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Karbstein K, Kösters L, Hodač L, Hofmann M, Hörandl E, Tomasello S, Wagner ND, Emerson BC, Albach DC, Scheu S, Bradler S, de Vries J, Irisarri I, Li H, Soltis P, Mäder P, Wäldchen J. Species delimitation 4.0: integrative taxonomy meets artificial intelligence. Trends Ecol Evol 2024; 39:771-784. [PMID: 38849221 DOI: 10.1016/j.tree.2023.11.002] [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: 05/08/2023] [Revised: 10/20/2023] [Accepted: 11/08/2023] [Indexed: 06/09/2024]
Abstract
Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.
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Affiliation(s)
- Kevin Karbstein
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany.
| | - Lara Kösters
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Ladislav Hodač
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Martin Hofmann
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany
| | - Elvira Hörandl
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Salvatore Tomasello
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Natascha D Wagner
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Brent C Emerson
- Institute of Natural Products and Agrobiology (IPNA-CSIC), Island Ecology and Evolution Research Group, 38206 La Laguna, Tenerife, Canary Islands, Spain
| | - Dirk C Albach
- Carl von Ossietzky-Universität Oldenburg, Institute of Biology and Environmental Science, 26129 Oldenburg, Germany
| | - Stefan Scheu
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany; University of Göttingen, Centre of Biodiversity and Sustainable Land Use (CBL), 37073 Göttingen, Germany
| | - Sven Bradler
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany
| | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, 37077 Göttingen, Germany; University of Göttingen, Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany; University of Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, 37077 Göttingen, Germany
| | - Iker Irisarri
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Centre for Molecular Biodiversity Research, Phylogenomics Section, Museum of Nature, 20146 Hamburg, Germany
| | - He Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Chenshan Botanical Garden, 201602 Shanghai, China
| | - Pamela Soltis
- University of Florida, Florida Museum of Natural History, 32611 Gainesville, USA
| | - Patrick Mäder
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Ecology and Evolution, Philosophenweg 16, 07743 Jena, Germany
| | - Jana Wäldchen
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
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2
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Davis HR, Sanford HT, Das I, Nashriq I, Leaché AD. Establishing species boundaries in Bornean geckos. Biol Lett 2024; 20:20240157. [PMID: 39140204 DOI: 10.1098/rsbl.2024.0157] [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: 03/26/2024] [Revised: 05/29/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024] Open
Abstract
Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering and delimiting species. However, delimiting species with a single locus (e.g. DNA barcoding) is biased towards overestimating species diversity. The highly diverse gecko genus Cyrtodactylus is one such group where delimitation using mtDNA remains the paradigm. In this study, we use genomic data to test putative species boundaries established using mtDNA within three recognized species of Cyrtodactylus on the island of Borneo. We predict that multi-locus genomic data will estimate fewer species than mtDNA, which could have important ramifications for the species diversity within the genus. We aim to (i) investigate the correspondence between species delimitations using mtDNA and genomic data, (ii) infer species trees for each target species, and (iii) quantify gene flow and identify migration patterns to assess population connectivity. We find that species diversity is overestimated and that species boundaries differ between mtDNA and nuclear data. This underscores the value of using genomic data to reassess mtDNA-based species delimitations for taxa lacking clear species boundaries. We expect the number of recognized species within Cyrtodactylus to continue increasing, but, when possible, genomic data should be included to inform more accurate species boundaries.
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Affiliation(s)
- Hayden R Davis
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington , Seattle, WA 98195, USA
| | - Henry T Sanford
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington , Seattle, WA 98195, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti of Malaysia, Sarawak , Kota Samarahan, Malaysia
| | - Izneil Nashriq
- Institute of Biodiversity and Environmental Conservation, Universiti of Malaysia, Sarawak , Kota Samarahan, Malaysia
| | - Adam D Leaché
- Department of Biology, Burke Museum of Natural History and Culture, University of Washington , Seattle, WA 98195, USA
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Liu Y, Fu X, Wang Y, Liu J, Liu Y, Li C, Dong J. Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida). PeerJ 2024; 12:e17480. [PMID: 38827288 PMCID: PMC11144392 DOI: 10.7717/peerj.17480] [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: 02/22/2023] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
Background Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae. Methods Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method. Results The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.
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Affiliation(s)
- Yingkui Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Xinxin Fu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Yu Wang
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Jing Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Yong Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Chong Li
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Jiajia Dong
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
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Davis CC, Choisy P. Medicinal plants meet modern biodiversity science. Curr Biol 2024; 34:R158-R173. [PMID: 38412829 DOI: 10.1016/j.cub.2023.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study of medicinal plants that combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, and ethnopharmacology - is poised to facilitate new breakthroughs in science, including pharmacological discoveries and rapid advancements in human health and well-being. Such interdisciplinary research leverages data and methods spanning space, time, and species associated with medicinal plant species evolution, ecology, genomics, and metabolomic trait diversity, all of which build heavily on traditional Indigenous knowledge. Such an interdisciplinary approach contrasts sharply with most well-funded and successful medicinal plant research during the last half-century, which, despite notable advancements, has greatly oversimplified the dynamic relationships between plants and humans, kept hidden the larger human narratives about these relationships, and overlooked potentially important research and discoveries into life-saving medicines. We suggest that medicinal plants and people should be viewed as partners whose relationship involves a complicated and poorly explored set of (socio-)ecological interactions including not only domestication but also commensalisms and mutualisms. In short, medicinal plant species are not just chemical factories for extraction and exploitation. Rather, they may be symbiotic partners that have shaped modern societies, improved human health, and extended human lifespans.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Patrick Choisy
- LVMH Research, 185 Avenue de Verdun, 45804 Saint Jean de Braye CEDEX, France
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5
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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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6
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Chan KO, Mulcahy DG, Anuar S. The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex). Syst Biol 2023; 72:1209-1219. [PMID: 37478480 DOI: 10.1093/sysbio/syad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/19/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiates the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
| | - Daniel G Mulcahy
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Shahrul Anuar
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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7
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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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8
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Dufresnes C, Poyarkov N, Jablonski D. Acknowledging more biodiversity without more species. Proc Natl Acad Sci U S A 2023; 120:e2302424120. [PMID: 37748058 PMCID: PMC10556632 DOI: 10.1073/pnas.2302424120] [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] [Indexed: 09/27/2023] Open
Abstract
Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research, College of Biology and Environment, Nanjing Forestry University, Nanjing210037, People’s Republic of China
| | - Nikolay Poyarkov
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi122000, Vietnam
- Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow119234, Russia
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava84215, Slovakia
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9
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Gijsbers JC, Englebert N, Prata KE, Pichon M, Dinesen Z, Brunner R, Eyal G, González-Zapata FL, Kahng SE, Latijnhouwers KRW, Muir P, Radice VZ, Sánchez JA, Vermeij MJA, Hoegh-Guldberg O, Jacobs SJ, Bongaerts P. Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths. BMC Biol 2023; 21:147. [PMID: 37365558 DOI: 10.1186/s12915-023-01630-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. RESULTS Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods. CONCLUSIONS The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.
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Affiliation(s)
- J C Gijsbers
- California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - N Englebert
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - K E Prata
- California Academy of Sciences, San Francisco, CA, 94118, USA
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - M Pichon
- Biodiversity Section, Queensland Museum, Townsville, 4810, Australia
| | - Z Dinesen
- Centre for Biodiversity and Conservation Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - R Brunner
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - G Eyal
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD, 4072, Australia
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - F L González-Zapata
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, 111711, Bogotá, Colombia
| | - S E Kahng
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, HI, 96822, USA
| | - K R W Latijnhouwers
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH, Amsterdam, The Netherlands
| | - P Muir
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - V Z Radice
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529, USA
| | - J A Sánchez
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, 111711, Bogotá, Colombia
| | - M J A Vermeij
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH, Amsterdam, The Netherlands
| | - O Hoegh-Guldberg
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - S J Jacobs
- California Academy of Sciences, San Francisco, CA, 94118, USA
| | - P Bongaerts
- California Academy of Sciences, San Francisco, CA, 94118, USA.
- Global Change Institute, The University of Queensland, St Lucia, QLD, 4072, Australia.
- CARMABI Foundation, Piscaderabaai Z/N, PO Box 2090, Willemstad, Curaçao.
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10
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Monjaraz-Ruedas R, Mendez RW, Hedin M. Species delimitation, biogeography, and natural history of dwarf funnel web spiders (Mygalomorphae, Hexurellidae, Hexurella) from the United States / Mexico borderlands. Zookeys 2023; 1167:109-157. [PMID: 37363739 PMCID: PMC10285686 DOI: 10.3897/zookeys.1167.103463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/29/2023] [Indexed: 06/28/2023] Open
Abstract
The rarely encountered spider genus Hexurella Gertsch & Platnick, 1979 includes some of the smallest mygalomorph spiders in the world, with four poorly known taxa from central and southeastern montane Arizona, southern California, and northern Baja California Norte. At time of description the genus was known from fewer than 20 individuals, with sparse natural history information suggesting a vagrant, web-building, litter-dwelling natural history. Here the first published taxonomic and natural history information for this taxon is provided in more than 50 years, working from extensive new geographic sampling, consideration of male and female morphology, and sequence capture-based nuclear phylogenomics and mitogenomics. Several new species are easily diagnosed based on distinctive male morphologies, while a complex of populations from central and northern Arizona required an integrative combination of genomic algorithmic species delimitation analyses and morphological study. Four new species are described, including H.ephedrasp. nov., H.uwiiltilsp. nov., H.xericasp. nov., and H.zassp. nov. Females of H.encina Gertsch & Platnick, 1979 are also described for the first time. It is predicted that additional new species will ultimately be found in the mountains of central and northwestern Arizona, northern mainland Mexico, and the Mojave Desert of California.
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Affiliation(s)
- Rodrigo Monjaraz-Ruedas
- Department of Biology, San Diego State University, San Diego, California 92182–4614, USASan Diego State UniversitySan DiegoUnited States of America
| | | | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California 92182–4614, USASan Diego State UniversitySan DiegoUnited States of America
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11
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Calixto-Rojas M, Lira-Noriega A, Rubio-Godoy M, Pérez-Ponce de León G, Pinacho-Pinacho CD. Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty. Mol Phylogenet Evol 2023:107856. [PMID: 37327830 DOI: 10.1016/j.ympev.2023.107856] [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: 12/10/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.
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Affiliation(s)
- Miguel Calixto-Rojas
- Doctorado en Ciencias, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico.
| | - Andrés Lira-Noriega
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Miguel Rubio-Godoy
- Instituto de Ecología, A.C., Red de Biología Evolutiva, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Gerardo Pérez-Ponce de León
- Escuela Nacional de Estudios Superiores unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Municipio de Ucú, Yucatán 97357, Mexico
| | - Carlos D Pinacho-Pinacho
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
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12
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Mera-Rodríguez D, Jourdan H, Ward PS, Shattuck S, Cover SP, Wilson EO, Rabeling C. Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics. Mol Phylogenet Evol 2023:107825. [PMID: 37244505 DOI: 10.1016/j.ympev.2023.107825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Studying the historical biogeography and life history transitions from eusocial colony life to social parasitism contributes to our understanding of the evolutionary mechanisms generating biodiversity in eusocial insects. The ants in the genus Myrmecia are a well-suited system for testing evolutionary hypotheses about how their species diversity was assembled through time because the genus is endemic to Australia with the single exception of the species M. apicalis inhabiting the Pacific Island of New Caledonia, and because at least one social parasite species exists in the genus. However, the evolutionary mechanisms underlying the disjunct biogeographic distribution of M. apicalis and the life history transition(s) to social parasitism remain unexplored. To study the biogeographic origin of the isolated, oceanic species M. apicalis and to reveal the origin and evolution of social parasitism in the genus, we reconstructed a comprehensive phylogeny of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements (UCEs) as molecular markers to generate a comprehensive molecular genetic dataset consisting of 2,287 loci per taxon on average for 66 out of the 93 known Myrmecia species as well as for the sister lineage Nothomyrmecia macrops and selected outgroups. Our time-calibrated phylogeny inferred that: (i) stem Myrmeciinae originated during the Paleocene ∼58 Ma ago; (ii) the current disjunct biogeographic distribution of M. apicalis was driven by long-distance dispersal from Australia to New Caledonia during the Miocene ∼14 Ma ago; (iii) the single social parasite species, M. inquilina, evolved directly from one of the two known host species, M. nigriceps, in sympatry via the intraspecific route of social parasite evolution; and (iv) 5 of the 9 previously established taxonomic species groups are non-monophyletic. We suggest minor changes to reconcile the molecular phylogenetic results with the taxonomic classification. Our study enhances our understanding of the evolution and biogeography of Australian bulldog ants, contributes to our knowledge about the evolution of social parasitism in ants, and provides a solid phylogenetic foundation for future inquiries into the biology, taxonomy, and classification of Myrmeciinae.
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Affiliation(s)
- Daniela Mera-Rodríguez
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany.
| | - Hervé Jourdan
- Institute of Research for Development. Promenade Roger Laroque, Nouméa 98848, New Caledonia
| | - Philip S Ward
- Department of Entomology and Nematology, University of California, Davis, CA 95616, United States of America
| | - Steven Shattuck
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Stefan P Cover
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Edward O Wilson
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Christian Rabeling
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany; Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America.
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13
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Oury N, Noël C, Mona S, Aurelle D, Magalon H. From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 2023; 184:107803. [PMID: 37120114 DOI: 10.1016/j.ympev.2023.107803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France.
| | - Cyril Noël
- IFREMER - IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; EPHE, PSL Research University, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Didier Aurelle
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
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14
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Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex. BIOLOGY 2023; 12:biology12030418. [PMID: 36979110 PMCID: PMC10045763 DOI: 10.3390/biology12030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.
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15
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Sierra-Patev S, Min B, Naranjo-Ortiz M, Looney B, Konkel Z, Slot JC, Sakamoto Y, Steenwyk JL, Rokas A, Carro J, Camarero S, Ferreira P, Molpeceres G, Ruiz-Dueñas FJ, Serrano A, Henrissat B, Drula E, Hughes KW, Mata JL, Ishikawa NK, Vargas-Isla R, Ushijima S, Smith CA, Donoghue J, Ahrendt S, Andreopoulos W, He G, LaButti K, Lipzen A, Ng V, Riley R, Sandor L, Barry K, Martínez AT, Xiao Y, Gibbons JG, Terashima K, Grigoriev IV, Hibbett D. A global phylogenomic analysis of the shiitake genus Lentinula. Proc Natl Acad Sci U S A 2023; 120:e2214076120. [PMID: 36848567 PMCID: PMC10013852 DOI: 10.1073/pnas.2214076120] [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: 08/20/2022] [Accepted: 12/22/2022] [Indexed: 03/01/2023] Open
Abstract
Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes. We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia-Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase (lecsl) and γ-glutamyl transpeptidase (leggt), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula. Paralogs of both genes that are unique to Lentinula (lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes. The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.
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Affiliation(s)
| | - Byoungnam Min
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | | | - Brian Looney
- Biology Department, Clark University, Worcester, MA01610
| | - Zachary Konkel
- Department of Plant Pathology, Ohio State University, Columbus, OH43210
| | - Jason C. Slot
- Department of Plant Pathology, Ohio State University, Columbus, OH43210
| | - Yuichi Sakamoto
- Iwate Biotechnology Research Center, Kitakami, Iwate024-0003, Japan
| | - Jacob L. Steenwyk
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN37235
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN37235
| | - Juan Carro
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Patricia Ferreira
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, 50009Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza,50018Zaragoza, Spain
| | - Gonzalo Molpeceres
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Université13288, Marseille, France
- INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques13009, Marseille, France
| | - Karen W. Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN37996
| | - Juan L. Mata
- Department of Biology, University of South Alabama, Mobile, AL36688
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, ManausAM 69067-375, Brazil
| | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, ManausAM 69067-375, Brazil
| | - Shuji Ushijima
- The Tottori Mycological Institute, Japan Kinoko Research Center Foundation, Tottori689-1125, Japan
| | - Chris A. Smith
- Manaaki Whenua - Landcare Research, Auckland1072, New Zealand
| | - John Donoghue
- Northwest Mycological Consultants, Corvallis, OR97330
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Guifen He
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Laura Sandor
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei430070, China
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA01003
| | - Kazuhisa Terashima
- The Tottori Mycological Institute, Japan Kinoko Research Center Foundation, Tottori689-1125, Japan
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA94720
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA01610
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Ortiz D, Pekár S, Bryjová A. Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider. Mol Phylogenet Evol 2023; 180:107682. [PMID: 36574825 DOI: 10.1016/j.ympev.2022.107682] [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: 08/17/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czechia
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17
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Picks in the Fabric of a Polyploidy Complex: Integrative Species Delimitation in the Tetraploid Leucanthemum Mill. (Compositae, Anthemideae) Representatives. BIOLOGY 2023; 12:biology12020288. [PMID: 36829565 PMCID: PMC9953438 DOI: 10.3390/biology12020288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Based on the results of a preceding species-delimitation analysis for the diploid representatives of the genus Leucanthemum (Compositae, Anthemideae), the present study aims at the elaboration of a specific and subspecific taxonomic treatment of the tetraploid members of the genus. Following an integrative taxonomic approach, species-level decisions on eight predefined morphotaxon hypotheses were based on genetic/genealogical, morphological, ecological, and geographical differentiation patterns. ddRADseq fingerprinting and SNP-based clustering revealed genetic integrity for six of the eight morphotaxa, with no clear differentiation patterns observed between the widespread L. ircutianum subsp. ircutianum and the N Spanish (Cordillera Cantábrica) L. cantabricum and the S French L. delarbrei subsp. delabrei (northern Massif Central) and L. meridionale (western Massif Central). The inclusion of differentiation patterns in morphological (leaf dissection and shape), ecological (climatological and edaphic niches), and geographical respects (pair-wise tests of sympatry vs. allopatry) together with the application of a procedural protocol for species-rank decisions (the 'Wettstein tesseract') led to the proposal of an acknowledgement of the eight predefined morphotaxon hypotheses as six species (two of them with two subspecies). Nomenclatural consequences following from these results are drawn and lead to the following new combinations: Leucanthemum delarbrei subsp. meridionale (Legrand) Oberpr., T.Ott & Vogt, comb. nov. and Leucanthemum ruscinonense (Jeanb. & Timb.-Lagr.) Oberpr., T.Ott & Vogt, comb. et stat. nov.
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18
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Dietz L, Eberle J, Mayer C, Kukowka S, Bohacz C, Baur H, Espeland M, Huber BA, Hutter C, Mengual X, Peters RS, Vences M, Wesener T, Willmott K, Misof B, Niehuis O, Ahrens D. Standardized nuclear markers improve and homogenize species delimitation in Metazoa. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Paris‐Lodron‐University Salzburg Austria
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Sandra Kukowka
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Hannes Baur
- Naturhistorisches Museum Bern/Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Marianne Espeland
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Bernhard A. Huber
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Carl Hutter
- Museum of Natural Sciences and Department of Biological Sciences Louisiana State University Baton Rouge Louisiana USA
| | - Ximo Mengual
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Ralph S. Peters
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Miguel Vences
- Technische Universität Braunschweig Braunschweig Germany
| | - Thomas Wesener
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Keith Willmott
- Florida Museum of Natural History University of Florida Gainesville Florida USA
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert‐Ludwigs‐Universität Freiburg Freiburg im Breisgau Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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19
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Noguerales V, Ortego J. Genomic evidence of speciation by fusion in a recent radiation of grasshoppers. Evolution 2022; 76:2618-2633. [PMID: 35695020 PMCID: PMC9796961 DOI: 10.1111/evo.14508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 01/22/2023]
Abstract
Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.
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Affiliation(s)
- Víctor Noguerales
- Department of Biological SciencesUniversity of CyprusNicosia1678Cyprus,Island Ecology and Evolution GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de La Laguna38206Spain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana (EBD‐CSIC)Sevilla41092Spain
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20
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Miranda FR, Garbino GST, Machado FA, Perini FA, Santos FR, Casali DM. Taxonomic revision of maned sloths, subgenus Bradypus ( Scaeopus), Pilosa, Bradypodidae, with revalidation of Bradypus crinitus Gray, 1850. J Mammal 2022. [DOI: 10.1093/jmammal/gyac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
We present a taxonomic revision of maned sloths, subgenus Bradypus (Scaeopus), a taxon endemic to the Brazilian Atlantic Forest and currently composed of a single species, the vulnerable Bradypus torquatus. Our review is based on coalescent species delimitation analyses using mitochondrial and nuclear DNA, morphological analyses, and field observations. Our integrative approach demonstrates that two species of maned sloth can be recognized: the northern maned sloth (Bradypus torquatusIlliger, 1811) occurring in the Brazilian states of Bahia and Sergipe, and the southern maned sloth (Bradypus crinitusGray, 1850), occurring in Rio de Janeiro and Espirito Santo states. The two species diverged in the Early Pliocene and are allopatrically distributed. We discuss the biogeographic pattern of the two maned sloth species, comparing it with other Atlantic Forest mammals. We also suggest that the conservation status of both maned sloths needs to be reassessed after this taxonomic rearrangement.
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Affiliation(s)
- Flavia R Miranda
- Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade , Rod. Jorge Amado, Km 16 - Salobrinho, 45662-900 Ilhéus, Bahia, 64200-240 , Brazil
- Instituto de Pesquisa e Conservação de Tamanduás no Brasil , Rua do Comercio, s/n, Sala 130 Conjunto Porto das Barcas, Parnaíba, Piauí, 64200-240 , Brazil
| | - Guilherme S T Garbino
- Universidade Federal de Viçosa (UFV), Museu de Zoologia João Moojen, Departamento de Biologia Animal , Avenida Peter Henry Rolfs, s/n, Campus Universitário, 36570-900 Viçosa, Minas Gerais , Brazil
| | - Fabio A Machado
- Department of Biological Sciences, Virginia Tech , 926 West Campus Drive, Blacksburg, Virginia 24061 , USA
| | - Fernando A Perini
- Universidade Federal de Minas Gerais, Laboratório de Evolução de Mamíferos , Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, Minas Gerais , Brazil
| | - Fabricio R Santos
- Universidade Federal de Minas Gerais, Laboratório de Biodiversidade e Evolução Molecular , Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, Minas Gerais , Brazil
| | - Daniel M Casali
- Universidade Federal de Minas Gerais, Laboratório de Evolução de Mamíferos , Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, Minas Gerais , Brazil
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21
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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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22
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Novaes-e-Fagundes G, Lyra ML, Loredam VSA, Carvalho TR, Haddad CFB, Rodrigues MT, Baldo D, Barrasso DA, Loebmann D, Ávila RW, Brusquetti F, Prudente ALC, Wheeler WC, Goyannes Dill Orrico V, Peloso P. A tale of two bellies: systematics of the oval frogs (Anura: Microhylidae: Elachistocleis Parker, 1927). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac057] [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
Oval frogs (Elachistocleis) have a broad geographic distribution covering nearly all of South America and parts of Central America. They also have a large inter- and intraspecific variation of the few morphological characters commonly used as diagnostic traits among species of the genus. Based on molecular data, we provide the most complete phylogeny of Elachistocleis to date, and explore its genetic diversity using distance-based and tree-based methods for putative species delimitation. Our results show that at least two of the most relevant traditional characters used in the taxonomy of this group (belly pattern and dorsal median white line) carry less phylogenetic information than previously thought. Based on our results, we propose some synonymizations and some candidate new species. This study is a first major step in disentangling the current systematics of Elachistocleis. Yet, a comprehensive review of morphological data is needed before any new species descriptions can be properly made.
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Affiliation(s)
- Gabriel Novaes-e-Fagundes
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Mariana L Lyra
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Vinicius S A Loredam
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Thiago R Carvalho
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Célio F B Haddad
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo , São Paulo , Brazil
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical `Claudio Juan Bidau’ (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones , Posadas, Misiones , Argentina
| | - Diego A Barrasso
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET) , Puerto Madryn, Chubut , Argentina
- Facultad de Ciencias Naturales y Ciencias de la Salud, Universidad Nacional de la Patagonia `San Juan Bosco’ , Puerto Madryn, Chubut , Argentina
| | - Daniel Loebmann
- Laboratório de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande , Rio Grande, Rio Grande do Sul , Brazil
| | - Robson W Ávila
- Departamento de Biologia, Núcleo Regional de Ofiologia da UFC, Universidade Federal do Ceará , Fortaleza, Ceará , Brazil
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay , Del Escudo, Asunción , Paraguay
| | - Ana L C Prudente
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History , New York, NY , USA
| | - Victor Goyannes Dill Orrico
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Pedro Peloso
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
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23
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Doyle JJ. Cell types as species: Exploring a metaphor. FRONTIERS IN PLANT SCIENCE 2022; 13:868565. [PMID: 36072310 PMCID: PMC9444152 DOI: 10.3389/fpls.2022.868565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/29/2022] [Indexed: 06/05/2023]
Abstract
The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.
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24
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Chambers EA, Marshall TL, Hillis DM. The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation. Syst Biol 2022:6673165. [PMID: 35993885 DOI: 10.1093/sysbio/syac056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/17/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (Lampropeltis triangulum) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species L. triangulum and L. gentilis, we examined a ∼700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of L. triangulum, thus providing strong support for a single species in this region (and no support for the recognition of L. gentilis as a distinct species). At a second contact zone between proposed species L. triangulum and L. elapsoides (but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported L. triangulum and L. elapsoides as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin TX 78712 USA.,Department of Environmental Science, Policy, and Management, The University of California Berkeley, Berkeley CA 94720 USA
| | - Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin TX 78712 USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin TX 78712 USA
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25
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Dueck LA, Steffens EA. Historical genetic diversity and population structure of wild red pandas (Ailurus fulgens) in Nepal. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00272-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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Main DC, van Vuuren BJ, Tilbury CR, Tolley KA. Out of southern Africa: Origins and cryptic speciation in Chamaeleo, the most widespread chameleon genus. Mol Phylogenet Evol 2022; 175:107578. [PMID: 35809854 DOI: 10.1016/j.ympev.2022.107578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/18/2022] [Accepted: 07/01/2022] [Indexed: 11/19/2022]
Abstract
Molecular phylogenetics and the application of species delimitation methods have proven useful in addressing limitations associated with morphology based taxonomy and have highlighted the inconsistencies in the current taxonomy for many groups. For example, the genus Chamaeleo, which comprises 14 species with large distributions across mainland Africa and parts of Eurasia, exhibits relatively minor phenotypic differentiation between species, leading to speculation regarding the presence of cryptic diversity in the genus. Therefore, the aims of the present study were to construct a robust and comprehensive phylogeny of the genus and highlight potential species-level cryptic diversity. Additionally, we sought to ascertain the most likely biogeographic origin of the genus and understand its spatio-temporal diversification. Accordingly, we made use of species delimitation methods (Bayesian and divergence based) to investigate the extent of cryptic diversity in Chamaeleo, and applied an ancestral area reconstruction to examine the biogeographic origin of the group. Our phylogenetic analyses suggested the presence of at least 18 taxa within Chamaeleo. Notably, three taxa could be recognised within C. dilepis, none of which are equivalent in context with any of the currently described subspecies. There were also three taxa within C. gracilis and two within C. anchietae. The single available tissue specimen identified as C. necasi was embedded within the C. gracilis clade. Our ancestral area reconstruction points to a southern African/Zambezian origin for Chamaeleo, with diversification beginning during the cooling and aridification of Africa that characterised the Oligocene Epoch, ca. 34-23 Mya (Million years ago). Species-level diversification began in the Miocene Epoch (ca. 23-5 Mya), possibly tracking the aridification that triggered the shift from forest to more open, mesic savanna for most clades, but with tectonic events influencing speciation in a Palearctic clade. These findings lay the foundation for a future integrative taxonomic re-evaluation of Chamaeleo, which will be supported with additional lines of evidence before implementing any taxonomic changes.
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Affiliation(s)
- Devon C Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | - Colin R Tilbury
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Krystal A Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa; South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7 Claremont, Cape Town, South Africa.
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27
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Hua X, Herdha T, Burden C. Protracted speciation under the state-dependent speciation and extinction approach. Syst Biol 2022; 71:1362-1377. [PMID: 35699529 PMCID: PMC9558848 DOI: 10.1093/sysbio/syac041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/16/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
How long does speciation take? The answer to this important question in evolutionary biology lies in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here, we propose such a model and test the model performance on both simulated data and real data. We show that maximum-likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened. [Micro–macro evolution; Protracted birth–death process; speciation completion rate; SSE approach.]
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Affiliation(s)
- Xia Hua
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
| | - Tyara Herdha
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
| | - Conrad Burden
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
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28
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Zhang Y, Clancy J, Jensen J, McMullin RT, Wang L, Leavitt SD. Providing Scale to a Known Taxonomic Unknown—At Least a 70-Fold Increase in Species Diversity in a Cosmopolitan Nominal Taxon of Lichen-Forming Fungi. J Fungi (Basel) 2022; 8:jof8050490. [PMID: 35628746 PMCID: PMC9146994 DOI: 10.3390/jof8050490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/06/2023] Open
Abstract
Robust species delimitations provide a foundation for investigating speciation, phylogeography, and conservation. Here we attempted to elucidate species boundaries in the cosmopolitan lichen-forming fungal taxon Lecanora polytropa. This nominal taxon is morphologically variable, with distinct populations occurring on all seven continents. To delimit candidate species, we compiled ITS sequence data from populations worldwide. For a subset of the samples, we also generated alignments for 1209 single-copy nuclear genes and an alignment spanning most of the mitochondrial genome to assess concordance among the ITS, nuclear, and mitochondrial inferences. Species partitions were empirically delimited from the ITS alignment using ASAP and bPTP. We also inferred a phylogeny for the L. polytropa clade using a four-marker dataset. ASAP species delimitations revealed up to 103 species in the L. polytropa clade, with 75 corresponding to the nominal taxon L. polytropa. Inferences from phylogenomic alignments generally supported that these represent evolutionarily independent lineages or species. Less than 10% of the candidate species were comprised of specimens from multiple continents. High levels of candidate species were recovered at local scales but generally with limited overlap across regions. Lecanora polytropa likely ranks as one of the largest species complexes of lichen-forming fungi known to date.
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Affiliation(s)
- Yanyun Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
- College of Life Science, Anhui Normal University, Wuhu 241000, China
| | - Jeffrey Clancy
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA; (J.C.); (J.J.)
| | - Jacob Jensen
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA; (J.C.); (J.J.)
| | | | - Lisong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
- Correspondence: (L.W.); (S.D.L.)
| | - Steven D. Leavitt
- Department of Biology, M. L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602, USA
- Correspondence: (L.W.); (S.D.L.)
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29
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Laidoudi Y, Bedjaoui S, Latrofa MS, Fanelli A, Dantas-Torres F, Otranto D. Genetic and geographical delineation of zoonotic vector-borne helminths of canids. Sci Rep 2022; 12:6699. [PMID: 35462560 PMCID: PMC9035454 DOI: 10.1038/s41598-022-10553-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/30/2022] [Indexed: 12/15/2022] Open
Abstract
Several zoonotic vector-borne helminths (VBHs) infesting canids cause serious veterinary and medical diseases worldwide. Increasing the knowledge about their genetic structures is pivotal to identify them and therefore to settle effective surveillance and control measures. To overcome the limitation due to the heterogeneity of large DNA sequence-datasets used for their genetic characterization, available cytochrome c oxidase subunit 1 (cox1) (n = 546) and the 12S rRNA (n = 280) sequences were examined using combined bioinformatic approach (i.e., distance-clustering, maximum likelihood phylogeny and phylogenetic evolutionary placement). Out of the 826 DNA available sequences from GenBank, 94.7% were characterized at the haplotype level regardless sequence size, completeness and/or their position. A total of 89 different haplotypes were delineated either by cox1 (n = 35), 12S rRNA (n = 21) or by both genes (n = 33), for 14 VBHs (e.g., Acanthocheilonema reconditum, Brugia spp., Dirofilaria immitis, Dirofilaria repens, Onchocerca lupi and Thelazia spp.). Overall, the present approach could be useful for studying global genetic diversity and phylogeography of VBHs. However, as barcoding sequences were restricted to two mitochondrial loci (cox1 and 12S rRNA), the haplotype delineation proposed herein should be confirmed by the characterization of other nuclear loci also to overcome potential limitations caused by the heteroplasmy phenomenon within the mitogenome of VBHs.
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Affiliation(s)
- Younes Laidoudi
- Parasitology Unit, Department of Veterinary Medicine, University of Bari, Valenzano, Italy
- PADESCA Laboratory, Veterinary Science Institute, University of Constantine 1, 25100, El Khroub, Algeria
| | - Samia Bedjaoui
- Laboratory of Food Hygiene and Quality Insurance System (HASAQ), Higher National Veterinary School, Issad Abbes, Oued Smar, 16000, Algiers, Algeria
| | - Maria Stefania Latrofa
- Parasitology Unit, Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Angela Fanelli
- Infectious Diseases Unit, Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Filipe Dantas-Torres
- Laboratory of Immunoparasitology, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, 50740-465, Brazil
| | - Domenico Otranto
- Parasitology Unit, Department of Veterinary Medicine, University of Bari, Valenzano, Italy.
- Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan, Iran.
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30
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Segovia NI, González-Wevar CA, Naretto J, Rosenfeld S, Brickle P, Hüne M, Bernal V, Haye PA, Poulin E. The right tool for the right question: contrasting biogeographic patterns in the notothenioid fish Harpagifer spp. along the Magellan Province. Proc Biol Sci 2022; 289:20212738. [PMID: 35382596 PMCID: PMC8984805 DOI: 10.1098/rspb.2021.2738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Molecular-based analysis has become a fundamental tool to understand the role of Quaternary glacial episodes. In the Magellan Province in southern South America, ice covering during the last glacial maximum (20 ka) radically altered the landscape/seascape, speciation rates and distribution of species. For the notothenioid fishes of the genus Harpagifer, in the area are described two nominal species. Nevertheless, this genus recently colonized South America from Antarctica, providing a short time for speciation processes. Combining DNA sequences and genotyping-by-sequencing SNPs, we evaluated the role of Quaternary glaciations over the patterns of genetic structure in Harpagifer across its distribution in the Magellan Province. DNA sequences showed low phylogeographic structure, with shared and dominant haplotypes between nominal species, suggesting a single evolutionary unit. SNPs identified contrastingly two groups in Patagonia and a third well-differentiated group in the Falkland/Malvinas Islands with limited and asymmetric gene flow. Linking the information of different markers allowed us to infer the relevance of postglacial colonization mediated by the general oceanographic circulation patterns. Contrasting rough- and fine-scale genetic patterns highlights the relevance of combined methodologies for species delimitation, which, depending on the question to be addressed, allows discrimination among phylogeographic structure, discarding incipient speciation, and contemporary spatial differentiation processes.
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Affiliation(s)
- N I Segovia
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.,Instituto Milenio en Socio-ecología Costera (SECOS), Coquimbo, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
| | - C A González-Wevar
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile.,Instituto de Ciencias Marinas y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.,Centro de Investigación en Dinámicas de Ecosistemas de Altas Latitudes (Fondap IDEAL), Universidad Austral de Chile
| | - J Naretto
- Costa Humboldt, Puerto Varas, Los Lagos, Chile
| | - S Rosenfeld
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Laboratorio de Ecosistemas Antárticos y sub-Antárticos, Universidad de Magallanes, Chile
| | - P Brickle
- South Atlantic Environmental Research Institute (SAERI), PO Box 609, Stanley Cottage, Port Stanley, Falkland Islands, UK
| | - M Hüne
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Centro de Investigación para la Conservación de los Ecosistemas Australes (ICEA), Punta Arenas, Chile
| | - V Bernal
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
| | - P A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.,Instituto Milenio en Socio-ecología Costera (SECOS), Coquimbo, Chile
| | - E Poulin
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
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31
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Derkarabetian S, Starrett J, Hedin M. Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Front Zool 2022; 19:8. [PMID: 35193622 PMCID: PMC8862334 DOI: 10.1186/s12983-022-00453-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, Briggs Hall, Davis, CA, 95616-5270, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
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32
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Dufresnes C, Litvinchuk SN. Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology & Environment, Nanjing Forestry University, Nanjing, China
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biology, Dagestan State University, Makhachkala, Russia
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33
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Jorna J, Linde JB, Searle PC, Jackson AC, Nielsen M, Nate MS, Saxton NA, Grewe F, Herrera‐Campos MDLA, Spjut RW, Wu H, Ho B, Lumbsch HT, Leavitt SD. Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi. Ecol Evol 2021; 11:18615-18632. [PMID: 35003697 PMCID: PMC8717302 DOI: 10.1002/ece3.8467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 12/05/2022] Open
Abstract
Species delimitation among closely related species is challenging because traditional phenotype-based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, for example, hybridization/introgression and incomplete lineage sorting, and computational limitations. Here, we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler, in the family Ramalinaceae by analyzing single-locus and genome-scale data consisting of (a) single-locus species delimitation analysis using ASAP, (b) maximum likelihood-based phylogenetic tree inference, (c) genome-scale species delimitation models, e.g., BPP and SNAPP+BFD, and (d) species validation using the genealogical divergence index (gdi). We specifically use these methods to cross-validate results between genome-scale and single-locus datasets, differently sampled subsets of genomic data and to control for population-level genetic divergence. Our species delimitation models tend to support more speciose groupings that were inconsistent with traditional taxonomy, supporting a hypothesis of micro-endemism, which may include morphologically cryptic species. However, the models did not converge on robust, consistent species delimitations. While the results of our analysis are somewhat ambiguous in terms of species boundaries, they provide a valuable perspective on how to use these empirical species delimitation methods in a nonmodel system. This study thus highlights the challenges inherent in delimiting species, particularly in groups such as Niebla, with complex, relatively recent phylogeographic histories.
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Affiliation(s)
- Jesse Jorna
- Department of BiologyBrigham Young UniversityProvoUtahUSA
| | | | | | | | | | | | | | - Felix Grewe
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | | | | | - Huini Wu
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - Brian Ho
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - H. Thorsten Lumbsch
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - Steven D. Leavitt
- Department of BiologyBrigham Young UniversityProvoUtahUSA
- Monte L. Bean Life Science MuseumBrigham Young UniversityProvoUtahUSA
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34
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Firneno TJ, O’Neill JR, Itgen MW, Kihneman TA, Townsend JH, Fujita MK. Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance. Ecol Evol 2021; 11:12739-12753. [PMID: 34594535 PMCID: PMC8462145 DOI: 10.1002/ece3.8018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/24/2022] Open
Abstract
The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation-related actions.
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Affiliation(s)
- Thomas J. Firneno
- Department of BiologyUniversity of Texas at ArlingtonArlingtonTXUSA
- Department of Biology, Amphibian and Reptile Diversity Research CenterUniversity of Texas at ArlingtonArlingtonTXUSA
| | | | | | | | - Josiah H. Townsend
- Department of BiologyIndiana University of PennsylvaniaIndianaPAUSA
- Departamento de Ambiente y DesarrolloCentro Zamorano de BiodiversidadEscuela Agrícola Panamericana ZamoranoMunicipalidad de San Antonio de OrienteFrancisco MorazánHonduras
| | - Matthew K. Fujita
- Department of BiologyUniversity of Texas at ArlingtonArlingtonTXUSA
- Department of Biology, Amphibian and Reptile Diversity Research CenterUniversity of Texas at ArlingtonArlingtonTXUSA
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35
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Leaché AD, Davis HR, Singhal S, Fujita MK, Lahti ME, Zamudio KR. Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.678110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.
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36
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Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N. SPART: A versatile and standardized data exchange format for species partition information. Mol Ecol Resour 2021; 22:430-438. [PMID: 34288531 DOI: 10.1111/1755-0998.13470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
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Affiliation(s)
- Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | - Sophie Brouillet
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Shiga, Japan
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - L Lacey Knowles
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
| | - Sangeeta Kumari
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jeet Sukumaran
- Biology Department, LS 262, San Diego State University, San Diego, CA, USA
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Miguel Vences
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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37
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Sklenář F, Jurjević Ž, Houbraken J, Kolařík M, Arendrup M, Jørgensen K, Siqueira J, Gené J, Yaguchi T, Ezekiel C, Silva Pereira C, Hubka V. Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species. Stud Mycol 2021; 99:100120. [PMID: 35003383 PMCID: PMC8688885 DOI: 10.1016/j.simyco.2021.100120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Since the last revision in 2015, the taxonomy of section Flavipedes evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section Flavipedes members using modern delimitation methods applied to an extended set of strains (n = 90) collected from various environments. The analysis used DNA sequences of three house-keeping genes (benA, CaM, RPB2) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to sort the isolates into putative species, which were subsequently validated using DELINEATE software that was applied for the first time in fungal taxonomy. As a result, four new species are introduced, i.e. A. alboluteus, A. alboviridis, A. inusitatus and A. lanuginosus, and A. capensis is synonymized with A. iizukae. Phenotypic analyses were performed for the new species and their relatives, and the results showed that the growth parameters at different temperatures and colonies characteristics were useful for differentiation of these taxa. The revised section harbors 18 species, most of them are known from soil. However, the most common species from the section are ecologically diverse, occurring in the indoor environment (six species), clinical samples (five species), food and feed (four species), droppings (four species) and other less common substrates/environments. Due to the occurrence of section Flavipedes species in the clinical material/hospital environment, we also evaluated the susceptibility of 67 strains to six antifungals (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, terbinafine) using the reference EUCAST method. These results showed some potentially clinically relevant differences in susceptibility between species. For example, MICs higher than those observed for A. fumigatus wild-type were found for both triazoles and amphotericin B for A. ardalensis, A. iizukae, and A. spelaeus whereas A. lanuginosus, A. luppiae, A. movilensis, A. neoflavipes, A. olivimuriae and A. suttoniae were comparable to or more susceptible as A. fumigatus. Finally, terbinafine was in vitro active against all species except A. alboviridis.
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Affiliation(s)
- F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | | | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - M. Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - M.C. Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - K.M. Jørgensen
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
| | - J.P.Z. Siqueira
- Laboratório de Microbiologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - C. Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
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