaries and niche divergence within the Speyeria atlantis-hesperis (Lepidoptera: Nymphalidae) complex, a confusing group of North American butterflies. This complex is notorious for its muddled species delimitations, morphological ambiguity, and extensive mito-nuclear discordance. Our admixture and multispecies coalescent-based analyses of single nucleotide polymorphisms identified substantial divergences between S. atlantis and S. hesperis in areas of contact, as well as between distinct northern and southern lineages within S. hesperis. Our results also provide evidence of past introgression relating to another species, S. zerene, which previous work has shown to be more distantly related to the S. atlantis-hesperis complex. We then used ecological models to predict habitat suitability for each of the three recovered genomic lineages in the S. atlantis-hesperis complex and assess their pairwise niche divergence. These analyses resolved that these three lineages are significantly diverged in their respective niches and are not separated by discontinuities in suitable habitat that might present barriers to gene flow. We therefore infer that ecologically-mediated selection resulting in disparate habitat associations is a principal mechanism reinforcing their genomic integrity. Overall, our results unambiguously support significant evolutionary and ecological divergence between the northern and southern lineages of S. hesperis, sufficient to recognize the southern evolutionary lineage as a distinct species, called S. nausicaa based on taxonomic priority.
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Affiliation(s)
- E O Campbell
- Department of Biological Sciences, Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - Z G MacDonald
- Department of Biological Sciences, Biosciences Centre, University of Alberta, Edmonton, AB, Canada.,Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - E V Gage
- Texas Museum of Entomology, Pipe Creek, TX, U.S.A
| | | | - F A H Sperling
- Department of Biological Sciences, Biosciences Centre, University of Alberta, Edmonton, AB, Canada
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5
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Fedosov A, Achaz G, Gontchar A, Puillandre N. MOLD, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions. Mol Ecol Resour 2022; 22:2038-2053. [DOI: 10.1111/1755-0998.13590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Leninsky prospect 33 119071 Moscow Russia
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
- UMR7206 Eco‐Anthropologie Université de Paris‐CNRS‐MNHN Paris
- UMR7241 Centre Interdisciplinaire de Recherche en Biologie Collége de France‐CNRS‐INSERM Paris
| | - Andrey Gontchar
- Molecular Immunology Laboratory Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology Samory Mashela street 1 117997 Moscow Russia
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
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6
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Bamberger S, Xu J, Hausdorf B. Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete. Syst Biol 2021; 71:439-460. [PMID: 34181027 DOI: 10.1093/sysbio/syab050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 06/11/2021] [Accepted: 06/26/2021] [Indexed: 01/25/2023] Open
Abstract
Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgression between several of the incipient species. Next generation sequencing data may help to overcome some of these problems. We evaluated methods for species delimitation based on genome-wide markers in a land snail radiation on Crete. Species delimitation in the Albinaria cretensis group was based exclusively on shell characters until now and resulted in classifications distinguishing 3-9 species. We generated sequences of 4270 loci for 140 specimens of the Albinaria cretensis group from 48 populations by double-digest restriction site-associated DNA sequencing. We evaluated three methods for species discovery. The multispecies coalescent approach implemented in the program Bayesian Phylogenetics and Phylogeography resulted in a drastic overestimating of the number of species, whereas Gaussian clustering resulted in an overlumping. Primary species hypotheses based on the maximum percentage of the genome of the individuals derived from ancestral populations as estimated with the program ADMIXTURE moderately overestimated the number of species, but this was the only approach that provided information about gene flow between groups. Two of the methods for species validation that we applied, BFD* and delimitR, resulted in an acceptance of almost all primary species hypotheses, even such based on arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast, secondary species hypotheses, resulting from an evaluation of primary species hypotheses based on ADMIXTURE with isolation by distance tests, approached the morphological classification, but also uncovered two cryptic species and indicated that some of the previously delimited units should be combined. Thus, we recommend this combination of approaches that provided more detailed insights in the distinctness of barriers between the taxa of a species complex and the spatial distribution of admixture between them than the other methods. The recognition and delimitation of undersampled species remained a major challenge.
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Affiliation(s)
- Sonja Bamberger
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Jie Xu
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Bernhard Hausdorf
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
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7
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Fernandes MR, Salgueiro F, Paula TS, Lôbo‐Hajdu G, Pimenta AD. Cryptic speciation in the “
Marshallora nigrocincta
” species complex (Gastropoda, Triphoridae) from the Western Atlantic. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maurício Romulo Fernandes
- Instituto de Biociências Universidade Federal do Estado do Rio de Janeiro Rio de Janeiro Brazil
- Departamento de Invertebrados Museu Nacional do Rio de Janeiro Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Fabiano Salgueiro
- Instituto de Biociências Universidade Federal do Estado do Rio de Janeiro Rio de Janeiro Brazil
| | - Thiago Silva Paula
- Departamento de Genética Instituto de Biologia Roberto Alcântara Gomes Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil
| | - Gisele Lôbo‐Hajdu
- Departamento de Genética Instituto de Biologia Roberto Alcântara Gomes Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil
| | - Alexandre Dias Pimenta
- Departamento de Invertebrados Museu Nacional do Rio de Janeiro Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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8
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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9
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Vaux F, Gemmell MR, Hills SFK, Marshall BA, Beu AG, Crampton JS, Trewick SA, Morgan-Richards M. Lineage Identification Affects Estimates of Evolutionary Mode in Marine Snails. Syst Biol 2020; 69:1106-1121. [PMID: 32163159 DOI: 10.1093/sysbio/syaa018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/13/2020] [Accepted: 03/09/2020] [Indexed: 11/14/2022] Open
Abstract
In order to study evolutionary pattern and process, we need to be able to accurately identify species and the evolutionary lineages from which they are derived. Determining the concordance between genetic and morphological variation of living populations, and then directly comparing extant and fossil morphological data, provides a robust approach for improving our identification of lineages through time. We investigate genetic and shell morphological variation in extant species of Penion marine snails from New Zealand, and extend this analysis into deep time using fossils. We find that genetic and morphological variation identify similar patterns and support most currently recognized extant species. However, some taxonomic over-splitting is detected due to shell size being a poor trait for species delimitation, and we identify incorrect assignment of some fossil specimens. We infer that a single evolutionary lineage (Penion sulcatus) has existed for 22 myr, with most aspects of shell shape and shell size evolving under a random walk. However, by removing samples previously classified as the extinct species P. marwicki, we instead detect morphological stasis for one axis of shell shape variation. This result demonstrates how lineage identification can change our perception of evolutionary pattern and process. [Genotyping by sequencing; geometric morphometrics; morphological evolution; Neogastropoda; phenotype; speciation; stasis.].
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Affiliation(s)
- Felix Vaux
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4410, New Zealand.,Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, 2030 SE Marine Science Dr, Newport, OR 97365, USA.,Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, Otago, New Zealand
| | - Michael R Gemmell
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4410, New Zealand
| | - Simon F K Hills
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4410, New Zealand
| | - Bruce A Marshall
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Alan G Beu
- GNS Science, PO Box 30-368, Lower Hutt 5011, New Zealand
| | - James S Crampton
- School of Geography, Environment & Earth Sciences, Victoria University of Wellington, PO Box 600, Wellington 6012, New Zealand
| | - Steven A Trewick
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4410, New Zealand
| | - Mary Morgan-Richards
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4410, New Zealand
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10
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Criscione F, Hallan A, Puillandre N, Fedosov A. Where the snails have no name: a molecular phylogeny of Raphitomidae (Neogastropoda: Conoidea) uncovers vast unexplored diversity in the deep seas of temperate southern and eastern Australia. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Although raphitomid snails are a dominant component of gastropod communities in deep seas worldwide, their systematics is still largely tentative. We assembled the most complete sampling of Raphitomidae from south-eastern Australia to date. Based on morphological and molecular data from this material, we produced a robust phylogenetic framework and used it to delimit genera. For the focus area, our results show a large proportion of undescribed species- and genus-level taxa, 11 of which are formally described herein. We demonstrate that the examination of purely morphological characters rarely suffices for the purpose of accurate genus delimitation. As a result, some traditionally highly diverse raphitomid genera (such as Gymnobela) turn out to be artificial assemblages of several unrelated, mostly undescribed, genus-level lineages. Our data suggest that comparable configurations of shell and radular features, observed at the genus level, commonly do not reflect true phylogenetic relationships. However, our results are inconclusive as to whether homoplasy or conservatism are the drivers of this phenomenon. Accommodating for the inevitable sampling biases, south-eastern Australia appears as a possible hotspot for both raphitomid diversity and endemism, when compared with adjacent areas.
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Affiliation(s)
| | | | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles. CP, Paris, France
| | - Alexander Fedosov
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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11
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Jossart Q, Kochzius M, Danis B, Saucède T, Moreau CVE. Diversity of the Pterasteridae (Asteroidea) in the Southern Ocean: a molecular and morphological approach. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
An integrative approach is crucial in discrimination of species, especially for taxa that are difficult to identify based on morphological characters. In this study, we combine genetics and morphology to assess the diversity of Pterasteridae, a sea star family diversified in deep-sea and polar environments. Because of their derived anatomy and the frequent loss of characters during preservation, Pterasteridae are a suitable case for an integrative study. The molecular identification of 191 specimens (mostly from the Southern Ocean) suggests 26–33 species in three genera (Diplopteraster, Hymenaster and Pteraster), which match the morphological identification in 54–62% of cases. The mismatches are either different molecular units that are morphologically indistinguishable (e.g. Pteraster stellifer units 2 and 4) or, conversely, nominal species that are genetically identical (e.g. Hymenaster coccinatus/densus/praecoquis). Several species are shared between the Northern and Southern Hemispheres (e.g. Pteraster jordani/affinis). In conclusion, the taxonomic status of some groups is confirmed, but for others we find the need to re-evaluate the taxonomy at both genus and species levels. This work significantly increases the DNA barcode library of the Southern Ocean species and merges taxonomic information into an identification key that could become a baseline for future studies (pterasteridae-so.identificationkey.org).
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Affiliation(s)
- Quentin Jossart
- Marine Biology, Ecology and Biodiversity, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology, Ecology and Biodiversity, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Bruno Danis
- Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Thomas Saucède
- Biogéosciences, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Camille V E Moreau
- Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Biogéosciences, Université Bourgogne Franche Comté (UBFC), Dijon, France
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12
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Fedosov AE, Puillandre N. Integrative taxonomy of the Clavus canalicularis species complex (Drilliidae, Conoidea, Gastropoda) with description of four new species. MOLLUSCAN RESEARCH 2020. [DOI: 10.1080/13235818.2020.1788695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- A. E. Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russian Federation
| | - N. Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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Zaharias P, Kantor YI, Fedosov AE, Criscione F, Hallan A, Kano Y, Bardin J, Puillandre N. Just the once will not hurt: DNA suggests species lumping over two oceans in deep-sea snails (Cryptogemma). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The practice of species delimitation using molecular data commonly leads to the revealing of species complexes and an increase in the number of delimited species. In a few instances, however, DNA-based taxonomy has led to lumping together of previously described species. Here, we delimit species in the genus Cryptogemma (Gastropoda: Conoidea: Turridae), a group of deep-sea snails with a wide geographical distribution, primarily by using the mitochondrial COI gene. Three approaches of species delimitation (ABGD, mPTP and GMYC) were applied to define species partitions. All approaches resulted in eight species. According to previous taxonomic studies and shell morphology, 23 available names potentially apply to the eight Cryptogemma species that were recognized herein. Shell morphometrics, radular characters and geographical and bathymetric distributions were used to link type specimens to these delimited species. In all, 23 of these available names are here attributed to seven species, resulting in 16 synonymizations, and one species is described as new: Cryptogemma powelli sp. nov. We discuss the possible reasons underlying the apparent overdescription of species within Cryptogemma, which is shown here to constitute a rare case of DNA-based species lumping in the hyper-diversified superfamily Conoidea.
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Affiliation(s)
- Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 26, Paris, France
| | - Yuri I Kantor
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander E Fedosov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russian Federation
| | - Francesco Criscione
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Anders Hallan
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Yasunori Kano
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Jérémie Bardin
- Centre de Recherche en Paléontologie – Paris (CR2P-UMR 7207), Sorbonne Université-CNRS-MNHN, Site Pierre et Marie Curie, 4 place Jussieu, Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 26, Paris, France
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Wu Y, Krishnankutty SM, Vieira KA, Wang B, Nadel H, Myers SW, Ray AM. Invasion of Trichoferus campestris (Coleoptera: Cerambycidae) into the United States characterized by high levels of genetic diversity and recurrent introductions. Biol Invasions 2020. [DOI: 10.1007/s10530-019-02182-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa. Mol Phylogenet Evol 2020; 142:106660. [DOI: 10.1016/j.ympev.2019.106660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
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Venom Diversity and Evolution in the Most Divergent Cone Snail Genus Profundiconus. Toxins (Basel) 2019; 11:toxins11110623. [PMID: 31661832 PMCID: PMC6891753 DOI: 10.3390/toxins11110623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023] Open
Abstract
Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also a significant percentage of other putative venom components such as chymotrypsin and L-rhamnose-binding lectin. The large majority of conotoxins appeared to be from new gene superfamilies, three of which are highly different from previously reported venom peptide toxins. Their low conotoxin diversity and the type of insulin found suggested that these species, for which no ecological information are available, have a worm or molluscan diet associated with a narrow dietary breadth. Our results indicate that Profundiconus venom is highly distinct from that of other cone snails, and therefore important for examining venom evolution in the Conidae family.
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Bocek M, Motyka M, Kusy D, Bocak L. Genomic and Mitochondrial Data Identify Different Species Boundaries in Aposematically Polymorphic Eniclases Net-Winged Beetles (Coleoptera: Lycidae). INSECTS 2019; 10:E295. [PMID: 31514482 PMCID: PMC6780303 DOI: 10.3390/insects10090295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 12/14/2022]
Abstract
Species delineation is essential for any evolutionary and biodiversity research, and recent advances in genomic sequencing have made it possible to robustly define species boundaries and detect hidden diversity. Here, we studied 14 species of aposematically colored New Guinean Eniclases (Coleoptera: Lycidae) whose conventional morphology- and single-locus mtDNA-based taxonomy has been contentious. We analyzed mitochondrial and restriction site associated DNA fragments to obtain a phylogenetic hypothesis and compared relationships recovered by the RAD analysis with species limits based on other information. The results show the presence of cryptic diversity and common mitonuclear discordance when over 30% of individuals were incorrectly assigned to species if only mitogenomic markers were considered. Nuclear data falsified the species rank of one species and identified one earlier unrecognized lineage deserving species rank. Further, our analyses demonstrate a highly variable phenotypic differentiation, with several pairs of cryptic species standing in contrast with genetically close but phenotypically highly divergent lineages. We show that morphological and mitogenomic analyses produce reliable information for taxonomy in most cases. Nevertheless, the species boundaries among closely related species should be based on all lines of evidence, including nuclear markers.
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Affiliation(s)
- Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
| | - Michal Motyka
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
| | - Dominik Kusy
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic.
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