51
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Puillandre N, Brouillet S, Achaz G. ASAP: assemble species by automatic partitioning. Mol Ecol Resour 2020; 21:609-620. [PMID: 33058550 DOI: 10.1111/1755-0998.13281] [Citation(s) in RCA: 375] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
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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, Paris, France
| | - Sophie Brouillet
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,SMILE Group, CIRB, UMR 7241, Collège de France, CNRS, INSERM, Paris, France.,Éco-anthropologie, Muséum National d'Histoire Naturelle, CNRS UMR 7206, Université de Paris, Paris, France
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52
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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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53
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Fawley MW, Fawley KP. Identification of Eukaryotic Microalgal Strains. JOURNAL OF APPLIED PHYCOLOGY 2020; 32:2699-2709. [PMID: 33542589 PMCID: PMC7853647 DOI: 10.1007/s10811-020-02190-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Proper identification and documentation of microalgae is often lacking in publications of applied phycology, algal physiology and biochemistry. Identification of many eukaryotic microalgae can be very daunting to the non-specialist. We present a systematic process for identifying eukaryotic microalgae using morphological evidence and DNA sequence analysis. Our intent was to provide an identification method that could be used by non-taxonomists, but which is grounded in the current techniques used by algal taxonomists. Central to the identification is database searches with DNA sequences of appropriate loci. We provide usable criteria for identification at the genus or species level, depending on the availability of sequence data in curated databases and repositories. Particular attention is paid to dealing with possible misidentifications in DNA databases and utilizing current taxonomy.
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Affiliation(s)
- Marvin W Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
| | - Karen P Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
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54
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Li C, Jiang S, Schneider K, Jin J, Lin H, Wang J, Elmer KR, Zhao J. Cryptic species in White Cloud Mountain minnow, Tanichthys albonubes: Taxonomic and conservation implications. Mol Phylogenet Evol 2020; 153:106950. [PMID: 32889137 DOI: 10.1016/j.ympev.2020.106950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Cryptic species describe two or more species that had mistakenly been considered to be a single species, a phenomenon that has been found throughout the tree of life. Recognizing cryptic species is key to estimating the real biodiversity of the world and understanding evolutionary processes. Molecular methods present an unprecedented opportunity for biologists to question whether morphologically similar populations are actually cryptic species. The minnow Tanichthys albonubes is a critically endangered freshwater fish and was classified as a second-class state-protected animal in China. Previous studies have revealed highly divergent lineages with similar morphological characters in this species. Herein, we tested for cryptic species across the ranges of all known wild populations of this minnow. Using multilocus molecular (one mitochondrial gene, two nuclear genes and 13 microsatellite loci) and morphological data for 230 individuals from eight populations, we found deep genetic divergence among these populations with subtle morphological disparity. Morphological examination found variance among these populations in the number of branched anal-fin rays. Based on genetic data, we inferred eight monophyletic groups that were well supported by haplotype network and population clustering analyses. Species delimitation methods suggested eight putative species in the T. albonubes complex. Molecular dating suggested that these cryptic species diverged in the period from the Pliocene to the Pleistocene. Based on these findings, we propose the existence of seven cryptic species in the T. albonubes complex. Our results highlight the need for a taxonomic revision of Tanichthys. What is more, the conservation status of and conservation strategies for the T. albonubes complex should be reassessed as soon as possible.
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Affiliation(s)
- Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Shuying Jiang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Kevin Schneider
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jinjin Jin
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Junjie Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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55
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Villamor A, Signorini LF, Costantini F, Terzin M, Abbiati M. Evidence of genetic isolation between two Mediterranean morphotypes of Parazoanthus axinellae. Sci Rep 2020; 10:13938. [PMID: 32811877 PMCID: PMC7434761 DOI: 10.1038/s41598-020-70770-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 08/04/2020] [Indexed: 11/20/2022] Open
Abstract
Coralligenous assemblages are among the most species-rich and vulnerable habitats of the Mediterranean Sea. Nevertheless, data on connectivity patterns on species inhabiting these habitats, crucial to define management and protection priorities, are largely lacking. Moreover, unreliable species-level taxonomy can confound ecological studies and mislead management strategies. In the northwestern Mediterranean two Parazoanthus axinellae morphotypes differing in size, color and preferred substrate are found in sympatry. In this study, we used COI and ITS sequence polymorphism to assess (1) the genetic divergence between the two morphotypes, (2) their connectivity patterns and (3) their phylogenetic position within the Parazoanthidae. Specimens of P. axinellae were sampled in 11 locations along the northwestern Mediterranean; in 6 locations, samples of the two morphotypes were collected in sympatry. Small genetic diversity and structure were found within morphotypes, while marked and consistent differentiation was detected between them. Moreover, the less widespread morphotype appeared to be closer to Pacific species as P. juanfernandezii and P. elongatus. Our findings confirmed the limited knowledge on Parazoanthus species complex, and how this gap can have important implication for the conservation strategies of this widespread and valuable genus in the Mediterranean Sea.
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Affiliation(s)
- Adriana Villamor
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, 48123, Ravenna, Italy.,International Council for the Exploration of the Sea, HC Andersen 22-24, 1553, Copenhagen, Denmark
| | - Lorenzo F Signorini
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, 48123, Ravenna, Italy.,Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Federica Costantini
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, 48123, Ravenna, Italy. .,CoNISMa, Piazzale Flaminio 9, 00196, Rome, Italy.
| | - Marko Terzin
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, 48123, Ravenna, Italy
| | - Marco Abbiati
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, 48123, Ravenna, Italy.,Consiglio Nazionale Delle Ricerche, Istituto di Scienze Marine, ISMAR, Bologna, Italy.,Dipartimento di Beni Culturali, Università di Bologna, Via degli Ariani, 1, 48121, Ravenna, RA, Italy
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56
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Elgetany AH, Rensburg H, Hektoen M, Matthee C, Budaeva N, Simon CA, Struck TH. Species delineation in the speciation grey zone—The case of
Diopatra
(Annelida, Onuphidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12421] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Asmaa H. Elgetany
- Zoology Department Faculty of Science Damietta University New Damietta, Central Zone Egypt
- Natural History Museum University of Oslo Oslo Norway
| | - Hendré Rensburg
- Department of Botany and Zoology Stellenbosch University Stellenbosch South Africa
| | - Martin Hektoen
- NTNU University Museum Norwegian University of Science and Technology Trondheim Norway
| | - Conrad Matthee
- Department of Botany and Zoology Stellenbosch University Stellenbosch South Africa
| | - Nataliya Budaeva
- Department of Natural History University Museum of Bergen University of Bergen Bergen Norway
| | - Carol A Simon
- Department of Botany and Zoology Stellenbosch University Stellenbosch South Africa
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57
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Cerca J, Meyer C, Purschke G, Struck TH. Delimitation of cryptic species drastically reduces the geographical ranges of marine interstitial ghost-worms (Stygocapitella; Annelida, Sedentaria). Mol Phylogenet Evol 2020; 143:106663. [DOI: 10.1016/j.ympev.2019.106663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
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58
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Leria L, Vila-Farré M, Álvarez-Presas M, Sánchez-Gracia A, Rozas J, Sluys R, Riutort M. Cryptic species delineation in freshwater planarians of the genus Dugesia (Platyhelminthes, Tricladida): Extreme intraindividual genetic diversity, morphological stasis, and karyological variability. Mol Phylogenet Evol 2020; 143:106496. [DOI: 10.1016/j.ympev.2019.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/10/2019] [Accepted: 05/17/2019] [Indexed: 01/04/2023]
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59
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Slavenko A, Tamar K, Tallowin OJS, Allison A, Kraus F, Carranza S, Meiri S. Cryptic diversity and non-adaptive radiation of montane New Guinea skinks (Papuascincus; Scincidae). Mol Phylogenet Evol 2020; 146:106749. [PMID: 32014575 DOI: 10.1016/j.ympev.2020.106749] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/12/2019] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
New Guinea, the world's largest and highest tropical island, has a rich but poorly known biota. Papuascincus is a genus of skinks endemic to New Guinea's mountain regions, comprising two wide-ranging species and two species known only from their type series. The phylogeny of the genus has never been examined and the relationships among its species - as well as between it and closely related taxa - are hitherto unknown. We performed the first large-scale molecular-phylogenetic study of Papuascincus, including sampling across the genus' range in Papua New Guinea. We sequenced three mitochondrial and two nuclear markers from 65 specimens of Papuascincus and reconstructed their phylogenetic relationships. We also performed species-delimitation analyses, estimated divergence times and ancestral biogeography, and examined body-size evolution within the genus. Papuascincus was strongly supported as monophyletic. It began radiating during the mid-Miocene in the area now comprising the Central Cordillera of New Guinea, then dispersed eastward colonising the Papuan Peninsula. We found evidence of extensive cryptic diversity within the genus, with between nine and 20 supported genetic lineages. These were estimated using three methods of species delimitation and predominantly occur in allopatry. Distribution and body-size divergence patterns indicated that character displacement in size took place during the evolutionary history of Papuascincus. We conclude that the genus requires comprehensive taxonomic revision and likely represents a species-rich lineage of montane skinks.
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Affiliation(s)
- Alex Slavenko
- School of Zoology, Tel Aviv University, 6997801 Tel Aviv, Israel.
| | - Karin Tamar
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | | | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, MI, USA
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Shai Meiri
- School of Zoology, Tel Aviv University, 6997801 Tel Aviv, Israel; The Steinhardt Museum of Natural History, Tel Aviv, Israel
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60
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Chambers EA, Hillis DM. The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa. Syst Biol 2020; 69:184-193. [PMID: 31180508 DOI: 10.1093/sysbio/syz042] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/14/2022] Open
Abstract
Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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61
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Engelbrecht HM, Branch WR, Greenbaum E, Burger M, Conradie W, Tolley KA. African Herald snakes,
Crotaphopeltis
, show population structure for a widespread generalist but deep genetic divergence for forest specialists. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hanlie M. Engelbrecht
- South African National Biodiversity Institute Kirstenbosch Research Centre Claremont South Africa
- Department of Botany & Zoology Stellenbosch University Matieland South Africa
| | - William R. Branch
- Port Elizabeth Museum (Bayworld) Port Elizabeth South Africa
- Department of Zoology Nelson Mandela University Port Elizabeth South Africa
| | - Eli Greenbaum
- Department of Biological Sciences University of Texas at El Paso El Paso TX USA
| | - Marius Burger
- African Amphibian Conservation Research Group Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
- Flora Fauna & Man Ecological Services Ltd. Tortola British Virgin Islands
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld) Port Elizabeth South Africa
- School of Natural Resource Management Nelson Mandela University George South Africa
- National Geographic Okovango Wilderness ProjectThe Wild Bird Trust Parktown South Africa
| | - Krystal A. Tolley
- South African National Biodiversity Institute Kirstenbosch Research Centre Claremont South Africa
- Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Auckland Park South Africa
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62
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Tóthné Bogdányi F, Petrikovszki R, Balog A, Putnoky-Csicsó B, Gódor A, Bálint J, Tóth F. Current Knowledge of the Entomopathogenic Fungal Species Metarhizium flavoviride Sensu Lato and Its Potential in Sustainable Pest Control. INSECTS 2019; 10:insects10110385. [PMID: 31684065 PMCID: PMC6920967 DOI: 10.3390/insects10110385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 11/29/2022]
Abstract
Fungal entomopathogens are gaining increasing attention as alternatives to chemical control of arthropod pests, and the literature on their use under different conditions and against different species keeps expanding. Our review compiles information regarding the entomopathogenic fungal species Metarhizium flavoviride (Gams and Rozsypal 1956) (Hypocreales: Clavicipitaceae) and gives account of the natural occurrences and target arthropods that can be controlled using M. flavoviride. Taxonomic problems around M. flavoviride species sensu lato are explained. Bioassays, laboratory and field studies examining the effect of fermentation, culture regimes and formulation are compiled along with studies on the effect of the fungus on target and non-target organisms and presenting the effect of management practices on the use of the fungus. Altogether, we provide information to help conducting basic studies, and by pointing out relatively uncharted territories, help to set new research areas.
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Affiliation(s)
| | - Renáta Petrikovszki
- Plant Protection Institute, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter Károly srt. 1, 2100 Gödöllő, Hungary.
| | - Adalbert Balog
- Department of Horticulture, Faculty of Technical and Human Sciences, Sapientia Hungarian University of Transylvania, Allea Sighișoarei 1C, 540485 Targu Mures/Corunca, Romania.
| | - Barna Putnoky-Csicsó
- Department of Horticulture, Faculty of Technical and Human Sciences, Sapientia Hungarian University of Transylvania, Allea Sighișoarei 1C, 540485 Targu Mures/Corunca, Romania.
| | - Anita Gódor
- Plant Protection Institute, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter Károly srt. 1, 2100 Gödöllő, Hungary.
| | - János Bálint
- Department of Horticulture, Faculty of Technical and Human Sciences, Sapientia Hungarian University of Transylvania, Allea Sighișoarei 1C, 540485 Targu Mures/Corunca, Romania.
| | - Ferenc Tóth
- Plant Protection Institute, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter Károly srt. 1, 2100 Gödöllő, Hungary.
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63
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Jossart Q, Sands CJ, Sewell MA. Dwarf brooder versus giant broadcaster: combining genetic and reproductive data to unravel cryptic diversity in an Antarctic brittle star. Heredity (Edinb) 2019; 123:622-633. [PMID: 31073238 PMCID: PMC6972741 DOI: 10.1038/s41437-019-0228-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/08/2019] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
Poecilogony, or multiple developmental modes in a single species, is exceedingly rare. Several species described as poecilogenous were later demonstrated to be multiple (cryptic) species with a different developmental mode. The Southern Ocean is known to harbor a high proportion of brooders (Thorson's Rule) but with an increasing number of counter examples over recent years. Here we evaluated poecilogony vs. crypticism in the brittle star Astrotoma agassizii across the Southern Ocean. This species was initially described from South America as a brooder before some pelagic stages were identified in Antarctica. Reproductive and mitochondrial data were combined to unravel geographic and genetic variation of developmental modes. Our results indicate that A. agassizii is composed of seven well-supported and deeply divergent clades (I: Antarctica and South Georgia; II: South Georgia and Sub-Antarctic locations including Kerguelen, Patagonian shelf, and New Zealand; III-VI-VII: Patagonian shelf, IV-V: South Georgia). Two of these clades demonstrated strong size dimorphism when in sympatry and can be linked to differing developmental modes (Clade V: dwarf brooder vs. Clade I: giant broadcaster). Based on their restricted geographic distributions and on previous studies, it is likely that Clades III-VI-VII are brooders. Clade II is composed of different morphological species, A. agassizii and A. drachi, the latter originally used as the outgroup. By integrating morphology, reproductive, and molecular data we conclude that the variation identified in A. agassizii is best described as crypticism rather than poecilogony.
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Affiliation(s)
- Quentin Jossart
- University of Auckland, Auckland, New Zealand.
- British Antarctic Survey, Cambridge, UK.
- Vrije Universiteit Brussel, Brussels, Belgium.
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64
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Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D. The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol 2019; 17:e3000483. [PMID: 31545807 PMCID: PMC6776362 DOI: 10.1371/journal.pbio.3000483] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/03/2019] [Indexed: 02/01/2023] Open
Abstract
Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
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Affiliation(s)
- Serge Planes
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- * E-mail:
| | - Denis Allemand
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
| | | | - Bernard Banaigs
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emilie Boissin
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - J. Michel Flores
- Weizmann Institute of Science, Dept. Earth and Planetary Science, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Paola Furla
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Pierre E. Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Jean-François Ghiglione
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université Laboratoire d’Océanographie Microbienne LOMIC, UMR 7621, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Stephane Pesant
- PANGEA, Data Publisher for Earth and Environment Science, Bremen, Germany
- MARUM—Center for Marine Environmental Sciences, Universität Bremen, Bremen, Germany
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | | | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, United States of America
| | - Shinichi Sunagawa
- Department of Biology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Olivier P. Thomas
- Marine Biodiscovery Laboratory, School of Chemistry and Ryan Institute, National University of Ireland, Galway (NUI Galway), Galway, Ireland
| | - Romain Troublé
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- La Fondation Tara Expéditions, “Base Tara” 11, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | | | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
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65
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Porro B, Mallien C, Hume BCC, Pey A, Aubin E, Christen R, Voolstra CR, Furla P, Forcioli D. The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs. Heredity (Edinb) 2019; 124:351-366. [PMID: 31527783 DOI: 10.1038/s41437-019-0266-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 07/30/2019] [Accepted: 08/15/2019] [Indexed: 11/09/2022] Open
Abstract
How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.
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Affiliation(s)
- Barbara Porro
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
| | - Cédric Mallien
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Benjamin C C Hume
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Alexis Pey
- THALASSA Marine research & Environmental awareness, 17 rue Gutenberg, 06000, Nice, France
| | - Emilie Aubin
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Laboratoire Génome et Développement des Plantes-UMR CNRS/UPVD 5096, Université de Perpignan, 66860, Perpignan, France
| | - Richard Christen
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paola Furla
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France
| | - Didier Forcioli
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
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66
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Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae). Mol Phylogenet Evol 2019; 138:89-101. [DOI: 10.1016/j.ympev.2019.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
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67
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Chiazzari B, Magalon H, Gélin P, Macdonald A. Living on the edge: Assessing the diversity of South African Pocillopora on the margins of the Southwestern Indian Ocean. PLoS One 2019; 14:e0220477. [PMID: 31374077 PMCID: PMC6677312 DOI: 10.1371/journal.pone.0220477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/16/2019] [Indexed: 11/19/2022] Open
Abstract
Scleractinia of the Maputaland reef complex (MRC) in South Africa exist at the margins of the Western Indian Ocean (WIO) coral distribution and are the only substantial hermatypic coral communities in South Africa. Pocillopora species occupy a conspicuous component of the MRC, and previous investigations identified three species of Pocillopora utilizing conventional taxonomy. Thus, our aims were four-fold: to elucidate Pocillopora species diversity using genetic techniques, primarily using species delimitation methods based on the ORF gene; to test for the presence of hybridisation within the Pocillopora community on the South-West margin of distribution in the Indian Ocean using two nuclear and two mitochondrial markers; to test the presence of cryptic species, using 13 microsatellite markers, finally, to elucidate the degree of genetic diversity within each Pocillopora species found and compare this to communities in lower latitudes. We illustrate taxonomic inconsistencies between these inventories and our phylogenetic data. The MRC harbours unique populations of Pocillopora, consisting of three species hypothetically co-occurring throughout the south WIO, namely: P. meandrina/P. eydouxi, commonly misidentified as P. verrucosa, P. verrucosa, sometimes correctly identified, but also commonly misidentified as P. damicornis sensu lato, and P. villosa, almost always misidentified as P. eydouxi. The hypothesis that hybrid swarms of Pocillopora occur in marginal environments such as the MRC was not supported, with low levels of introgressive hybridization reported instead. Analyses illustrate low genetic diversity at the species and population resolutions, suggesting a small founder population for each species. Nevertheless, these populations are demographically unique, exhibiting high levels of ITS2 haplotype endemism compared to higher latitude populations and the rest of the WIO. Pocillopora diversity on the MRC represents a unique assemblage and warrants further protection.
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Affiliation(s)
- Brent Chiazzari
- School of Life Sciences, University of KwaZulu-Natal, Westville, KwaZulu-Natal, South Africa
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d’excellence CORAIL, Faculté des Sciences et Technologies, La Réunion, France
| | - Pauline Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d’excellence CORAIL, Faculté des Sciences et Technologies, La Réunion, France
| | - Angus Macdonald
- School of Life Sciences, University of KwaZulu-Natal, Westville, KwaZulu-Natal, South Africa
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68
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Lin YJ, Qurban MA, Shen KN, Chao NL. Delimitation of Tigertooth Croaker Otolithes Species (Teleostei: Sciaenidae) from the Western Arabian Gulf Using an Integrative Approach, with a Description of Otolithes arabicus sp. nov. Zool Stud 2019; 58:e10. [PMID: 31966311 PMCID: PMC6759924 DOI: 10.6620/zs.2019.58-10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/24/2019] [Indexed: 12/26/2022]
Abstract
Two species, Otolithes ruber and Otolithes cuvieri, are currently recognized in the sciaenid genus Otolithes. Recent findings suggest that Otolithes ruber likely has multiple genetically and morphologically distinct lineages and one of them, Otolithes sp. West Indian Ocean II group (WIO II group), has been previously identified in the Arabian Gulf. In this study, the specimens of Otolithes sp. collected from the western Arabian Gulf were examined using an integrative approach by combining mitochondrial cytochrome c oxidase 1 gene, morphological characteristics, and otolith-shape analyses. Three groups were found to have small within-group and large between-group genetic distance: the Otolithes sp. Western Arabian Gulf (WA) group, and the Otolithes sp. WIO II groups type A and type B. Accordingly, three primary species hypotheses were proposed. Evidence from conventional morphological comparisons, multivariate statistical analysis, geometric morphometric landmark analysis on morphological characteristics, and otolith shape analysis based on wavelet transformation all favor the hypothesis that the Otolithes sp. WA group is a distinct lineage. For this new species, the name Otolithes arabicus sp. nov. is proposed. A detailed description of Otolithes arabicus sp. nov. and a key to identifing species in the genus Otolithes are also provided. However, the primary species hypotheses for Otolithes sp. West Indian Ocean II group type A and type B cannot be fully supported because of partial congruence, which may result from recent divergence.
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Affiliation(s)
- Yu-Jia Lin
- Marine Studies Section, Center for Environment and
Waters, King Fahd University of Petroleum and Minerals, Kingdom of Saudi Arabia; Marine
Studies Section, Center for Environment and Waters, King Fahd University of Petroleum and
Minerals, Kingdom of Saudi Arabia. E-mail: (Qurban)
| | - Mohammad A. Qurban
- Marine Studies Section, Center for Environment and
Waters, King Fahd University of Petroleum and Minerals, Kingdom of Saudi Arabia; Marine
Studies Section, Center for Environment and Waters, King Fahd University of Petroleum and
Minerals, Kingdom of Saudi Arabia. E-mail: (Qurban)
| | - Kang Ning Shen
- Department of Environmental Biology and Fisheries
Science, National Taiwan Ocean University, Taiwan. E-mail:
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69
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Riquet F, Liautard-Haag C, Woodall L, Bouza C, Louisy P, Hamer B, Otero-Ferrer F, Aublanc P, Béduneau V, Briard O, El Ayari T, Hochscheid S, Belkhir K, Arnaud-Haond S, Gagnaire PA, Bierne N. Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages. Evolution 2019; 73:817-835. [PMID: 30854632 DOI: 10.1111/evo.13696] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/19/2019] [Accepted: 01/24/2019] [Indexed: 01/02/2023]
Abstract
Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both reduce gene flow between groups. Rarely are these two patterns of spatial distribution reported in the same study system. Here, we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry-i.e., in the same geographical zone-with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon-like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus-specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. We find that fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome-wide pattern of structure that mostly follow geography. These parallel outlier SNPs cluster on a single chromosome-wide island of differentiation. Since Atlantic lineages do not map to lagoon-sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts-i.e., spatial versus ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated both with space and with a patchy environment in a single study system.
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Affiliation(s)
- Florentine Riquet
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Cathy Liautard-Haag
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Lucy Woodall
- Department of Zoology, University of Oxford, Wytham, OX2 8QJ, United Kingdom.,Natural History Museum, London, SW7 5BD, United Kingdom
| | - Carmen Bouza
- Department of Genetics, Faculty of Veterinary Science, Universidade de Santiago de Compostela, Lugo, Spain
| | - Patrick Louisy
- ECOMERS Laboratory, University of Nice Sophia Antipolis, Faculty of Sciences, Parc Valrose, Nice, France.,Association Peau-Bleue, 46 rue des Escais, Agde, France
| | - Bojan Hamer
- Center for Marine Research, Ruder Boskovic Institute, Giordano Paliaga 5, 52210, Rovinj, Croatia
| | - Francisco Otero-Ferrer
- Grupo en Biodiversidad y Conservación, IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214, Telde, Spain
| | - Philippe Aublanc
- Institut océanographique Paul Ricard, Ile des Embiez, Six-Fours-les-Plages, France
| | - Vickie Béduneau
- Océarium du Croisic, Avenue de Saint Goustan, Le Croisic, France
| | - Olivier Briard
- Aquarium de Biarritz, Biarritz Océan, Plateau de l'Atalaye, Biarritz, France
| | - Tahani El Ayari
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Sandra Hochscheid
- Stazione Zoologica Anton Dohrn, Department Research Infrastructures for Marine Biological Resources, Aquarium Unit, Napoli, Italy
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Sophie Arnaud-Haond
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,Ifremer-MARine Biodiversity, Exploitation and Conservation, UMR 9190 IRD-IFREMER-UM-CNRS, Sète, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, Montpellier, France.,CNRS Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Sète, France
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70
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Phillips JD, Gillis DJ, Hanner RH. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol Evol 2019; 9:2996-3010. [PMID: 30891232 PMCID: PMC6406011 DOI: 10.1002/ece3.4757] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/03/2018] [Accepted: 10/12/2018] [Indexed: 02/01/2023] Open
Abstract
DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present levels of haplotype diversity, as well as patterning of standing genetic variation that exists within and between species. Typical sample sizes for molecular biodiversity assessment using DNA barcodes range from 5 to 10 individuals per species. However, required levels that are necessary to fully gauge haplotype variation at the species level are presumed to be strongly taxon-specific. Importantly, little attention has been paid to determining appropriate specimen sample sizes that are necessary to reveal the majority of intraspecific haplotype variation within any one species. In this paper, we present a brief outline of the current literature and methods on intraspecific sample size estimation for the assessment of COI DNA barcode haplotype sampling completeness. The importance of adequate sample sizes for studies of molecular biodiversity is stressed, with application to a variety of metazoan taxa, through reviewing foundational statistical and population genetic models, with specific application to ray-finned fishes (Chordata: Actinopterygii). Finally, promising avenues for further research in this area are highlighted.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer ScienceUniversity of GuelphGuelphOntarioCanada
- Centre for Biodiversity GenomicsBiodiversity Institute of OntarioUniversity of GuelphGuelphOntarioCanada
| | - Daniel J. Gillis
- School of Computer ScienceUniversity of GuelphGuelphOntarioCanada
| | - Robert H. Hanner
- Centre for Biodiversity GenomicsBiodiversity Institute of OntarioUniversity of GuelphGuelphOntarioCanada
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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Chenuil A, Cahill AE, Délémontey N, Du Salliant du Luc E, Fanton H. Problems and Questions Posed by Cryptic Species. A Framework to Guide Future Studies. HISTORY, PHILOSOPHY AND THEORY OF THE LIFE SCIENCES 2019. [DOI: 10.1007/978-3-030-10991-2_4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AbstractSpecies are the currency of biology and important units of biodiversity, thus errors in species delimitations potentially have important consequences. During the last decades, owing to the use of genetic markers, many nominal species appeared to consist of several reproductively isolated entities called cryptic species (hereafter CS). In this chapter we explain why CS are important for practical reasons related to community and ecosystem monitoring, and for biological knowledge, particularly for understanding ecological and evolutionary processes. To find solutions to practical problems and to correct biological errors, a thorough analysis of the distinct types of CS reported in the literature is necessary and some general rules have to be identified. Here we explain how to identify CS, and we propose a rational and practical classification of CS (and putative CS), based on the crossing of distinct levels of genetic isolation with distinct levels of morphological differentiation. We also explain how to identify likely explanations for a given CS (either inherent to taxonomic processes or related to taxon biology, ecology and geography) and how to build a comprehensive database aimed at answering these practical and theoretical questions. Our pilot review of the literature in marine animals established that half of the reported cases are not CS sensu stricto (i.e. where morphology cannot distinguish the entities) and just need taxonomic revision. It also revealed significant associations between CS features, such as a higher proportion of diagnostic morphological differences in sympatric than in allopatric CS and more frequent ecological differentiation between sympatric than allopatric CS, both observations supporting the competitive exclusion theory, thus suggesting that ignoring CS causes not only species diversity but also functional diversity underestimation.
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72
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Hakala SM, Seppä P, Heikkilä M, Punttila P, Sorvari J, Helanterä H. Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta. PeerJ 2018; 6:e6013. [PMID: 30564515 PMCID: PMC6286808 DOI: 10.7717/peerj.6013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/27/2018] [Indexed: 12/27/2022] Open
Abstract
Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.
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Affiliation(s)
- Sanja Maria Hakala
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Perttu Seppä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Maria Heikkilä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | - Jouni Sorvari
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Heikki Helanterä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland.,Ecology and genetics research unit, University of Oulu, Oulu, Finland
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73
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Tamar K, Mitsi P, Carranza S. Cryptic diversity revealed in the leaf‐toed gecko Asaccus montanus(Squamata, Phyllodactylidae) from the Hajar Mountains of Arabia. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12258] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karin Tamar
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Pelagia Mitsi
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
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74
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Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae). Mol Phylogenet Evol 2018; 129:242-257. [DOI: 10.1016/j.ympev.2018.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/01/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022]
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75
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Abdelkrim J, Aznar-Cormano L, Buge B, Fedosov A, Kantor Y, Zaharias P, Puillandre N. Delimiting species of marine gastropods (Turridae, Conoidea) using RAD sequencing in an integrative taxonomy framework. Mol Ecol 2018; 27:4591-4611. [DOI: 10.1111/mec.14882] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 08/27/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Jawad Abdelkrim
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
- Service de Systématique Moléculaire SSM- UMS2700 - Muséum National d'Histoire Naturelle; Paris France
| | - Laetitia Aznar-Cormano
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
| | - Barbara Buge
- Muséum National d'Histoire Naturelle; Paris France
| | - Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution; Russian Academy of Sciences; Moscow Russia
| | - Yuri Kantor
- A.N. Severtsov Institute of Ecology and Evolution; Russian Academy of Sciences; Moscow Russia
| | - Paul Zaharias
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
| | - Nicolas Puillandre
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
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76
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Engelbrecht HM, Branch WR, Greenbaum E, Alexander GJ, Jackson K, Burger M, Conradie W, Kusamba C, Zassi-Boulou AG, Tolley KA. Diversifying into the branches: Species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae). Mol Phylogenet Evol 2018; 130:357-365. [PMID: 30366085 DOI: 10.1016/j.ympev.2018.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 08/30/2018] [Accepted: 10/16/2018] [Indexed: 10/28/2022]
Abstract
The African green and bush snakes of the genus Philothamnus currently comprises 21 species and three subspecies and occurs throughout sub-Saharan Africa. The genus has been the subject of previous taxonomic revisions based on traditional morphological characters and limited genetic assessment, and may not reflect their evolutionary history. Indeed, previous findings based on phylogenetics show discordant results of interspecific relationships and question the monophyly of the genus, although taxon sampling has been limited to date. We investigated phylogenetic affinities within Philothamnus with more inclusive genetic and geographical sampling, with the aim of better understanding their evolutionary history, so that future taxonomic revision of Philothamnus can be better informed. Species relationships were examined within a phylogenetic context and sampling included 133 ingroup samples from 16 taxa. Phylogenies were constructed in Bayesian and likelihood frameworks using three mitochondrial (16S, cyt b and ND4) and two nuclear (c-mos and RAG1) markers. Competing hypotheses relating to the monophyly of the genus were tested with a Shimodaira-Hasegawa test. To examine species boundaries, Bayesian General Mixed Yule-Coalescent Model and multi-rate Poisson Tree Processes analyses were conducted. In addition, a barcoding approach was used to further clarify species-level relationships by comparing frequency distributions between intra- and interspecific sequence divergence. The genus was recovered as monophyletic; however, species-delimitation results suggest that the current taxonomy does not reflect the evolutionary history of this group. For example, Philothamnus s. semivariegatus is paraphyletic, with at least four distinct clades. Philothamnus carinatus consists of two cryptic (sister) lineages from Central and West Africa that are deeply divergent, suggesting a long history of isolation between those regions. Furthermore, the subspecies P. n. natalensis and P. n. occidentalis show strong support for species-level divergence, which reflects their morphological and ecological differences. Accordingly, we elevate P. occidentalisnov. comb. to a full species. A fully informed taxonomic revision of these taxa will require additional morphological and ecological data for corroboration, but it seems that the morphological characters (e.g. scalation, dentition) used to describe these species to date are labile within and between species. This most likely has clouded our understanding of the species boundaries within the genus. Our phylogeny and species-delimitation analyses should provide a sounder framework for taxonomy, but may also prove useful toward understanding the morphological adaptations of these species to their respective habitats.
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Affiliation(s)
- Hanlie M Engelbrecht
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Claremont 7735, South Africa; Department of Botany & Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa; Department of Biology, Whitman College, 345 Boyer Ave, Walla Walla, WA 99362, USA.
| | - William R Branch
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Zoology, P. O. Box 77000, Nelson Mandela University, Port Elizabeth 6031, South Africa
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX 79968, USA
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P.O. Wits, Johannesburg 2050, South Africa
| | - Kate Jackson
- Department of Biology, Whitman College, 345 Boyer Ave, Walla Walla, WA 99362, USA
| | - Marius Burger
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa; Flora Fauna & Man, Ecological Services Ltd., Tortola, British Virgin Islands
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; School of Natural Resource Management, George Campus, Nelson Mandela University, George 6530, South Africa
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, The Democratic Republic of the Congo
| | - Ange-Ghislain Zassi-Boulou
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), BP 2400 Brazzaville, The Democratic Republic of the Congo
| | - Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Claremont 7735, South Africa; Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2000, South Africa
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77
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Hierarchical biogeographical processes largely explain the genomic divergence pattern in a species complex of sea anemones (Metridioidea: Sagartiidae: Anthothoe). Mol Phylogenet Evol 2018; 127:217-228. [DOI: 10.1016/j.ympev.2018.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 11/20/2022]
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78
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Buckley SJ, Domingos FMCB, Attard CRM, Brauer CJ, Sandoval-Castillo J, Lodge R, Unmack PJ, Beheregaray LB. Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172125. [PMID: 30110415 PMCID: PMC6030323 DOI: 10.1098/rsos.172125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east-west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east-west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.
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Affiliation(s)
- Sean J. Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Fabricius M. C. B. Domingos
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso, Pontal do Araguaia, MT 78698-000, Brazil
| | - Catherine R. M. Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Chris J. Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Ryan Lodge
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Peter J. Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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79
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Page MJ. Colonial ascidians from the Foveaux Strait region of New Zealand. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1450903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- M. J. Page
- Marine Ecology and Aquaculture, National Institute of Water and Atmospheric Research Ltd (NIWA), Nelson, New Zealand
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80
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Three new species of Clinostomum Leidy, 1856 (Trematoda) from Middle American fish-eating birds. Parasitol Res 2018; 117:2171-2185. [PMID: 29730726 DOI: 10.1007/s00436-018-5905-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
We recently engaged in a two-part study of Clinostomum Leidy, 1856 across a geographic range comprising central Mexico southwards to Costa Rica, in Central America. In the first study, we investigated the species boundaries by using DNA sequences of mitochondrial and nuclear molecular markers, implementing several analytical tools and species delimitation methods. The result of that approach revealed five highly divergent genetic lineages that were interpreted as independent evolutionary units, or species. Here, we present the second part of the study, where we describe three of the five species for which we have sexually mature adult specimens obtained from the mouth cavity of fish-eating birds. Additionally, we characterise morphologically the metacercariae of the other two species, collected from freshwater fishes; these species cannot be formally described since no adults were found in their definitive hosts. We further discuss the characters that are more reliable for species identification within Clinostomum, such as the cirrus sac shape and relative position with respect to testes and ovary, the shape of the reproductive organs, and the diverticulated condition of the caeca.
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81
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Struck TH, Feder JL, Bendiksby M, Birkeland S, Cerca J, Gusarov VI, Kistenich S, Larsson KH, Liow LH, Nowak MD, Stedje B, Bachmann L, Dimitrov D. Cryptic Species – More Than Terminological Chaos: A Reply to Heethoff. Trends Ecol Evol 2018; 33:310-312. [DOI: 10.1016/j.tree.2018.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 01/15/2023]
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82
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Underwood JN, Richards ZT, Miller KJ, Puotinen ML, Gilmour JP. Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral. Mol Ecol 2018; 27:1586-1602. [DOI: 10.1111/mec.14559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/22/2018] [Accepted: 02/24/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Jim N. Underwood
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Perth WA Australia
| | - Karen J. Miller
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Marji L. Puotinen
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - James P. Gilmour
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
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83
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Singhal S, Hoskin CJ, Couper P, Potter S, Moritz C. A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Syst Biol 2018; 67:1061-1075. [DOI: 10.1093/sysbio/syy026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University—Dominguez Hills, Carson, CA 90747, USA
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Patrick Couper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
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84
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Finding Evolutionary Processes Hidden in Cryptic Species. Trends Ecol Evol 2018; 33:153-163. [DOI: 10.1016/j.tree.2017.11.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/18/2022]
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85
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Meik JM, Schaack S, Flores-Villela O, Streicher JW. Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1429689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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86
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Malfant M, Darras S, Viard F. Coupling molecular data and experimental crosses sheds light about species delineation: a case study with the genus Ciona. Sci Rep 2018; 8:1480. [PMID: 29367599 PMCID: PMC5784138 DOI: 10.1038/s41598-018-19811-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/19/2017] [Indexed: 01/03/2023] Open
Abstract
Molecular studies sometimes reveal evolutionary divergence within accepted species. Such findings can initiate taxonomic revision, as exemplified in the formerly recognized species Ciona intestinalis. While an increasing number of studies have examined the ecology, reproductive barriers and genetics of C. intestinalis and C. robusta, there are still much uncertainties regarding other species of this genus. Using experimental crosses and mitochondrial data, we investigated the evolutionary relationships among four native and introduced Ciona spp., found in sympatry in the Mediterranean Sea or English Channel. Outcome of 62 bi-parental reciprocal crosses between C. intestinalis, C. robusta, C. roulei and C. edwardsi showed that C. edwardsi is reproductively isolated from the other taxa, which is in agreement with its distinct location in the phylogenetic tree. Conversely, hybrids are easily obtained in both direction when crossing C. intestinalis and C. roulei, reinforcing the hypothesis of two genetically differentiated lineages but likely being from a same species. Altogether, this study sheds light on the evolutionary relationship in this complex genus. It also calls for further investigation notably based on genome-wide investigation to better describe the evolutionary history within the genus Ciona, a challenging task in a changing world where biological introductions are shuffling species distribution.
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Affiliation(s)
- Marine Malfant
- Sorbonne Universite, CNRS - UMR 7144 'AD2M' - Station Biologique, Roscoff, 29680, France.
| | - Sébastien Darras
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Frédérique Viard
- Sorbonne Universite, CNRS - UMR 7144 'AD2M' - Station Biologique, Roscoff, 29680, France.
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87
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88
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Gélin P, Fauvelot C, Bigot L, Baly J, Magalon H. From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals. Ecol Evol 2018; 8:1411-1426. [PMID: 29375807 PMCID: PMC5773318 DOI: 10.1002/ece3.3747] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
Here, we examined the genetic variability in the coral genus Pocillopora, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods [also named Pocillopora eydouxi/meandrina complex sensu, Schmidt-Roach, Miller, Lundgren, & Andreakis (2014)] and which was found to split into three secondary species hypotheses (SSH09a, SSH09b, and SSH09c) according to assignment tests using multi-locus genotypes (13 microsatellites). From a large sampling (2,507 colonies) achieved in three marine provinces [Western Indian Ocean (WIO), Tropical Southwestern Pacific (TSP), and Southeast Polynesia (SEP)], genetic structuring analysis conducted with two clustering analyses (structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels (PSH > SSH > cluster), each level hiding highly differentiated genetic groups. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. The issue is now to understand which hierarchical level (SSH, cluster, or even below) corresponds to the species one. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.
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Affiliation(s)
- Pauline Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
| | - Cécile Fauvelot
- Laboratoire d'excellence‐CORAILPerpignanFrance
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS)Centre IRD de NouméaNoumeaNew Caledonia
- Present address:
Université Côte d'AzurCNRSNiceFrance
| | - Lionel Bigot
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
| | - Joseph Baly
- Laboratoire d'excellence‐CORAILPerpignanFrance
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS)Centre IRD de NouméaNoumeaNew Caledonia
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
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89
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Darling JA, Carlton JT. A Framework for Understanding Marine Cosmopolitanism in the Anthropocene. FRONTIERS IN MARINE SCIENCE 2018; 5:293. [PMID: 31019910 PMCID: PMC6475922 DOI: 10.3389/fmars.2018.00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recent years have witnessed growing appreciation for the ways in which human-mediated species introductions have reshaped marine biogeography. Despite this we have yet to grapple fully with the scale and impact of anthropogenic dispersal in both creating and determining contemporary distributions of marine taxa. In particular, the past several decades of research on marine biological invasions have revealed that broad geographic distributions of coastal marine organisms-historically referred to simply as "cosmopolitanism"-may belie complex interplay of both natural and anthropogenic processes. Here we describe a framework for understanding contemporary cosmopolitanism, informed by a synthesis of the marine bioinvasion literature. Our framework defines several novel categories in an attempt to provide a unified terminology for discussing cosmopolitan distributions in the world's oceans. We reserve the term eucosmopolitan to refer to those species for which data exist to support a true, natural, and prehistorically global (or extremely broad) distribution. While in the past this has been the default assumption for species observed to exhibit contemporary cosmopolitan distributions, we argue that given recent advances in marine invasion science this assignment should require positive evidence. In contrast, neocosmopolitan describes those species that have demonstrably achieved extensive geographic ranges only through historical anthropogenic dispersal, often facilitated over centuries of human maritime traffic. We discuss the history and human geography underpinning these neocosmopolitan distributions, and illustrate the extent to which these factors may have altered natural biogeographic patterns. We define the category pseudocosmopolitan to encompass taxa for which a broad distribution is determined (typically after molecular investigation) to reflect multiple, sometimes regionally endemic, lineages with uncertain taxonomic status; such species may remain cosmopolitan only so long as taxonomic uncertainty persists, after which they may splinter into multiple geographically restricted species. We discuss the methods employed to identify such species and to resolve both their taxonomic status and their biogeographic histories. We argue that recognizing these different types of cosmopolitanism, and the important role that invasion science has played in understanding them, is critically important for the future study of both historical and modern marine biogeography, ecology, and biodiversity.
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Affiliation(s)
- John A. Darling
- United States Environmental Protection Agency, National Exposure Research Laboratory, Research Triangle Park, NC, United States
| | - James T. Carlton
- Maritime Studies Program, Williams College-Mystic Seaport, Mystic, CT, United States
- Department of Biology, Williams College, Williamstown, MA, United States
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90
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Gabriel D, Draisma SGA, Schmidt WE, Schils T, Sauvage T, Maridakis C, Gurgel CFD, Harris DJ, Fredericq S. Beneath the hairy look: the hidden reproductive diversity of the Gibsmithia hawaiiensis complex (Dumontiaceae, Rhodophyta). JOURNAL OF PHYCOLOGY 2017; 53:1171-1192. [PMID: 28990202 DOI: 10.1111/jpy.12593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/10/2017] [Indexed: 06/07/2023]
Abstract
The tropical alga previously recognized as Gibsmithia hawaiiensis (Dumontiaceae, Rhodophyta) was recently suggested to represent a complex of species distributed throughout the Indo-Pacific Ocean and characterized by a peculiar combination of hairy (pilose) gelatinous lobes growing on cartilaginous stalks. Phylogenetic reconstructions based on three genetic markers are presented here with the inclusion of new samples. Further diversity is reported within the complex, with nine lineages spread in four major phylogenetic groups. The threshold between intra- and interspecific relationships was assessed by species delimitation methods, which indicate the existence of 8-10 putative species in the complex. Two species belonging to the G. hawaiiensis complex are described here: Gibsmithia malayensis sp. nov. from the Coral Triangle and Gibsmithia indopacifica sp. nov., widely distributed in the Central and Eastern Indo-Pacific. Morphological differences in the vegetative and reproductive structures of the newly described species are provided and compared to the previously described species of the complex. Additional lineages represent putative species, which await further investigation to clarify their taxonomic status. Gibsmithia hawaiiensis sensu stricto is confirmed to be endemic to the Hawaiian Islands, and Gibsmithia eilatensis is apparently confined to the Red Sea, with an expanded distribution in the region. New records of the G. hawaiiensis complex are reported from Egypt, Saudi Arabia, Indonesia, Philippines, and the Federated States of Micronesia, indicating that the complex is more broadly distributed than previously considered. The isolated position of Gibsmithia within the Dumontiaceae is corroborated by molecular data.
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Affiliation(s)
- Daniela Gabriel
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Research Network in Biodiversity and Evolutionary Biology, University of the Azores, 9501-801, Ponta Delgada, Portugal
| | - Stefano G A Draisma
- Faculty of Science, Excellence Center for Biodiversity of Peninsular Thailand, Seaweed and Seagrass Research Unit, Prince of Songkla University, Songkhla, 90112, Thailand
| | - William E Schmidt
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | - Tom Schils
- UOG Station, University of Guam Marine Laboratory, Mangilao, Guam, 96923, USA
| | - Thomas Sauvage
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | - Clio Maridakis
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Research Network in Biodiversity and Evolutionary Biology, University of the Azores, 9501-801, Ponta Delgada, Portugal
| | - C Frederico D Gurgel
- Center of Biological Sciences, Department of Botany, Federal University of Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - D James Harris
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Research Network in Biodiversity and Evolutionary Biology, University of Porto, 4485-661, Vairão, Portugal
| | - Suzanne Fredericq
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
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91
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Trevisan B, Primon JF, Marques FPL. Systematics and diversification of Anindobothrium Marques, Brooks & Lasso, 2001 (Eucestoda: Rhinebothriidea). PLoS One 2017; 12:e0184632. [PMID: 28953933 PMCID: PMC5617167 DOI: 10.1371/journal.pone.0184632] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/04/2017] [Indexed: 12/17/2022] Open
Abstract
Tapeworms of the genus Anindobothrium Marques, Brooks & Lasso, 2001 are found in both marine and Neotropical freshwater stingrays of the family Potamotrygonidae. The patterns of host association within the genus support the most recent hypothesis about the history of diversification of potamotrygonids, which suggests that the ancestor of freshwater lineages of the Potamotrygonidae colonized South American river systems through marine incursion events. Despite the relevance of the genus Anindobothrium to understand the history of colonization and diversification of potamotrygonids, no additional efforts were done to better investigate the phylogenetic relationship of this taxon with other lineages of cestodes since its erection. This study is a result of recent collecting efforts to sample members of the genus in marine and freshwater potamotrygonids that enabled the most extensive documentation of the fauna of Anindobothrium parasitizing species of Styracura de Carvalho, Loboda & da Silva, Potamotrygon schroederi Fernández-Yépez, P. orbignyi (Castelnau) and P. yepezi Castex & Castello from six different countries, representing the eastern Pacific Ocean, Caribbean Sea, and river basins in South America (Rio Negro, Orinoco, and Maracaibo). The newly collected material provided additional specimens for morphological studies and molecular samples for subsequent phylogenetic analyses that allowed us to address the phylogenetic position of Anindobothrium and provide molecular and morphological evidence to recognize two additional species for the genus. The taxonomic actions that followed our analyses included the proposition of a new family, Anindobothriidae fam. n., to accommodate the genus Anindobothrium in the order Rhinebothriidea Healy, Caira, Jensen, Webster & Littlewood, 2009 and the description of two new species-one from the eastern Pacific Ocean, A. carrioni sp. n., and the other from the Caribbean Sea, A. inexpectatum sp. n. In addition, we also present a redescription of the type species of the genus, A. anacolum (Brooks, 1977) Marques, Brooks & Lasso, 2001, and of A. lisae Marques, Brooks & Lasso, 2001. Finally, we discuss the paleogeographical events mostly linked with the diversification of the genus and the protocols adopted to uncover cryptic diversity in Anindobothrium.
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Affiliation(s)
- Bruna Trevisan
- Curso de Pós-graduação/Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Departamento de Zoologia/Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Juliana F. Primon
- Departamento de Zoologia/Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Fernando P. L. Marques
- Departamento de Zoologia/Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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92
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El Ayari T, Trigui El Menif N, Saavedra C, Cordero D, Viard F, Bierne N. Unexpected mosaic distribution of two hybridizing sibling lineages in the teleplanically dispersing snail Stramonita haemastoma suggests unusual postglacial redistribution or cryptic invasion. Ecol Evol 2017; 7:9016-9026. [PMID: 29177037 PMCID: PMC5689492 DOI: 10.1002/ece3.3418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 08/04/2017] [Accepted: 08/11/2017] [Indexed: 01/29/2023] Open
Abstract
Molecular approaches have proven efficient to identify cryptic lineages within single taxonomic entities. Sometimes these cryptic lineages maybe previously unreported or unknown invasive taxa. The genetic structure of the marine gastropod Stramonita haemastoma has been examined in the Western Mediterranean and North‐Eastern Atlantic populations with mtDNA COI sequences and three newly developed microsatellite markers. We identified two cryptic lineages, differentially fixed for alternative mtDNA COI haplogroups and significantly differentiated at microsatellite loci. The mosaic distribution of the two lineages is unusual for a warm‐temperate marine invertebrate with a teleplanic larval stage. The Atlantic lineage was unexpectedly observed as a patch enclosed in the north of the Western Mediterranean Sea between eastern Spain and the French Riviera, and the Mediterranean lineage was found in Macronesian Islands. Although cyto‐nuclear disequilibrium is globally maintained, asymmetric introgression occurs in the Spanish region where the two lineages co‐occur in a hybrid zone. A first interpretation of our results is mito‐nuclear discordance in a stable postglacial hybrid zone. Under this hypothesis, though, the location of genetic discontinuities would be unusual among planktonic dispersers. An alternative interpretation is that the Atlantic lineage, also found in Senegal and Venezuela, has been introduced by human activities in the Mediterranean area and is introgressing Mediterranean genes during its propagation, as theoretically expected. This second hypothesis would add an additional example to the growing list of cryptic marine invasions revealed by molecular studies.
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Affiliation(s)
- Tahani El Ayari
- Université de Montpellier Montpellier Cedex 5 France.,ISEM - CNRS UMR 5554 Station Marine OREME Sète France.,Laboratory of Environment Bio-monitoring Faculty of Sciences of Bizerta University of Carthage Bizerta Tunisia
| | - Najoua Trigui El Menif
- Laboratory of Environment Bio-monitoring Faculty of Sciences of Bizerta University of Carthage Bizerta Tunisia
| | - Carlos Saavedra
- Instituto de Acuicultura Torre de la Sal Consejo Superior de Investigaciones Cientίficas Ribera de Cabanes (Castellόn) Spain
| | - David Cordero
- Instituto de Acuicultura Torre de la Sal Consejo Superior de Investigaciones Cientίficas Ribera de Cabanes (Castellόn) Spain
| | - Frédérique Viard
- UPMC Université Paris 6CNRS UMR 7144 Adaptation et Diversité en Milieu Marin Equipe DIVCO Station Biologique de Roscoff Sorbonne Université Roscoff France
| | - Nicolas Bierne
- Université de Montpellier Montpellier Cedex 5 France.,ISEM - CNRS UMR 5554 Station Marine OREME Sète France
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93
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Chen W, Zhong Z, Dai W, Fan Q, He S. Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China. BMC Evol Biol 2017; 17:216. [PMID: 28899345 PMCID: PMC5596851 DOI: 10.1186/s12862-017-1058-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. RESULTS Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61-2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively. CONCLUSIONS Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai-Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zaixuan Zhong
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei Dai
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qi Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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94
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Postaire B, Gélin P, Bruggemann JH, Pratlong M, Magalon H. Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea. Ecol Evol 2017; 7:8170-8186. [PMID: 29075441 PMCID: PMC5648676 DOI: 10.1002/ece3.3236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 01/18/2023] Open
Abstract
Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive FIS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise FST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo‐Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.
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Affiliation(s)
- Bautisse Postaire
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France.,IMBE UMR 7263 Aix Marseille Université/CNRS/IRD/Avignon Université Marseille France
| | - Pauline Gélin
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
| | - J Henrich Bruggemann
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
| | - Marine Pratlong
- IMBE UMR 7263 Aix Marseille Université/CNRS/IRD/Avignon Université Marseille France.,I2M Equipe Evolution Biologique et Modélisation Aix Marseille Université/CNRS/Centrale Marseille Marseille France
| | - Hélène Magalon
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
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95
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Taylor ML, Roterman CN. Invertebrate population genetics across Earth's largest habitat: The deep-sea floor. Mol Ecol 2017; 26:4872-4896. [PMID: 28833857 DOI: 10.1111/mec.14237] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/04/2023]
Abstract
Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made.
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Affiliation(s)
- M L Taylor
- Department of Zoology, University of Oxford, Oxford, UK
| | - C N Roterman
- Department of Zoology, University of Oxford, Oxford, UK
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96
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Puillandre N, Fedosov AE, Zaharias P, Aznar-Cormano L, Kantor YI. A quest for the lost types of Lophiotoma (Gastropoda: Conoidea: Turridae): integrative taxonomy in a nomenclatural mess. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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97
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Korshunova T, Martynov A, Bakken T, Picton B. External diversity is restrained by internal conservatism: New nudibranch mollusc contributes to the cryptic species problem. ZOOL SCR 2017. [DOI: 10.1111/zsc.12253] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tatiana Korshunova
- Koltzov Institute of Developmental Biology RAS; Moscow Russia
- Zoological Museum; Moscow State University; Moscow Russia
| | | | - Torkild Bakken
- NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
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98
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Aurelle D, Pivotto ID, Malfant M, Topçu NE, Masmoudi MB, Chaoui L, Kara HM, Coelho MA, Castilho R, Haguenauer A. Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes. ZOOL SCR 2017. [DOI: 10.1111/zsc.12245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
| | - Isabelle D. Pivotto
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Department of Computer Science and Operations Research (DIRO); University of Montreal; Montréal QC 2194 Canada
| | - Marine Malfant
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Lab. « Adaptation et Diversité en Milieu Marin »; Team Div&Co; Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144; 29682 Roscoff France
| | - Nur E. Topçu
- Fisheries Faculty; Istanbul University; Ordu Cad No 200 34130 Laleli Istanbul Turkey
| | - Mauatassem B. Masmoudi
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Lamya Chaoui
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Hichem M. Kara
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Márcio A.G. Coelho
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Centre for Marine Sciences; CCMAR-CIMAR Laboratório Associado; Universidade do Algarve; Campus do Gambelas 8005-139 Faro Portugal
| | - Rita Castilho
- Centre for Marine Sciences; CCMAR-CIMAR Laboratório Associado; Universidade do Algarve; Campus do Gambelas 8005-139 Faro Portugal
- Graduate Program in Evolution, Ecology and Behavior; University at Buffalo; Buffalo NY 14260 USA
| | - Anne Haguenauer
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
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99
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Merényi Z, Varga T, Hubai AG, Pitlik P, Erős Á, Trappe JM, Bratek Z. Challenges in the delimitation of morphologically similar species: a case study of Tuber brumale agg. (Ascomycota, Pezizales). Mycol Prog 2017. [DOI: 10.1007/s11557-017-1296-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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100
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Willis SC. One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes. PLoS One 2017; 12:e0172349. [PMID: 28235096 PMCID: PMC5325279 DOI: 10.1371/journal.pone.0172349] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/03/2017] [Indexed: 11/18/2022] Open
Abstract
Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.
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Affiliation(s)
- Stuart C. Willis
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, United States of America
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