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Coca-de-la-Iglesia M, Gallego-Narbón A, Alonso A, Valcárcel V. High rate of species misidentification reduces the taxonomic certainty of European biodiversity databases of ivies (Hedera L.). Sci Rep 2024; 14:4876. [PMID: 38418501 PMCID: PMC10902322 DOI: 10.1038/s41598-024-54735-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 03/01/2024] Open
Abstract
The digitization of natural history specimens and the popularization of citizen science are creating an unprecedented availability of large amounts of biodiversity data. These biodiversity inventories can be severely affected by species misidentification, a source of taxonomic uncertainty that is rarely acknowledged in biodiversity data management. For these reasons, taxonomists debate the use of online repositories to address biological questions at the species level. Hedera L. (ivies) provides an excellent case study as it is well represented in both herbaria and online repositories with thousands of records likely to be affected by high taxonomic uncertainty. We analyze the sources and extent of taxonomic errors in the identification of the European ivy species by reviewing herbarium specimens and find a high misidentification rate (18% on average), which varies between species (maximized in H. hibernica: 55%; H. azorica: 48%; H. iberica: 36%) and regions (maximized in the UK: 38% and Spain: 27%). We find a systematic misidentification of all European ivies with H. helix behind the high misidentification rates in herbaria and warn of even higher rates in online records. We compile a spatial database to overcome the large discrepancies we observed in species distributions between online and morphologically reviewed records.
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Affiliation(s)
- Marina Coca-de-la-Iglesia
- Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- TRAGSATEC, Madrid, Spain
| | | | - Alejandro Alonso
- Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain.
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2
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Rodríguez-Vivas RI, Ojeda-Chi MM, Thompson AT, Yabsley MJ, Colunga-Salas P, Montes SS. Population genetics of the Ixodes affinis (Ixodida: Ixodidae) complex in America: new findings and a host-parasite review. Parasitol Res 2023; 123:78. [PMID: 38158425 DOI: 10.1007/s00436-023-08091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Ticks are hematophagous ectoparasites associated with a wide range of vertebrate hosts. Within this group, the Ixodidae family stands out, in which the Ixodes genus contains at least 245 species worldwide, from which 55 species are present in the Neotropical region. Ixodes affinis, a tick described in 1899, has a wide distribution from the Southern Cone of America to the United States. However, since its description, morphological variability has been reported among its populations. Furthermore, attempts have been made to clarify its status as a species complex using mitochondrial markers, but mainly in restricted populations of South and Central America. Thus, information related to populations of the transition region between the Neotropical and Nearctic zones is lacking. For these reasons, the objectives of the study were to evaluate the genetic diversity and structure of I. affinis across the Americas and to compile all the published records of I. affinis in America, to elucidate the host-parasite relationships and to identify their geographical distribution. For this, a phylogeny, and AMOVA analyses were performed to assess the genetic structure of samples obtained by field work in South Carolina, USA and Yucatán, Mexico. A total of 86 sequences were retrieved from a fragment of the 16S region. Phylogeny and genetic structure analysis showed four groups that were geographically and genetically related with high branch support and Fst values, all of them statistically significant. The results obtained support the hypothesis that I. affinis it corresponds to a complex of four species, which must be validated through future morphological comparisons.
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Affiliation(s)
- Roger I Rodríguez-Vivas
- Campus de Ciencias Biológicas y Agropecuarias. Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Melina M Ojeda-Chi
- Campus de Ciencias Biológicas y Agropecuarias. Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
- Facultad de Ciencias Biológicas y Agropecuarias Región Poza Rica-Tuxpan, Universidad Veracruzana, Carretera Tuxpan Tampico Kilómetro 7.5, Universitaria, Tuxpan de Rodríguez Cano, Veracruz, C.P. 92870, México
| | - Alec T Thompson
- Southeastern Cooperative Wildlife Disease Study (SCWDS), College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Michael J Yabsley
- Southeastern Cooperative Wildlife Disease Study (SCWDS), College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Pablo Colunga-Salas
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa de Enríquez, Veracruz, 91090, México.
- Centro de Medicina Tropical, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico, México.
| | - Sokani Sánchez Montes
- Centro de Medicina Tropical, División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico, México.
- Facultad de Ciencias Biológicas y Agropecuarias Región Poza Rica-Tuxpan, Universidad Veracruzana, Carretera Tuxpan Tampico Kilómetro 7.5, Universitaria, Tuxpan de Rodríguez Cano, Veracruz, C.P. 92870, México.
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3
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Chia SY, Fang YT, Su YT, Tsai PY, Hsieh C, Tsao SH, Juang JY, Hung CM, Tuanmu MN. A global database of bird nest traits. Sci Data 2023; 10:923. [PMID: 38129417 PMCID: PMC10739861 DOI: 10.1038/s41597-023-02837-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
The reproductive success of birds is closely tied to the characteristics of their nests. It is crucial to understand the distribution of nest traits across phylogenetic and geographic dimensions to gain insight into bird evolution and adaptation. Despite the extensive historical documentation on breeding behavior, a structured dataset describing bird nest characteristics has been lacking. To address this gap, we have compiled a comprehensive dataset that characterizes three ecologically and evolutionarily significant nest traits-site, structure, and attachment-for 9,248 bird species, representing all 36 orders and 241 out of the 244 families. By defining seven sites, seven structures, and four attachment types, we have systematically classified the nests of each species using information from text descriptions, photos, and videos sourced from online databases and literature. This nest traits dataset serves as a valuable addition to the existing body of morphological and ecological trait data for bird species, providing a useful resource for a wide range of avian macroecological and macroevolutionary research.
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Affiliation(s)
- Stephanie Yuan Chia
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Yi-Ting Fang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Ting Su
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Yu Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia Hsieh
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Program in Ecology and Evolutionary Biology, BioSciences Department, Rice University, Houston, Texas, USA
| | - Shu-Han Tsao
- Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan
| | - Jia-Yang Juang
- Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan
- Program in Nanoengineering and Nanoscience, Graduate School of Advanced Technology, National Taiwan University, Taipei, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| | - Mao-Ning Tuanmu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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Noll NW, Scherber C, Schäffler L. taxalogue: a toolkit to create comprehensive CO1 reference databases. PeerJ 2023; 11:e16253. [PMID: 38077427 PMCID: PMC10702336 DOI: 10.7717/peerj.16253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/18/2023] [Indexed: 12/18/2023] Open
Abstract
Background Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding. Metabarcoding allows for the simultaneous identification of thousands of organisms from bulk samples with high taxonomic resolution. However, reliable identifications can only be achieved with comprehensive and curated reference databases. Therefore, custom reference databases are often created to meet the needs of specific research questions. Due to taxonomic inconsistencies, formatting issues, and technical difficulties, building a custom reference database requires tremendous effort. Here, we present taxalogue, an easy-to-use software for creating comprehensive and customized reference databases that provide clean and taxonomically harmonized records. In combination with extensive geographical filtering options, taxalogue opens up new possibilities for generating and testing evolutionary hypotheses. Methods taxalogue collects DNA sequences from several online sources and combines them into a reference database. Taxonomic incongruencies between the different data sources can be harmonized according to available taxonomies. Dereplication and various filtering options are available regarding sequence quality or metadata information. taxalogue is implemented in the open-source Ruby programming language, and the source code is available at https://github.com/nwnoll/taxalogue. We benchmark four reference databases by sequence identity against eight queries from different localities and trapping devices. Subsamples from each reference database were used to compare how well another one is covered. Results taxalogue produces reference databases with the best coverage at high identities for most tested queries, enabling more accurate, reliable predictions with higher certainty than the other benchmarked reference databases. Additionally, the performance of taxalogue is more consistent while providing good coverage for a variety of habitats, regions, and sampling methods. taxalogue simplifies the creation of reference databases and makes the process reproducible and transparent. Multiple available output formats for commonly used downstream applications facilitate the easy adoption of taxalogue in many different software pipelines. The resulting reference databases improve the taxonomic classification accuracy through high coverage of the query sequences at high identities.
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Affiliation(s)
- Niklas W. Noll
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
| | - Christoph Scherber
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
| | - Livia Schäffler
- Centre for Biodiversity Monitoring and Conservation Science, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, North Rhine-Westphalia, Germany
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5
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Coca-De-La-Iglesia M, Valcárcel V, Medina NG. A Protocol to Retrieve and Curate Spatial and Climatic Data from Online Biodiversity Databases Using R. Bio Protoc 2023; 13:e4847. [PMID: 37900105 PMCID: PMC10603197 DOI: 10.21769/bioprotoc.4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 10/31/2023] Open
Abstract
Ecological and evolutionary studies often require high quality biodiversity data. This information is readily available through the many online databases that have compiled biodiversity data from herbaria, museums, and human observations. However, the process of preparing this information for analysis is complex and time consuming. In this study, we have developed a protocol in R language to process spatial data (download, merge, clean, and correct) and extract climatic data, using some genera of the ginseng family (Araliaceae) as an example. The protocol provides an automated way to process spatial and climatic data for numerous taxa independently and from multiple online databases. The script uses GBIF, BIEN, and WorldClim as the online data sources, but can be easily adapted to include other online databases. The script also uses genera as the sampling unit but provides a way to use species as the target. The cleaning process includes a filter to remove occurrences outside the natural range of the taxa, gardens, and other human environments, as well as erroneous locations and a spatial correction for misplaced occurrences (i.e., occurrences within a distance buffer from the coastal boundary). Additionally, each step of the protocol can be run independently. Thus, the protocol can begin with data cleaning, if the database has already been compiled, or with climatic data extraction, if the database has already been parsed. Each line of the R script is commented so that it can also be run by users with little knowledge of R.
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Affiliation(s)
- Marina Coca-De-La-Iglesia
- Departamento de Biología, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- TRAGSATEC, Madrid, Spain
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Madrid, Spain
| | - Nagore G. Medina
- Departamento de Biología, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Madrid, Spain
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6
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Sterner B, Elliott S, Gilbert EE, Franz NM. Unified and pluralistic ideals for data sharing and reuse in biodiversity. Database (Oxford) 2023; 2023:baad048. [PMID: 37465916 PMCID: PMC10354506 DOI: 10.1093/database/baad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/30/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
How should billions of species observations worldwide be shared and made reusable? Many biodiversity scientists assume the ideal solution is to standardize all datasets according to a single, universal classification and aggregate them into a centralized, global repository. This ideal has known practical and theoretical limitations, however, which justifies investigating alternatives. To support better community deliberation and normative evaluation, we develop a novel conceptual framework showing how different organizational models, regulative ideals and heuristic strategies are combined to form shared infrastructures supporting data reuse. The framework is anchored in a general definition of data pooling as an activity of making a taxonomically standardized body of information available for community reuse via digital infrastructure. We describe and illustrate unified and pluralistic ideals for biodiversity data pooling and show how communities may advance toward these ideals using different heuristic strategies. We present evidence for the strengths and limitations of the unification and pluralistic ideals based on systemic relationships of power, responsibility and benefit they establish among stakeholders, and we conclude the pluralistic ideal is better suited for biodiversity data.
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Affiliation(s)
- Beckett Sterner
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA
| | - Steve Elliott
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA
| | - Edward E Gilbert
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA
| | - Nico M Franz
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA
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7
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Capurucho JMG, Hains T, Pirro S, Bates J, Hackett S. The Complete Genome Sequences of 19 Species of Snipes (Scolopacidae, Charadriiformes, Aves). Biodivers Genomes 2023; 2023:10.56179/001c.74632. [PMID: 37153853 PMCID: PMC10162776 DOI: 10.56179/001c.74632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We present the complete genome sequences of 19 species of snipes from 7 genera. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
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Affiliation(s)
- João Marcos G Capurucho
- Coordenação de Biodiversidade, Field Museum of Natural History
- Committee on Evolutionary Biology, Instituto Nacional de Pesquisas da Amazônia
| | - Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago, Committee on Evolutionary Biology
| | | | - John Bates
- Negaunee Integrative Research Center, Field Museum of Natural History
| | - Shannon Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History
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8
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Catanach TA, Pirro S. The Complete Genome Sequences of 87 Species of Hawks (Accipitriformes, Aves). Biodivers Genomes 2023; 2023:1-5. [PMID: 36686854 PMCID: PMC9851080 DOI: 10.56179/001c.67877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present the complete genome sequences of 87 species of hawks from 39 genera. Illumina sequencing was performed on genetic material from single individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
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Affiliation(s)
- Therese A Catanach
- Department of Ornithology, Academy of Natural Sciences, Drexel University
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9
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Hains T, Pirro S, O'Neill K, Valez J, Speed N, Clubb S, Oleksyk T, Bates J, Hackett S. The Complete Genome Sequences of 94 Species of Parrots (Psittaciformes, Aves). Biodivers Genomes 2022; 2022:10.56179/001c.40338. [PMID: 36405343 PMCID: PMC9671223 DOI: 10.56179/001c.40338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
We present the complete genome sequences of 94 species of parrots from 40 genera. Illumina sequencing was performed on genetic material from single individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.
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Affiliation(s)
- Taylor Hains
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago Committee on Evolutionary Biology
| | | | | | - Jafet Valez
- Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service
| | - Nancy Speed
- Rainforest Clinic for Birds & Exotics, Hurricane Aviaries Inc
| | - Susan Clubb
- Rainforest Clinic for Birds & Exotics, Hurricane Aviaries Inc
| | - Taras Oleksyk
- Department of Biological Sciences, Oakland University
| | - John Bates
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago Committee on Evolutionary Biology
| | - Shannon Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History
- University of Chicago Committee on Evolutionary Biology
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10
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Walsh MG, Pattanaik A, Vyas N, Saxena D, Webb C, Sawleshwarkar S, Mukhopadhyay C. A biogeographical description of the wild waterbird species associated with high-risk landscapes of Japanese encephalitis virus in India. Transbound Emerg Dis 2022; 69:e3015-e3023. [PMID: 35809085 PMCID: PMC9796264 DOI: 10.1111/tbed.14656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 01/01/2023]
Abstract
Wild reservoirs of Japanese encephalitis virus are under-studied globally, which presents critical knowledge gaps for JEV epidemiology and infection ecology despite decades of received wisdom regarding this high-impact mosquito-borne virus. As a result, ardeid birds, generally understood to be the primary reservoirs for JEV, as well as other waterbirds occupying landscapes at high risk for spillover to humans, are frequently ignored by current surveillance mechanisms and infrastructure. This is particularly true in India, which experiences a high annual burden of human outbreaks. Incorporating wild reservoirs into surveillance of human and livestock populations is therefore essential but will first require a data-driven approach to target individual host species. The current study sought to identify preliminary waterbird target species for JEV surveillance development based on species' distributions in high-risk landscapes. Twenty-one target species were identified after adjusting species presence and abundance for the biotic constraints of sympatry. Furthermore, ardeid bird species richness demonstrated a strong non-linear association with the distribution of human JEV outbreaks, which suggested areas with the highest ardeid species richness corresponded to low JEV outbreak risk. No association was identified between JEV outbreaks and anatid or rallid richness. The lack of association between Anatidae and Rallidae family-level diversity and JEV outbreak risk notwithstanding, this study did identify several individual species among these two bird families in high-risk landscapes. The findings from this work provide the first data-driven evidence base to inform wildlife sampling for the monitoring of JEV circulation in outbreak hotspots in India and thus identify good preliminary targets for the development of One Health JEV surveillance.
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Affiliation(s)
- Michael G. Walsh
- Faculty of Medicine and Health, School of Public HealthThe University of SydneyCamperdownNew South WalesAustralia,Faculty of Medicine and Health, Sydney Institute for Infectious DiseasesThe University of SydneyWestmeadNew South WalesAustralia,One Health Centre, The Prasanna School of Public HealthManipal Academy of Higher EducationManipalKarnatakaIndia,The Prasanna School of Public HealthManipal Academy of Higher EducationManipalKarnatakaIndia
| | - Amrita Pattanaik
- Manipal Institute of VirologyManipal Academy of Higher EducationManipalKarnatakaIndia
| | - Navya Vyas
- One Health Centre, The Prasanna School of Public HealthManipal Academy of Higher EducationManipalKarnatakaIndia,The Prasanna School of Public HealthManipal Academy of Higher EducationManipalKarnatakaIndia
| | - Deepak Saxena
- Department of EpidemiologyIndian Institute of Public Health GandhinagarGandhinagarGujaratIndia
| | - Cameron Webb
- Faculty of Medicine and Health, Sydney Institute for Infectious DiseasesThe University of SydneyWestmeadNew South WalesAustralia,Department of Medical EntomologyNSW Health Pathology, Westmead HospitalWestmeadNew South WalesAustralia
| | - Shailendra Sawleshwarkar
- Faculty of Medicine and Health, Sydney Institute for Infectious DiseasesThe University of SydneyWestmeadNew South WalesAustralia,One Health Centre, The Prasanna School of Public HealthManipal Academy of Higher EducationManipalKarnatakaIndia,The Prasanna School of Public HealthManipal Academy of Higher EducationManipalKarnatakaIndia,Faculty of Medicine and Health, Westmead Clinical SchoolThe University of SydneyWestmeadNew South WalesAustralia
| | - Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical CollegeManipal Academy of Higher EducationManipalKarnatakaIndia,Centre for Emerging and Tropical Diseases, Kasturba Medical CollegeManipal Academy of Higher EducationManipalKarnatakaIndia
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11
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Tobias JA, Sheard C, Pigot AL, Devenish AJM, Yang J, Sayol F, Neate-Clegg MHC, Alioravainen N, Weeks TL, Barber RA, Walkden PA, MacGregor HEA, Jones SEI, Vincent C, Phillips AG, Marples NM, Montaño-Centellas FA, Leandro-Silva V, Claramunt S, Darski B, Freeman BG, Bregman TP, Cooney CR, Hughes EC, Capp EJR, Varley ZK, Friedman NR, Korntheuer H, Corrales-Vargas A, Trisos CH, Weeks BC, Hanz DM, Töpfer T, Bravo GA, Remeš V, Nowak L, Carneiro LS, Moncada R AJ, Matysioková B, Baldassarre DT, Martínez-Salinas A, Wolfe JD, Chapman PM, Daly BG, Sorensen MC, Neu A, Ford MA, Mayhew RJ, Fabio Silveira L, Kelly DJ, Annorbah NND, Pollock HS, Grabowska-Zhang AM, McEntee JP, Carlos T Gonzalez J, Meneses CG, Muñoz MC, Powell LL, Jamie GA, Matthews TJ, Johnson O, Brito GRR, Zyskowski K, Crates R, Harvey MG, Jurado Zevallos M, Hosner PA, Bradfer-Lawrence T, Maley JM, Stiles FG, Lima HS, Provost KL, Chibesa M, Mashao M, Howard JT, Mlamba E, Chua MAH, Li B, Gómez MI, García NC, Päckert M, Fuchs J, Ali JR, Derryberry EP, Carlson ML, Urriza RC, Brzeski KE, Prawiradilaga DM, Rayner MJ, Miller ET, Bowie RCK, Lafontaine RM, Scofield RP, Lou Y, Somarathna L, Lepage D, Illif M, Neuschulz EL, Templin M, Dehling DM, Cooper JC, Pauwels OSG, Analuddin K, Fjeldså J, Seddon N, Sweet PR, DeClerck FAJ, Naka LN, Brawn JD, Aleixo A, Böhning-Gaese K, Rahbek C, Fritz SA, Thomas GH, Schleuning M. AVONET: morphological, ecological and geographical data for all birds. Ecol Lett 2022; 25:581-597. [PMID: 35199922 DOI: 10.1111/ele.13898] [Citation(s) in RCA: 138] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/10/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023]
Abstract
Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.
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Affiliation(s)
- Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Catherine Sheard
- Department of Zoology, University of Oxford, Oxford, UK.,School of Earth Sciences, University of Bristol, Bristol, UK
| | - Alex L Pigot
- Department of Zoology, University of Oxford, Oxford, UK.,Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Jingyi Yang
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Ferran Sayol
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Montague H C Neate-Clegg
- Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Nico Alioravainen
- Department of Zoology, University of Oxford, Oxford, UK.,Natural Resources Institute Finland, Natural resources - Migratory fish and regulated rivers, Oulu, Finland
| | - Thomas L Weeks
- Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Robert A Barber
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Patrick A Walkden
- Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Hannah E A MacGregor
- Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, University of Bristol, Bristol, UK
| | - Samuel E I Jones
- Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, Royal Holloway, University of London, Egham, UK
| | - Claire Vincent
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Anna G Phillips
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Flavia A Montaño-Centellas
- Instituto de Ecología, Universidad Mayor de San Andres, La Paz, Bolivia.,Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
| | - Victor Leandro-Silva
- Laboratório de Ecologia e Evolução de Aves, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Santiago Claramunt
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Bianca Darski
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Benjamin G Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom P Bregman
- Department of Zoology, University of Oxford, Oxford, UK.,Future-Fit Foundation, Spitalfields, London, UK
| | | | - Emma C Hughes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Elliot J R Capp
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Zoë K Varley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, UK
| | - Nicholas R Friedman
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Heiko Korntheuer
- Department of Ecology, Institute of Zoology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andrea Corrales-Vargas
- Central American Institute for Studies on Toxic Substances (IRET), Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Christopher H Trisos
- Department of Zoology, University of Oxford, Oxford, UK.,African Climate and Development Initiative, University of Cape Town, Cape Town, South Africa.,Centre for Statistics in Ecology, the Environment and Conservation, University of Cape Town, Cape Town, South Africa
| | - Brian C Weeks
- School for Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA.,Department of Ornithology, American Museum of Natural History, New York, New York, USA
| | - Dagmar M Hanz
- Biogeography and Biodiversity Lab, Institute of Physical Geography, Goethe University Frankfurt, , Frankfurt am Main, Germany
| | - Till Töpfer
- Ornithology Section, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Gustavo A Bravo
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Vladimír Remeš
- Department of Zoology, Palacký University, Olomouc, Czech Republic.,Department of Ecology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Larissa Nowak
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lincoln S Carneiro
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| | - Amilkar J Moncada R
- CATIE (Centro Agronómico Tropical de Investigación y Enseñanza), Cartago, Turrialba, Costa Rica
| | | | | | | | - Jared D Wolfe
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Marjorie C Sorensen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alexander Neu
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michael A Ford
- South African Ringing Unit, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Rebekah J Mayhew
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Luis Fabio Silveira
- Museu de Zoologia da Universidade de Sao Paulo (MZUSP), São Paulo, SP, Brazil
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Nathaniel N D Annorbah
- Department of Biological, Physical and Mathematical Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | - Henry S Pollock
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Jay P McEntee
- Department of Biology, Missouri State University, Springfield, Missouri, USA
| | - Juan Carlos T Gonzalez
- Department of Zoology, University of Oxford, Oxford, UK.,Museum of Natural History, University of the Philippines Los, Baños, Los Baños, Laguna, Philippines.,Animal Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los, Baños, Los Baños, Laguna, Philippines
| | - Camila G Meneses
- Museum of Natural History, University of the Philippines Los, Baños, Los Baños, Laguna, Philippines
| | - Marcia C Muñoz
- Programa de Biología, Universidad de la Salle, Bogotá, Colombia
| | - Luke L Powell
- Institute of Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, UK.,Biodiversity Initiative, Houghton, Michigan, USA.,CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Gabriel A Jamie
- Department of Zoology, University of Cambridge, Cambridge, UK.,FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Thomas J Matthews
- GEES (School of Geography, Earth and Environmental Sciences) and Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK.,CE3C (Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade, dos Açores), Depto de Ciências Agráriase Engenharia do Ambiente, Angra do Heroísmo, Açores, Portugal
| | - Oscar Johnson
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisina, USA
| | - Guilherme R R Brito
- Depto. de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Kristof Zyskowski
- Peabody Museum of Natural History, Yale University, New Haven, Connecticut, USA
| | - Ross Crates
- Fenner School of Environment and Society, Australian National University, Canberra, Australia
| | - Michael G Harvey
- Department of Biological Sciences and Biodiversity Collections, The University of Texas at El Paso, El Paso, Texas, USA
| | | | - Peter A Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - James M Maley
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California, USA
| | - F Gary Stiles
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Hevana S Lima
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Kaiya L Provost
- Department of Ornithology, American Museum of Natural History, New York, New York, USA.,Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, Ohio, USA
| | - Moses Chibesa
- Department of Zoology and Aquatic Sciences, Copperbelt University, Kitwe, Zambia
| | | | - Jeffrey T Howard
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisina, USA.,Louisiana State University, Health Sciences Center Shreveport, Shreveport, Louisina, USA
| | - Edson Mlamba
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Marcus A H Chua
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Bicheng Li
- Natural History Research Center, Shanghai Natural History Museum, Shanghai, China
| | - M Isabel Gómez
- Colección Boliviana de Fauna - Museo Nacional de Historia Natural, Ministerio de Medio Ambiente y Agua, La Paz, Bolivia
| | - Natalia C García
- División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Buenos Aires, Argentina
| | - Martin Päckert
- Senckenberg Natural History Collections, Museum of Zoology, Dresden, Germany
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, SU, EPHE, UA, Paris, France
| | - Jarome R Ali
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Monica L Carlson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Rolly C Urriza
- Ornithology Section, Zoology Division, Philippine National Museum, Rizal Park, Manila, Philippines
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Dewi M Prawiradilaga
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Bogor, Indonesia
| | - Matt J Rayner
- Auckland Museum, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - René-Marie Lafontaine
- Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences (RBINS), Brussels, Belgium
| | | | - Yingqiang Lou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lankani Somarathna
- Natural History Section, Department of National Museum, Colombo, Sri Lanka
| | | | | | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Mathias Templin
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - D Matthias Dehling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | | | - Olivier S G Pauwels
- Department of Recent Vertebrates, Royal Belgian Institute of Natural Sciences (RBINS), Brussels, Belgium
| | - Kangkuso Analuddin
- Department of Biotechnology, Halu Oleo University, Kendari, Sulawesi Tenggara, Indonesia
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Seddon
- Nature-based Solutions Initiative, Department of Zoology, University of Oxford, Oxford, UK
| | - Paul R Sweet
- Department of Ornithology, American Museum of Natural History, New York, New York, USA
| | - Fabrice A J DeClerck
- Bioversity International, CGIAR, Parc Scientifique Agropolis II, Montpellier, France
| | - Luciano N Naka
- Laboratório de Ecologia e Evolução de Aves, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Jeffrey D Brawn
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Katrin Böhning-Gaese
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Carsten Rahbek
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.,Institute of Ecology, Peking University, Beijing, China
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institut für Geowissenschaften, Goethe University, Frankfurt, Frankfurt am Main, Germany
| | - Gavin H Thomas
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, UK
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
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12
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Grenié M, Berti E, Carvajal‐Quintero J, Dädlow GML, Sagouis A, Winter M. Harmonizing taxon names in biodiversity data: a review of tools, databases, and best practices. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13802] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
| | - Emilio Berti
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Friedrich‐Schiller University Jena Jena Germany
| | - Juan Carvajal‐Quintero
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
| | - Gala Mona Louise Dädlow
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
| | - Alban Sagouis
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Department of Computer Science Martin Luther University Halle‐Wittenberg, Halle Germany
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Puschstraße 4 04103 Leipzig Germany
- Leipzig University Ritterstraße 26 04109 Leipzig Germany
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13
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Yu J, Liu J, Li C, Wu W, Feng F, Wang Q, Ying X, Qi D, Qi G. Characterization of the complete mitochondrial genome of Otus lettia: exploring the mitochondrial evolution and phylogeny of owls (Strigiformes). Mitochondrial DNA B Resour 2021; 6:3443-3451. [PMID: 34805524 PMCID: PMC8604474 DOI: 10.1080/23802359.2021.1995517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Large-scale molecular phylogenetic studies of the avian order Strigiformes have been performed, and numerous mitochondrial genomes have been determined. However, their intergeneric relationships are still controversial, and few comprehensive comparative analyses of mitochondrial genomes have been conducted on Strigiformes. In this study, the mitochondrial genome of Otus lettia was determined and compared with other Strigiformes. The O. lettia mitochondrial genome was 16,951 bp in size. For Strigiformes, atp8 can be used as a suitable molecular marker for population genetic diversity, while cox1 is a candidate barcoding marker for species identification. All protein-coding genes may be under strong purifying selection pressure, and one extra cytosine insertion located in nad3 is common to all owls except Tyto longimembris, T. alba, and Athene noctua. Four different mitochondrial gene arrangement types were found among the Strigiformes mitogenomes, and their evolutionary relationship between each other can be perfectly explained by the tandem duplication and random loss model. The phylogenetic topologies using the mitochondrial genomes showed that target species O. lettia had a closer relationship with O. scops + O. sunia than O. bakkamoena, the genus Glaucidium was paraphyletic, and the Ninox clade was located at the basal position of Strigidae lineage. Our phylogenetic trees also supported the previous recommendations that Sceloglaux albifacies, Ciccaba nigrolineata, and Ketupa flavipes should be transferred to Ninox, Strix, and Bubo, respectively. These findings will be helpful in further unraveling the mitochondrial evolution and phylogeny of Strigiformes.
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Affiliation(s)
- Jiaojiao Yu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Jiabin Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Cheng Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Wei Wu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Feifei Feng
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Qizhi Wang
- Sichuan Nanshan Forestry Judicial Appraisal Center, Chengdu, China
| | - Xiaofeng Ying
- Sichuan Nanshan Forestry Judicial Appraisal Center, Chengdu, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, China
| | - Guilan Qi
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
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14
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Pyle RL, Barik SK, Christidis L, Conix S, Costello MJ, van Dijk PP, Garnett ST, Hobern D, Kirk PM, Lien AM, Orrell TM, Remsen D, Thomson SA, Wambiji N, Zachos FE, Zhang ZQ, Thiele KR. Towards a global list of accepted species V. The devil is in the detail. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00504-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Affiliation(s)
- Kari E. A. Norman
- Department of Environmental Science, Policy, and Management University of California Berkeley Berkeley CA USA
| | - Scott Chamberlain
- The rOpenSci Project University of California Berkeley Berkeley CA USA
| | - Carl Boettiger
- Department of Environmental Science, Policy, and Management University of California Berkeley Berkeley CA USA
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16
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Campbell DL, Thessen AE, Ries L. A novel curation system to facilitate data integration across regional citizen science survey programs. PeerJ 2020; 8:e9219. [PMID: 32821528 PMCID: PMC7395600 DOI: 10.7717/peerj.9219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 04/28/2020] [Indexed: 11/20/2022] Open
Abstract
Integrative modeling methods can now enable macrosystem-level understandings of biodiversity patterns, such as range changes resulting from shifts in climate or land use, by aggregating species-level data across multiple monitoring sources. This requires ensuring that taxon interpretations match up across different sources. While encouraging checklist standardization is certainly an option, coercing programs to change species lists they have used consistently for decades is rarely successful. Here we demonstrate a novel approach for tracking equivalent names and concepts, applied to a network of 10 regional programs that use the same protocols (so-called “Pollard walks”) to monitor butterflies across America north of Mexico. Our system involves, for each monitoring program, associating the taxonomic authority (in this case one of three North American butterfly fauna treatments: Pelham, 2014; North American Butterfly Association, Inc., 2016; Opler & Warren, 2003) that shares the most similar overall taxonomic interpretation to the program’s working species list. This allows us to define each term on each program’s list in the context of the appropriate authority’s species concept and curate the term alongside its authoritative concept. We then aligned the names representing equivalent taxonomic concepts among the three authorities. These stepping stones allow us to bridge a species concept from one program’s species list to the name of the equivalent in any other program, through the intermediary scaffolding of aligned authoritative taxon concepts. Using a software tool we developed to access our curation system, a user can link equivalent species concepts between data collecting agencies with no specialized knowledge of taxonomic complexities.
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Affiliation(s)
- Dana L Campbell
- Division of Biological Sciences, School of STEM, University of Washington, Bothell, WA, USA
| | - Anne E Thessen
- The Ronin Institute for Independent Scholarship, Montclair, NJ, USA.,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Leslie Ries
- Department of Biology, Georgetown University, Washington, DC, USA
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17
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McClure CJW, Lepage D, Dunn L, Anderson DL, Schulwitz SE, Camacho L, Robinson BW, Christidis L, Schulenberg TS, Iliff MJ, Rasmussen PC, Johnson J. Towards reconciliation of the four world bird lists: hotspots of disagreement in taxonomy of raptors. Proc Biol Sci 2020; 287:20200683. [PMID: 32546096 DOI: 10.1098/rspb.2020.0683] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There are currently four world bird lists referenced by different stakeholders including governments, academic journals, museums and citizen scientists. Consolidation of these lists is a conservation and research priority. In reconciling lists, care must be taken to ensure agreement in taxonomic concepts-the actual groups of individual organisms circumscribed by a given scientific epithet. Here, we compare species-level taxonomic concepts for raptors across the four lists, highlighting areas of disagreement. Of the 665 species-level raptor taxa observed at least once among the four lists, only 453 (68%) were consistent across all four lists. The Howard and Moore Checklist of the Birds of the World contains the fewest raptor species (528), whereas the International Ornithological Community World Bird List contains the most (580) and these two lists are in the most disagreement. Of the disagreements, 67% involved owls, and Indonesia was the country containing the most disagreed upon species (169). Finally, we calculated the amount of species-level agreement across lists for each avian order and found raptor orders spread throughout the rankings of agreement. Our results emphasize the need to reconcile the four world bird lists for all avian orders, highlight broad disagreements across lists and identify hotspots of disagreement for raptors, in particular.
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Affiliation(s)
| | - Denis Lepage
- Birds Canada, PO Box 160, 115 Front Street, Port Rowan, Ontario, Canada N0E 1M0
| | - Leah Dunn
- The Peregrine Fund, 5668 West Flying Hawk Lane, Boise, ID 83709, USA
| | - David L Anderson
- The Peregrine Fund, 5668 West Flying Hawk Lane, Boise, ID 83709, USA
| | - Sarah E Schulwitz
- The Peregrine Fund, 5668 West Flying Hawk Lane, Boise, ID 83709, USA
| | - Leticia Camacho
- The Peregrine Fund, 5668 West Flying Hawk Lane, Boise, ID 83709, USA.,Department of Biological Sciences and Raptor Research Center, Boise State University, 1910, Boise, ID 83725, USA
| | | | - Les Christidis
- Southern Cross University, Coffs Harbour, New South Wales, Australia
| | | | - Marshall J Iliff
- Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Pamela C Rasmussen
- Department of Integrative Biology, Michigan State University Museum, East Lansing, MI, USA
| | - Jeff Johnson
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #310559, Denton, TX 76203, USA
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18
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Abstract
Costly interactions between species that arise as a by-product of ancestral similarities in communication signals are expected to persist only under specific evolutionary circumstances. Territorial aggression between species, for instance, is widely assumed to persist only when extrinsic barriers prevent niche divergence or selection in sympatry is too weak to overcome gene flow from allopatry. However, recent theoretical and comparative studies have challenged this view. Here we present a large-scale, phylogenetic analysis of the distribution and determinants of interspecific territoriality. We find that interspecific territoriality is widespread in birds and strongly associated with hybridization and resource overlap during the breeding season. Contrary to the view that territoriality only persists between species that rarely breed in the same areas or where niche divergence is constrained by habitat structure, we find that interspecific territoriality is positively associated with breeding habitat overlap and unrelated to habitat structure. Furthermore, our results provide compelling evidence that ancestral similarities in territorial signals are maintained and reinforced by selection when interspecific territoriality is adaptive. The territorial signals linked to interspecific territoriality in birds depend on the evolutionary age of interacting species, plumage at shallow (within-family) timescales, and song at deeper (between-family) timescales. Evidently, territorial interactions between species have persisted and shaped phenotypic diversity on a macroevolutionary timescale.
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Affiliation(s)
- Jonathan P Drury
- Department of Biosciences, Durham University, DH1 3LE Durham, United Kingdom;
| | - Madeline C Cowen
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Gregory F Grether
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA 90095
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19
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Levy H, Fiddaman SR, Vianna JA, Noll D, Clucas GV, Sidhu JKH, Polito MJ, Bost CA, Phillips RA, Crofts S, Miller GD, Pistorius P, Bonnadonna F, Le Bohec C, Barbosa A, Trathan P, Raya Rey A, Frantz LAF, Hart T, Smith AL. Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird. Mol Biol Evol 2020; 37:1708-1726. [PMID: 32096861 PMCID: PMC7253215 DOI: 10.1093/molbev/msaa040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.
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Affiliation(s)
- Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
| | - Daly Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Gemma V Clucas
- Cornell Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY
| | | | - Michael J Polito
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA
| | - Charles A Bost
- Centre d’Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS‐Université de La Rochelle, Villiers‐en‐Bois, France
| | | | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands, United Kingdom
| | - Gary D Miller
- Microbiology and Immunology, PALM, University of Western Australia, Crawley, Western Australia, Australia
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Francesco Bonnadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Céline Le Bohec
- Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
- Département de Biologie Polaire, Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Andrés Barbosa
- Museo Nacional de Ciencias Naturales, Departamento de Ecología Evolutiva, CSIC, Madrid, Spain
| | - Phil Trathan
- British Antarctic Survey, Cambridge, United Kingdom
| | - Andrea Raya Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Tierra del Fuego, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
- Wildlife Conservation Society, Buenos Aires, Argentina
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Sterner B, Witteveen J, Franz N. Coordinating dissent as an alternative to consensus classification: insights from systematics for bio-ontologies. Hist Philos Life Sci 2020; 42:8. [PMID: 32030540 DOI: 10.1007/s40656-020-0300-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or "settled" science.
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Affiliation(s)
- Beckett Sterner
- School of Life Sciences, Arizona State University, Tempe, USA.
| | - Joeri Witteveen
- Department of Science Education, Section for History and Philosophy of Science, University of Copenhagen, Copenhagen, Denmark
| | - Nico Franz
- School of Life Sciences, Arizona State University, Tempe, USA
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Abstract
Contrary to the traditional claim that needs for unambiguous communication about animal and plant species are best served by a single set of names (Linnaean nomenclature) ruled by international Codes, I suggest that a more diversified system is required, especially to cope with problems emerging from aggregation of biodiversity data in large databases. Departures from Linnaean nomenclature are sometimes intentional, but there are also other, less obvious but widespread forms of not Code-compliant grey nomenclature. A first problem is due to the circumstance that the Codes are intended to rule over the way names are applied to species and other taxonomic units, whereas users of taxonomy need names to be applied to specimens. For different reasons, it is often impossible to refer a specimen with certainty to a named species, and in those cases an open nomenclature is employed. Second, molecular taxonomy leads to the discovery of clusters of gene sequence diversity not necessarily equivalent to the species recognized and named by taxonomists. Those clusters are mostly indicated with informal names or formulas that challenge comparison between different publications or databases. In several instances, it is not even clear if a formula refers to an individual voucher specimen, or is a provisional species name. The use of non-Linnaean names and formulas must be revised and strengthened by fixing standard formats for the different kinds of objects or hypotheses and providing permanent association of 'grey names' with standardized source information such as author and year. In the context of a broad-scope revisitation of aims and scope of scientific nomenclature, it may be worth rethinking if natural objects like plant galls and lichens, although other than the 'single-entity' objects traditionally covered by biological classifications, may nevertheless deserve taxonomic names.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via Ugo Bassi 58 B, 35131, Padua, Italy.
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22
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Affiliation(s)
- Jeffrey O. Hanson
- School of Biological Sciences The University of Queensland Brisbane QLD Australia
| | - Richard Schuster
- Department of Biology Carleton University Ottawa ON Canada
- Ecosystem Science and Management Program University of Northern British Prince George BC Canada
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Cacho NI, Monteverde-Suárez MJ, McIntyre PJ. Convergent evolution in floral morphology in a plant ring species, the Caribbean Euphorbia tithymaloides. Am J Bot 2019; 106:1032-1045. [PMID: 31281963 DOI: 10.1002/ajb2.1318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Ring species have long fascinated evolutionary biologists for their potential insights into lineage divergence and speciation across space. Few studies have investigated the potential for convergent or parallel evolution along the diverging fronts of ring species. We investigated a potential case of parallel floral variation in the Caribbean spurge Euphorbia tithymaloides, the only plant system with molecular support as a ring species. The terminal populations of each front, despite being the most divergent, exhibit such similar floral traits that they were originally considered each other's closest relative. METHODS We evaluated convergence in floral and leaf traits in relation to geography across 95 populations spanning the distribution of E. tithymaloides. We also reanalyzed available genetic data (from previous phylogenetic analyses) in an explicitly spatial framework. RESULTS Floral morphology appears to have shifted in a convergent fashion along both geographic fronts of E. tithymaloides, resulting in shorter and more compact inflorescences in Antillean populations compared to the typical elongate "slipper-like" cyathia characteristic of the area of origin. Patterns of spatial genetic variation were more consistent with a two-fronted invasion of the Caribbean than with a simpler model of isolation-by-distance. CONCLUSIONS Floral divergence in E. tithymaloides is consistent with convergent evolution along the two fronts of a ring species. We outline several (not mutually exclusive) mechanisms that could be driving patterns in morphology, including shifts toward generalized pollination with reduced reliance on hummingbirds, shifts in floral structure closely matching available hummingbird bill traits, and shifts toward increased selfing.
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Affiliation(s)
- N Ivalú Cacho
- Instituto de Biología, Universidad Nacional Autónoma de México, CDMX 04510, Mexico
| | | | - Patrick J McIntyre
- NatureServe, Western Regional Office, 1680 38th St., Suite 120, Boulder, Colorado, 80301, USA
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24
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Penev L, Dimitrova M, Senderov V, Zhelezov G, Georgiev T, Stoev P, Simov K. OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science. Publications 2019; 7:38. [DOI: 10.3390/publications7020038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Hundreds of years of biodiversity research have resulted in the accumulation of a substantial pool of communal knowledge; however, most of it is stored in silos isolated from each other, such as published articles or monographs. The need for a system to store and manage collective biodiversity knowledge in a community-agreed and interoperable open format has evolved into the concept of the Open Biodiversity Knowledge Management System (OBKMS). This paper presents OpenBiodiv: An OBKMS that utilizes semantic publishing workflows, text and data mining, common standards, ontology modelling and graph database technologies to establish a robust infrastructure for managing biodiversity knowledge. It is presented as a Linked Open Dataset generated from scientific literature. OpenBiodiv encompasses data extracted from more than 5000 scholarly articles published by Pensoft and many more taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version of the Global Biodiversity Information Facility (GBIF) taxonomic backbone. Through the application of semantic technologies, the project showcases the value of open publishing of Findable, Accessible, Interoperable, Reusable (FAIR) data towards the establishment of open science practices in the biodiversity domain.
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Ross SRPJ, Friedman NR, Janicki J, Economo EP. A test of trophic and functional island biogeography theory with the avifauna of a continental archipelago. J Anim Ecol 2019; 88:1392-1405. [PMID: 31132149 DOI: 10.1111/1365-2656.13029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/02/2019] [Indexed: 01/10/2023]
Abstract
The classical MacArthur-Wilson theory of island biogeography (TIB) emphasizes the role of island area and isolation in determining island biotas, but is neutral with respect to species differences that could affect community assembly and persistence. Recent extensions of island biogeography theory address how functional differences among species may lead to non-random community assembly processes and different diversity-area scaling patterns. First, the trophic TIB considers how diversity scaling varies across trophic position in a community, with species at higher trophic levels being most strongly influenced by island area. Second, further extensions have predicted how trait distributions, and hence functional diversity, should scale with area. Trait-based theory predicts richness-corrected functional diversity should be low on small islands but converge to null on larger islands. Conversely, competitive assembly predicts high diversity on small islands converging to null with increasing size. However, despite mounting interest in diversity-area relationships across different dimensions of diversity, these predictions derived from theory have not been extensively tested across taxa and island systems. Here, we develop and test predictions of the trophic TIB and extensions to functional traits, by examining the diversity-area relationship across multiple trophic ranks and dimensions of avian biodiversity in the Ryūkyū archipelago of Japan. We find evidence for a positive species- and phylogenetic diversity-area relationship, but functional diversity was not strongly affected by island area. Counter to the trophic TIB, we found no differences in the slopes of species-area relationships among trophic ranks, although slopes varied among trophic guilds at the same rank. We revealed differential assembly of trophic ranks, with evidence of trait-based assembly of intermediate predators but otherwise neutral community assembly. Our results suggest that niche space differs among trophic guilds of birds, but that differences are mostly not predicted by current extensions of island biogeography theory. While predicted patterns do not fit the empirical data well in this case, the development of such theory provides a useful framework to analyse island patterns from new perspectives. The application of empirical datasets such as ours should help provide a basis for developing further iterations of island biogeography theory.
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Affiliation(s)
- Samuel R P-J Ross
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan.,Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Nicholas R Friedman
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
| | - Julia Janicki
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
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Franz NM, Musher LJ, Brown JW, Yu S, Ludäscher B. Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion. PLoS Comput Biol 2019; 15:e1006493. [PMID: 30768597 PMCID: PMC6395011 DOI: 10.1371/journal.pcbi.1006493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/28/2019] [Accepted: 09/10/2018] [Indexed: 11/24/2022] Open
Abstract
Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference-such as newly supported clade concepts-have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences. Here we develop a novel solution to the conflict verbalization challenge, based on a logic representation and reasoning approach that utilizes the language of Region Connection Calculus (RCC-5) to produce consistent alignments of node concepts endorsed by incongruent phylogenomic studies. The approach employs clade concept labels to individuate concepts used by each source, even if these carry identical names. Indirect RCC-5 modeling of intensional (property-based) node concept definitions, facilitated by the local relaxation of coverage constraints, allows parent concepts to attain congruence in spite of their differentially sampled children. To demonstrate the feasibility of this approach, we align two recent phylogenomic reconstructions of higher-level avian groups that entail strong conflict in the "neoavian explosion" region. According to our representations, this conflict is constituted by 26 instances of input "whole concept" overlap. These instances are further resolvable in the output labeling schemes and visualizations as "split concepts", which provide the labels and relations needed to build truly synthetic phylogenomic data environments. Because the RCC-5 alignments fundamentally reflect the trained, logic-enabled judgments of systematic experts, future designs for such environments need to promote a culture where experts routinely assess the intensionalities of node concepts published by our peers-even and especially when we are not in agreement with each other.
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Affiliation(s)
- Nico M. Franz
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Lukas J. Musher
- Richard Gilder Graduate School and Department of Ornithology, American Museum of Natural History, New York, New York, United States of America
| | - Joseph W. Brown
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Shizhuo Yu
- Department of Computer Science, University of California at Davis, Davis, California, United States of America
| | - Bertram Ludäscher
- School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
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Doña J, Serrano D, Mironov S, Montesinos-Navarro A, Jovani R. Unexpected bird-feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario. Mol Ecol 2019; 28:379-390. [PMID: 30536745 DOI: 10.1111/mec.14968] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/16/2018] [Indexed: 12/24/2022]
Abstract
The high relevance of host-switching for the diversification of highly host-specific symbionts (i.e., those commonly inhabiting a single host species) demands a better understanding of host-switching dynamics at an ecological scale. Here, we used DNA metabarcoding to study feather mites on passerine birds in Spain, sequencing mtDNA (COI) for 25,540 individual mites (representing 64 species) from 1,130 birds (representing 71 species). Surprisingly, 1,228 (4.8%) mites from 84 (7.4%) birds were found on host species that were not the expected to be a host according to a recent bird-feather mite associations catalog. Unexpected associations were widespread across studied mite (40.6%) and bird (43.7%) species and showed smaller average infrapopulation sizes than typical associations. Unexpected mite species colonized hosts being distantly related to the set of their usual hosts, but with similar body size. The network of bird-mite associations was modular (i.e., some groups of bird and mite species tended to be more associated with each other than with the others), with 75.9% of the unexpected associations appearing within the module of the typical hosts of the mite species. Lastly, 68.4% of mite species found on unexpected hosts showed signatures of genetic differentiation, and we found evidence for reproduction or the potential for it in many of the unexpected associations. Results show host colonization as a common phenomenon even for these putatively highly host-specific symbionts. Thus, host-switching by feather mites, rather than a rare phenomenon, appears as a relatively frequent phenomenon shaped by ecological filters such as host morphology and is revealed as a fundamental component for a dynamic coevolutionary and codiversification scenario.
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Affiliation(s)
- Jorge Doña
- Department of Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - David Serrano
- Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Sergey Mironov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Embankment 1, Saint Petersburg, Russia
| | - Alicia Montesinos-Navarro
- Centro de Investigaciones sobre Desertificación (CSIC-UV-GV), Carretera Moncada-Náquera, Valencia, Spain
| | - Roger Jovani
- Department of Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Folk RA, Sun M, Soltis PS, Smith SA, Soltis DE, Guralnick RP. Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids. Am J Bot 2018; 105:433-445. [PMID: 29665035 DOI: 10.1002/ajb2.1059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/19/2017] [Indexed: 06/08/2023]
Abstract
Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data-and doing this with rigor despite all the attendant challenges-is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems is hampered by a lingering series of theoretical and practical bottlenecks. The community is still wrestling with the challenges of how to develop species-level, comprehensively sampled phylogenies and associated geographic and phenotypic resources that enable global-scale analyses. We illustrate difficulties and opportunities using the rosids as a case study, arguing that assembly of biodiversity data that is scale-appropriate-and therefore comprehensive and global in scope-is required to test global-scale hypotheses. Synthesizing comprehensive biodiversity data sets in clades such as the rosids will be key to understanding the origin and present-day evolutionary and ecological dynamics of the angiosperms.
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Affiliation(s)
- Ryan A Folk
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
| | - Miao Sun
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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Senderov V, Simov K, Franz N, Stoev P, Catapano T, Agosti D, Sautter G, Morris RA, Penev L. OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system. J Biomed Semantics 2018; 9:5. [PMID: 29347997 PMCID: PMC5774086 DOI: 10.1186/s13326-017-0174-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy. RESULTS OpenBiodiv-O introduces classes, properties, and axioms in the domains of scholarly biodiversity publishing and biological taxonomy and aligns them with several important domain ontologies (FaBiO, DoCO, DwC, Darwin-SW, NOMEN, ENVO). By doing so, it bridges the ontological gap across scholarly biodiversity publishing and biological taxonomy and allows for the creation of a Linked Open Dataset (LOD) of biodiversity information (a biodiversity knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System. A key feature of the ontology is that it is an ontology of the scientific process of biological taxonomy and not of any particular state of knowledge. This feature allows it to express a multiplicity of scientific opinions. The resulting OpenBiodiv knowledge system may gain a high level of trust in the scientific community as it does not force a scientific opinion on its users (e.g. practicing taxonomists, library researchers, etc.), but rather provides the tools for experts to encode different views as science progresses. CONCLUSIONS OpenBiodiv-O provides a conceptual model of the structure of a biodiversity publication and the development of related taxonomic concepts. It also serves as the basis for the OpenBiodiv Knowledge Management System.
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Affiliation(s)
- Viktor Senderov
- Pensoft Publishers, Prof. Georgi Zlatarski 12, Sofia, 1700 Bulgaria
- Institute of Biodiversity and Ecosystems Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kiril Simov
- Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nico Franz
- Arizona State University, School of Life Sciences, Tempe Campus, Tempe, 4501 AZ USA
| | - Pavel Stoev
- Pensoft Publishers, Prof. Georgi Zlatarski 12, Sofia, 1700 Bulgaria
- National Museum of Natural History, 1 Tsar Osvoboditel Blvd., Sofia, 1000 Bulgaria
| | | | | | | | | | - Lyubomir Penev
- Pensoft Publishers, Prof. Georgi Zlatarski 12, Sofia, 1700 Bulgaria
- Institute of Biodiversity and Ecosystems Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Franz NM, Sterner BW. To increase trust, change the social design behind aggregated biodiversity data. Database (Oxford) 2018; 2018:4791171. [PMID: 29315357 PMCID: PMC7206650 DOI: 10.1093/database/bax100] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 01/07/2023]
Abstract
Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors 'at the source.' We show that this strategy falls systematically short of a full diagnosis of the underlying causes of distrust. In particular, trust in an aggregator is not just a feature of the data signal quality provided by the sources to the aggregator, but also a consequence of the social design of the aggregation process and the resulting power balance between individual data contributors and aggregators. The latter have created an accountability gap by downplaying the authorship and significance of the taxonomic hierarchies-frequently called 'backbones'-they generate, and which are in effect novel classification theories that operate at the core of data-structuring process. The Darwin Core standard for sharing occurrence records plays an under-appreciated role in maintaining the accountability gap, because this standard lacks the syntactic structure needed to preserve the taxonomic coherence of data packages submitted for aggregation, potentially leading to inferences that no individual source would support. Since high-quality data packages can mirror competing and conflicting classifications, i.e. unsettled systematic research, this plurality must be accommodated in the design of biodiversity data integration. Looking forward, a key directive is to develop new technical pathways and social incentives for experts to contribute directly to the validation of taxonomically coherent data packages as part of a greater, trustworthy aggregation process.
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Affiliation(s)
- Nico M Franz
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Beckett W Sterner
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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Kissling WD, Ahumada JA, Bowser A, Fernandez M, Fernández N, García EA, Guralnick RP, Isaac NJB, Kelling S, Los W, McRae L, Mihoub J, Obst M, Santamaria M, Skidmore AK, Williams KJ, Agosti D, Amariles D, Arvanitidis C, Bastin L, De Leo F, Egloff W, Elith J, Hobern D, Martin D, Pereira HM, Pesole G, Peterseil J, Saarenmaa H, Schigel D, Schmeller DS, Segata N, Turak E, Uhlir PF, Wee B, Hardisty AR. Building essential biodiversity variables (
EBV
s) of species distribution and abundance at a global scale. Biol Rev Camb Philos Soc 2017; 93:600-625. [DOI: 10.1111/brv.12359] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- W. Daniel Kissling
- Department Theoretical and Computational Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED) University of Amsterdam, P.O. Box 94248 1090 GE Amsterdam The Netherlands
| | - Jorge A. Ahumada
- TEAM Network, Moore Center for Science, Conservation International, 2011 Crystal Dr. Suite 500 Arlington VA 22202 U.S.A
| | - Anne Bowser
- Woodrow Wilson International Center for Scholars, 1300 Pennsylvania Ave NW Washington DC 20004 U.S.A
| | - Miguel Fernandez
- Biodiversity Conservation Group, German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig, Deutscher Platz 5e 04103 Leipzig Germany
- Institute of Biology Martin Luther University Halle‐Wittenberg Halle Germany
- Instituto de Ecología Universidad Mayor de San Andrés (UMSA), Campus Universitario, Cota cota La Paz Bolivia
| | - Néstor Fernández
- Biodiversity Conservation Group, German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig, Deutscher Platz 5e 04103 Leipzig Germany
- Estación Biológica de Doñana EBD‐CSIC, Américo Vespucio s.n 41092 Sevilla Spain
| | - Enrique Alonso García
- Councillor of State of the Kingdom of Spain and Honorary Researcher of the Franklin Institute of the University of Alcalá Madrid Spain
| | - Robert P. Guralnick
- University of Florida Museum of Natural History, University of Florida at Gainesville Gainesville FL 32611‐2710 U.S.A
| | - Nick J. B. Isaac
- Biological Records Centre, Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford OX10 8BB Wallingford U.K
| | - Steve Kelling
- Cornell Lab of Ornithology Cornell University, 158 Sapsucker Woods Rd Ithaca NY 14850 U.S.A
| | - Wouter Los
- Department Theoretical and Computational Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED) University of Amsterdam, P.O. Box 94248 1090 GE Amsterdam The Netherlands
| | - Louise McRae
- Institute of Zoology, Zoological Society of London, Regent's Park NW1 4RY London U.K
| | - Jean‐Baptiste Mihoub
- UPMC Université Paris 06, Muséum National d'Histoire Naturelle, CNRS, CESCO, UMR 7204 Sorbonne Universités, 61 rue Buffon 75005 Paris France
- Department of Conservation Biology UFZ‐Helmholtz Centre for Environmental Research, Permoserstr. 15 04318 Leipzig Germany
| | - Matthias Obst
- Department of Marine Sciences Göteborg University, Box 463 SE‐40530 Göteborg Sweden
- Gothenburg Global Biodiversity Centre, Box 461 SE‐405 30 Göteborg Sweden
| | - Monica Santamaria
- CNR‐Institute of Biomembranes and Bioenergetics, Amendola 165/A Street 70126 Bari Italy
| | - Andrew K. Skidmore
- Department of Natural Resources, Faculty of Geo‐Information Science and Earth Observation (ITC) University of Twente, P.O. Box 217 7500AE Enschede The Netherlands
| | - Kristen J. Williams
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), PO Box 1600 Canberra Australian Capital Territory 2601 Australia
| | | | - Daniel Amariles
- Decision and Policy Analysis (DAPA), International Center for Tropical Agriculture (CIAT) AA6713 Cali Colombia
- Instituto Alexander von Humboldt CALLE 28A # 15‐09 Bogota D.C. Colombia
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassokosmos, Former US Base at Gournes 71003 Heraklion, Crete Greece
| | - Lucy Bastin
- School of Engineering and Applied Science Aston University, Aston Triangle B4 7ET Birmingham U.K
- Knowledge Management Unit Joint Research Centre of the European Commission, Via Enrico Fermi 21027 Varese Italy
| | - Francesca De Leo
- CNR‐Institute of Biomembranes and Bioenergetics, Amendola 165/A Street 70126 Bari Italy
| | | | - Jane Elith
- School of BioSciences (Building 143) University of Melbourne Melbourne VIC 3010 Australia
| | - Donald Hobern
- Global Biodiversity Information Facility Secretariat, Universitetsparken 15 2100 København Ø Denmark
| | - David Martin
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), PO Box 1600 Canberra Australian Capital Territory 2601 Australia
| | - Henrique M. Pereira
- Biodiversity Conservation Group, German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig, Deutscher Platz 5e 04103 Leipzig Germany
- Institute of Biology Martin Luther University Halle‐Wittenberg Halle Germany
| | - Graziano Pesole
- CNR‐Institute of Biomembranes and Bioenergetics, Amendola 165/A Street 70126 Bari Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics University of Bari “A. Moro”, via Orabona 4 70125 Bari Italy
| | - Johannes Peterseil
- Department for Ecosystem Research & Environmental Information Management Umweltbundesamt GmbH, Spittelauer Lände 5 1090 Vienna Austria
| | - Hannu Saarenmaa
- Department of Forest Sciences, University of Eastern Finland, Joensuu Science Park, Länsikatu 15 FI‐80110 Joensuu Finland
| | - Dmitry Schigel
- Global Biodiversity Information Facility Secretariat, Universitetsparken 15 2100 København Ø Denmark
| | - Dirk S. Schmeller
- UPMC Université Paris 06, Muséum National d'Histoire Naturelle, CNRS, CESCO, UMR 7204 Sorbonne Universités, 61 rue Buffon 75005 Paris France
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS Toulouse France
| | - Nicola Segata
- Centre for Integrative Biology University of Trento, Via Sommarive 9 38123 Trento Italy
| | - Eren Turak
- NSW Office of Environment and Heritage, PO Box A290 Sydney South NSW 1232 Australia
- Australian Museum, 6 College Street Sydney NSW 2000 Australia
| | - Paul F. Uhlir
- Consultant, Data Policy and Management, P.O. Box 305, Callicoon NY 12723 U.S.A
| | - Brian Wee
- Massive Connections, 2410 17th St NW, Apt 306 Washington DC 20009 U.S.A
| | - Alex R. Hardisty
- School of Computer Science & Informatics Cardiff University, Queens Buildings, 5 The Parade Cardiff CF24 3AA U.K
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Gordy MA, Locke SA, Rawlings TA, Lapierre AR, Hanington PC. Molecular and morphological evidence for nine species in North American Australapatemon (Sudarikov, 1959): a phylogeny expansion with description of the zygocercous Australapatemon mclaughlini n. sp. Parasitol Res 2017. [PMID: 28623502 DOI: 10.1007/s00436-017-5523-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Zygocercous (aggregating) cercarial larvae were recently discovered emerging from a physid snail during a molecular survey of cercariae from molluscs in lakes in central Alberta, Canada. This manuscript delves into the characterization of these cercariae through morphological and molecular techniques and provides the first genetic information for a zygocercous larval trematode. Analyses of cytochrome c oxidase I of mitochondrial DNA and two partial regions of nuclear ribosomal DNA sequences revealed the zygocercous cercariae to belong to the genus Australapatemon Sudarikov, 1959. Further analyses of sequences of Australapatemon burti (Miller, 1923), from cercariae and adults collected from across North America, indicate a complex of nine genetically-distinct lineages within this species, a surprising level of diversity. The zygocercous cercariae, along with adult worms collected from ducks in Manitoba, Canada, and from Mexico, represent one of these lineages, and are herein described as Australapatemon mclaughlini n. sp. Seven lineages cannot yet be identified, but one is tentatively identified as Australapatemon burti.
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Affiliation(s)
- Michelle A Gordy
- University of Alberta School of Public Health, 357F South Academic Building, Edmonton, AB, T6G 2G7, Canada
| | - Sean A Locke
- Department of Biology, University of Puerto Rico at Mayagüez, Box 9000, Mayagüez, 00681-9000, Puerto Rico
| | - Timothy A Rawlings
- Department of Biology, Cape Breton University, 1250 Grand Lake Road, PO Box 5300, Sydney, NS, B1P 6L2, Canada
| | - Angela R Lapierre
- Department of Biology, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada
| | - Patrick C Hanington
- University of Alberta School of Public Health, 357F South Academic Building, Edmonton, AB, T6G 2G7, Canada.
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Franz N, Gilbert E, Ludäscher B, Weakley A. Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal. RIO 2016. [DOI: 10.3897/rio.2.e10610] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Overview. Taxonomic names are imperfect identifiers of specific and sometimes conflicting taxonomic perspectives in aggregated biodiversity data environments. The inherent ambiguities of names can be mitigated using syntactic and semantic conventions developed under the taxonomic concept approach. These include: (1) representation of taxonomic concept labels (TCLs: name sec. source) to precisely identify name usages and meanings, (2) use of parent/child relationships to assemble separate taxonomic perspectives, and (3) expert provision of Region Connection Calculus articulations (RCC–5: congruence, [inverse] inclusion, overlap, exclusion) that specify how data identified to different-sourced TCLs can be integrated. Application of these conventions greatly increases trust in biodiversity data networks, most of which promote unitary taxonomic 'syntheses' that obscure the actual diversity of expert-held views. Better design solutions allow users to control the taxonomic variable and thereby assess the robustness of their biological inferences under different perspectives. A unique constellation of prior efforts – including the powerful Symbiota collections software platform, the Euler/X multi-taxonomy alignment toolkit, and the "Weakley Flora" which entails 7,000 concepts and more than 75,000 RCC–5 articulations – provides the opportunity to build a first full-scale concept resolution service for SERNEC, the SouthEast Regional Network of Expertise and Collections, currently with 60 member herbaria and 2 million occurrence records.
Intellectual merit. We have developed a multi-dimensional, step-wise plan to transition SERNEC's data culture from name- to concept-based practices. (1) We will engage SERNEC experts through annual, regional workshops and follow-up interactions that will foster buy-in and ultimately the completion of 12 community-identified use cases. (2). We will leverage RCC–5 data from the Weakley Flora and further development of the Euler/X logic reasoning toolkit to provide comprehensive genus- to variety-level concept alignments for at least 10 major flora treatments with highest relevance to SERNEC. The visualizations and estimated > 1 billion inferred concept-to-concept relations will effectively drive specimen data integration in the transformed portal. (3) We will expand Symbiota's taxonomy and occurrence schemas and related user interfaces to support the new concept data, including novel batch and map-based specimen determination modules, with easy output options in Darwin Core Archive format. (4) Through combinations of the new technology, enlisted taxonomic expertise, and SERNEC's large image resources, we will upgrade minimally 80% of all SERNEC specimen identifications from names to the narrowest suitable TCLs, or add "uncertainty" flags to specimens needing further study. (5) We will utilize the novel tools and data to demonstrate how controlling for the taxonomic variable in 12 use cases variously drives the outcomes of evolutionary, ecological, and conservation-based research hypotheses.
Broader impacts. Our project is focused on just one herbarium network, but the potential impact is as wide as Darwin Core or even comparative biology. We believe that trust in networked biodiversity data depends on open and dynamic system designs, allowing expert access and resolution of multiple conflicting views that reflect the complex realities of ongoing taxonomic research. Taking well over 1 million SERNEC records from name- to TCL-resolution will show that "big" specimen data can pass the credibility threshold needed to validate the substantive data mobilization investment. We will mentor one postdoctoral researcher (UNC), two Ph.D. students (ASU, UIUC), and at least 15 undergraduate students (ASU). Each of our workshops will capacitate 10-15 SERNEC experts, who in turn can recruit colleagues and students at their home collections. We will incorporate the project theme and use cases into undergraduate courses taught at six institutions and reaching an estimated 300-500 students annually (10-40% minority students). At each institution, project members will make a systematic effort to recruit new students from underrepresented groups. Our group's leadership of Symbiota (with close ties to iDigBio), SERNEC, and local biodiversity projects and centers will further promote the new data culture. We will create a feature story "Where do plant species occur?" for ASU's popular "Ask A Biologist" website, and a series of undergraduate student-led "How-To" videos that illustrate the use case workflows, including the creation of multi-taxonomy alignments.
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Jarić I, Courchamp F, Gessner J, Roberts DL. Data mining in conservation research using Latin and vernacular species names. PeerJ 2016; 4:e2202. [PMID: 27547528 PMCID: PMC4957995 DOI: 10.7717/peerj.2202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/10/2016] [Indexed: 12/01/2022] Open
Abstract
In conservation science, assessments of trends and priorities for actions often focus on species as the management unit. Studies on species coverage in online media are commonly conducted by using species vernacular names. However, the use of species vernacular names for web-based data search is problematic due to the high risk of mismatches in results. While the use of Latin names may produce more consistent results, it is uncertain whether a search using Latin names will produce unbiased results as compared to vernacular names. We assessed the potential of Latin names to be used as an alternative to vernacular names for the data mining within the field of conservation science. By using Latin and vernacular names, we searched for species from four species groups: diurnal birds of prey, Carnivora, Primates and marine mammals. We assessed the relationship of the results obtained within different online sources, such as Internet pages, newspapers and social media networks. Results indicated that the search results based on Latin and vernacular names were highly correlated, and confirmed that one may be used as an alternative for the other. We also demonstrated the potential of the number of images posted on the Internet to be used as an indication of the public attention towards different species.
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Affiliation(s)
- Ivan Jarić
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Franck Courchamp
- Ecologie, Systématique, and Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris Sud (Paris XI) , Orsay , France
| | - Jörn Gessner
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin , Germany
| | - David L Roberts
- Durrell Institute of Conservation and Ecology, School of Anthropology & Conservation, Marlowe Building, University of Kent , Canterbury , Kent , United Kingdom
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Affiliation(s)
- Marco Sigovini
- CNR – National Research Council of Italy ISMAR – Marine Sciences Institute Arsenale Tesa 104 Castello 2737/F I‐30122 Venice Italy
| | - Erica Keppel
- CNR – National Research Council of Italy ISMAR – Marine Sciences Institute Arsenale Tesa 104 Castello 2737/F I‐30122 Venice Italy
- Smithsonian Environmental Research Center (SERC) 647, Contees Wharf Road Edgewater MD 21037 USA
| | - Davide Tagliapietra
- CNR – National Research Council of Italy ISMAR – Marine Sciences Institute Arsenale Tesa 104 Castello 2737/F I‐30122 Venice Italy
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Franz NM, Pier NM, Reeder DM, Chen M, Yu S, Kianmajd P, Bowers S, Ludäscher B. Two Influential Primate Classifications Logically Aligned. Syst Biol 2016; 65:561-82. [PMID: 27009895 PMCID: PMC4911943 DOI: 10.1093/sysbio/syw023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/11/2016] [Accepted: 03/17/2016] [Indexed: 01/02/2023] Open
Abstract
Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments-in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms.
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Affiliation(s)
- Nico M Franz
- School of Life Sciences, PO Box 874501, Arizona State University, Tempe, AZ 85287, USA;
| | - Naomi M Pier
- School of Life Sciences, PO Box 874501, Arizona State University, Tempe, AZ 85287, USA
| | - Deeann M Reeder
- Department of Biology, Bucknell University, 1 Dent Drive, Lewisburg, PA 17837, USA
| | - Mingmin Chen
- Department of Computer Science, 2063 Kemper Hall, 1 Shields Avenue, University of California at Davis, CA 95616, USA
| | - Shizhuo Yu
- Department of Computer Science, 2063 Kemper Hall, 1 Shields Avenue, University of California at Davis, CA 95616, USA
| | - Parisa Kianmajd
- Department of Computer Science, 2063 Kemper Hall, 1 Shields Avenue, University of California at Davis, CA 95616, USA
| | - Shawn Bowers
- Department of Computer Science, 502 East Boone Avenue, AD Box 26, Gonzaga University, Spokane, WA 99258, USA
| | - Bertram Ludäscher
- Gradate School of Library and Information Science, 510 East Daniel Street, University of Illinois at Urbana-Champaign, Champaign, IL 61820
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Patterson D, Mozzherin D, Shorthouse DP, Thessen A. Challenges with using names to link digital biodiversity information. Biodivers Data J 2016; 4:e8080. [PMID: 27346955 PMCID: PMC4910497 DOI: 10.3897/bdj.4.e8080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/19/2016] [Indexed: 01/05/2023] Open
Affiliation(s)
| | - Dmitry Mozzherin
- Illinois Natural History Survey, Champaign, IL, United States of America
| | | | - Anne Thessen
- The Data Detektive, Waltham, United States of America
- The Ronin Institute for Independent Scholarship, Montclair, United States of America
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Dickinson EC. Reinforcing the foundations of ornithological nomenclature: Filling the gaps in Sherborn's and Richmond's historical legacy of bibliographic exploration. Zookeys 2016:107-34. [PMID: 26877655 PMCID: PMC4741217 DOI: 10.3897/zookeys.550.10170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 11/13/2022] Open
Abstract
Due to its public popularity, ornithology has a huge corpus of scientific publication for a relatively small number of species. Although there are global checklists of currently recognised taxa, there has been only limited, mainly individual, effort to build a nomenclatural database that the science of ornithology deserves. This is especially true in relation to concise synonymies. With the arrival of ZooBank and the Biodiversity Heritage Library, the time has come to develop synonymies and to add fuller bibliographic detail to databases. The preparation for both began at the start of the 20th century with extensive work by Sherborn and Richmond. I discuss their legacy, offer notes on significant work since then, and provide suggestions for what remains to be done. To make solid the foundations for ornithological nomenclature and taxonomy, especially for synonymies, ornithologists will need to collaborate much more and contribute to the digital infrastructure.
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Zermoglio PF, Guralnick RP, Wieczorek JR. A Standardized Reference Data Set for Vertebrate Taxon Name Resolution. PLoS One 2016; 11:e0146894. [PMID: 26760296 DOI: 10.1371/journal.pone.0146894] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/24/2015] [Indexed: 11/19/2022] Open
Abstract
Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only once during accessioning of specimens, or have a history of label changes without clear provenance. Before records are reliably usable in research, it is critical that these issues be addressed. However, still missing is an assessment of the scope of the problem, the effort needed to solve it, and a way to improve effectiveness of tools developed to aid the process. We present a carefully human-vetted analysis of 1000 verbatim scientific names taken at random from those published via the data aggregator VertNet, providing the first rigorously reviewed, reference validation data set. In addition to characterizing formatting problems, human vetting focused on detecting misspelling, synonymy, and the incorrect use of Darwin Core. Our results reveal a sobering view of the challenge ahead, as less than 47% of name strings were found to be currently valid. More optimistically, nearly 97% of name combinations could be resolved to a currently valid name, suggesting that computer-aided approaches may provide feasible means to improve digitized content. Finally, we associated names back to biocollections records and fit logistic models to test potential drivers of issues. A set of candidate variables (geographic region, year collected, higher-level clade, and the institutional digitally accessible data volume) and their 2-way interactions all predict the probability of records having taxon name issues, based on model selection approaches. We strongly encourage further experiments to use this reference data set as a means to compare automated or computer-aided taxon name tools for their ability to resolve and improve the existing wealth of legacy data.
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Abstract
Scientific names serve to label biodiversity information: information related to species. Names, and their underlying taxonomic definitions, however, are unstable and ambiguous. This negatively impacts the utility of names as identifiers and as effective indexing tools in biological informatics where names are commonly utilized for searching, retrieving and integrating information about species. Semiotics provides a general model for describing the relationship between taxon names and taxon concepts. It distinguishes syntactics, which governs relationships among names, from semantics, which represents the relations between those labels and the taxa to which they refer. In the semiotic context, changes in semantics (i.e., taxonomic circumscription) do not consistently result in a corresponding and reflective change in syntax. Further, when syntactic changes do occur, they may be in response to semantic changes or in response to syntactic rules. This lack of consistency in the cardinal relationship between names and taxa places limits on how scientific names may be used in biological informatics in initially anchoring, and in the subsequent retrieval and integration, of relevant biodiversity information. Precision and recall are two measures of relevance. In biological taxonomy, recall is negatively impacted by changes or ambiguity in syntax while precision is negatively impacted when there are changes or ambiguity in semantics. Because changes in syntax are not correlated with changes in semantics, scientific names may be used, singly or conflated into synonymous sets, to improve recall in pattern recognition or search and retrieval. Names cannot be used, however, to improve precision. This is because changes in syntax do not uniquely identify changes in circumscription. These observations place limits on the utility of scientific names within biological informatics applications that rely on names as identifiers for taxa. Taxonomic systems and services used to organize and integrate information about taxa must accommodate the inherent semantic ambiguity of scientific names. The capture and articulation of circumscription differences (i.e., multiple taxon concepts) within such systems must be accompanied with distinct concept identifiers that can be employed in association with, or in replacement of, traditional scientific names.
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Affiliation(s)
- David Remsen
- Department of Marine Resources, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543
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