1
|
Liu D, Semenchuk P, Essl F, Lenzner B, Moser D, Blackburn TM, Cassey P, Biancolini D, Capinha C, Dawson W, Dyer EE, Guénard B, Economo EP, Kreft H, Pergl J, Pyšek P, van Kleunen M, Nentwig W, Rondinini C, Seebens H, Weigelt P, Winter M, Purvis A, Dullinger S. The impact of land use on non-native species incidence and number in local assemblages worldwide. Nat Commun 2023; 14:2090. [PMID: 37045818 PMCID: PMC10097616 DOI: 10.1038/s41467-023-37571-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
While the regional distribution of non-native species is increasingly well documented for some taxa, global analyses of non-native species in local assemblages are still missing. Here, we use a worldwide collection of assemblages from five taxa - ants, birds, mammals, spiders and vascular plants - to assess whether the incidence, frequency and proportions of naturalised non-native species depend on type and intensity of land use. In plants, assemblages of primary vegetation are least invaded. In the other taxa, primary vegetation is among the least invaded land-use types, but one or several other types have equally low levels of occurrence, frequency and proportions of non-native species. High land use intensity is associated with higher non-native incidence and frequency in primary vegetation, while intensity effects are inconsistent for other land-use types. These findings highlight the potential dual role of unused primary vegetation in preserving native biodiversity and in conferring resistance against biological invasions.
Collapse
Affiliation(s)
- Daijun Liu
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria.
| | - Philipp Semenchuk
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
- Department of Arctic Biology, UNIS-The University Centre in Svalbard, 9171, Longyearbyen, Norway
| | - Franz Essl
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Bernd Lenzner
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Dietmar Moser
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Tim M Blackburn
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Institute of Zoology, Zoological Society of London, London, UK
| | - Phillip Cassey
- Invasion Science and Wildlife Ecology Lab, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Dino Biancolini
- Global Mammal Assessment programme, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
- National Research Council of Italy - Institute for Bioeconomy (CNR-IBE), Via dei Taurini 19, Rome, Italy
| | - César Capinha
- Centro de Estudos Geográficos, Instituto de Geografia e Ordenamento do Território da Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado TERRA, Tapada da Ajuda, 1349-017, Lisboa, Portugal
| | - Wayne Dawson
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Ellie E Dyer
- UK Centre for Ecology and Hydrology, Wallingford, UK
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution, and Environment, University College London, London, UK
| | - Benoit Guénard
- Insect Biodiversity and Biogeography Laboratory, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Rd, Lung Fu Shan, Hong Kong SAR, China
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, 02138, USA
| | - Holger Kreft
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, D-37077, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, D-37077, Göttingen, Germany
| | - Jan Pergl
- Czech Academy of Sciences, Institute of Botany, Department of Invasion Ecology, CZ-252 43, Průhonice, Czech Republic
| | - Petr Pyšek
- Czech Academy of Sciences, Institute of Botany, Department of Invasion Ecology, CZ-252 43, Průhonice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-128 44, Prague, Czech Republic
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Universitätsstrasse 10, D-78457, Konstanz, Germany
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Wolfgang Nentwig
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland
| | - Carlo Rondinini
- Global Mammal Assessment programme, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Hanno Seebens
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Patrick Weigelt
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, D-37077, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, D-37077, Göttingen, Germany
- Campus-Institut Data Science, University of Göttingen, Goldschmidtstraße 1, D-37077, Göttingen, Germany
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- Department of Life Sciences, Imperial College London, Ascot, SL5 7PY, UK
| | - Stefan Dullinger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| |
Collapse
|
2
|
Gorneau JA, Kulkarni S, Cala-Riquelme F, Esposito LA. Measuring What We Don't Know: Biodiversity Catalogs Reveal Bias in Taxonomic Effort. Bioscience 2023. [DOI: 10.1093/biosci/biac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Abstract
Biodiversity catalogs are an invaluable resource for biological research. Efforts to scientifically document biodiversity have not been evenly applied, either because of charisma or because of ease of study. Spiders are among the most precisely cataloged and diverse invertebrates, having surpassed 50,000 described species globally. The World Spider Catalog presents a unique opportunity to assess the disproportionate documentation of spider diversity. In the present article, we develop a taxonomic ratio relating new species descriptions to other taxonomic activity as a proxy for taxonomic effort, using spiders as a case study. We use this taxonomic effort metric to examine biases along multiple axes: phylogeny, zoogeography, and socioeconomics. We also use this metric to estimate the number of species that remain to be described. This work informs arachnologists in identifying high-priority taxa and regions for species discovery and highlights the benefits of maintaining open-access taxonomic databases—a necessary step in overcoming bias and documenting the world's biodiversity.
Collapse
Affiliation(s)
- Jacob A Gorneau
- Biology Department of San Francisco State University , San Francisco, California , United States
| | - Siddharth Kulkarni
- Department of Integrative Biology, University of Wisconsin–Madison , Madison, Wisconsin , United States
| | - Franklyn Cala-Riquelme
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco , California , United States
| | - Lauren A Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco , California , United States
| |
Collapse
|
3
|
Waterhouse RM, Adam-Blondon AF, Agosti D, Baldrian P, Balech B, Corre E, Davey RP, Lantz H, Pesole G, Quast C, Glöckner FO, Raes N, Sandionigi A, Santamaria M, Addink W, Vohradsky J, Nunes-Jorge A, Willassen NP, Lanfear J. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR. F1000Res 2022; 10. [PMID: 35999898 PMCID: PMC9360911 DOI: 10.12688/f1000research.73825.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 12/03/2022] Open
Abstract
Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.
Collapse
Affiliation(s)
- Robert M. Waterhouse
- Department of Ecology and Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Vaud, 1015, Switzerland
| | | | | | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Praha, 142 20, Czech Republic
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, 70126, Italy
| | - Erwan Corre
- CNRS/Sorbonne Université, Station Biologique de Roscoff, Roscoff, 29680, France
| | | | - Henrik Lantz
- Department of Medical Biochemistry and Microbiology/NBIS, Uppsala University, Uppsala, Sweden
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, 70126, Italy
- Department of Biosciences. Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Bari, 70126, Italy
| | - Christian Quast
- Life Sciences & Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| | - Frank Oliver Glöckner
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremerhaven, 27570, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Bremerhaven, 27570, Germany
| | - Niels Raes
- NLBIF - Netherlands Biodiversity Information Facility, Naturalis Biodiversity Center, Leiden, 2300 RA, The Netherlands
| | | | - Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, 70126, Italy
| | - Wouter Addink
- DiSSCo - Distributed System of Scientific Collections, Naturalis Biodiversity Center, Leiden, 2300 RA, The Netherlands
| | - Jiri Vohradsky
- Laboratory of Bioinformatics, Institute of Microbiology, Prague, 142 20, Czech Republic
| | | | | | - Jerry Lanfear
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| |
Collapse
|
4
|
Rivera-Quiroz FA, Petcharad B, Miller JA. Mining data from legacy taxonomic literature and application for sampling spiders of the Teutamus group (Araneae; Liocranidae) in Southeast Asia. Sci Rep 2020; 10:15787. [PMID: 32978432 PMCID: PMC7519673 DOI: 10.1038/s41598-020-72549-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/02/2020] [Indexed: 11/12/2022] Open
Abstract
Taxonomic literature contains information about virtually ever known species on Earth. In many cases, all that is known about a taxon is contained in this kind of literature, particularly for the most diverse and understudied groups. Taxonomic publications in the aggregate have documented a vast amount of specimen data. Among other things, these data constitute evidence of the existence of a particular taxon within a spatial and temporal context. When knowledge about a particular taxonomic group is rudimentary, investigators motivated to contribute new knowledge can use legacy records to guide them in their search for new specimens in the field. However, these legacy data are in the form of unstructured text, making it difficult to extract and analyze without a human interpreter. Here, we used a combination of semi-automatic tools to extract and categorize specimen data from taxonomic literature of one family of ground spiders (Liocranidae). We tested the application of these data on fieldwork optimization, using the relative abundance of adult specimens reported in literature as a proxy to find the best times and places for collecting the species (Teutamus politus) and its relatives (Teutamus group, TG) within Southeast Asia. Based on these analyses we decided to collect in three provinces in Thailand during the months of June and August. With our approach, we were able to collect more specimens of T. politus (188 specimens, 95 adults) than all the previous records in literature combined (102 specimens). Our approach was also effective for sampling other representatives of the TG, yielding at least one representative of every TG genus previously reported for Thailand. In total, our samples contributed 231 specimens (134 adults) to the 351 specimens previously reported in the literature for this country. Our results exemplify one application of mined literature data that allows investigators to more efficiently allocate effort and resources for the study of neglected, endangered, or interesting taxa and geographic areas. Furthermore, the integrative workflow demonstrated here shares specimen data with global online resources like Plazi and GBIF, meaning that others can freely reuse these data and contribute to them in the future. The contributions of the present study represent an increase of more than 35% on the taxonomic coverage of the TG in GBIF based on the number of species. Also, our extracted data represents 72% of the occurrences now available through GBIF for the TG and more than 85% of occurrences of T. politus. Taxonomic literature is a key source of undigitized biodiversity data for taxonomic groups that are underrepresented in the current biodiversity data sphere. Mobilizing these data is key to understanding and protecting some of the less well-known domains of biodiversity.
Collapse
Affiliation(s)
- F Andres Rivera-Quiroz
- Department of Terrestrial Zoology, Understanding Evolution group, Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, The Netherlands.
- Institute of Biology Leiden (IBL), Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
| | - Booppa Petcharad
- Faculty of Science and Technology, Thammasat University, Rangsit, 12121, Pathum Thani, Thailand
| | - Jeremy A Miller
- Department of Terrestrial Zoology, Understanding Evolution group, Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, The Netherlands
- Plazi, Zinggstrasse 16, CH 3007, Bern, Switzerland
| |
Collapse
|
5
|
Miller JA, Freund C, Rambonnet L, Koets L, Barth N, van der Linden C, Geml J, Schilthuizen M, Burger R, Goossens B. Dispatch from the field II: the mystery of the red and blue Opadometa male (Araneae, Tetragnathidae, Opadometa sarawakensis). Biodivers Data J 2018:e24777. [PMID: 29674940 PMCID: PMC5904518 DOI: 10.3897/bdj.6.e24777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/26/2018] [Indexed: 11/12/2022] Open
Abstract
Background Males of Opadometa are difficult to associate with conspecific females, and sex-matching errors may persist in the taxonomic literature. Recommended best practices for definitive sex matching in this genus suggest finding a male in the web of a female, or better yet, mating pairs. New information A male Opadometa was observed hanging on a frame line of the web of a female Opadometa sarawakensis, a species for which the male was previously undescribed. This occurred during a tropical ecology field course held at the Danau Girang Field Centre in Sabah, Malaysia. A taxonomic description was completed as a course activity.
Collapse
Affiliation(s)
- Jeremy A Miller
- Naturalis Biodiversity Center, Leiden, Netherlands.,Plazi.org, Bern, Switzerland
| | | | | | | | | | | | - József Geml
- Naturalis Biodiversity Center, Leiden, Netherlands.,Leiden University, Leiden, Netherlands
| | - Menno Schilthuizen
- Naturalis Biodiversity Center, Leiden, Netherlands.,Taxon Expeditions, Leiden, Netherlands.,Universiti Malaysia, Kota Kinabalu, Malaysia
| | - Richard Burger
- Danau Girang Field Centre, Sabah, Malaysia.,Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Benoit Goossens
- Danau Girang Field Centre, Sabah, Malaysia.,Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom.,Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom.,Sabah Wildlife Department, Sabah, Malaysia
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Nelson G, Sweeney P, Gilbert E. Use of globally unique identifiers (GUIDs) to link herbarium specimen records to physical specimens. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1027. [PMID: 29732258 PMCID: PMC5851565 DOI: 10.1002/aps3.1027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/09/2017] [Indexed: 05/11/2023]
Abstract
With the advent of the U.S. National Science Foundation's Advancing Digitization of Biodiversity Collections program and related worldwide digitization initiatives, the rate of herbarium specimen digitization in the United States has expanded exponentially. As the number of electronic herbarium records proliferates, the importance of linking these records to the physical specimens they represent as well as to related records from other sources will intensify. Although a rich and diverse literature has developed over the past decade that addresses the use of specimen identifiers for facilitating linking across the internet, few implementable guidelines or recommended practices for herbaria have been advanced. Here we review this literature with the express purpose of distilling a specific set of recommendations especially tailored to herbarium specimen digitization, curation, and management. We argue that associating globally unique identifiers (GUIDs) with physical herbarium specimens and including these identifiers in all electronic records about those specimens is essential to effective digital data curation. We also address practical applications for ensuring these associations.
Collapse
Affiliation(s)
- Gil Nelson
- iDigBioFlorida State University142 Collegiate Loop, P.O. Box 3062664TallahasseeFlorida32306‐2664USA
| | - Patrick Sweeney
- Division of BotanyPeabody Museum of Natural HistoryYale UniversityP.O. Box 208118New HavenConnecticut06520USA
| | - Edward Gilbert
- School of Life SciencesArizona State UniversityP.O. Box 874501TempeArizona85287USA
| |
Collapse
|
8
|
Page RDM. DNA barcoding and taxonomy: dark taxa and dark texts. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0334. [PMID: 27481786 PMCID: PMC4971186 DOI: 10.1098/rstb.2015.0334] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 01/19/2023] Open
Abstract
Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline ('dark texts'). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These 'dark taxa' hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global 'digital dashboard' to assess the extent to which biodiversity data are available online.This article is part of the themed issue 'From DNA barcodes to biomes'.
Collapse
Affiliation(s)
- Roderic D M Page
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| |
Collapse
|
9
|
Ng TH, Dulipat J, Foon JK, Lopes-Lima M, Alexandra Zieritz, Liew TS. A preliminary checklist of the freshwater snails of Sabah (Malaysian Borneo) deposited in the BORNEENSIS collection, Universiti Malaysia Sabah. Zookeys 2017:105-123. [PMID: 28769673 PMCID: PMC5523197 DOI: 10.3897/zookeys.673.12544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/25/2017] [Indexed: 11/24/2022] Open
Abstract
Sabah, a Malaysian state at the north-eastern tip of Borneo, is situated in one of the Earth’s biodiversity hotspots yet its freshwater gastropod diversity remains poorly known. An annotated checklist of the freshwater gastropods is presented, based on specimens deposited in the BORNEENSIS collection of the Institute for Tropical Biology and Conservation at Universiti Malaysia Sabah, Malaysia. A KMZ file is also provided, which acts as a repository of digital images and complete collection data of all examined material, so that it can be shared and adapted to facilitate future research.
Collapse
Affiliation(s)
- Ting Hui Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore.,Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan District, Bangkok 10330, Thailand
| | - Jasrul Dulipat
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah. Jalan UMS, 88450 Kota Kinabalu, Sabah, Malaysia
| | - Junn Kitt Foon
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah. Jalan UMS, 88450 Kota Kinabalu, Sabah, Malaysia
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Alexandra Zieritz
- School of Environmental and Geographical Sciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Malaysia
| | - Thor-Seng Liew
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah. Jalan UMS, 88450 Kota Kinabalu, Sabah, Malaysia
| |
Collapse
|
10
|
Rees JA, Cranston K. Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodivers Data J 2017:e12581. [PMID: 28765728 PMCID: PMC5515096 DOI: 10.3897/bdj.5.e12581] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/12/2017] [Indexed: 12/24/2022] Open
|
11
|
Dietrich CH, Dmitriev DA. Insect phylogenetics in the digital age. CURRENT OPINION IN INSECT SCIENCE 2016; 18:48-52. [PMID: 27939710 DOI: 10.1016/j.cois.2016.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Insect systematists have long used digital data management tools to facilitate phylogenetic research. Web-based platforms developed over the past several years support creation of comprehensive, openly accessible data repositories and analytical tools that support large-scale collaboration, accelerating efforts to document Earth's biota and reconstruct the Tree of Life. New digital tools have the potential to further enhance insect phylogenetics by providing efficient workflows for capturing and analyzing phylogenetically relevant data. Recent initiatives streamline various steps in phylogenetic studies and provide community access to supercomputing resources. In the near future, automated, web-based systems will enable researchers to complete a phylogenetic study from start to finish using resources linked together within a single portal and incorporate results into a global synthesis.
Collapse
Affiliation(s)
- Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S Oak St., Champaign, IL 61820, USA.
| | - Dmitry A Dmitriev
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S Oak St., Champaign, IL 61820, USA
| |
Collapse
|
12
|
Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Catapano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M. EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e10445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
13
|
Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M. EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e9774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
14
|
Stoev P, Smirnova L, Mergen P, Groom Q, De Wever A, Penev L, Pe’er I, Runnel V, Camacho A, Vincent T, Agosti D, Arvanitidis C, Bonet F, Saarenmaa H. Data sharing tools adopted by the European Biodiversity Observation Network Project. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e9390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
15
|
Senderov V, Penev L. The Open Biodiversity Knowledge Management System in Scholarly Publishing. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e7757] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
|
16
|
Dikow T, Agosti D. Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae). Biodivers Data J 2015:e5707. [PMID: 26491392 PMCID: PMC4609823 DOI: 10.3897/bdj.3.e5707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/30/2015] [Indexed: 11/12/2022] Open
Abstract
A cybercatalog to the Apioceridae (apiocerid flies) of the Afrotropical Region is provided. Each taxon entry includes links to open-access, online repositories such as ZooBank, BHL/BioStor/BLR, Plazi, GBIF, Morphbank, EoL, and a research web-site to access taxonomic information, digitized literature, morphological descriptions, specimen occurrence data, and images. Cybercatalogs as the one presented here will need to become the future of taxonomic catalogs taking advantage of the growing number of online repositories, linked data, and be easily updatable. Comments on the deposition of the holotype of Apiocera braunsi Melander, 1907 are made.
Collapse
Affiliation(s)
- Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | | |
Collapse
|