1
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Callaghan CT, Borda-de-Água L, van Klink R, Rozzi R, Pereira HM. Unveiling global species abundance distributions. Nat Ecol Evol 2023; 7:1600-1609. [PMID: 37667000 PMCID: PMC10555817 DOI: 10.1038/s41559-023-02173-y] [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: 04/29/2023] [Accepted: 07/18/2023] [Indexed: 09/06/2023]
Abstract
Whether most species are rare or have some intermediate abundance is a long-standing question in ecology. Here, we use more than one billion observations from the Global Biodiversity Information Facility to assess global species abundance distributions (gSADs) of 39 taxonomic classes of eukaryotic organisms from 1900 to 2019. We show that, as sampling effort increases through time, the shape of the gSAD is unveiled; that is, the shape of the sampled gSAD changes, revealing the underlying gSAD. The fraction of species unveiled for each class decreases with the total number of species in that class and increases with the number of individuals sampled, with some groups, such as birds, being fully unveiled. The best statistical fit for almost all classes was the Poisson log-normal distribution. This strong evidence for a universal pattern of gSADs across classes suggests that there may be general ecological or evolutionary mechanisms governing the commonness and rarity of life on Earth.
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Affiliation(s)
- Corey T Callaghan
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany.
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, USA.
| | - Luís Borda-de-Água
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Roel van Klink
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Department of Computer Science, Martin Luther University-Halle Wittenberg, Halle, Germany
| | - Roberto Rozzi
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Zentralmagazin Naturwissenschaftlicher Sammlungen, Martin Luther University, Halle, Germany
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Henrique M Pereira
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
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2
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Hartebrodt L, Wilson S, Costello MJ. Progress in the discovery of isopods (Crustacea: Peracarida)-is the description rate slowing down? PeerJ 2023; 11:e15984. [PMID: 37692117 PMCID: PMC10484202 DOI: 10.7717/peerj.15984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Taxonomic species are the best standardised metric of biodiversity. Therefore, there is broad scientific and public interest in how many species have already been named and how many more may exist. Crustaceans comprise about 6% of all named animal species and isopods about 15% of all crustaceans. Here, we review progress in the naming of isopods in relation to the number of people describing new species and estimate how many more species may yet be named by 2050 and 2100, respectively. In over two and a half centuries of discovery, 10,687 isopod species in 1,557 genera and 141 families have been described by 755 first authors. The number of authors has increased over time, especially since the 1950s, indicating increasing effort in the description of new species. Despite that the average number of species described per first author has declined since the 1910s, and the description rate has slowed down over the recent decades. Authors' publication lifetimes did not change considerably over time, and there was a distinct shift towards multi-authored publications in recent decades. Estimates from a non-homogeneous renewal process model predict that an additional 660 isopod species will be described by 2100, assuming that the rate of description continues at its current pace.
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Affiliation(s)
- Lena Hartebrodt
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Simon Wilson
- School of Computer Science and Statistics, University of Dublin, Trinity College, Dublin, Ireland
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3
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Dillon EM, Dunne EM, Womack TM, Kouvari M, Larina E, Claytor JR, Ivkić A, Juhn M, Carmona PSM, Robson SV, Saha A, Villafaña JA, Zill ME. Challenges and directions in analytical paleobiology. PALEOBIOLOGY 2023; 49:377-393. [PMID: 37809321 PMCID: PMC7615171 DOI: 10.1017/pab.2023.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.
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Affiliation(s)
- Erin M. Dillon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, U.S.A.; Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Emma M. Dunne
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tom M. Womack
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Miranta Kouvari
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Ekaterina Larina
- Jackson School of Geosciences, University of Texas, Austin, Texas 78712, U.S.A
| | - Jordan Ray Claytor
- Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A; Burke Museum of Natural History and Culture, Seattle, Washington 98195, U.S.A
| | - Angelina Ivkić
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2,1090 Vienna, Austria
| | - Mark Juhn
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, U.S.A
| | - Pablo S. Milla Carmona
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Geológicas, Buenos Aires C1428EGA, Argentina; Instituto de Estudios Andinos “Don Pablo Groeber” (IDEAN, UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Selina Viktor Robson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Anwesha Saha
- Institute of Palaeobiology, Polish Academy of Sciences, ul. Twarda 51/55, 00-818 Warsaw, Poland; Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Jaime A. Villafaña
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria; Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O ‘Higgins, Santiago 8370993, Chile
| | - Michelle E. Zill
- Department of Earth and Planetary Sciences, University of California Riverside, Riverside, California 92521, U.S.A
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4
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Jossart Q, Bauman D, Moreau CV, Saucède T, Christiansen H, Brasier MJ, Convey P, Downey R, Figuerola B, Martin P, Norenburg J, Rosenfeld S, Verheye M, Danis B. A pioneer morphological and genetic study of the intertidal fauna of the Gerlache Strait (Antarctic Peninsula). ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:514. [PMID: 36973586 DOI: 10.1007/s10661-023-11066-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The underexplored intertidal ecosystems of Antarctica are facing rapid changes in important environmental factors. Associated with temperature increase, reduction in coastal ice will soon expose new ice-free areas that will be colonized by local or distant biota. To enable detection of future changes in faunal composition, a biodiversity baseline is urgently required. Here, we evaluated intertidal faunal diversity at 13 locations around the Gerlache Strait (western Antarctic Peninsula), using a combination of a quadrat approach, morphological identification and genetic characterization. Our data highlight a community structure comprising four generally distributed and highly abundant species (the flatworm Obrimoposthia wandeli, the bivalve Kidderia subquadrata, and the gastropods Laevilitorina umbilicata and Laevilitorina caliginosa) as well as 79 rarer and less widely encountered species. The most abundant species thrive in the intertidal zone due to their ability to either survive overwinter in situ or to rapidly colonize this zone when conditions allow. In addition, we confirmed the presence of multiple trophic levels at nearly all locations, suggesting that complex inter-specific interactions occur within these communities. Diversity indices contrasted between sampling locations (from 3 to 32 species) and multivariate approaches identified three main groups. This confirms the importance of environmental heterogeneity in shaping diversity patterns within the investigated area. Finally, we provide the first genetic and photographic baseline of the Antarctic intertidal fauna (106 sequences, 137 macrophotographs), as well as preliminary insights on the biogeography of several species. Taken together, these results provide a timely catalyst to assess the diversity and to inform studies of the potential resilience of these intertidal communities.
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Affiliation(s)
- Quentin Jossart
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Marine Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
- UMR CNRS 6282, Université de Bourgogne, Dijon, France.
| | - David Bauman
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, Montpellier, IRD, France
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Camille Ve Moreau
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Madeleine J Brasier
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Peter Convey
- British Antarctic Survey, NERC, Cambridge, United Kingdom
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
- Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (MI-BASE), Santiago, Chile
| | - Rachel Downey
- Fenner School of Environment & Society, Australian National University, Canberra, Australia
| | | | - Patrick Martin
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Jon Norenburg
- Smithsonian Institution National Museum of Natural History, Washington, United States of America
| | - Sebastian Rosenfeld
- Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (MI-BASE), Santiago, Chile
- Laboratorio de Ecosistemas Marinos Antarticos y Subantarticos, Universidad de Magallanes, Punta Arenas, Chile
- Centro de Investigación Gaia‑Antártica, Universidad de Magallanes, Punta Arenas, Chile
| | - Marie Verheye
- Laboratory of Trophic and Isotopes Ecology (LETIS), Université de Liège, Liège, Belgium
- Laboratory of Evolutionary Ecology, Université de Liège, Liège, Belgium
| | - Bruno Danis
- Marine Biology, Université Libre de Bruxelles (ULB), Brussels, Belgium
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5
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Kessel GM, Alderslade P, Bilewitch JP, Schnabel KE, Gardner JPA. The use of integrative taxonomy in Octocorallia (Cnidaria: Anthozoa): a literature survey. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abstract
Octocorals are problematic in their systematics, and the extent of their biodiversity is poorly understood. Integrative taxonomy (the use of two or more lines of evidence for the delimitation and description of taxa) is seen as a promising way to produce more robust species hypotheses and achieve taxonomic progress in this group. However, many octocoral descriptions continue to rely on morphological evidence alone, and the prevalence of integrative methods is unclear. Here, a literature survey was conducted to gain an overview of historical description rates and to examine trends in the publication of integrative descriptions between the years 2000 and 2020. We find that recent description rates are among the highest in the history of octocoral taxonomy, and although increasing, integrative taxon descriptions remain in the minority overall. We also find that integrative taxonomy has been applied unevenly across octocoral groups and geographical regions. Description rates show no signs of slowing, and no ceiling of total species richness has yet come into view. Coupled with a continued overreliance on morphological variation, particularly at the species level, this suggests that we might be adding to the workload of taxa requiring future revision faster than such instances can be resolved.
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Affiliation(s)
- Gustav M Kessel
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
| | - Philip Alderslade
- CSIRO Oceans and Atmosphere , Castray Esplanade, Hobart, TAS 7000 , Australia
| | - Jaret P Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Kareen E Schnabel
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Jonathan P A Gardner
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
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6
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Ranasinghe UGSL, Eberle J, Thormann J, Bohacz C, Benjamin SP, Ahrens D. Multiple species delimitation approaches with
COI
barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae). Ecol Evol 2022; 12:e8942. [PMID: 35600695 PMCID: PMC9120212 DOI: 10.1002/ece3.8942] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 11/07/2022] Open
Abstract
DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.
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Affiliation(s)
| | - Jonas Eberle
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- University of Salzburg Salzburg Austria
| | - Jana Thormann
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Suresh P. Benjamin
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- National Institute of Fundamental Studies Kandy Sri Lanka
| | - Dirk Ahrens
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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7
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Lum D, Rheindt FE, Chisholm RA. Tracking scientific discovery of avian phylogenetic diversity over 250 years. Proc Biol Sci 2022; 289:20220088. [PMID: 35440208 PMCID: PMC9019523 DOI: 10.1098/rspb.2022.0088] [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] [Indexed: 11/24/2022] Open
Abstract
Estimating the total number of species on Earth has been a longstanding pursuit. Models project anywhere between 2 and 10 million species, and discovery of new species continues to the present day. Despite this, we hypothesized that our current knowledge of phylogenetic diversity (PD) may be almost complete because new discoveries may be less phylogenetically distinct than past discoveries. Focusing on birds, which are well studied, we generated a robust phylogenetic tree for most extant species by combining existing published trees and calculated each discovery's marginal contribution to known PD since the first formal species descriptions in 1758. We found that PD contributions began to plateau in the early 1900s, about half a century earlier than species richness. Relative contributions of each phylogenetic order to known PD shifted over the first 150 years, with a growing contribution of the hyper-diverse perching birds (Passeriformes) in particular, but after the early 1900s this has remained relatively stable. Altogether, this suggests that our knowledge of the evolutionary history of extant birds is mostly complete, with few discoveries of high evolutionary novelty left to be made, and that conclusions of studies using avian phylogenies are likely to be robust to future species discoveries.
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Affiliation(s)
- Deon Lum
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore
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8
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Poulin R, Presswell B. Is parasite taxonomy really in trouble? A quantitative analysis. Int J Parasitol 2022; 52:469-474. [DOI: 10.1016/j.ijpara.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/25/2022]
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9
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Brown MK, Gibbons MJ. Null models for null hypotheses in taxonomy: a test using Scyphozoa. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Although molecular tools are becoming more important in the delineation of scyphozoan species there is, perforce, a need to substantiate new species definitions using morphological data. Access to type material is often difficult and detailed, raw morphometric data are rarely provided in older type descriptions, which makes comparisons of new with old challenging. Here, we use null models based on simple measures of central tendency to generate morphometric data sets for four species of Aurelia, three species of Chrysaora and two species of Crambionella. The results of PERMANOVA and CAP analyses indicate no significant differences between random and real data within species, but significant differences between congeneric species (null or real), suggesting that this multivariate approach may be a useful tool for defining species when comparative data are scant.
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Affiliation(s)
- Michael K Brown
- Biodiversity and Conservation Biology, University of the Western Cape, Belville, Western Cape, South Africa
| | - Mark J Gibbons
- Biodiversity and Conservation Biology, University of the Western Cape, Belville, Western Cape, South Africa
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10
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Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glaw F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner SS, Vences M. Repositories for Taxonomic Data: Where We Are and What is Missing. Syst Biol 2020; 69:1231-1253. [PMID: 32298457 PMCID: PMC7584136 DOI: 10.1093/sysbio/syaa026] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/20/2020] [Accepted: 03/24/2020] [Indexed: 12/05/2022] Open
Abstract
Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].
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Affiliation(s)
- Aurélien Miralles
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Teddy Bruy
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Katherine Wolcott
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mark D Scherz
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Biology, Universität Konstanz, Universitätstraße 10, 78464 Konstanz, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Bank Beszteri
- Department of Phycology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Center of Excellence in Plant Sciences (CEPLAS), Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674 Köln, Germany
| | - Janine Felden
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Leobenerstraße 8, 28359 Bremen, Germany
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Birgit Gemeinholzer
- Department of Systematic Botany, Justus Liebig University Gießen, Heinrich-Buff Ring 38, 35392 Giessen, Germany
| | - Frank Glaw
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Frank Oliver Glöckner
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Oliver Hawlitschek
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Scientific Infrastructure, Centrum für Naturkunde (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ivaylo Kostadinov
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Center of Biotechnology (CeBiTec), Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
| | - Christian Printzen
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Jasmin Renz
- Zooplankton Research Group, DZMB – Senckenberg am Meer, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Nataliya Rybalka
- Department of Experimental Phycology and Culture Collection of Algae, University Göttingen, Nikolausberger-Weg 18, 37073 Göttingen, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Tanja Weibulat
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Gießen, Heinrich-Buff Ring 26, 35392 Giessen, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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11
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Jossart Q, Kochzius M, Danis B, Saucède T, Moreau CVE. Diversity of the Pterasteridae (Asteroidea) in the Southern Ocean: a molecular and morphological approach. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
An integrative approach is crucial in discrimination of species, especially for taxa that are difficult to identify based on morphological characters. In this study, we combine genetics and morphology to assess the diversity of Pterasteridae, a sea star family diversified in deep-sea and polar environments. Because of their derived anatomy and the frequent loss of characters during preservation, Pterasteridae are a suitable case for an integrative study. The molecular identification of 191 specimens (mostly from the Southern Ocean) suggests 26–33 species in three genera (Diplopteraster, Hymenaster and Pteraster), which match the morphological identification in 54–62% of cases. The mismatches are either different molecular units that are morphologically indistinguishable (e.g. Pteraster stellifer units 2 and 4) or, conversely, nominal species that are genetically identical (e.g. Hymenaster coccinatus/densus/praecoquis). Several species are shared between the Northern and Southern Hemispheres (e.g. Pteraster jordani/affinis). In conclusion, the taxonomic status of some groups is confirmed, but for others we find the need to re-evaluate the taxonomy at both genus and species levels. This work significantly increases the DNA barcode library of the Southern Ocean species and merges taxonomic information into an identification key that could become a baseline for future studies (pterasteridae-so.identificationkey.org).
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Affiliation(s)
- Quentin Jossart
- Marine Biology, Ecology and Biodiversity, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology, Ecology and Biodiversity, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Bruno Danis
- Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Thomas Saucède
- Biogéosciences, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Camille V E Moreau
- Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Biogéosciences, Université Bourgogne Franche Comté (UBFC), Dijon, France
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12
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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13
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Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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14
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Systematics Association Special Volumes. Cladistics 2020. [DOI: 10.1017/9781139047678.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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15
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Relationship Diagrams. Cladistics 2020. [DOI: 10.1017/9781139047678.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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16
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The Separation of Classification and Phylogenetics. Cladistics 2020. [DOI: 10.1017/9781139047678.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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17
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Beyond Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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18
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The Interrelationships of Organisms. Cladistics 2020. [DOI: 10.1017/9781139047678.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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19
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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20
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Modern Artificial Methods and Raw Data. Cladistics 2020. [DOI: 10.1017/9781139047678.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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21
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Further Myths and More Misunderstandings. Cladistics 2020. [DOI: 10.1017/9781139047678.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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22
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Afterword. Cladistics 2020. [DOI: 10.1017/9781139047678.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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23
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Systematics: Exposing Myths. Cladistics 2020. [DOI: 10.1017/9781139047678.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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24
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Essentialism and Typology. Cladistics 2020. [DOI: 10.1017/9781139047678.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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25
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Beyond Classification: How to Study Phylogeny. Cladistics 2020. [DOI: 10.1017/9781139047678.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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26
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How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data. Cladistics 2020. [DOI: 10.1017/9781139047678.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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27
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What This Book Is About. Cladistics 2020. [DOI: 10.1017/9781139047678.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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28
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How to Study Classification. Cladistics 2020. [DOI: 10.1017/9781139047678.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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29
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The Cladistic Programme. Cladistics 2020. [DOI: 10.1017/9781139047678.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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30
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Index. Cladistics 2020. [DOI: 10.1017/9781139047678.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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31
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Parameters of Classification: Ordo Ab Chao. Cladistics 2020. [DOI: 10.1017/9781139047678.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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32
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Monothetic and Polythetic Taxa. Cladistics 2020. [DOI: 10.1017/9781139047678.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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33
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How to Study Classification: Consensus Techniques and General Classifications. Cladistics 2020. [DOI: 10.1017/9781139047678.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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34
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Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly. Cladistics 2020. [DOI: 10.1017/9781139047678.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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35
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Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes. Cladistics 2020. [DOI: 10.1017/9781139047678.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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36
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Preface. Cladistics 2020. [DOI: 10.1017/9781139047678.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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37
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Poulin R, Presswell B, Jorge F. The state of fish parasite discovery and taxonomy: a critical assessment and a look forward. Int J Parasitol 2020; 50:733-742. [PMID: 32151615 DOI: 10.1016/j.ijpara.2019.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/05/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Efforts to find and characterise new parasite species in fish hosts are crucial not just to complete our inventory of Earth's biodiversity, but also to monitor and mitigate disease threats in fisheries and aquaculture in the face of global climate change. Here, we review recent quantitative assessments of research efforts into fish parasite discovery and taxonomy. We address broad questions including: Are efforts aimed at finding new parasite species targeted at geographical hotspots of fish biodiversity, where there should be more parasite species to be found? Is the application of molecular tools to study parasite genetic diversity deployed strategically across regions of the world, or focused disproportionately on certain areas? How well coordinated is the search for new parasite species of fish among workers specialising on different higher helminth taxa? Are parasite discovery efforts in any geographical area consistent over time, or subject to idiosyncrasies due to the waxing and waning of highly prolific research careers? Is the quality of taxonomic descriptions of new species improving over time, with the incorporation of new tools to characterise species? Are taxonomic descriptions moving away from a focus on the adult stage only toward attempts to characterise the full life cycle of newly-discovered helminth species? By using empirical evidence to answer these questions, we assess the current state of research into fish parasite discovery and taxonomy. We also explore the far-reaching implications of recent research on parasite microbiomes for parasite taxonomy. We end with recommendations aimed at maximising the knowledge gained per fish sacrificed, and per dollar and time invested into research on fish parasite biodiversity.
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Affiliation(s)
- Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
| | - Bronwen Presswell
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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38
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Abstract
The use of the "integrative approach" for classification of organisms since its formal establishment in 2005 has become a recurrent theme of zoosystematics. A bibliometric survey of the publications on integrative taxonomy of animals, which is aimed at exploring the most popular areas of research and characterizing the practical systematists' attitudes to this new approach, is presented. An analysis of 582 papers, which appeared between 2005 and 2017 in journals indexed by Scopus and the Web of Science Core Collection, has illustrated the gradual growth of the popularity of integrative taxonomy as well as some biases in the representation of higher taxa in "integrated" studies. It has been shown that the "integrative" papers have more chance of appearing in a top-ranking journal and gain relatively more citations as compared with non-integrative papers. The obtained results are discussed in the context of the "taxonomic impediment" problem thought to be a consequence of the institutional crisis of traditional taxonomy, which has been vividly debated over the past decades.
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Affiliation(s)
- Maxim V Vinarski
- Laboratory of Macroecology and Biogeography of Invertebrates, Saint-Petersburg State University, Saint-Petersburg, Russia
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39
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Hofstetter V, Buyck B, Eyssartier G, Schnee S, Gindro K. The unbearable lightness of sequenced-based identification. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00428-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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40
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Abstract
Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a “biodiversity knowledge graph” for the Australian fauna. The data cleaning and reconciliation steps involved in constructing the knowledge graph are described in detail. Examples are given of its application to understanding changes in patterns of taxonomic publication over time. A web interface to the knowledge graph (called “Ozymandias”) is available at https://ozymandias-demo.herokuapp.com.
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41
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Cryptic diversity in Brazilian endemic monkey frogs (Hylidae, Phyllomedusinae, Pithecopus) revealed by multispecies coalescent and integrative approaches. Mol Phylogenet Evol 2019; 132:105-116. [DOI: 10.1016/j.ympev.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/22/2022]
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42
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Conix S. Radical pluralism, classificatory norms and the legitimacy of species classifications. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2019; 73:27-34. [PMID: 30429047 DOI: 10.1016/j.shpsc.2018.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/16/2018] [Accepted: 11/03/2018] [Indexed: 06/09/2023]
Abstract
Moderate pluralism is a popular position in contemporary philosophy of biology. Despite its popularity, various authors have argued that it tends to slide off into a radical form of pluralism that is both normatively and descriptively unacceptable. This paper looks at the case of biological species classification, and evaluates a popular way of avoiding radical pluralism by relying on the shared aims and norms of a discipline. The main contention is that while these aims and norms may play an important role in the legitimacy of species classifications, they fail to fend off radical pluralism. It follows from this that the legitimacy of species classifications is also determined by local decisions about the aims of research and how to operationalize and balance these. This is important, I argue, because it means that any acceptable view on the legitimacy of classification should be able to account for these local decisions.
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Affiliation(s)
- Stijn Conix
- Centre for Logic and Philosophy of Science, KU Leuven, Andreas Vesaliusstraat 2, 3000, Leuven, Belgium.
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43
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Vaidya G, Lepage D, Guralnick R. The tempo and mode of the taxonomic correction process: How taxonomists have corrected and recorrected North American bird species over the last 127 years. PLoS One 2018; 13:e0195736. [PMID: 29672539 PMCID: PMC5909608 DOI: 10.1371/journal.pone.0195736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
While studies of taxonomy usually focus on species description, there is also a taxonomic correction process that retests and updates existing species circumscriptions on the basis of new evidence. These corrections may themselves be subsequently retested and recorrected. We studied this correction process by using the Check-List of North and Middle American Birds, a well-known taxonomic checklist that spans 130 years. We identified 142 lumps and 95 splits across sixty-three versions of the Check-List and found that while lumping rates have markedly decreased since the 1970s, splitting rates are accelerating. We found that 74% of North American bird species recognized today have never been corrected (i.e., lumped or split) over the period of the checklist, while 16% have been corrected exactly once and 10% have been corrected twice or more. Since North American bird species are known to have been extensively lumped in the first half of the 20th century with the advent of the biological species concept, we determined whether most splits seen today were the result of those lumps being recorrected. We found that 5% of lumps and 23% of splits fully reverted previous corrections, while a further 3% of lumps and 13% of splits are partial reversions. These results show a taxonomic correction process with moderate levels of recorrection, particularly of previous lumps. However, 81% of corrections do not revert any previous corrections, suggesting that the majority result in novel circumscriptions not previously recognized by the Check-List. We could find no order or family with a significantly higher rate of correction than any other, but twenty-two genera as currently recognized by the AOU do have significantly higher rates than others. Given the currently accelerating rate of splitting, prediction of the end-point of the taxonomic recorrection process is difficult, and many entirely new taxonomic concepts are still being, and likely will continue to be, proposed and further tested.
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Affiliation(s)
- Gaurav Vaidya
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail:
| | - Denis Lepage
- Bird Studies Canada, Port Rowan, Ontario, Canada
| | - Robert Guralnick
- Department of Natural History and the Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
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44
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Abstract
Marine biogeographic realms have been inferred from small groups of species in particular environments (e.g., coastal, pelagic), without a global map of realms based on statistical analysis of species across all higher taxa. Here we analyze the distribution of 65,000 species of marine animals and plants, and distinguish 30 distinct marine realms, a similar proportion per area as found for land. On average, 42% of species are unique to the realms. We reveal 18 continental-shelf and 12 offshore deep-sea realms, reflecting the wider ranges of species in the pelagic and deep-sea compared to coastal areas. The most widespread species are pelagic microscopic plankton and megafauna. Analysis of pelagic species recognizes five realms within which other realms are nested. These maps integrate the biogeography of coastal and deep-sea, pelagic and benthic environments, and show how land-barriers, salinity, depth, and environmental heterogeneity relate to the evolution of biota. The realms have applications for marine reserves, biodiversity assessments, and as an evolution relevant context for climate change studies.
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45
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Costello MJ, Chaudhary C. Marine Biodiversity, Biogeography, Deep-Sea Gradients, and Conservation. Curr Biol 2017; 27:R511-R527. [DOI: 10.1016/j.cub.2017.04.060] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Edie SM, Smits PD, Jablonski D. Probabilistic models of species discovery and biodiversity comparisons. Proc Natl Acad Sci U S A 2017; 114:3666-3671. [PMID: 28325881 PMCID: PMC5389289 DOI: 10.1073/pnas.1616355114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inferring large-scale processes that drive biodiversity hinges on understanding the phylogenetic and spatial pattern of species richness. However, clades and geographic regions are accumulating newly described species at an uneven rate, potentially affecting the stability of currently observed diversity patterns. Here, we present a probabilistic model of species discovery to assess the uncertainty in diversity levels among clades and regions. We use a Bayesian time series regression to estimate the long-term trend in the rate of species description for marine bivalves and find a distinct spatial bias in the accumulation of new species. Despite these biases, probabilistic estimates of future species richness show considerable stability in the currently observed rank order of regional diversity. However, absolute differences in richness are still likely to change, potentially modifying the correlation between species numbers and geographic, environmental, and biological factors thought to promote biodiversity. Applied to scallops and related clades, we find that accumulating knowledge of deep-sea species will likely shift the relative richness of these three families, emphasizing the need to consider the incomplete nature of bivalve taxonomy in quantitative studies of its diversity. Along with estimating expected changes to observed patterns of diversity, the model described in this paper pinpoints geographic areas and clades most urgently requiring additional systematic study-an important practice for building more complete and accurate models of biodiversity dynamics that can inform ecological and evolutionary theory and improve conservation practice.
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Affiliation(s)
- Stewart M Edie
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637;
| | - Peter D Smits
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637;
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637
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47
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Mateos E, Sluys R, Riutort M, Álvarez-Presas M. Species richness in the genus Microplana (Platyhelminthes, Tricladida, Microplaninae) in Europe: as yet no asymptote in sight. INVERTEBR SYST 2017. [DOI: 10.1071/is16038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study forms a major step towards a comprehensive morphological and molecular analysis of the species diversity of European microplanid land planarians. It presents a molecular phylogenetic tree on the basis of information from the genes Cox1, 18S, 28S and elongation factor 1-α, and applies molecular and morphological species delimitation methodologies for Microplana specimens sampled over a wide geographic range within Europe. The study suggests that as yet there is no plateau or asymptote in the accumulation curve for European Microplana species, as our results facilitated an integrative delimitation of seven new species as well as the diagnosis of new populations of three already known species and one doubtful or problematic species. In some cases, the new records considerably enlarged the known range of a species. An integrative account is provided of each of these species. Molecular sequence information on newly collected land flatworms may quickly point the planarian systematist to taxa that need to be examined morphologically and thus may considerably reduce laborious and time-consuming histological analyses.
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48
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Deng J, Li K, Chen C, Wu S, Huang X. Discovery pattern and species number of scale insects (Hemiptera: Coccoidea). PeerJ 2016; 4:e2526. [PMID: 27703864 PMCID: PMC5047223 DOI: 10.7717/peerj.2526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/04/2016] [Indexed: 11/30/2022] Open
Abstract
Few investigations have been made of the species description trend of scale insects. The present study reports the discovery pattern and taxonomic efforts for this group based on global species and a literature dataset. In addition, three asymptotic models (Logistic, Gompertz, and Extreme Value) based on a discovery curve were used to predict the species number of scale insects. Our results showed that the species description rate has been changing over time, with certain peaks and valleys in the past 250 years. The mean number of species described per year was 30, with the highest number of 195 described species in 1985. The increasing number of authors and the almost constant proportion of species described by 10% most prolific authors since the 1900s suggested that taxonomic effort has been increasing over time. The Gompertz model with lowest AIC value suggested that there are about 10,450 species of scale insects on Earth, nearly 30% of which remain to be described. Our study offers insights into the discovery pattern of scale insect diversity.
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Affiliation(s)
- Jun Deng
- College of Plant Protection, Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Kunming Li
- College of Economics, Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Cui Chen
- College of Plant Protection, Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Sanan Wu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University , Beijing , China
| | - Xiaolei Huang
- College of Plant Protection, Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
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49
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Costello MJ. Parasite Rates of Discovery, Global Species Richness and Host Specificity. Integr Comp Biol 2016; 56:588-99. [PMID: 27400977 DOI: 10.1093/icb/icw084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
If every metazoan species has at least one host-specific parasite, as several local scale studies have suggested, then half of all species could be parasites. However, host specificity varies significantly depending on host phylogeny, body size, habitat, and geographic distribution. The best studied hosts tend to be vertebrates, larger animals, and/or widespread, and thus have a higher number of parasites and host-specific parasites. Thus, host specificity for these well-known taxa cannot be simply extrapolated to other taxa, notably invertebrates, small sized, and more endemic species, which comprise the major portion of yet to be discovered species. At present, parasites of animals comprise about 5% of named species. This article analyzed the rate of description of several largely parasitic taxa within crustaceans (copepods, amphipods, isopods, pentastomids, cirripeds), marine helminths (nematodes, acanthocephalans, flukes), gastropod molluscs, insects (ticks, fleas, biting flies, strepispterans), and microsporidia. The period of highest discovery has been most recent for the marine helminths and microsporids. The number of people describing parasites has been increasing since the 1960s, as it has for all other taxa. However, the number of species being described per decade relative to the number of authors has been decreasing except for the helminths. The results indicate that more than half of all parasites have been described, and two-thirds of host taxa, although the proportion varies between taxa. It is highly unlikely that the number of named species of parasites will ever approach that of their hosts. This contrast between the proportion that parasites comprise of local and global faunas suggests that parasites are less host specific and more widespread than local scale studies suggest.
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Affiliation(s)
- Mark John Costello
- Institute of Marine Science, University of Auckland, Auckland, 1142, New Zealand
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Poulin R, Presswell B. Taxonomic Quality of Species Descriptions Varies over Time and with the Number of Authors, but Unevenly among Parasitic Taxa. Syst Biol 2016; 65:1107-1116. [DOI: 10.1093/sysbio/syw053] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/14/2016] [Accepted: 06/01/2016] [Indexed: 11/13/2022] Open
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