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Talavera A, Valbuena-Ureña E, Burriel-Carranza B, Mochales-Riaño G, Adams DC, Amat F, Carbonell F, Carranza S. Integrative systematic revision of the Montseny brook newt ( Calotriton arnoldi), with the description of a new subspecies. PeerJ 2024; 12:e17550. [PMID: 38881865 PMCID: PMC11180430 DOI: 10.7717/peerj.17550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
The Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxa.
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Affiliation(s)
- Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
- Museu de Ciències Naturals de Barcelona, Barcelona, Catalonia, Spain
| | - Gabriel Mochales-Riaño
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Dean C Adams
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States
| | - Fèlix Amat
- Àrea d'Herpetologia, Museu de Granollers-Ciències Naturals, Granollers, Catalonia, Spain
| | - Francesc Carbonell
- Centre de Fauna Salvatge de Torreferrussa, Santa Perpètua de Mogoda, Catalonia, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
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2
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Souza LHB, Pierson TW, Tenório RO, Ferro JM, Gatto KP, Silva BC, de Andrade GV, Suárez P, Haddad CFB, Lourenço LB. Multiple contact zones and karyotypic evolution in a neotropical frog species complex. Sci Rep 2024; 14:1119. [PMID: 38212602 PMCID: PMC10784582 DOI: 10.1038/s41598-024-51421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
Previous studies of DNA sequence and karyotypic data have revealed high genetic diversity in the Physalaemus cuvieri - Physalaemus ephippifer species complex-a group of small leptodactylid frogs in South America. To date, seven major genetic lineages have been recognized in this group, with species delimitation tests supporting four to seven of them as valid species. Among these, only P. ephippifer shows heteromorphic sex chromosomes, but the implications of cytogenetic divergence for the evolution of this group are unknown. We analyzed karyotypic, mitochondrial DNA, and 3RAD genomic data to characterize a putative contact zone between P. ephippifer and P. cuvieri Lineage 1, finding evidence for admixture and karyotypic evolution. We also describe preliminary evidence for admixture between two other members of this species complex-Lineage 1 and Lineage 3 of P. cuvieri. Our study sheds new light on evolutionary relationships in the P. cuvieri - P. ephippifer species complex, suggesting an important role of karyotypic divergence in its evolutionary history and underscoring the importance of hybridization as a mechanism of sex chromosome evolution in amphibians.
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Affiliation(s)
- Lucas H B Souza
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil.
| | - Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Renata O Tenório
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Juan M Ferro
- Laboratorio de Genética Evolutiva "Dr. Claudio J. Bidau", Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Kaleb P Gatto
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Bruno C Silva
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Gilda V de Andrade
- Departamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão (UFMA), Campus do Bacanga, São Luís, MA, 65080-040, Brazil
| | - Pablo Suárez
- Instituto de Biología Subtropical (CONICET-UNaM), Puerto Iguazú, Argentina
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Luciana B Lourenço
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
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3
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Pyron RA, Kakkera A, Beamer DA, O'Connell KA. Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype. Mol Ecol 2024; 33:e17219. [PMID: 38015012 DOI: 10.1111/mec.17219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Anvith Kakkera
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia, USA
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University, Greenville, North Carolina, USA
| | - Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
- Deloitte Consulting LLP, Health and Data AI, Arlington, Virginia, USA
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4
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Alexander Pyron R. Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation. Mol Phylogenet Evol 2023; 189:107939. [PMID: 37804960 DOI: 10.1016/j.ympev.2023.107939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or "Kohonen") Maps (SOMs) for such purposes. Recent extensions called "SuperSOMs" can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA.
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5
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Cook CN, Redford KH, Schwartz MW. Species conservation in the era of genomic science. Bioscience 2023; 73:885-890. [PMID: 38162573 PMCID: PMC10755706 DOI: 10.1093/biosci/biad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024] Open
Abstract
The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.
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Affiliation(s)
- Carly N Cook
- Monash University's School of Biological Sciences, Melbourne, Australia
| | - Kent H Redford
- University of New England's Department of Environmental Studies, Biddeford, Maine, United States
| | - Mark W Schwartz
- Department of Environmental Science and Policy, University of California, Davis, Davis, California, United States
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6
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Harbach RE, Wilkerson RC. The insupportable validity of mosquito subspecies (Diptera: Culicidae) and their exclusion from culicid classification. Zootaxa 2023; 5303:1-184. [PMID: 37518540 DOI: 10.11646/zootaxa.5303.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 08/01/2023]
Abstract
Beginning about 80 years ago, the recognition of morphological varieties of mosquitoes was gradually replaced by the recognition of subspecies. As an examination of revisionary and detailed taxonomic studies of mosquitoes clearly shows, subspecies are untenable concepts which have been synonymized with nominotypical forms or recognized as distinct species. Thus, from our perspective, subspecies is not a functional or practical taxonomic rank. Consequently, in this study we critically assessed the taxonomic status of the 120 nominal taxa distinguished as subspecies before now to determine whether they should be recognized as separate species or synonymous names. As a result, 96 subspecies are formally elevated to specific rank, 22 are relegated to synonymy with nominotypical forms, one is considered a nomen dubium, one a species inquirenda and the names of four nominal species regarded as synonyms are revalidated. The subspecies and their new status are listed in a conspectus. The revalidated species include Anopheles argentinus (Brèthes, 1912), from synonymy with An. pseudopunctipennis Theobald, 1901c; An. peruvianus Tamayo, 1907, from synonymy with An. pseudopunctipennis as nomen dubium; Culex major Edwards, 1935, from synonymy with Cx. annulioris consimilis Newstead, 1907; and Trichoprosopon trichorryes (Dyar & Knab, 1907), from synonymy with Tr. compressum Lutz, 1905. Additionally, the type locality of Anopheles sergentii Theobald, 1907 is restricted to El Outaya, Biskra Province, Algeria. A complete list of species to be retained, added to or removed from the Encyclopedia of Life, with a few corrections, is provided.
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Affiliation(s)
- Ralph E Harbach
- Department of Science; Natural History Museum; Cromwell Road; London SW7 5BD; UK.
| | - Richard C Wilkerson
- Department of Entomology; National Museum of Natural History; Smithsonian Institution; Washington DC 20013; USA; Walter Reed Biosystematics Unit; Museum Support Center; Smithsonian Institution; Suitland; MD 20746; USA; One Health Branch; Walter Reed Army Institute of Research; Silver Spring; MD 20910; USA.
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7
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Korshunova T, Lundin K, Malmberg K, Martynov A. Narrowly defined taxa on a global scale: The phylogeny and taxonomy of the genera Catriona and Tenellia (Nudibranchia, Trinchesiidae) favours fine-scale taxonomic differentiation and dissolution of the "lumpers & splitters" dilemma. Evol Appl 2023; 16:428-460. [PMID: 36793683 PMCID: PMC9923469 DOI: 10.1111/eva.13468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022] Open
Abstract
By applying morphological and molecular data on two genera of the nudibranch molluscs it is shown that the tension between taxonomic practice and evolutionary processes persists. A review of the related genera Catriona and Tenellia is used to demonstrate that the fine-scale taxonomic differentiation is an important tool in the integration of morphological and molecular data. This is highlighted by the hidden species problem and provides strong argument that the genus must be kept as a maximally narrowly-defined entity. Otherwise, we are forced to compare a highly disparate species under the putatively lumped name "Tenellia". We demonstrate this in the present study by applying a suite of delimitation methods and describing a new species of Tenellia from the Baltic Sea. The new species possesses fine-scale morphological distinguishing features, which were not investigated before. The true, narrowly defined genus Tenellia represents a peculiar taxon with a clearly expressed paedomorphic characters and predominantly brackish-water habitats. The phylogenetically related genus Catriona, of which three new species are described here, clearly demonstrates different features. A lumping decision to call many morphologically and evolutionary different taxa as "Tenellia" will downgrade the taxonomic and phylogenetic resolution of the entire family Trinchesiidae to just a single genus. The dissolution of the dilemma of "lumpers & splitters", which still significantly affects taxonomy, will further help to make systematics a true evolutionary discipline.
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Affiliation(s)
| | - Kennet Lundin
- Gothenburg Natural History Museum Gothenburg Sweden.,Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden
| | - Klas Malmberg
- Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden.,Aquatilis Gothenburg Sweden
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8
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Molinari J. A bare-bones scheme to choose between the species, subspecies, and ‘evolutionarily significant unit’ categories in taxonomy and conservation. J Nat Conserv 2023. [DOI: 10.1016/j.jnc.2023.126335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Penna A, Dillon R, Bearder SK, Karlsson J, Perkin A, Pozzi L. Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.
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Affiliation(s)
- Anna Penna
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Rosemarie Dillon
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Johan Karlsson
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Luca Pozzi
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
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10
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Prates I, Doughty P, Rabosky DL. Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard ( Ctenotus pantherinus). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.
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Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan , Ann Arbor, MI , USA
- Museum of Zoology, University of Michigan , Ann Arbor, MI , USA
| | - Paul Doughty
- Collections & Research, Western Australian Museum , Welshpool , WA 6106 , Australia
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11
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Juman MM, Woodman N, Miller-Murthy A, Olson LE, Sargis EJ. Taxonomic boundaries in Lesser Treeshrews (Scandentia, Tupaiidae: Tupaia minor ). J Mammal 2022. [DOI: 10.1093/jmammal/gyac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The Lesser Treeshrew, Tupaia minor Günther, 1876, is a small mammal from Southeast Asia with four currently recognized subspecies: T. m. minor from Borneo; T. m. malaccana from the Malay Peninsula; T. m. humeralis from Sumatra; and T. m. sincepis from Singkep Island and Lingga Island. A fifth subspecies, T. m. caedis, was previously synonymized with T. m. minor; it was thought to occur in northern Borneo and on the nearby islands of Banggi and Balambangan. These subspecies were originally differentiated based on pelage color, a plastic feature that has proven to be an unreliable indicator of taxonomic boundaries in treeshrews and other mammals. To explore infraspecific variation among T. minor populations across the Malay Peninsula, Borneo, Sumatra, and smaller islands, we conducted multivariate analyses of morphometric data collected from the hands and skulls of museum specimens. Principal component and discriminant function analyses reveal limited differentiation in manus and skull proportions among populations of T. minor from different islands. We find no morphometric support for the recognition of the four allopatric subspecies and no support for the recognition of T. m. caedis as a separate subspecies on Borneo.
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Affiliation(s)
- Maya M Juman
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, Connecticut 06520 , USA
| | - Neal Woodman
- U.S. Geological Survey, Eastern Ecological Science Center , Laurel, Maryland 20708 , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
| | - Ananth Miller-Murthy
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, Connecticut 06520 , USA
| | - Link E Olson
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
- Department of Mammalogy, University of Alaska Museum, University of Alaska Fairbanks , Fairbanks, Alaska 99775 , USA
| | - Eric J Sargis
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, Connecticut 06520 , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, District of Columbia 20013 , USA
- Division of Vertebrate Zoology, Yale Peabody Museum of Natural History , New Haven, Connecticut 06520 , USA
- Department of Anthropology, Yale University , New Haven, Connecticut 06520 , USA
- Yale Institute for Biospheric Studies , New Haven, Connecticut 06520 , USA
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12
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Reilly SB, Karin BR, Stubbs AL, Arida E, Arifin U, Kaiser H, Bi K, Hamidy A, Iskandar DT, McGuire JA. Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago. Evolution 2022; 76:2281-2301. [PMID: 35932243 DOI: 10.1111/evo.14592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Zoology Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Hinrich Kaiser
- Department of Biology, Victor Valley College, 18422 Bear Valley Road, Victorville, California, 92395, USA.,Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djoko T Iskandar
- Basic Sciences Commission, Indonesian Academy of Sciences, 11, Jl. Medan Merdeka, Selatan Jakarta, 10110, Indonesia.,School of Life Sciences and Technology, Institut Teknologi Bandung, 10 Jalan Ganesha, Bandung, 40132, Indonesia
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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13
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Barrett CF, Santee MV, Fama NM, Freudenstein JV, Simon SJ, Sinn BT. Lineage and role in integrative taxonomy of a heterotrophic orchid complex. Mol Ecol 2022; 31:4762-4781. [PMID: 35837745 PMCID: PMC9452484 DOI: 10.1111/mec.16617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Mathilda V. Santee
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Nicole M. Fama
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - John V. Freudenstein
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 1315 Kinnear Rd., Columbus, Ohio, USA 43212
| | - Sandra J. Simon
- Department of Biology, West Virginia University Institute of Technology, Beckley, WV, USA
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, USA
- Department of Botany and Ecology, University of Latvia, Jelgavas iela 1, Riga, LV-1004, Latvia
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14
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Smith LT, Magdalena C, Przelomska NAS, Pérez-Escobar OA, Melgar-Gómez DG, Beck S, Negrão R, Mian S, Leitch IJ, Dodsworth S, Maurin O, Ribero-Guardia G, Salazar CD, Gutierrez-Sibauty G, Antonelli A, Monro AK. Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation. FRONTIERS IN PLANT SCIENCE 2022; 13:883151. [PMID: 35860537 PMCID: PMC9289450 DOI: 10.3389/fpls.2022.883151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus Victoria (Nymphaeaceae). The systematics of Victoria has thus far been poorly characterized due to difficulty in attributing species identities to biological collections. This research gap stems from an absence of type material and biological collections, also the confused diagnosis of V. cruziana. With the goal of improving systematic knowledge of the genus, we compiled information from historical records, horticulture and geography and assembled a morphological dataset using citizen science and specimens from herbaria and living collections. Finally, we generated genomic data from a subset of these specimens. Morphological and geographical observations suggest four putative species, three of which are supported by nuclear population genomic and plastid phylogenomic inferences. We propose these three confirmed entities as robust species, where two correspond to the currently recognized V. amazonica and V. cruziana, the third being new to science, which we describe, diagnose and name here as V. boliviana Magdalena and L. T. Sm. Importantly, we identify new morphological and molecular characters which serve to distinguish the species and underpin their delimitations. Our study demonstrates how combining different types of character data into a heuristic, total-evidence approach can enhance the reliability with which biological diversity of morphologically challenging groups can be identified, documented and further studied.
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Affiliation(s)
- Lucy T. Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Darío G. Melgar-Gómez
- Herbario German Coimbra Sanz, Jardín Botánico Municipal de Santa Cruz de la Sierra, Santa Cruz de la Sierra, Bolivia
| | - Stephan Beck
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Raquel Negrão
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Sahr Mian
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | | | | | | | - Gloria Gutierrez-Sibauty
- Herbario German Coimbra Sanz, Jardín Botánico Municipal de Santa Cruz de la Sierra, Santa Cruz de la Sierra, Bolivia
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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15
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Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology American Museum of Natural History New York New York USA
| | - Brian I Crother
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Christopher M Murray
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Brian Tilston Smith
- Department of Ornithology American Museum of Natural History New York New York USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center Field Museum of Natural History Chicago Illinois USA
| | - Edward A Myers
- Department of Herpetology American Museum of Natural History New York New York USA.,Department of Biological Sciences Clemson University Clemson South Carolina USA.,Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA
| | - Robert Alexander Pyron
- Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA.,Department of Biological Sciences The George Washington University Washington District of Columbia USA
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16
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Wells T, Carruthers T, Scotland RW. Heuristics, species, and the analysis of systematic data. TRENDS IN PLANT SCIENCE 2022; 27:524-527. [PMID: 35450796 DOI: 10.1016/j.tplants.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Disagreements over how to define species potentially render them incomparable, yet biologists routinely count and compare species. This 'species problem' persists despite the wealth of data and methods available to contemporary systematists. A heuristic approach to species provides a consistent yet flexible means of selecting, assessing, and integrating different biological data.
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Affiliation(s)
- Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, UK.
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17
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Werhahn G, Senn H, Macdonald DW, Sillero-Zubiri C. The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.782528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.
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18
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Hope AG, Frey JK. Misinterpretation of Genomic Data Matters for Endangered Species Listing: The Sub-specific Status of the Peñasco Least Chipmunk (Neotamias minimus atristriatus). FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2021.793277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We provide a response to a recently published evaluation of the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus). The work we discuss used exon capture genomic approaches and concluded that their results did not support the distinction of this taxon as a subspecies, with recommendation that it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic recommendations of this study, and explain in clearer terms how to interpret genomic analyses for applied management. We identify four broad conceptual issues that led to errant recommendations: (1) interpretation of subspecies and diagnosability, (2) inappropriate use of reciprocal monophyly as a criterion for subspecies, (3) importance of geographic isolation, and (4) error in hypothesis testing and misinterpretation of results. We conclude that the data from this genomic appraisal add to information from prior studies providing strong support for recognition of N. m. atristriatus as a subspecies. Our conclusions have important and immediate implications for the proposed listing of N. m. atristriatus as an endangered species under the U.S. Endangered Species Act.
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19
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Radulovici AE, Vieira PE, Duarte S, Teixeira MAL, Borges LMS, Deagle BE, Majaneva S, Redmond N, Schultz JA, Costa FO. Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.67862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.
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20
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Westergaard KB, Kyrkjeeide MO, Brandrud MK. Using genomics to guide seed-sourcing at the right taxonomical level for ecological restoration projects: The complex case of Carex bigelowii s.lat. in Norway. Ecol Evol 2021; 11:17117-17131. [PMID: 34938497 PMCID: PMC8668773 DOI: 10.1002/ece3.8350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
There is a growing demand for ecological restoration using suitable seeds following international standards or national legal demands for local seed-sourcing. However, before selecting the appropriate geographic origin of seeds, it is vital to explore taxonomic complexity related to the focal taxa. We used ddRAD-seq to screen genomic diversity within Carex bigelowii s.lat. focussing on Norway. This species complex is considered a candidate for seeding, but presents considerable morphological, ecological, and genetic variation. The genetic structure of 132 individuals of C. bigelowii s.lat., including Carex nigra as an outgroup, was explored using ordinations, clustering analyses, and a genetic barrier algorithm. Two highly divergent clusters were evident, supporting the recognition of two taxonomic units "C. dacica" and C. bigelowii "subsp. bigelowii". Previously defined seed-sourcing regions for C. bigelowii s.lat. did not consider the known taxonomic complexity, and therefore interpreted the overall genetic structure as seed-sourcing regions, not taxa. We estimated genetic neighborhood sizes within each taxon to be 100-150 km and 300 km, respectively, indicating species-specific delimitations of local seed-sourcing regions. Frequent hybrids, local genetic distinctiveness, and suggested ecotypes add complexity to the discussed seed-sourcing regions. Our results show how genomic screening of diversity and structure in a species complex can alleviate the taxonomic impediment, inform practical questions, and legal requirements related to seed-sourcing, and together with traditional taxonomic work provide necessary information for a sound management of biodiversity.
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21
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Chou MH, Tseng WZ, Sang YD, Morgan B, De Vivo M, Kuan YH, Wang LJ, Chen WY, Huang JP. Incipient speciation and its impact on taxonomic decision: a case study using a sky island sister-species pair of stag beetles (Lucanidae: Lucanus). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Species delimitation can be difficult when the divergence between focal taxa is in the incipient stage of speciation, because conflicting results are expected among different data sets, and the species limits can differ depending on the species concept applied. We studied speciation history and investigated the impact on taxonomic decision-making when using different types of data in a Taiwanese endemic sister-species pair of stag beetles, Lucanus miwai and Lucanus yulaoensis, from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3%; however, L. miwai might not be monophyletic. The result of our multispecies coalescent-based species delimitation using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of the genealogical divergence index (gdi) corresponded to the ambiguous zone of species delimitation. We also showed that post-divergence gene flow is unlikely. Our study demonstrates challenges in the delineation of incipient species, but shows the importance of understanding the speciation history and adopting integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions.
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Affiliation(s)
- Ming-Hsun Chou
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Zhe Tseng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yao-De Sang
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Liang-Jong Wang
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Wei-Yun Chen
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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22
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Wells T, Carruthers T, Muñoz-Rodríguez P, Sumadijaya A, Wood JRI, Scotland RW. Species as a heuristic: reconciling theory and practice. Syst Biol 2021; 71:1233-1243. [PMID: 34672346 PMCID: PMC9366457 DOI: 10.1093/sysbio/syab087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/07/2021] [Accepted: 10/16/2021] [Indexed: 11/21/2022] Open
Abstract
Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the “species problem” stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and comparable unit of biology. Here, we suggest that treating species as a heuristic can be consistent with a theoretical definition of what species are and with the practical means by which they are identified and delimited. Specifically, we suggest that theoretically species are heuristic since they comprise clusters of closely related individuals responding in a similar manner to comparable sets of evolutionary and ecological forces, whilst they are practically heuristic because they are identifiable by the congruence of contingent properties indicative of those forces. This reconciliation of the theoretical basis of species with their practical applications in biological research allows for a loose but relatively consistent definition of species based on the strategic analysis and integration of genotypic, phenotypic, and ecotypic data. [Cohesion; heuristic; homeostasis; lineage; species problem.]
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Affiliation(s)
- Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | - Alex Sumadijaya
- Department of Plant Sciences, University of Oxford, Oxford, UK.,National Research and Innovation Agency, Cibinong Science Center, Indonesia
| | - John R I Wood
- Department of Plant Sciences, University of Oxford, Oxford, UK.,Royal Botanic Gardens, Kew, Richmond, UK
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23
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Brower AVZ. A slippery reality: the epistemological shifting sands of tokogeny, phylogeny, lineages and species delimitation. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1929545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Andrew V. Z. Brower
- National Identification Services, Plant Protection and Quarantine, USDA-APHIS, 4700 River Road, Riverdale, 20737, MD, USA
- Division of Invertebrates, American Museum of Natural History, Central Park West at 79th Street, New York, 10024, NY, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D. C., 20013-7012, USA
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24
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Athreya S, Hopkins A. Conceptual issues in hominin taxonomy: Homo heidelbergensis and an ethnobiological reframing of species. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175 Suppl 72:4-26. [PMID: 34117636 DOI: 10.1002/ajpa.24330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/29/2022]
Abstract
Efforts to name and classify Middle Pleistocene Homo, often referred to as "Homo heidelbergensis" are hampered by confusing patterns of morphology but also by conflicting paleoanthropological ideologies that are embedded in approaches to hominin taxonomy, nomenclature, and the species concept. We deconstruct these issues to show how the field's search for a "real" species relies on strict adherence to pre-Darwinian essentialist naming rules in a post-typological world. We then examine Middle Pleistocene Homo through the framework of ethnobiology, which examines on how Indigenous societies perceive, classify, and name biological organisms. This research reminds us that across human societies, taxonomies function to (1) identify and classify organisms based on consensus pattern recognition and (2) construct a stable nomenclature for effective storage, retrieval and communication of information. Naming Middle Pleistocene Homo as a "real" species cannot be verified with the current data; and separating regional groups into distinct evolutionary lineages creates taxa that are not defined by readily perceptible or universally salient differences. Based on ethnobiological studies of this kind of patterning, referring to these hominins above the level of the species according to their generic category with modifiers (e.g., "European Middle Pleistocene Homo") is consistent with observed human capabilities for cognitive differentiation, is both necessary and sufficient given the current data, and will allow for the most clear communication across ideologies going forward.
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Affiliation(s)
- Sheela Athreya
- Liberal Arts Program, Texas A&M University-Qatar, Doha, Qatar.,Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - Allison Hopkins
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
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25
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Singh PR, Karssen G, Couvreur M, Subbotin SA, Bert W. Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes. PLANTS (BASEL, SWITZERLAND) 2021; 10:408. [PMID: 33671787 PMCID: PMC7926417 DOI: 10.3390/plants10020408] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/18/2023]
Abstract
Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.
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Affiliation(s)
- Phougeishangbam Rolish Singh
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
- National Plant Protection Organization, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Marjolein Couvreur
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
| | - Sergei A. Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA;
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian, Academy of Sciences, Leninskii Prospect 33, 117071 Moscow, Russia
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium; (G.K.); (M.C.); (W.B.)
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