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Meier R, Hartop E, Pylatiuk C, Srivathsan A. Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230120. [PMID: 38705187 PMCID: PMC11070263 DOI: 10.1098/rstb.2023.0120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/25/2024] [Indexed: 05/07/2024] Open
Abstract
Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rudolf Meier
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
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2
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Vences M, Patmanidis S, Schmidt JC, Matschiner M, Miralles A, Renner SS. Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction, and haploweb calculation. BIOINFORMATICS ADVANCES 2024; 4:vbae083. [PMID: 38895561 PMCID: PMC11184345 DOI: 10.1093/bioadv/vbae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/15/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other datasets in the framework of integrative taxonomy. In diploid organisms, this often requires separating (phasing) sequences with heterozygotic positions, and typically separate programs are required for phasing, reformatting of input files, and haplotype network construction. We therefore developed Hapsolutely, a user-friendly program with an ergonomic graphical user interface that integrates haplotype phasing from single-locus sequences with five approaches for network/genealogy reconstruction. Results Among the novel options implemented, Hapsolutely integrates phasing and graphical reconstruction steps of haplotype networks, supports input of species partition data in the common SPART and SPART-XML formats, and calculates and visualizes haplowebs and fields for recombination, thus allowing graphical comparison of allele distribution and allele sharing among subsets for the purpose of species delimitation. The new tool has been specifically developed with a focus on the workflow in alpha-taxonomy, where exploring fields for recombination across alternative species partitions may help species delimitation. Availability and implementation Hapsolutely is written in Python, and integrates code from Phase, SeqPHASE, and PopART in C++ and Haxe. Compiled stand-alone executables for MS Windows and Mac OS along with a detailed manual can be downloaded from https://www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/Hapsolutely).
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Affiliation(s)
- Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Stefanos Patmanidis
- Department of Computer Science, School of Electrical and Computer Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - Jan-Christopher Schmidt
- Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | | | - Aurélien Miralles
- Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 75005 Paris, France
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, United States
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3
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Zaharias P, Kantor YI, Fedosov AE, Puillandre N. Coupling DNA barcodes and exon-capture to resolve the phylogeny of Turridae (Gastropoda, Conoidea). Mol Phylogenet Evol 2024; 191:107969. [PMID: 38007006 DOI: 10.1016/j.ympev.2023.107969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Taxon sampling in most phylogenomic studies is often based on known taxa and/or morphospecies, thus ignoring undescribed diversity and/or cryptic lineages. The family Turridae is a group of venomous snails within the hyperdiverse superfamily Conoidea that includes many undescribed and cryptic species. Therefore 'traditional' taxon sampling could constitute a strong risk of undersampling or oversampling Turridae lineages. To minimize potential biases, we establish a robust sampling strategy, from species delimitation to phylogenomics. More than 3,000 cox-1 "barcode" sequences were used to propose 201 primary species hypotheses, nearly half of them corresponding to species potentially new to science, including several cryptic species. A 110-taxa exon-capture tree, including species representatives of the diversity uncovered with the cox-1 dataset, was build using up to 4,178 loci. Our results show the polyphyly of the genus Gemmula, that is split into up to 10 separate lineages, of which half would not have been detected if the sampling strategy was based only on described species. Our results strongly suggest that the use of blind, exploratory and intensive barcode sampling is necessary to avoid sampling biases in phylogenomic studies.
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Affiliation(s)
- Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France.
| | - Yuri I Kantor
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Alexander E Fedosov
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France
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4
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Xu Y, Ge LL, Cheng XF, Xiang XL, Wen XL, Wang YJ, Fu H, Ge YL, Xi YL. Temporal Distribution Patterns of Cryptic Brachionus calyciflorus (Rotifera) Species in Relation to Biogeographical Gradient Associated with Latitude. Animals (Basel) 2024; 14:244. [PMID: 38254413 PMCID: PMC10812649 DOI: 10.3390/ani14020244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Sympatric distribution and temporal overlap of cryptic zooplankton species pose a challenge to the framework of the niche differentiation theory and the mechanisms allowing competitor coexistence. We applied the methods of phylogenetic analysis, DNA taxonomy, and statistical analysis to study the temporal distribution patterns of the cryptic B. calyciflorus species, an excellent model, in three lakes, and to explore the putative mechanisms for their seasonal succession and temporal overlap. The results showed that in the warm-temperate Lake Yunlong, B. fernandoi and B. calyciflorus s.s. underwent a seasonal succession, which was largely attributed to their differential adaptation to water temperature. In the subtropical Lake Jinghu, B. fernandoi, B. calyciflorus s.s., and B. dorcas exhibited both seasonal succession and temporal overlap. Seasonal successions were largely attributed to their differential adaptation to temperature, and temporal overlap resulted from their differential responses to algal food concentration. In the tropical Lake Jinniu, B. calyciflorus s.s. persisted throughout the year and overlapped with B. dorcas for 5 months. The temporal overlap resulted from their differential responses to copepod predation. These results indicated that the temporal distribution pattern of the cryptic B. calyciforus species and the mechanism that allows competitor coexistence vary with different climate zones.
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Affiliation(s)
- Yuan Xu
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Le-Le Ge
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Xin-Feng Cheng
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Xian-Ling Xiang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Xin-Li Wen
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Yong-Jin Wang
- Management Committee of Scenic Attraction of Lake Yunlong, Xuzhou 221007, China;
| | - Hao Fu
- Reservoir Management Office of Lake Yunlong, Xuzhou 221007, China;
| | - Ya-Li Ge
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Yi-Long Xi
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
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Miralles A, Puillandre N, Vences M. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy. Methods Mol Biol 2024; 2744:77-104. [PMID: 38683312 DOI: 10.1007/978-1-0716-3581-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.
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Affiliation(s)
- Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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6
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Vences M, Miralles A, DeSalle R. A Glossary of DNA Barcoding Terms. Methods Mol Biol 2024; 2744:561-572. [PMID: 38683343 DOI: 10.1007/978-1-0716-3581-0_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.
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Affiliation(s)
- Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Robert DeSalle
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
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7
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Deng X, Liao Y, Wong D, Yu H. The genetic structuring in pollinating wasps of Ficus hispida in continental Asia. Ecol Evol 2023; 13:e10518. [PMID: 37745788 PMCID: PMC10511832 DOI: 10.1002/ece3.10518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/26/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
The interaction between figs and fig wasps provides a striking example of obligate brood site pollination mutualism. Monoecious figs, constituting independent radiations in each tropical biome, are present in significant proportions worldwide, but in continental Asia, dioecious figs have diverged into various niches, making the region's assemblage remarkably diverse. However, the reproductive success of figs and fig wasps largely depends on the fig wasp dispersal process. Monoecious fig pollinators in continental Asian tropical rain forests exhibit high gene flow of the plant, while many dioecious fig pollinators have a more restricted gene flow. However, there are limited studies on the genetic structure of dioecious Ficus pollinators that pollinate figs with intermediate gene flow. Here, we used molecular methods to investigate the genetic structure of pollinating wasps of the widely distributed dioecious Ficus hispida in China and Southeast Asia. Sequence data from two gene regions were used: the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S genes. Both molecular and morphological results support two fig wasp species at our sampling sites. Our findings suggest that for widely sympatric Ficus species in continental Asia, monoecious figs presenting long gene glow have the fewest fig wasp species, followed by dioecious figs presenting intermediate gene flow, and dioecious figs presenting local gene flow have the most fig wasp species.
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Affiliation(s)
- Xiaoxia Deng
- Key Laboratory of Plant Resource Conservation and Sustainable UtilizationSouth China Botanical Garden, CASGuangzhouChina
- South China National Botanical GardenGuangzhouChina
- CEFECNRS, Univ Montpellier, EPHE, IRDMontpellierFrance
| | - Yaolin Liao
- Key Laboratory of Plant Resource Conservation and Sustainable UtilizationSouth China Botanical Garden, CASGuangzhouChina
- South China National Botanical GardenGuangzhouChina
| | - Da‐Mien Wong
- Key Laboratory of Plant Resource Conservation and Sustainable UtilizationSouth China Botanical Garden, CASGuangzhouChina
- South China National Botanical GardenGuangzhouChina
| | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable UtilizationSouth China Botanical Garden, CASGuangzhouChina
- South China National Botanical GardenGuangzhouChina
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8
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Ansari L, Asgari B, Zare R, Zamanizadeh HR. Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676702 DOI: 10.1099/ijsem.0.006028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30T (=IRAN 4042CT=CBS 149737T).
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Affiliation(s)
- Laleh Ansari
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Bita Asgari
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Rasoul Zare
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Hamid Reza Zamanizadeh
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
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9
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Chimeno C, Schmidt S, Cancian de Araujo B, Perez K, von Rintelen T, Schmidt O, Hamid H, Pramesa Narakusumo R, Balke M. Abundant, diverse, unknown: Extreme species richness and turnover despite drastic undersampling in two closely placed tropical Malaise traps. PLoS One 2023; 18:e0290173. [PMID: 37585425 PMCID: PMC10431641 DOI: 10.1371/journal.pone.0290173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Arthropods account for a large proportion of animal biomass and diversity in terrestrial systems, making them crucial organisms in our environments. However, still too little is known about the highly abundant and megadiverse groups that often make up the bulk of collected samples, especially in the tropics. With molecular identification techniques ever more evolving, analysis of arthropod communities has accelerated. In our study, which was conducted within the Global Malaise trap Program (GMP) framework, we operated two closely placed Malaise traps in Padang, Sumatra, for three months. We analyzed the samples by DNA barcoding and sequenced a total of more than 70,000 insect specimens. For sequence clustering, we applied three different delimitation techniques, namely RESL, ASAP, and SpeciesIdentifier, which gave similar results. Despite our (very) limited sampling in time and space, our efforts recovered more than 10,000 BINs, of which the majority are associated with "dark taxa". Further analysis indicates a drastic undersampling of both sampling sites, meaning that the true arthropod diversity at our sampling sites is even higher. Regardless of the close proximity of both Malaise traps (< 360 m), we discovered significantly distinct communities.
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Affiliation(s)
| | - Stefan Schmidt
- Zoologische Staatssammlung München (SNSB-ZSM), Munich, Germany
| | - Bruno Cancian de Araujo
- Zoologische Staatssammlung München (SNSB-ZSM), Munich, Germany
- Entomological Biodiversity Laboratory, Federal University of Espirito Santo, Vitoria, Brazil
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Thomas von Rintelen
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde—Leibniz-Institut fur Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Olga Schmidt
- Zoologische Staatssammlung München (SNSB-ZSM), Munich, Germany
| | - Hasmiandy Hamid
- Department of Plant Protection, Faculty of Agriculture, Universitas Andalas, Padang, Indonesia
| | - Raden Pramesa Narakusumo
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Museum Zoologicum Bogoriense, Cibinong, Indonesia
| | - Michael Balke
- Zoologische Staatssammlung München (SNSB-ZSM), Munich, Germany
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10
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Baptista L, Fassio G, Gofas S, Oliverio M, P Ávila S, M Santos A. Evaluating the taxonomic status of the large sized Tricolia Risso, 1826 in the Northeast Atlantic and Mediterranean Sea. Mol Phylogenet Evol 2023:107857. [PMID: 37315708 DOI: 10.1016/j.ympev.2023.107857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
Despite a long history of taxonomic studies on the genus Tricolia Risso, 1826, there is a shortfall on thorough systematic molecular reviews of the taxon from the NE Atlantic and Mediterranean coasts. Aiming to assess the genetic distinctness among morphospecies and the taxonomic status of currently accepted large sized species in these areas, we conducted a molecular phylogenetic analysis of the genus based on one mitochondrial (cox1) and two nuclear (28S and ITS2) markers. Seven Tricolia species were consistently retrieved in the analyses, including a new genetic lineage in the NE Atlantic designated as Tricolia sp. 1. Molecular analyses revealed that only one species, T. azorica, occurs in the NE Atlantic archipelagos. The sister taxa T. pullus (Mediterranean) and T. picta (NE Atlantic) should be classified as distinct species, instead of subspecies of the T. pullus group (sensu Gofas 1982). Tricolia miniata is also a complex of species in the Mediterranean and future studies across the distribution range are necessary to clarify its status.
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Affiliation(s)
- Lara Baptista
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801 Ponta Delgada, Açores, Portugal; MPB-Marine Palaeontology and Biogeography Lab, University of the Azores, Rua da Mãe de Deus, 9501-801 Ponta Delgada, Açores, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, R. Mãe de Deus 13A, 9500-321 Ponta Delgada, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal.
| | - Giulia Fassio
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, Viale dell'Università 32, I-00185, Rome, Italy and NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| | - Serge Gofas
- Departamento de Biología Animal, Facultad de Ciencias, Universidad de MálagaE-29071 Málaga, Spain; Muséum National d'Histoire Naturelle, Paris, France
| | - Marco Oliverio
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, Viale dell'Università 32, I-00185, Rome, Italy and NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| | - Sérgio P Ávila
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-801 Ponta Delgada, Açores, Portugal; MPB-Marine Palaeontology and Biogeography Lab, University of the Azores, Rua da Mãe de Deus, 9501-801 Ponta Delgada, Açores, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; UNESCO Chair - Land Within Sea: Biodiversity & Sustainability in Atlantic Islands, Universidade dos Açores, R. Mãe de Deus 13A, 9500-321 Ponta Delgada, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal; Departamento de Biologia, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal
| | - António M Santos
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, no. 7, 4485-661 Vairão, Portugal
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11
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Whitelaw BL, Finn JK, Zenger KR, Cooke IR, Morse P, Strugnell JM. SNP data reveals the complex and diverse evolutionary history of the blue-ringed octopus genus (Octopodidae: Hapalochlaena) in the Asia-Pacific. Mol Phylogenet Evol 2023:107827. [PMID: 37257797 DOI: 10.1016/j.ympev.2023.107827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
The blue-ringed octopus species complex (Hapalochlaena spp.), known to occur from Southern Australia to Japan, currently contains four formally described species (Hapalochlaena maculosa, Hapalochlaena fasciata, Hapalochlaena lunulata and Hapalochlaena nierstraszi). These species are distinguished based on morphological characters (iridescent blue rings and/or lines) along with reproductive strategies. However, the observation of greater morphological diversity than previously captured by the current taxonomic framework indicates that a revision is required. To examine species boundaries within the genus we used mitochondrial (12S rRNA, 16S rRNA, cytochrome c oxidase subunit 1 [COI], cytochrome c oxidase subunit 3 [COIII] and cytochrome b [Cytb]) and genome-wide SNP data (DaRT seq) from specimens collected across its geographic range including variations in depth from 3m to >100m. This investigation indicates substantially greater species diversity present within the genus Hapalochlaena than is currently described. We identified 10,346 SNPs across all locations, which when analysed support a minimum of 11 distinct clades. Bayesian phylogenetic analysis of the mitochondrial COI gene on a more limited sample set dates the diversification of the genus to ∼30mya and corroborates eight of the lineages indicated by the SNP analyses. Furthermore, we demonstrate that the diagnostic lined patterning of H. fasciata found in North Pacific waters and NSW, Australia is polyphyletic and therefore likely the result of convergent evolution. Several "deep water" (> 100m) lineages were also identified in this study with genetic convergence likely to be driven by external selective pressures. Examination of morphological traits, currently being undertaken in a parallel morphological study, is required to describe additional species within the complex.
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Affiliation(s)
- Brooke L Whitelaw
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia; Sciences, Museums Victoria Research Institute, Carlton, Victoria 3053, Australia
| | - Julian K Finn
- Sciences, Museums Victoria Research Institute, Carlton, Victoria 3053, Australia
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Ira R Cooke
- College of Public Health, Medical and Vet Sciences, James Cook University, Townsville, Queensland, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, 4811, Australia
| | - Peter Morse
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia; Department of Environment and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia
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12
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Canoglu H, Aksu I, Turan D, Bektas Y. DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey. ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.94333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.
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13
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Mediterranean Matters: Revision of the Family Onchidorididae (Mollusca, Nudibranchia) with the Description of a New Genus and a New Species. DIVERSITY 2022. [DOI: 10.3390/d15010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Mediterranean Sea hosts a great Nudibranchia diversity and has proved to be particularly intriguing in the case of the family Onchidorididae, a group of dorid nudibranchs that lately increased its diversity with the addition of one recently described Mediterranean species. The Onchidorididae family has a troubled systematic history to date, characterized by uncertainties and genera that are considered valid or not, according to the different authors. This confused taxonomy reflects the lack of a broad and comprehensive view on the phylogenetic relationships occurring between Onchidorididae members, an incorrect interpretation of the diagnostic morphological characters, and a poor knowledge of important biological aspects characterizing the different genera included in the family. To shed some light on the systematics of Onchidorididae, an integrative taxonomic revision was carried out involving morphological, ecological, and molecular analyses on an updated dataset. Mediterranean specimens and species were added to the dataset of the already known Onchidorididae and a new species from the Adriatic Sea (Central Mediterranean Sea) is described here. Furthermore, historical controversies are clarified due to the discovery of new important synapomorphies useful to define genera belonging to the Onchidorididae family and to describe a new genus. Finally, the taxonomic status of all the known Onchidorididae species is investigated and discussed, filling the gap of knowledge on neglected species.
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14
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Zhou LY, Zhan ZH, Zhu XL, Wan X. Multilocus phylogeny and species delimitation suggest synonymies of two Lucanus Scopoli, 1763 (Coleoptera, Lucanidae) species names. Zookeys 2022; 1135:139-155. [PMID: 36761796 PMCID: PMC9836572 DOI: 10.3897/zookeys.1135.89257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
Phylogenetic relationsships of four nominal Lucanus Scopoli, 1763 species, L.swinhoei Parry, 1874, L.continentalis Zilioli, 1998, L.liuyei Huang & Chen, 2010, and L.wuyishanensis Schenk, 1999, are assessed based on mitochondrial (16S rDNA, COI) and nuclear (28S rDNA, Wingless) genes. The genetic distance is 0.0072 between L.swinhoei and L.continentalis, and 0.0094 between L.wuyishanensis and L.liuyei. Three species-delimitation approaches (ABGD, PTP, and GMYC) consistently showed L.swinhoei + L.continentalis and L.wuyishanensis + L.liuyei as two MOTUs. A new synonymy, L.liuyei = L.wuyishanensis, is proposed. Synonymy of L.swinhoei over L.continentalis is confirmed.
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Affiliation(s)
- Li Yang Zhou
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
| | - Zhi Hong Zhan
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, 111 Jiulong Rd., Hefei, 230601, China
| | - Xue Li Zhu
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
| | - Xia Wan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
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15
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Fassio G, Stefani M, Russini V, Buge B, Bouchet P, Treneman N, Malaquias MAE, Schiaparelli S, Modica MV, Oliverio M. Neither slugs nor snails: a molecular reappraisal of the gastropod family Velutinidae. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Abstract
The systematics of the marine mollusc family Velutinidae has long been neglected by taxonomists, mainly because their often internal and fragile shells offer no morphological characters. Velutinids are usually undersampled owing to their cryptic mantle coloration on the solitary, social or colonial ascidians on which they feed and lay eggs. In this study, we address the worldwide diversity and phylogeny of Velutinidae based on the largest molecular dataset (313 specimens) to date, accounting for > 50% of the currently accepted genera, coupled with morphological and ecological data. Velutinids emerge as a diverse group, encompassing four independent subfamily-level lineages, two of which are newly described herein: Marseniopsinae subfam. nov. and Hainotinae subfam. nov. High diversity was found at genus and species levels, with two newly described genera (Variolipallium gen. nov. and Pacifica gen. nov.) and ≥ 86 species in the assayed dataset, 58 of which are new to science (67%). Velutinidae show a remarkable morphological plasticity in shell morphology, mantle extension and chromatic patterns. This variability is likely to be the result of different selective forces, including habitat, depth and trophic interactions.
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Affiliation(s)
- Giulia Fassio
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome , Viale dell’Universitá 32, 00185 Rome , Italy
| | - Matteo Stefani
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome , Viale dell’Universitá 32, 00185 Rome , Italy
| | - Valeria Russini
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome , Viale dell’Universitá 32, 00185 Rome , Italy
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana ‘M. Aleandri’ , Via Appia Nuova 1411, 00178 Rome , Italy
| | - Barbara Buge
- Muséum national d’Histoire naturelle, Direction des Collections , 55, Rue de Buffon, 75005 Paris , France
| | - Philippe Bouchet
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 (CNRS, EPHE, MNHN, UPMC), Muséum national d’Histoire naturelle, Sorbonne Universités , 43 Rue Cuvier, 75231 Paris Cedex 05 , France
| | - Nancy Treneman
- Oregon Institute of Marine Biology , POB 5389, 63466 Boat Basin Road, Charleston, OR 97420 , USA
| | | | - Stefano Schiaparelli
- DiSTAV, University of Genoa , Corso Europa 26, 16132 Genoa , Italy
- Italian National Antarctic Museum (MNA, Section of Genoa) , Viale Benedetto XV n. 5, 16132 Genoa , Italy
| | - Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn , Villa Comunale, 80121 Naples , Italy
| | - Marco Oliverio
- Department of Biology and Biotechnologies ‘Charles Darwin’, Sapienza University of Rome , Viale dell’Universitá 32, 00185 Rome , Italy
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16
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Kantor Y, Hallan A, Criscione F. Integrative taxonomy reveals new Australian species of the deep-water snail genera Comispira (Conoidea: Cochlespiridae) and Leucosyrinx (Conoidea: Pseudomelatomidae). MOLLUSCAN RESEARCH 2022. [DOI: 10.1080/13235818.2022.2102887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Yuri Kantor
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Anders Hallan
- Australian Museum Research Institute, Sydney, Australia
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17
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Bektas Y, Aksu İ, Kaya C, Bayçelebi E, Turan D. DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia. JOURNAL OF FISH BIOLOGY 2022; 101:505-514. [PMID: 35607971 DOI: 10.1111/jfb.15114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.
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Affiliation(s)
- Yusuf Bektas
- Deparment of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - İsmail Aksu
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cüneyt Kaya
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Esra Bayçelebi
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - Davut Turan
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdogan University, Rize, Turkey
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18
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Zamani A, Dal Pos D, Fric ZF, Orfinger AB, Scherz MD, Bartoňová AS, Gante HF. The future of zoological taxonomy is integrative, not minimalist. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2063964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Zamani
- Zoological Museum, Biodiversity Unit, University of Turku, 20500 Turku, Finland
| | - Davide Dal Pos
- Department of Biology, University of Central Florida, 4110 Libra dr. Rm 442, Orlando, FL 32816, USA
| | - Zdenek Faltýnek Fric
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Alexander B. Orfinger
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Center for Water Resources, Florida A&M University, Tallahassee, FL 32301, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Alena Sucháčková Bartoňová
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Hugo F. Gante
- cE3c—Center for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
- Department of Biology, KU Leuven, Section Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 32 box 2439, Leuven, B-3000, Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 17, Tervuren, 3080, Belgium
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19
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Hartop E, Srivathsan A, Ronquist F, Meier R. Towards Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa. Syst Biol 2022; 71:1404-1422. [PMID: 35556139 PMCID: PMC9558837 DOI: 10.1093/sysbio/syac033] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa,” here defined as groups for which \documentclass[12pt]{minimal}
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}{}$\%$\end{document} of all species are described and the estimated diversity exceeds 1,000 species. Species delimitation for these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop large-scale integrative taxonomy (LIT), an explicit method where preliminary species hypotheses are generated based on inexpensive data that can be obtained quickly and cost-effectively. These hypotheses are then evaluated based on a more expensive type of “validation data” that is only obtained for specimens selected based on objective criteria applied to the preliminary species hypotheses. We here use this approach to sort 18,000 scuttle flies (Diptera: Phoridae) into 315 preliminary species hypotheses based on next-generation sequencing barcode (313 bp) clusters (using objective clustering [OC] with a 3\documentclass[12pt]{minimal}
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}{}$\%$\end{document} threshold). These clusters are then evaluated with morphology as the validation data. We develop quantitative indicators for predicting which barcode clusters are likely to be incongruent with morphospecies by randomly selecting 100 clusters for in-depth validation with morphology. A linear model demonstrates that the best predictors for incongruence between barcode clusters and morphology are maximum p-distance within the cluster and a newly proposed index that measures cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that are incongruent with morphology. In our study, all morphospecies are true or disjoint subsets of the initial barcode clusters so that all incongruence can be eliminated by varying clustering thresholds. This leads to a discussion of when a third data source is needed to resolve incongruent grouping statements. The morphological validation step in our study involved 1,039 specimens (5.8\documentclass[12pt]{minimal}
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}{}$\%$\end{document} of the total). The formal LIT protocol we propose would only have required the study of 915 (5.1\documentclass[12pt]{minimal}
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}{}$\%$\end{document}: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of incongruence are similar across OC, Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Refined Single Linkage (RESL) (used by Barcode of Life Data System to assign Barcode Index Numbers [BINs]). OC and ABGD achieved a maximum congruence score with the morphology of 89\documentclass[12pt]{minimal}
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}{}$\%$\end{document} while PTP was slightly less effective (84\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1,714 haplotypes were 86\documentclass[12pt]{minimal}
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}{}$\%$\end{document} congruent with morphology while the values were 89\documentclass[12pt]{minimal}
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}{}$\%$\end{document} for OC, 74\documentclass[12pt]{minimal}
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}{}$\%$\end{document} for PTP, and 72\documentclass[12pt]{minimal}
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}{}$\%$\end{document} for ABGD. [Biodiversity discovery; dark taxa; DNA barcodes; integrative taxonomy.]
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Affiliation(s)
- Emily Hartop
- Zoology Department, Stockholm University, Stockholm, Sweden.,Station Linné, Öland, Sweden.,Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde, Berlin
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore.,Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde, Berlin
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore.,Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde, Berlin
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20
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Hlebec D, Sivec I, Podnar M, Kučinić M. DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera). PeerJ 2022; 10:e13213. [PMID: 35469200 PMCID: PMC9034701 DOI: 10.7717/peerj.13213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/12/2022] [Indexed: 01/12/2023] Open
Abstract
Background The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy. Methods A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies. Results Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.
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Affiliation(s)
- Dora Hlebec
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia,Zoological Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany,Croatian Biospeleological Society, Zagreb, Croatia
| | - Ignac Sivec
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | | | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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21
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Somoza-Valdeolmillos E, Gómez-Moliner BJ, Caro A, Chueca LJ, Martínez-Ortí A, Puente AI, Madeira MJ. Molecular phylogeny of the genus Chondrina (Gastropoda, Panpulmonata, Chondrinidae) in the Iberian Peninsula. Mol Phylogenet Evol 2022; 172:107480. [PMID: 35452839 DOI: 10.1016/j.ympev.2022.107480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 11/29/2022]
Abstract
Chondrina Reichenbach, 1828 is a highly diverse genus of terrestrial molluscs currently including 44 species with about 28 subspecific taxa. It is distributed through North Africa, central and southern Europe, from Portugal in the West to the Caucasus and Asia Minor in the East. Approximately 70% of the species are endemic to the Iberian Peninsula constituting its main center of speciation with 34 species. This genus includes many microendemic taxa, some of them not yet described, confined to limestone habitats (being strictly rock-dwelling species). They are distributed on rocky outcrops up to 2000 m.a.s.l. It is a genus of conical-fusiform snails that differ mainly in shell characters and in the number and position of teeth in their aperture. So far, molecular studies on Chondrina have been based exclusively on the mitochondrial Cytochrome Oxidase subunit I region (COI). These studies gave a first view of the phylogeny of the genus but many inner nodes were not statistically supported. The main objective of the study is to obtain a better understanding of the phylogeny and systematics of the genus Chondrina on the Iberian Peninsula, using multilocus molecular analysis. Partial sequences of the COI and 16S rRNA genes, as well as of the nuclear Internal Transcribed Spacer 1 (ITS1-5.8S) and Internal Transcribed Spacer 2 (5.8S-ITS2-28S) were obtained from individuals of all the extant Chondrina species known from the Iberian Peninsula. In addition to this, the newly obtained COI sequences were combined with those previously published in the GenBank. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods. The reconstructed phylogenies showed high values of support for more recent branches and basal nodes. Moreover, molecular species delimitation allowed to better definethe studied species and check the presence of new taxa.
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Affiliation(s)
- Eder Somoza-Valdeolmillos
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain.
| | - Benjamín J Gómez-Moliner
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain
| | - Amaia Caro
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain
| | - Luis J Chueca
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Alberto Martínez-Ortí
- Museu Valencià d'Història Natural, Apto. 8460, E-46018, Valencia and Universitat de València, Faculty of Pharmacy, Parasitology Departament, Burjassot, Valencia, (Spain)
| | - Ana I Puente
- University of the Basque Country (UPV/EHU), Faculty of Science and Technology, Department of Zoology and Animal Cell Biology: Barrio Sarriena s/n, 48015 Leioa, Spain
| | - María J Madeira
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain
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22
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Ji Y, Yang J, Landis JB, Wang S, Jin L, Xie P, Liu H, Yang JB, Yi TS. Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:832034. [PMID: 35444671 PMCID: PMC9014178 DOI: 10.3389/fpls.2022.832034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.
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Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jacob B. Landis
- Section of Plant Biology and the L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Lei Jin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Pingxuan Xie
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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23
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Identifying the Genetic Distance Threshold for Entiminae (Coleoptera: Curculionidae) Species Delimitation via COI Barcodes. INSECTS 2022; 13:insects13030261. [PMID: 35323559 PMCID: PMC8953793 DOI: 10.3390/insects13030261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/27/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023]
Abstract
The subfamily Entiminae is the largest group in the family Curculionidae, and it has long represented a challenge in traditional and molecular classification. Here, we analyzed intra- and interspecific genetic distances of 621 public COI barcode sequences (658bp) from 39 genera and 110 species of Entiminae, to determine parameters most congruent in retaining established species. We found that the mean intraspecific genetic distance (3.07%) was much smaller than the mean interspecific one (21.96%), but there is a wide range of overlap between intra- and interspecific genetic distances (0.77−18.01%), indicating that there is no consistent, universal barcoding gap. Specifically, DNA barcoding gap analysis for morphospecies revealed that 102 of 110 morphospecies had barcoding gaps, and 9.18% was the optimum threshold of genetic distances for 97 species delimitation. We further confirmed this threshold with barcodes from 27 morphologically identified specimens (including 21 newly reported barcodes) sequenced from five genera and seven species. We also identified thresholds to delimit congeneric species within 14 selected genera (species > 2), which varied from 7.42% (Trichalophus) to 13.48% (Barypeithes). We herein present optimal parameters for species identification in the Entiminae. Our study suggests that despite no universal genetic distance threshold value in subfamily Entiminae, 9.18% is optimal for most species. We recommend a wider sampling of geographic populations to better account for intraspecific distance variation, and that genetic distance thresholds for species delimitation should be refined at the genus level.
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Fassio G, Bouchet P, Oliverio M, Strong EE. Re-evaluating the case for poecilogony in the gastropod Planaxis sulcatus (Cerithioidea, Planaxidae). BMC Ecol Evol 2022; 22:13. [PMID: 35130841 PMCID: PMC8822645 DOI: 10.1186/s12862-022-01961-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background Planaxis sulcatus has been touted as a textbook example of poecilogony, with members of this wide-ranging Indo-Pacific marine gastropod said to produce free-swimming veligers as well as brooded juveniles. A recent paper by Wiggering et al. (BMC Evol Biol 20:76, 2020) assessed a mitochondrial gene phylogeny based on partial COI and 16S rRNA sequences for 31 individuals supplemented by observations from the brood pouch of 64 mostly unsequenced individuals. ABGD and bGYMC supported three reciprocally monophyletic clades, with two distributed in the Indo-Pacific, and one restricted to the northern Indian Ocean and Red Sea. Given an apparent lack of correlation between clade membership and morphological differentiation or mode of development, the reported 3.08% maximum K2P model-corrected genetic divergence in COI among all specimens was concluded to represent population structuring. Hence, the hypothesis that phylogenetic structure is evidence of cryptic species was rejected and P. sulcatus was concluded to represent a case of geographic poecilogony. Results Our goal was to reassess the case for poecilogony in Planaxis sulcatus with a larger molecular dataset and expanded geographic coverage. We sequenced an additional 55 individuals and included published and unpublished sequence data from other sources, including from Wiggering et al. Our dataset comprised 108 individuals (88 COI, 81 16S rRNA) and included nine countries unrepresented in the previous study. The expanded molecular dataset yielded a maximum K2P model-corrected genetic divergence among all sequenced specimens of 12.09%. The value of 3.08% erroneously reported by Wiggering et al. is the prior maximal distance value that yields a single-species partition in ABGD, and not the maximum K2P intraspecific divergence that can be calculated for the dataset. The bGMYC analysis recognized between two and six subdivisions, while the best-scoring ASAP partitions recognized two, four, or five subdivisions, not all of which were robustly supported in Bayesian and maximum likelihood phylogenetic analyses of the concatenated and single gene datasets. These hypotheses yielded maximum intra-clade genetic distances in COI of 2.56–6.19%, which are more consistent with hypothesized species-level thresholds for marine caenogastropods. Conclusions Based on our analyses of a more comprehensive dataset, we conclude that the evidence marshalled by Wiggering et al. in support of Planaxis sulcatus comprising a single widespread, highly variable species with geographic poecilogony is unconvincing and requires further investigation in an integrative taxonomic framework. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01961-7.
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25
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Barbo FE, Booker WW, Duarte MR, Chaluppe B, Portes-Junior JA, Franco FL, Grazziotin FG. Speciation process on Brazilian continental islands, with the description of a new insular lancehead of the genus Bothrops (Serpentes, Viperidae). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2017059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Fausto E. Barbo
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - William W. Booker
- Department of Biological Sciences, Florida State University, 319 Stadium Drive, Tallahassee, 32306 FL, USA
| | - Marcelo R. Duarte
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - Betina Chaluppe
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - José A. Portes-Junior
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - Francisco L. Franco
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
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26
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Abouabdallah MA, Peyrard N, Franc A. Does clustering of DNA barcodes agree with botanical classification directly at high taxonomic levels? Trees in French Guiana as a case study. Mol Ecol Resour 2022; 22:1746-1761. [PMID: 34995403 DOI: 10.1111/1755-0998.13579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 12/16/2021] [Indexed: 11/29/2022]
Abstract
Characterising biodiversity is one of the main challenges for the coming decades. Most diversity has not been morphologically described and barcoding is now complementing morphological-based taxonomy to further develop inventories. Both approaches have been cross-validated at the level of species and OTUs. However, many known species are not listed in reference databases. One path to speed up inventories using barcoding is to directly identify individuals at coarser taxonomic levels. We therefore studied in barcoding of plants whether morphological-based and molecular-based approaches are in agreement at genus, family and order levels. We used Agglomerative Hierarchical Clustering (with Ward, Complete and Single Linkage) and Stochastic Block Models (SBM), with two dissimilarity measures (Smith-Waterman scores, kmers). The agreement between morphological-based and molecular-based classifications ranges in most of the cases from good to very good at taxonomic levels above species, even though it decreases when taxonomic levels increase, or when using the tetramer-based distance. Agreement is correlated with the entropy of morphological-based classification and with the ratio of the mean within- and mean between-groups dissimilarities. The Ward method globally leads to the best agreement whereas Single Linkage can show poor behaviours. SBM provides a useful tool to test whether or not the dissimilarities are structured by the botanical groups. These results suggest that automatic clustering and group identification at taxonomic levels above species are possible in barcoding.
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Affiliation(s)
- Mohamed Anwar Abouabdallah
- BIOGECO, INRAE, Université de Bordeaux, 33612, Cestas, France.,Pleiade, EPC INRIA-INRAE-CNRS, Université de Bordeaux, 33405, Talence, France
| | - Nathalie Peyrard
- Université de Toulouse, INRAE, UR MIAT, F-31320, Castanet-Tolosan, France
| | - Alain Franc
- BIOGECO, INRAE, Université de Bordeaux, 33612, Cestas, France.,Pleiade, EPC INRIA-INRAE-CNRS, Université de Bordeaux, 33405, Talence, France
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27
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28
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Taft JM, Maritz B, Tolley KA. Stable climate corridors promote gene flow in the Cape sand snake species complex (Psammophiidae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jody M. Taft
- Department of Biodiversity and Conservation Biology University of the Western Cape Private Bag X17 Bellville South Africa
- Kirstenbosch Research Center South African National Biodiversity Institute Cape Town South Africa
| | - Bryan Maritz
- Department of Biodiversity and Conservation Biology University of the Western Cape Private Bag X17 Bellville South Africa
| | - Krystal A. Tolley
- Kirstenbosch Research Center South African National Biodiversity Institute Cape Town South Africa
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Johannesburg South Africa
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29
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Lagourgue L, Payri CE. Diversity and taxonomic revision of tribes Rhipileae and Rhipiliopsideae (Halimedaceae, Chlorophyta) based on molecular and morphological data. JOURNAL OF PHYCOLOGY 2021; 57:1450-1471. [PMID: 34003495 DOI: 10.1111/jpy.13186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Genera and species of the tribes Rhipileae and Rhipiliopsideae are abundant in most coral reef ecosystems worldwide. However, the group has been largely overlooked, and very little genetic data is available to accurately assess its diversity, phylogenetic relationships, and geographic distribution. Our study provided an in-depth reassessment of tribes Rhipileae and Rhipiliopsideae based on a species-rich dataset and the combination of molecular species delimitation, multilocus phylogenetic analyses (tufA, rbcL, and 18S rDNA), and morpho-anatomic observations. Our results revealed an unexpected diversity of 38 morphologically validated species hypotheses, including 20 new species, two of which are described in this paper and one resurrected species (Rhipilia diaphana). Based on our phylogenetic results we proposed to redefine the genera Rhipilia and Rhipiliopsis and described two new genera, Kraftalia gen. nov. (Rhipileae) and Rhipiliospina gen. nov. (Rhipiliopsideae). Finally, we validated Rhipiliella Kraft and included it in the tribe Rhipileae. Although Rhipilia and Rhipiliopsis have a pantropical distribution, none of the species studied here appeared cosmopolitan; instead, they have restricted distributions.
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Affiliation(s)
- Laura Lagourgue
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, Paris Cedex 05, 75252, France
- UMR ENTROPIE (IRD, UR, UNC, Ifremer, CNRS), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France
| | - Claude E Payri
- UMR ENTROPIE (IRD, UR, UNC, Ifremer, CNRS), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France
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30
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Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R. ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 2021; 19:217. [PMID: 34587965 PMCID: PMC8479912 DOI: 10.1186/s12915-021-01141-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. RESULTS We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. CONCLUSIONS We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Johnathan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany.
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31
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Ramírez-Portilla C, Baird AH, Cowman PF, Quattrini AM, Harii S, Sinniger F, Flot JF. Solving the Coral Species Delimitation Conundrum. Syst Biol 2021; 71:461-475. [PMID: 34542634 DOI: 10.1093/sysbio/syab077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022] Open
Abstract
Distinguishing coral species is not only crucial for physiological, ecological and evolutionary studies, but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that inter-specific hybridization might be responsible for this apparent conundrum. Here, we used three lines of evidence - morphology, breeding trials and molecular approaches - to identify species boundaries in a group of ecologically important tabular Acropora corals. In contrast to previous studies, our morphological analyses yielded groups that were congruent with experimental crosses as well as with coalescent-based and allele sharing-based multilocus approaches to species delimitation. Our results suggest that species of the genus Acropora are reproductively isolated and independently evolving units that can be distinguished morphologically. These findings not only pave the way for a taxonomic revision of coral species, but also outline an approach that can provide a solid basis to address species delimitation and provide conservation support to a wide variety of keystone organisms.
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Affiliation(s)
- Catalina Ramírez-Portilla
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, B-1050, Belgium.,Systematics & Biodiversity, Justus-Liebig University, Giessen, D-35392, Germany
| | - Andrew H Baird
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Peter F Cowman
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - Saki Harii
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Frederic Sinniger
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, B-1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)2, Brussels, B-1050, Belgium
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32
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Borges LMS, Treneman NC, Haga T, Shipway JR, Raupach MJ, Altermark B, Carlton JT. Out of taxonomic crypsis: A new trans-arctic cryptic species pair corroborated by phylogenetics and molecular evidence. Mol Phylogenet Evol 2021; 166:107312. [PMID: 34530118 DOI: 10.1016/j.ympev.2021.107312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/06/2021] [Accepted: 09/09/2021] [Indexed: 01/17/2023]
Abstract
Cryptic species are a common phenomenon in cosmopolitan marine species. The use of molecular tools has often uncovered cryptic species occupying a fraction of the geographic range of the original morphospecies. Shipworms (Teredinidae) are marine bivalves, living in drift and fixed wood, many of which have a conserved morphology across cosmopolitan distributions. Herein novel and GenBank mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S rRNA) DNA sequences are employed to produce a phylogeny of the Teredinidae and delimit a cryptic species pair in the Psiloteredo megotara complex. The anatomy, biogeography, and ecology of P. megotara, Psiloteredo sp. and Nototeredo edax are compared based on private and historic museum collections and a thorough literature review. Morphological and anatomical characters of P. megotara from the North Atlantic and Psiloteredo sp. from Japan were morphologically indistinguishable, and differ in pallet architecture and soft tissue anatomy from N. edax. The two Psiloteredo species were then delimited as genetically distinct species using four molecular-based methods. Consequently, the Northwest Pacific species, Psiloteredo pentagonalis, first synonymized with N. edax and then with P. megotara, is resurrected. Nototeredo edax, P. megotara and P. pentagonalis are redescribed based upon morphological and molecular characters. Phylogenetic analysis further revealed cryptic species complexes within the cosmopolitan species Bankia carinata and possibly additional cryptic lineages within the cosmopolitan Lyrodus pedicellatus.
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Affiliation(s)
- Luísa M S Borges
- L(3) Scientific Solutions, Runder Berg 7e, 21502 Geesthacht, Germany.
| | - Nancy C Treneman
- Oregon Institute of Marine Biology, P.O. Box 5389, Charleston, OR 97420, USA.
| | - Takuma Haga
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan.
| | - J Reuben Shipway
- Institute of Marine Sciences, University of Portsmouth, Ferry Rd, Portsmouth, UK. & Microbiology Department, University of Massachusetts, Amherst, MA, USA.
| | - Michael J Raupach
- Sektion Hemiptera, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany.
| | - Bjørn Altermark
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, PB 6050 Langnes, 9037 Tromsø, Norway.
| | - James T Carlton
- Ocean & Coastal Studies Program, Williams College-Mystic Seaport, Mystic, CT 06355, USA.
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33
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Meier R, Blaimer BB, Buenaventura E, Hartop E, von Rintelen T, Srivathsan A, Yeo D. A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science. Cladistics 2021; 38:264-275. [PMID: 34487362 DOI: 10.1111/cla.12489] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.
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Affiliation(s)
- Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Bonnie B Blaimer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Eliana Buenaventura
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Emily Hartop
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
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34
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Criscione F, Hallan A, Fedosov A, Puillandre N. Deep Downunder: Integrative taxonomy of
Austrobela
,
Spergo
,
Theta
and
Austrotheta
(Gastropoda: Conoidea: Raphitomidae) from the deep sea of Australia. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Anders Hallan
- Australian Museum Research Institute Sydney NSW Australia
| | - Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences Moscow Russia
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Muséum National d'Histoire Naturelle CNRS Sorbonne Université EPHE Université des AntillesParis France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Muséum National d'Histoire Naturelle CNRS Sorbonne Université EPHE Université des AntillesParis France
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35
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Collado GA, Torres-Díaz C, Valladares MA. Phylogeography and molecular species delimitation reveal cryptic diversity in Potamolithus (Caenogastropoda: Tateidae) of the southwest basin of the Andes. Sci Rep 2021; 11:15735. [PMID: 34344905 PMCID: PMC8333322 DOI: 10.1038/s41598-021-94900-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
The species of the genus Potamolithus inhabiting the southwestern basin of the Andes are difficult to distinguish due to small size and similar shell morphology. Only Potamolithus australis and Potamolithus santiagensis have been traditionally recognized in this region, but the occurrence of several morphologically similar undescribed populations could increase the regional richness. Here we delimit described and potentially undescribed cryptic species of the genus using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis and diversity indices inferred six highly differentiated haplogroups, many of them sympatric and widespread in the study area. Phylogeographic analyses suggest a scenario of recent diversification and the occurrence of multiple refuges during the successive Pleistocene glaciations. Phylogenetic analysis also recovered six major clades that showed no relationship with physiography. Species delimitation analyses consistently recognized three or four candidate species apart from P. australis and P. santiagensis. Divergence times indicate that speciation of Chilean Potamolithus began at the end of the Pliocene, probably driven by climatic rather than geographic events. Considering the high inter- and intra-basin genetic diversity, conservation efforts should be focused on protecting sympatric taxa in the basins with the highest species richness.
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Affiliation(s)
- Gonzalo A. Collado
- grid.440633.6Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán, Chile ,grid.440633.6Grupo de Investigación en Biodiversidad y Cambio Global (GBCG), Universidad del Bío-Bío, Chillán, Chile
| | - Cristian Torres-Díaz
- grid.440633.6Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán, Chile ,grid.440633.6Grupo de Investigación en Biodiversidad y Cambio Global (GBCG), Universidad del Bío-Bío, Chillán, Chile
| | - Moisés A. Valladares
- grid.440633.6Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán, Chile ,grid.440633.6Grupo de Investigación en Biodiversidad y Cambio Global (GBCG), Universidad del Bío-Bío, Chillán, Chile
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36
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Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N. SPART: A versatile and standardized data exchange format for species partition information. Mol Ecol Resour 2021; 22:430-438. [PMID: 34288531 DOI: 10.1111/1755-0998.13470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
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Affiliation(s)
- Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | - Sophie Brouillet
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Shiga, Japan
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - L Lacey Knowles
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
| | - Sangeeta Kumari
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jeet Sukumaran
- Biology Department, LS 262, San Diego State University, San Diego, CA, USA
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Miguel Vences
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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37
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Lopes-Lima M, Gürlek ME, Kebapçı Ü, Şereflişan H, Yanık T, Mirzajani A, Neubert E, Prié V, Teixeira A, Gomes-Dos-Santos A, Barros-García D, Bolotov IN, Kondakov AV, Vikhrev IV, Tomilova AA, Özcan T, Altun A, Gonçalves DV, Bogan AE, Froufe E. Diversity, biogeography, evolutionary relationships, and conservation of Eastern Mediterranean freshwater mussels (Bivalvia: Unionidae). Mol Phylogenet Evol 2021; 163:107261. [PMID: 34273504 DOI: 10.1016/j.ympev.2021.107261] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022]
Abstract
Located at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater mussels (Bivalvia, Unionidae) from the Western Palearctic have been widely studied in their European range, but little attention has been dedicated to these taxa in the Eastern Mediterranean region and their diversity and phylogeography are still poorly understood. The present study aims to resolve the diversity, biogeography, and evolutionary relationships of the Eastern Mediterranean freshwater mussels. To that end, we performed multiple field surveys, phylogenetic analyses, and a thorough taxonomic revaluation. We reassessed the systematics of all Unionidae species in the region, including newly collected specimens across Turkey, Israel, and Iran, combining COI + 16S + 28S and COI phylogenies with molecular species delineation methods. Phylogeographical patterns were characterized based on published molecular data, newly sequenced specimens, and species distribution data, as well as ancestral range estimations. We reveal that Unionidae species richness in the Eastern Mediterranean is over 70% higher than previously assumed, counting 19 species within two subfamilies, the Unioninae (14) and Gonideinae (5). We propose two new species, Anodonta seddonisp. nov. and Leguminaia anatolicasp. nov. Six additional taxa, Unio delicatusstat. rev., Unio eucirrusstat. rev., Unio huetistat. rev., Unio sesirmensisstat. rev., Unio terminalisstat. rev. removed from the synonymy of Unio tigridis, as well as Unio damascensisstat. rev. removed from the synonymy of Unio crassus, are re-described. The nominal taxa Unio rothi var. komarowi O. Boettger, 1880 and Unio armeniacus Kobelt, 1911 are proposed as new synonyms of Unio bruguierianus, and Anodonta cyrea Drouët, 1881 and Anodonta cilicica Kobelt & Rolle, 1895 as new synonyms of Anodonta anatina. Also, the presence of Unio tumidus in the Maritza River is confirmed. The phylogeographic patterns described here are interpreted concerning major past geological events. Conservation needs and implications are presented, together with populations and species conservation priorities.
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Affiliation(s)
- Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal; SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, CB2 3QZ Cambridge, United Kingdom.
| | - Mustafa Emre Gürlek
- Burdur Vocational School of Food Agriculture and Livestock, Mehmet Akif Ersoy University, 15100 Burdur, Turkey
| | - Ümit Kebapçı
- Biology Department of Art and Science Faculty, Mehmet Akif Ersoy University, Burdur, Turkey
| | - Hülya Şereflişan
- Marine Sciences and Technology Faculty, Iskenderun Technical University, 31200 Iskenderun, Hatay, Turkey
| | - Telat Yanık
- Ataturk University, Faculty of Fishery, 25240 Erzurum, Turkey
| | - Alireza Mirzajani
- Inland Waters Aquaculture Research Center, Iranian Fisheries Science Research Institute, Agricultural Research Education and Extension Organization (AREEO), P.O. Box 66, Bandar-e Anzali, Iran
| | - Eike Neubert
- Natural History Museum Bern, Bernastr. 15, CH-3005 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Vincent Prié
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Institute of Systematics, Evolution, Biodiversity (ISYEB), National Museum of Natural History (MNHN), CNRS, SU, EPHE, UA CP 51, 57 rue Cuvier, 75005 Paris, France
| | - Amilcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 1021/1055 Porto, Portugal
| | - David Barros-García
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
| | - Ivan N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163017 Arkhangelsk, Russia; Saint-Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia
| | - Alexander V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163017 Arkhangelsk, Russia; Saint-Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia
| | - Ilya V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia; Northern Arctic Federal University, Northern Dvina Emb. 17, 163017 Arkhangelsk, Russia; Saint-Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia
| | - Alena A Tomilova
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000 Arkhangelsk, Russia
| | - Tahir Özcan
- Marine Sciences and Technology Faculty, Iskenderun Technical University, 31200 Iskenderun, Hatay, Turkey
| | - Ayhan Altun
- Marine Sciences and Technology Faculty, Iskenderun Technical University, 31200 Iskenderun, Hatay, Turkey
| | - Duarte V Gonçalves
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones St, Raleigh, NC 27601, United States
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
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38
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Levicoy D, Rosenfeld S, Cárdenas L. Divergence time and species delimitation of microbivalves in the Southern Ocean: the case of Kidderia species. Polar Biol 2021; 44:1365-1377. [PMID: 34092908 PMCID: PMC8169414 DOI: 10.1007/s00300-021-02885-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/18/2022]
Abstract
The systematics of Subantarctic and Antarctic near-shore marine benthic invertebrates requires major revision and highlights the necessity to incorporate additional sources of information in the specimen identification chart in the Southern Ocean (SO). In this study, we aim to improve our understanding of the biodiversity of Kidderia (Dall 1876) through molecular and morphological comparisons of Antarctic and Subantarctic taxa. The microbivalves of the genus Kidderia are small brooding organisms that inhabit intertidal and shallow subtidal rocky ecosystems. This genus represents an interesting model to test the vicariance and dispersal hypothesis in the biogeography of the SO. However, the description of Kidderia species relies on a few morphological characters and biogeographic records that raise questions about the true diversity in the group. Here we will define the specimens collected with genetic tools, delimiting their respective boundaries across provinces of the SO, validating the presence of two species of Kidderia. Through the revision of taxonomic issues and species delimitation, it was possible to report that the Antarctic species is Kidderia subquadrata and the species recorded in the Subantarctic islands Diego Ramirez, South Georgia and the Kerguelen Archipelago is Kidderia minuta. The divergence time estimation suggests the origin and diversification of Kidderia lineages are related to historical vicariant processes probably associated with the separation of the continental landmasses close to the late Eocene.
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Affiliation(s)
- Daniela Levicoy
- Centro FONDAP- IDEAL, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Chile
| | - Sebastián Rosenfeld
- Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras #3425, Ñuñoa, Santiago Chile.,Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Avenida Bulnes 01890, Punta Arenas, Chile.,Instituto de Ecología y Biodiversidad, Las Palmeras 3425, Ñuñoa, Santiago Chile.,Centro de Investigación Gaia-Antártica, Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas, Chile
| | - Leyla Cárdenas
- Centro FONDAP- IDEAL, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Chile
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39
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Zhang Y, Wang Z, Guo Y, Chen S, Xu X, Wang R. Complete chloroplast genomes of Leptodermis scabrida complex: Comparative genomic analyses and phylogenetic relationships. Gene 2021; 791:145715. [PMID: 33984444 DOI: 10.1016/j.gene.2021.145715] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022]
Abstract
Leptodermis scabrida complex is one of the important components of genus Leptodermis, which is mainly distributed in the Himalaya Mountains. It includes species of L. gracilis, L. hirsutiflora, L. hirsutiflora var. ciliata, L. kumaonensis, L. pilosa var. acanthoclada and L. scabrida. However, species boundaries and relationships within this complex are unclear based on current morphological and molecular evidence. We sequenced 13 complete chloroplast (cp) genomes representing seven taxa of the complex and two non-Leptodermis scabrida complex taxa. After de novo assembly and annotation, we performed comparative genomic analysis. All cp genomes showed highly conserved structures, and the genome sizes ranged from 154,369 bp to 154,885 bp and possessed the same GC content (37.5%). A total of 113 unique genes were identified in each cp sample, including 79 protein coding genes, 30 tRNAs, and four rRNAs. Repeat sequences and SSRs were detected, showing great similarity among all taxa in this complex. Six highly variable regions, including trnS-trnG, rps2-rpoC2, ndhF, rpl32-ccsA, ccsA-ndhD, and ndhA, were screened as potential molecular markers for phylogenetic reconstruction. Based on a total of 27 complete cp genome sequences, the consistent and robust phylogenetic relationships were firstly constructed and the same species within L. scabrida complex clustered into a group. The divergence time of Leptodermis from ancestral taxa occurred at the middle Eocene, which might be due to geological and climatic changes. The 13 complete cp genome sequences reported will provide new clues for phylogeny elucidation, species identification and evolutionary history speculation of Leptodermis, as well as in Rubiaceae.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengfeng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yanan Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Sheng Chen
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xianyi Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ruijiang Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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40
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Onn Chan K, Hutter CR, Wood PL, Su YC, Brown RM. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis). Syst Biol 2021; 71:40-57. [PMID: 33964168 DOI: 10.1093/sysbio/syab034] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022] Open
Abstract
In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L Wood
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, Alabama 36849, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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41
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Caccavale F, Osca D, D’Aniello S, Crocetta F. Molecular taxonomy confirms that the northeastern Atlantic and Mediterranean Sea harbor a single lancelet, Branchiostoma lanceolatum (Pallas, 1774) (Cephalochordata: Leptocardii: Branchiostomatidae). PLoS One 2021; 16:e0251358. [PMID: 33956890 PMCID: PMC8101936 DOI: 10.1371/journal.pone.0251358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/23/2021] [Indexed: 12/02/2022] Open
Abstract
Branchiostomatidae (lancelets or amphioxus) comprises about 30 species, several of which are well-established models in evolutionary development. Our zoological and ecological knowledge of the family is nonetheless limited. Despite evident differences can be found among known populations, the taxonomy of Branchiostoma lanceolatum (type species of the genus Branchiostoma) has never been investigated with modern methods through its range in the northeastern Atlantic and Mediterranean Sea. We address this via a multilocus molecular approach and comparing specimens collected from different European populations. Results obtained here confirm the presence of a single species inhabiting the range between the topotypical localities of B. lanceolatum (Atlantic Ocean) and of its junior synonym B. lubricum (Mediterranean Sea), without evincing geographical structure between populations. This suggests that environment most likely drives the characteristics observed in different geographic areas. The long larval phase and the slow mutation rate in lancelets may have played a key role in the evolutionary history of this iconic species.
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Affiliation(s)
- Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - David Osca
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Fabio Crocetta
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
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Moraes SDS, Murillo‐Ramos L, Machado PA, Ghanavi HR, Magaldi LM, Silva‐Brandão KL, Kato MJ, Freitas AVL, Wahlberg N. A double‐edged sword: Unrecognized cryptic diversity and taxonomic impediment in
Eois
(Lepidoptera, Geometridae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simeão de Souza Moraes
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
- Department of Biology Lund University Lund Sweden
| | - Leidys Murillo‐Ramos
- Department of Biology Lund University Lund Sweden
- Departamento de Biología Universidad de Sucre Sincelejo Colombia
| | - Patrícia A. Machado
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
| | | | - Luiza M. Magaldi
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
| | | | - Massuo J. Kato
- Laboratório de Química de Produtos Naturais Instituto de Química Universidade de São Paulo São Paulo Brazil
| | - André V. L. Freitas
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
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43
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Furfaro G, Salvi D, Trainito E, Vitale F, Mariottini P. When morphology does not match phylogeny: The puzzling case of two sibling nudibranchs (Gastropoda). ZOOL SCR 2021. [DOI: 10.1111/zsc.12484] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Giulia Furfaro
- Department of Science and Biological and Environmental Technologies ‐ DiSTeBA University of Salento Lecce Italy
| | - Daniele Salvi
- Department of Health, Life and Environmental Sciences University of L’Aquila L’Aquila Italy
- CIBIO‐InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Egidio Trainito
- Marine Protected Area 'Tavolara‐Punta Coda Cavallo' Olbia Italy
| | - Fabio Vitale
- Museum of Natural History of Salento (Calimera) Lecce Italy
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44
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Yuan JJ, Chen D, Wan X. A multilocus assessment reveals two new synonymies for East Asian Cyclommatus stag beetles (Coleoptera, Lucanidae). Zookeys 2021; 1021:65-79. [PMID: 33727883 PMCID: PMC7943532 DOI: 10.3897/zookeys.1021.58832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/31/2021] [Indexed: 11/12/2022] Open
Abstract
Cyclommatus scutellaris Möllenkamp, 1912, Cyclommatus elsae Kriesche, 1921 and Cyclommatus tamdaoensis Fujita, 2010 are East Asian stag beetle species with long-debated taxonomic relationships due to high intraspecific morphological variability. In this study, we applied multilocus phylogenetic analyses to reassess their relationships. Two mitochondrial genes (16S rDNA, COI) and two nuclear genes (28S rDNA, Wingless) were used to reconstruct the phylogeny through the Bayesian inference (BI) and Maximum Likelihood (ML) methods. Both topologies supported two clades: the clade C. scutellaris was sister to the clade (C. elsae + C. tamdaoensis) with the subclade C. tamdaoensis embedded in the subclade C. elsae. The Kimura 2-parameter (K2P) genetic distance analysis yielded a low mean value (≤0.035) among the three taxa, which was well below the minimum mean value between other Cyclommatus species (≥0.122). We also compared the accuracy and efficiency of two approaches, GMYC and ABGD, in delimitating the three lineages. The result shows that ABGD is a better approach than GMYC. Our molecular data recognizes the three species as different populations of a single species, ranging from Taiwan Island to the continent. Therefore, we propose two new junior synonyms for C. scutellaris: C. tamdaoensis, syn. nov. and C. elsae syn. nov.
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Affiliation(s)
- Jiao Jiao Yuan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
| | - Dan Chen
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
| | - Xia Wan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
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Unveiling cryptic diversity among Müllerian co-mimics: insights from the Western Palaearctic Syntomis moths (Lepidoptera: Erebidae: Arctiinae). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-020-00474-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractAccurate species delimitation is of primary importance in biodiversity assessments and in reconstructing patterns and processes in the diversification of life. However, the discovery of cryptic species in virtually all taxonomic groups unveiled significant gaps in our knowledge of biodiversity. Mimicry complexes are good candidates to source for cryptic species. Indeed, members of mimicry complexes undergo selective pressures on their habitus, which results in strong resemblance even between distantly related species. In this study, we used a multi-locus genetic approach to investigate the presence of cryptic diversity within a group of mimetic day-flying moths whose systematics has long been controversial, the Euro-Anatolian Syntomis. Results showed incongruence between species boundaries and the currently accepted taxonomy of this group. Both mitochondrial and nuclear markers indicate the presence of four, well-distinct genetic lineages. The genetic distance and time of divergence between the Balkan and Italian populations of S. marjana are the same as those found between S. phegea and S. ragazzii, the last two being well-distinct, broadly sympatrically occurring species. The divergence between the two lineages of S. marjana dates back to the Early Pleistocene, which coincided with substantial changes in climatic conditions and vegetation cover in Southern Europe that have likely induced geographic and ecological vicariance. Syntomis populations belonging to the taxa kruegeri (s. str.), albionica and quercii are now considered a separate species from marjana s. str. and are thus distinguished as Syntomis quercii Verity, 1914, bona sp., stat. nov. Our results show that the species richness of mimicry complexes inhabiting temperate regions might still be severely underestimated.
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Singh PR, Karssen G, Couvreur M, Subbotin SA, Bert W. Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes. PLANTS (BASEL, SWITZERLAND) 2021; 10:408. [PMID: 33671787 PMCID: PMC7926417 DOI: 10.3390/plants10020408] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/18/2023]
Abstract
Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.
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Affiliation(s)
- Phougeishangbam Rolish Singh
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
- National Plant Protection Organization, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Marjolein Couvreur
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
| | - Sergei A. Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA;
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian, Academy of Sciences, Leninskii Prospect 33, 117071 Moscow, Russia
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
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Paz-Sedano S, Wilson NG, Carmona L, Gosliner TM, Pola M. An ocean yet to be discovered: increasing systematic knowledge of Indo-Pacific Okenia Menke, 1830 (Nudibranchia:Goniodorididae). INVERTEBR SYST 2021. [DOI: 10.1071/is20088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Numerous faunistic and ecological studies have been conducted throughout the Indo-Pacific Ocean to assess its biodiversity. Despite the abundance of research, studies on the species that inhabit the Indo-Pacific are still necessary due to its extent and high species richness. The major species richness of the genus Okenia Menke, 1830 (Nudibranchia, Goniodorididae) is found in the Indo-Pacific Ocean, including 38 of 60 valid species. Nevertheless, this number does not represent the real biodiversity, since at least 20 more species are already reported in field-guides as undescribed species belonging to this genus. The systematics of the genus Okenia are still unclear since it has been the subject of only a few and incomplete studies. In the present paper, we describe five new Okenia species from the coastlines of Japan, Mozambique and Australia: Okenia aurorapapillata sp. nov., Okenia elisae sp. nov., Okenia nakanoae sp. nov., Okenia siderata sp. nov. and Okenia tenuifibrata sp. nov. Moreover, anatomical details not previously described of Okenia atkinsonorum, Okenia barnardi, Okenia cf. echinata, Okenia hallucigenia, Okenia hiroi, Okenia japonica, Okenia pellucida, Okenia pilosa and Okenia rhinorma are provided. New partial sequences of standard markers (COI, 16S rRNA and H3) were obtained and a phylogenetic analysis that included all species with available data was performed.
ZOOBANK urn:lsid:zoobank.org:pub:28AE2536-A264–4194–8AE3-C430620572E7
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Hallan A, Criscione F, Fedosov A, Puillandre N. Few and far apart: integrative taxonomy of Australian species of Gladiobela and Pagodibela (Conoidea : Raphitomidae) reveals patterns of wide distributions and low abundance. INVERTEBR SYST 2021. [DOI: 10.1071/is20017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The deep-sea malacofauna of temperate Australia remains comparatively poorly known. However, a recent influx of DNA-suitable material obtained from a series of deep-sea cruises has facilitated integrative taxonomic study on the Conoidea (Caenogastropoda:Neogastropoda). Building on a recent molecular phylogeny of the conoidean family Raphitomidae, this study focussed on the genera Gladiobela and Pagodibela (both Criscione, Hallan, Puillandre & Fedosov, 2020). We subjected a representative mtDNA cox1 dataset of deep-sea raphitomids to ABGD, which recognised 14 primary species hypotheses (PSHs), 9 of which were converted to secondary species hypotheses (SSHs). Following the additional examination of the shell and hypodermic radula features, as well as consideration of bathymetric and geographic data, seven of these SSHs were recognised as new to science and given full species rank. Subsequently, systematic descriptions are provided herein. Of these, five are attributed to Gladiobela (three of which are endemic to Australia and two more widely distributed) and two are placed in Pagodibela (one endemic to southern Australia and one widespread in the Pacific). The rarity of many ‘turrids’ reported in previous studies is confirmed herein, as particularly indicated by highly disjunct geographic records for two taxa. Additionally, several of the studied taxa exhibit wide Indo-Pacific distributions, suggesting that wide geographic ranges in deep-sea ‘turrids’ may be more common than previously assumed. Finally, impediments to deep-sea ‘turrid’ taxonomy in light of such comparative rarity and unexpectedly wide distributions are discussed.
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Ji Y, Yang J, Landis JB, Wang S, Yang Z, Zhang Y. Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes. FRONTIERS IN PLANT SCIENCE 2021; 12:681270. [PMID: 34335651 PMCID: PMC8320023 DOI: 10.3389/fpls.2021.681270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/10/2021] [Indexed: 05/08/2023]
Abstract
Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.
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Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Yunheng Ji,
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Zhenyan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yonghong Zhang
- School of Life Sciences, Yunnan Normal University, Kunming, China
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Criscione F, Hallan A, Puillandre N, Fedosov A. Snails in depth: integrative taxonomy of Famelica, Glaciotomella and Rimosodaphnella (Conoidea: Raphitomidae) from the deep sea of temperate Australia. INVERTEBR SYST 2021. [DOI: 10.1071/is21008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The deep sea of temperate south-eastern Australia appears to be a ‘hotspot’ for diversity and endemism of conoidean neogastropods of the family Raphitomidae. Following a series of expeditions in the region, a considerable amount of relevant DNA-suitable material has become available. A molecular phylogeny based on this material has facilitated the identification of diagnostic morphological characters, allowing the circumscription of monophyletic genera and the introduction of several new genus-level taxa. Both named and new genera are presently being investigated through integrative taxonomy, with the discovery of a significant number of undescribed species. As part of this ongoing investigation, our study focuses on the genera Famelica Bouchet & Warén, 1980, Glaciotomella Criscione, Hallan, Fedosov & Puillandre, 2020 and Rimosodaphnella Cossmann, 1914. We subjected a comprehensive mitochondrial DNA dataset of representative deep-sea raphitomids to the species delimitation methods ABGD and ASAP that recognised 18 and 15 primary species hypotheses (PSHs) respectively. Following additional evaluation of shell and radular features, and examination of geographic and bathymetric ranges, nine of these PSHs were converted to secondary species hypotheses (SSHs). Four SSHs (two in Famelica and two in Rimosodaphnella) were recognised as new, and formal descriptions are provided herein.
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