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Budaeva N, Agne S, Ribeiro PA, Straube N, Preick M, Hofreiter M. Wide-spread dispersal in a deep-sea brooding polychaete: the role of natural history collections in assessing the distribution in quill worms (Onuphidae, Annelida). Front Zool 2024; 21:1. [PMID: 38233869 PMCID: PMC10795374 DOI: 10.1186/s12983-023-00520-0] [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: 10/16/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Modern integrative taxonomy-based annelid species descriptions are detailed combining morphological data and, since the last decades, also molecular information. Historic species descriptions are often comparatively brief lacking such detail. Adoptions of species names from western literature in the past led to the assumption of cosmopolitan ranges for many species, which, in many cases, were later found to include cryptic or pseudocryptic lineages with subtle morphological differences. Natural history collections and databases can aid in assessing the geographic ranges of species but depend on correct species identification. Obtaining DNA sequence information from wet-collection museum specimens of marine annelids is often impeded by the use of formaldehyde and/or long-term storage in ethanol resulting in DNA degradation and cross-linking. RESULTS The application of ancient DNA extraction methodology in combination with single-stranded DNA library preparation and target gene capture resulted in successful sequencing of a 110-year-old collection specimen of quill worms. Furthermore, a 40-year-old specimen of quill worms was successfully sequenced using a standard extraction protocol for modern samples, PCR and Sanger sequencing. Our study presents the first molecular analysis of Hyalinoecia species including the previously known species Hyalinoecia robusta, H. tubicloa, H. artifex, and H. longibranchiata, and a potentially undescribed species from equatorial western Africa morphologically indistinguishable from H. tubicola. The study also investigates the distribution of these five Hyalinoecia species. Reassessing the distribution of H. robusta reveals a geographical range covering both the Atlantic and the Indian Oceans as indicated by molecular data obtained from recent and historical specimens. CONCLUSION Our results represent an example of a very wide geographical distribution of a brooding deep-sea annelid with a complex reproduction strategy and seemingly very limited dispersal capacity of its offspring, and highlights the importance of molecular information from museum specimens for integrative annelid taxonomy and biogeography.
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Affiliation(s)
- Nataliya Budaeva
- Department of Natural History, University Museum of Bergen, University of Bergen, Allégaten 41, 5007, Bergen, Norway.
| | - Stefanie Agne
- Evolutionary Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Pedro A Ribeiro
- Department of Biological Sciences and Centre for Deep-Sea Research, University of Bergen, Thormøhlens Gate 53B, 5006, Bergen, Norway
| | - Nicolas Straube
- Department of Natural History, University Museum of Bergen, University of Bergen, Allégaten 41, 5007, Bergen, Norway
| | - Michaela Preick
- Evolutionary Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Neal L, Abrahams E, Wiklund H, Rabone M, Bribiesca-Contreras G, Stewart ECD, Dahlgren TG, Glover AG. Taxonomy, phylogeny, and biodiversity of Lumbrineridae (Annelida, Polychaeta) from the Central Pacific Clarion-Clipperton Zone. Zookeys 2023; 1172:61-100. [PMID: 37538355 PMCID: PMC10394509 DOI: 10.3897/zookeys.1172.100483] [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: 01/12/2023] [Accepted: 05/02/2023] [Indexed: 08/05/2023] Open
Abstract
The DNA taxonomy of six species of the annelid family Lumbrineridae collected from the Clarion-Clipperton Zone (CCZ) in the Central Pacific, an area of potential mining interest for polymetallic nodules, is presented. Lumbrinerids are an ecologically important and understudied annelid family within the deep sea, with many species still undescribed. This study aims to document the taxonomy and biodiversity of the CCZ using specimens collected from the UK-1, OMS, and NORI-D exploration contract areas and Areas of Particular Environmental Interest. Species were identified through a combination of morphological and molecular phylogenetic analysis. We present informal species descriptions associated with voucher specimens, accessible through the Natural History Museum (London) collections, to improve future taxonomic and biodiversity studies of this region. Five taxa in this study had no morphological or genetic matches within the literature and therefore are possibly new to science, but their suboptimal morphological preservation prevented the formalisation of new species. The most abundant taxon Lumbrineridescf.laubieri (NHM_0020) was compared with the holotype of Lumbrinerideslaubieri Miura, 1980 from the deep Northeast Atlantic. Currently no reliable morphological characters separating the Pacific and Atlantic specimens have been found and molecular data from the Atlantic specimens was not available.
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Affiliation(s)
- Lenka Neal
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| | - Emily Abrahams
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| | - Helena Wiklund
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
- Department of Marine Sciences, University of Gothenburg, Box 463, 40530 Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity Centre, Box 463, 40530 Gothenburg, SwedenGothenburg Global Biodiversity CentreGothenburgSweden
| | - Muriel Rabone
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
| | | | - Eva C. D. Stewart
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
- School of Ocean and Earth Sciences, University of Southampton, Southampton, SO14 3ZH, UKUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Thomas G. Dahlgren
- Department of Marine Sciences, University of Gothenburg, Box 463, 40530 Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity Centre, Box 463, 40530 Gothenburg, SwedenGothenburg Global Biodiversity CentreGothenburgSweden
- NORCE Norwegian Research Centre, Bergen, NorwayNORCE Norwegian Research CentreBergenNorway
| | - Adrian G. Glover
- Life Sciences Department, Natural History Museum, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
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Korshunova T, Grøtan VV, Johnson KB, Bakken T, Picton BE, Martynov A. Similar Ones Are Not Related and Vice Versa—New Dendronotus Taxa (Nudibranchia: Dendronotidae) from the North Atlantic Ocean Provide a Platform for Discussion of Global Marine Biodiversity Patterns. DIVERSITY 2023. [DOI: 10.3390/d15040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
One new species of the genus Dendronotus (Nudibranchia: Dendronotidae) is described from Norway and Northern Ireland, as well as from the adjacent North Sea, and one new subspecies of Dendronotus arcticus is described from Norway by applying a combination of fine-scale morphological and molecular phylogenetic data. The present case demonstrates multilevel morphological and molecular similarities and differences considering on the one hand a grouping of three similar looking sympatric taxa (D. yrjargul, D. arcticus gartensis n. subsp. and D. keatleyae n. sp.), and on the other hand two different looking apparently allopatric subspecies (D. arcticus arcticus and D. arcticus gartensis n. subsp.). The type species of the genus, D. frondosus, which is the commonest dendronotid in Norway and the United Kingdom, consistently demonstrates substantial molecular and fine-scale morphological differences from D. keatleyae n. sp. The present study, apart from providing purely taxonomic information, also provides new data for a broad discussion of global biodiversity patterns.
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Affiliation(s)
| | | | | | - Torkild Bakken
- NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Bernard E. Picton
- National Museums Northern Ireland, Holywood BT18 0EU, UK
- Marine Laboratory, Queen’s University Belfast, Belfast BT22 1PF, Northern Ireland, UK
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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5
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Muffett K, Miglietta MP. Demystifying Cassiopea species identity in the Florida Keys: Cassiopea xamachana and Cassiopea andromeda coexist in shallow waters. PLoS One 2023; 18:e0283441. [PMID: 36989331 PMCID: PMC10058153 DOI: 10.1371/journal.pone.0283441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
The phylogeny of the Upside-Down Jellyfish (Cassiopea spp.) has been revised multiple times in its history. This is especially true in the Florida Keys, where much of the Cassiopea stock for research and aquarium trade in the United States are collected. In August 2021, we collected 55 Cassiopea medusae at eight shallow water sites throughout the Florida Keys and sequenced COI, 16S, and 28S genes. Mitochondrial genes demonstrate that the shallow waters in Florida are inhabited by both Cassiopea xamachana and a non-native Cassiopea andromeda lineage, identified in multispecies assemblages at least thrice. While C. xamachana were present at all sites, the C. andromeda-mitotype individuals were present at only a minority of sites. While we cannot confirm hybridization or lack thereof between the C. xamanchana and C. andromeda lineages, these previously unknown multispecies assemblages are a likely root cause for the confusing and disputed COI-based species identities of Cassiopea in the Florida Keys. This also serves as a cautionary note to all Cassiopea researchers to barcode their individuals regardless of the location in which they were collected.
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Affiliation(s)
- Kaden Muffett
- Texas A&M University at Galveston, Galveston, Texas, United States of America
| | - Maria Pia Miglietta
- Texas A&M University at Galveston, Galveston, Texas, United States of America
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Teixeira MAL, Langeneck J, Vieira PE, Hernández JC, Sampieri BR, Kasapidis P, Mucciolo S, Bakken T, Ravara A, Nygren A, Costa FO. Reappraisal of the hyperdiverse. INVERTEBR SYST 2022. [DOI: 10.1071/is21084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D
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Decoupling in Diversification and Body Size Rates During the Radiation of Phyllodactylus: Evidence Suggests Minor Role of Ecology in Shaping Phenotypes. Evol Biol 2022. [DOI: 10.1007/s11692-022-09575-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Teixeira MAL, Vieira PE, Ravara A, Costa FO, Nygren A. From 13 to 22 in a second stroke: revisiting the European Eumida sanguinea (Phyllodocidae: Annelida) species complex. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Eumida sanguinea is a recognized polychaete species complex which, in previous studies, has been reported to have additional undescribed diversity. We detected nine additional lineages by analysing DNA sequence data (mitochondrial: COI, 16S rRNA and nuclear loci: ITS region and 28S rRNA) of E. sanguinea morphotype populations from a broader sampling effort in European marine waters. Traditional morphological features failed to provide consistent differences or unique characters that could be used to distinguish these Eumida species. However, by complementing DNA data with morphometrics, geographic range, colour and pigmentation patterns, we revealed five new species. Two of these undescribed species derived from the previously signalled Eumida lineages S21 and GB22, which are here named as E. schanderi sp. nov. and E. fenwicki sp. nov., respectively. Three other species are based on newly discovered lineages, namely E. fauchaldi sp. nov., E. langenecki sp. nov. and E. pleijeli sp. nov. From the six new lineages remaining, three are represented by fewer than two well-preserved specimens, which prevented further comprehensive analysis. The last three lineages were only distinct when using mitochondrial markers. Integrative taxonomy is essential to elucidate evolutionary phenomena and eventually allow informed use of species complexes exhibiting stasis in biomonitoring or other ecological studies.
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Affiliation(s)
- Marcos A L Teixeira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Ascensão Ravara
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Arne Nygren
- Institutionen for marina vetenskaper, Göteborgs Universitet, Tjärnö, Strömstad, Sweden
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9
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Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters. BIOLOGY 2021; 10:biology10111092. [PMID: 34827084 PMCID: PMC8614736 DOI: 10.3390/biology10111092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022]
Abstract
Simple Summary The biodiversity and ecological status assessment of transitional water ecosystems by benthic macroinvertebrates investigation could use DNA barcode tools for more rapid and efficient outputs. The principal limits of this application are the incompleteness of DNA barcode databases, the identification of optimal primers set, and the gap in the species sequences. The influence of the incompleteness of DNA barcode libraries on species diversity indices, ecological indicators, and ecological status assessment in transitional waters of the southeast Mediterranean were analysed, underlying the importance to implement DNA barcode libraries and to put an effort toward specific species at a local level. Abstract The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. The morphological identification of benthic macroinvertebrates is the current tool for their assessment. Recently, DNA-based tools have been proposed as effective alternatives. The main current limits of DNA-based applications include the incompleteness of species recorded in the DNA barcode reference libraries and the primers bias. Here, we analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species. The ecological quality status assigned through the potential application of both approaches to the analysed transitional water ecosystems was different in 27% of sites. We also analysed the inter-specific genetic distances to evaluate the potential application of the DNA metabarcoding method. Overall, this work highlights the importance to expand the barcode databases and to analyse, at the regional level, the gaps in the DNA barcodes.
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10
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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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11
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Korshunova TA, Driessen FMF, Picton BE, Martynov AV. The multilevel organismal diversity approach deciphers difficult to distinguish nudibranch species complex. Sci Rep 2021; 11:18323. [PMID: 34526521 PMCID: PMC8443629 DOI: 10.1038/s41598-021-94863-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/30/2021] [Indexed: 11/09/2022] Open
Abstract
Species identification is a key procedure for broad-scoped ecological, phylogeographic and evolutionary studies. However, to perform a taxonomic study in the molecular era is a complicated task that has many pitfalls. In the present study we use particular examples of common but difficult to distinguish European species within the genus of Polycera (Nudibranchia, Mollusca) to discuss the general issues of the "cryptic species" problem that has broad biological and interdisciplinary importance and can significantly impede ecological, evolutionary, and other biodiversity-related research. The largest dataset of molecular and morphological information for European nudibranchs ever applied encompasses a wide geographical area and shapes a robust framework in this study. Four species are recognized in the species complex, including a new one. It is shown that a lack of appropriate taxonomic analysis led recently to considerable errors in species identity assessment of this complex. Chromatic polymorphism for each species is mapped in a periodic-like framework and combined with statistical analysis of the diagnostic features that considerably facilitates identification of particular species in the complex for biologists and practitioners. The present study evidently shows that "cryptic" and "non-cryptic" components are present within the same species. Therefore, this species complex is well suited for the exploring and testing of general biological problems. One of the main conclusions of this study is that division of biological diversity into "cryptic" and "non-cryptic" components is counterproductive. We propose that the central biological phenomenon of a species can instead be universally designated as multilevel organismal diversity thereby provide a practical set of methods for its investigation.
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Affiliation(s)
- Tatiana A Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334, Moscow, Russia
| | - Floor M F Driessen
- Bureau Waardenburg BV, Aquatic Ecology, Varkensmarkt 9, 4101 CK, Culemborg, The Netherlands.,Royal Netherlands Institute for Sea Research (NIOZ), PO Box 59, 1790 AB, Den Burg, The Netherlands
| | - Bernard E Picton
- National Museums Northern Ireland, Holywood, Northern Ireland, BT18 0EU, UK.,Queen's University, Belfast, Northern Ireland, UK
| | - Alexander V Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009, Moscow, Russia.
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12
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Tessens B, Monnens M, Backeljau T, Jordaens K, Van Steenkiste N, Breman FC, Smeets K, Artois T. Is ‘everything everywhere’? Unprecedented cryptic diversity in the cosmopolitan flatworm
Gyratrix hermaphroditus. ZOOL SCR 2021. [DOI: 10.1111/zsc.12507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Bart Tessens
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Marlies Monnens
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Thierry Backeljau
- Department of Biology Evolutionary Ecology Group University of Antwerp Antwerp Belgium
- Royal Belgian Institute of Natural Sciences (RBINS: Taxonomy and Phylogeny & JEMU) Brussels Belgium
| | - Kurt Jordaens
- Royal Museum for Central Africa (RMCA: Entomology Section & JEMU) Tervuren Belgium
| | - Niels Van Steenkiste
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
- Departments of Botany and Zoology University of British Columbia Vancouver BC Canada
| | - Floris C. Breman
- Royal Belgian Institute of Natural Sciences (RBINS: Taxonomy and Phylogeny & JEMU) Brussels Belgium
| | - Karen Smeets
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Tom Artois
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
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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: 23] [Impact Index Per Article: 7.7] [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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Abstract
Members of the following marine annelid families are found almost exclusively in the interstitial environment and are highly adapted to move between sand grains, relying mostly on ciliary locomotion: Apharyngtidae n. fam., Dinophilidae, Diurodrilidae, Nerillidae, Lobatocerebridae, Parergodrilidae, Polygordiidae, Protodrilidae, Protodriloididae, Psammodrilidae and Saccocirridae. This article provides a review of the evolution, systematics, and diversity of these families, with the exception of Parergodrilidae, which was detailed in the review of Orbiniida by Meca, Zhadan, and Struck within this Special Issue. While several of the discussed families have previously only been known by a few described species, recent surveys inclusive of molecular approaches have increased the number of species, showing that all of the aforementioned families exhibit a high degree of cryptic diversity shadowed by a limited number of recognizable morphological traits. This is a challenge for studies of the evolution, taxonomy, and diversity of interstitial families as well as for their identification and incorporation into ecological surveys. By compiling a comprehensive and updated review on these interstitial families, we hope to promote new studies on their intriguing evolutionary histories, adapted life forms and high and hidden diversity.
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Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ 2021; 9:e10896. [PMID: 33614296 PMCID: PMC7879940 DOI: 10.7717/peerj.10896] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
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Affiliation(s)
- José Cerca
- Department of Environmental Science, Policy, and Management, University of California, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Angel G. Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
| | - Mafalda S. Ferreira
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
- Departamento de Biologia, Universidade do Porto, Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Porto, Portugal
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
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Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview. DIVERSITY-BASEL 2021. [DOI: 10.3390/d13020036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.
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17
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The Early Branching Group of Orbiniida Sensu Struck et al., 2015: Parergodrilidae and Orbiniidae. DIVERSITY 2021. [DOI: 10.3390/d13010029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review addresses the state of the art of the systematics and the improvements in the biology, ecology and species diversity of the two annelid taxa Parergodrilidae and Orbiniidae, the early branching group of Orbiniida sensu Struck et al., 2015 according to molecular studies. An effort to identify gaps of knowledge is given to understand the distribution, dispersal and the diversity Parergodrilidae and Orbiniidae hold, as well as to give several directions for future research. Parergodrilidae is a taxon of interstitial annelids constituted by the terrestrial Parergodrilus heideri (monotypic genus up to date), reported throughout Europe but also in Korea and North America, and the genus Stygocapitella, which includes eleven species from the upper shore of sandy beaches distributed along Europe and other regions of the world. Orbiniidae contains more than 200 described species spread over 20 valid genera, varying in size from a few millimeters up to 30 cm, distributed globally and living in a wide variety of soft bottoms. Improving the knowledge on these two sister-taxa is crucial for the understanding of the evolution to interstitial forms by progenesis in Annelida.
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Gąsiorek P, Oczkowski A, Blagden B, Kristensen RM, Bartels PJ, Nelson DR, Suzuki AC, Michalczyk Ł. New Asian and Nearctic Hypechiniscus species (Heterotardigrada: Echiniscidae) signalize a pseudocryptic horn of plenty. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The cosmopolitan echiniscid genus Hypechiniscus contains exclusively rare species. In this contribution, by combining statistical morphometry and molecular phylogeny, we present qualitative and quantitative aspects of Hypechiniscus diversity, which remained hidden under the two purportedly cosmopolitan species: H. gladiator and H. exarmatus. A neotype is designated for H. gladiator from Creag Meagaidh (Scotland), and an informal re-description is provided for H. exarmatus based on animals from Creag Meagaidh and the Isle of Skye (Inner Hebrides). Subspecies/forms of H. gladiator are suppressed due to the high developmental variability of the cirrus dorsalis. At the same time, four species of the genus are described: H. daedalus sp. nov. from Roan Mountain and the Great Smoky Mountains (Southern Appalachian Mountains, USA), H. flavus sp. nov. and H. geminus sp. nov. from the Yatsugatake Mountains (Honshu, Japan), and H. cataractus sp. nov. from the Malay Archipelago (Borneo and the Moluccas). Dorsal and ventral sculpturing, together with morphometric traits, are shown to be the key characters that allow for the phenotypic discrimination of species within the genus. Furthermore, the morphology of Hypechiniscus is discussed and compared to that of the most similar genera, Pseudechiniscus and Stellariscus. Finally, a diagnostic key to all recognized Hypechiniscus species is provided.
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Affiliation(s)
- Piotr Gąsiorek
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - Artur Oczkowski
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - Brian Blagden
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - Reinhardt M Kristensen
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, Copenhagen Ø, Denmark
| | - Paul J Bartels
- Department of Biology, Warren Wilson College, Asheville, NC, USA
| | - Diane R Nelson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA
| | | | - Łukasz Michalczyk
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa, Kraków, Poland
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Hedenäs L. Cryptic and morphologically recognizable species diversity within Scandinavian Plagiopus oederianus (Bryophyta: Bartramiaceae). LINDBERGIA 2020. [DOI: 10.25227/linbg.01130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Lars Hedenäs
- L. Hedenäs ✉ , Dept of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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20
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Grosse M, Bakken T, Nygren A, Kongsrud JA, Capa M. Species delimitation analyses of NE Atlantic Chaetozone (Annelida, Cirratulidae) reveals hidden diversity among a common and abundant marine annelid. Mol Phylogenet Evol 2020; 149:106852. [PMID: 32417496 DOI: 10.1016/j.ympev.2020.106852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 01/04/2023]
Abstract
The polychaetes of the family Cirratulidae (Annelida) are common inhabitants in continental shelf benthic environments and considered an important group of organisms in environmental monitoring surveys. The family represents a taxonomic and systematic challenge, as monophyly of genera and evolutionary relationships within the family remain to be explored in a proper phylogenetic framework. Bitentaculate cirratulids, especially the genus Chaetozone, form one of the most species-diverse group of polychaetes worldwide. In this study, we aimed at evaluating the species diversity of the genus Chaetozonein benthic environments in the North East Atlantic by molecular means. We tested whether traditional morphological diagnostic characters are able to discriminate between the species hypothesis after species delimitation analyses, and assessed monophyly of the genera involved. Two DNA markers were sequenced from about 200 specimens belonging to Chaetozone, Aphelochaeta, Dodecaceria, Cirriformia and Cirratulus - the universal mitochondrial barcoding region COI, and the D1-D2 regions of the nuclear 28S rRNA - and analyzed with Bayesian inference, Maximum Likelihood and the species delimitation methods mPTP and GMYC. The first phylogeny of the family Cirratulidae is inferred and the genera Chaetozone, Dodecaceria and Cirratulus are recovered monophyletic. A total of 14 clusters of sequences - corresponding to species of Chaetozone - were found in the study area, and only one of them is here referred to a nominal species, Chaetozone setosa. Our results reveal several species complexes in the genus Chaetozone, that some of these independent lineages are unnamed and undescribed, and that morphological diagnostic features are in most cases unable to discriminate between the most similar species.
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Affiliation(s)
- Maël Grosse
- Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway; University of the Balearic Island, Department of Biology, Ctra. Valldemossa km 7.5, Balearic Islands, Spain.
| | - Torkild Bakken
- Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
| | - Arne Nygren
- Institutionen för marina vetenskaper, Göteborgs Universitet, Göteborg, Sweden
| | - Jon A Kongsrud
- Department of Natural History, University Museum of Bergen, Bergen, Norway
| | - María Capa
- University of the Balearic Island, Department of Biology, Ctra. Valldemossa km 7.5, Balearic Islands, Spain; Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
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