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Klimov PB, Kolesnikov VB, Vorontsov DD, Ball AD, Bolton SJ, Mellish C, Edgecombe GD, Pepato AR, Chetverikov PE, He Q, Perotti MA, Braig HR. The evolutionary history and timeline of mites in ancient soils. Sci Rep 2025; 15:13555. [PMID: 40253405 PMCID: PMC12009363 DOI: 10.1038/s41598-025-96115-2] [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: 12/06/2024] [Accepted: 03/26/2025] [Indexed: 04/21/2025] Open
Abstract
Acariform mites play a crucial role as primary soil decomposers, impacting the carbon cycle. However, the timing of their diversification is uncertain, with estimated dates ranging from the Precambrian (no land plants) to the Carboniferous (diverse terrestrial ecosystems). One factor affecting these time estimates is an uncertain phylogenetic position of the earliest unequivocal fossil mites from the Devonian Rhynie Chert, which have been classified in five modern families and three suborders. Here, we thoroughly examine these specimens, assign them to a single species Protacarus crani (family Protoacaridae, fam. nov., suborder Endeostigmata) and integrate this information into a time-calibrated phylogenetic analysis. Our phylogeny suggests a Cambrian basal divergence of Acariformes (508-486 Ma), coinciding with the land colonization by bryophytes. At this time, the mites' ecological niches were probably diversified beyond the upper soil. Our study provides temporal context, improves the accuracy of fossil dating, and underscores the importance of mites' diverse habitats and their potential roles in soil food webs.
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Affiliation(s)
- Pavel B Klimov
- Department of Biological Sciences, Purdue University, Mitch Daniels Blvd, West Lafayette, IN, 47907, USA.
| | - Vasiliy B Kolesnikov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl, 152742, Russia
| | - Dmitry D Vorontsov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | | | - Samuel J Bolton
- Division of Plant Industry, Florida State Collection of Arthropods, Florida Department of Agriculture and Consumer Services, Gainesville, FL, 32608, USA
| | - Claire Mellish
- The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | | | - Almir R Pepato
- Laboratório de Sistemática e Evolução de Ácaros Acariformes, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Philipp E Chetverikov
- Zoological Institute of Russian Academy of Sciences, Universitetskaya Nab., 1, St. Petersburg, 199034, Russia
| | - Qixin He
- Department of Biological Sciences, Purdue University, Mitch Daniels Blvd, West Lafayette, IN, 47907, USA
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK
| | - Henk R Braig
- Institute and Museum of Natural Sciences, Faculty of Natural and Exact Sciences, National University of San Juan, J5400 DNQ, San Juan, Argentina
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2
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Matthews AE, Trevelline BK, Wijeratne AJ, Boves TJ. Picky eaters: Selective microbial diet of avian ectosymbionts. J Anim Ecol 2025; 94:466-481. [PMID: 39538981 DOI: 10.1111/1365-2656.14215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 10/14/2024] [Indexed: 11/16/2024]
Abstract
Individual organisms can function as ecosystems inhabited by symbionts. Symbionts may interact with each other in ways that subsequently influence their hosts positively or negatively, although the details of how these interactions operate collectively are usually not well understood. Vane-dwelling feather mites are common ectosymbionts of birds and are proposed to confer benefits to hosts by consuming feather-degrading microbes. However, it is unknown whether these mites exhibit generalist or selective diets, or how their dietary selection could potentially impact their symbiotic functional nature. In this study, we conducted 16S rDNA and ITS1 amplicon sequencing to examine the microbial diet of feather mites. We characterized and compared the diversity and composition of bacteria and fungi in the bodies of mites living on feathers of the Prothonotary Warbler, Protonotaria citrea, to microbial assemblages present on the same feathers. We found less diverse, more compositionally similar microbial assemblages within mites than on feathers. We also found that mites were resource-selective. Based on the identity and known functions of microbes found within and presumably preferred by mites, our results suggest that these mites selectively consume feather-degrading microbes. Therefore, our results support the proposition that mites confer benefits to their hosts. This study provides insight into symbioses operating at multiple biological levels, highlights the ecological and evolutionary importance of the synergistic interactions between species, and greatly expands our understanding of feather mite biology.
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Affiliation(s)
- Alix E Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, Arkansas, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
- Department of Biology, Rhodes College, Memphis, Tennessee, USA
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, New York, USA
| | - Brian K Trevelline
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
| | - Asela J Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Than J Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
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3
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Blakemore RJ. Biodiversity restated: > 99.9% of global species in Soil Biota. Zookeys 2025; 1224:283-316. [PMID: 39935608 PMCID: PMC11811713 DOI: 10.3897/zookeys.1224.131153] [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: 07/03/2024] [Accepted: 01/03/2025] [Indexed: 02/13/2025] Open
Abstract
More than a decade of research led to the conclusion in 2022 that the Soil Biome is home to ~ 2.1 × 1024 taxa and thus supports > 99.9% of global species biodiversity, mostly Bacteria or other microbes, based upon topographic field data. A subsequent 2023 report tabulated a central value of just 1.04 × 1010 taxa claiming soils had 59 ± 15%, i.e., 44-74% (or truly 10-50%?) of the global total, while incidentally confirming upper values of ~ 90% for soil Bacteria. Incompatibility of these two studies is reviewed, supporting prior biodiversity data with the vast majority of species inhabiting soils, despite excluding viruses (now with ~ 5 × 1031 virions and 1026 species most, ~ 80%, in soils). The status of Oligochaeta (earthworms) and other taxa marked "?" in the 2023 paper are clarified. Although biota totals are increased considerably, inordinate threats of topsoil erosion and poisoning yet pertain with finality of extinction. Species affected include Keystone taxa, especially earthworms and microbes, essential for a healthy Soil foundation to sustain the Tree-of-Life inhabiting the Earth.
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Affiliation(s)
- Robert J. Blakemore
- VermEcology, 101 Suidomichi, Nogeyama, Yokohama-shi, Kanagawa-ken 231-0064, JapanVermEcologyKanagawa-kenJapan
- ENSSER, Marienstr. 19/20, 10117 Berlin, GermanyENSSERBerlinGermany
- IUCN Species Survival Commission, Rue Mauverney 28, 1196 Gland, SwitzerlandIUCN Species Survival CommissionGlandSwaziland
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Aguilar-Colorado ÁS, Morales-Jiménez J, Rivera-Chávez J. Harnessing Molecular and Bioactivity Network Analysis to Prioritize Antibacterial Compound Isolation From Ant-Associated Fungi. PHYTOCHEMICAL ANALYSIS : PCA 2025. [PMID: 39887489 DOI: 10.1002/pca.3513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 12/05/2024] [Accepted: 01/07/2025] [Indexed: 02/01/2025]
Abstract
INTRODUCTION Antimicrobial resistance is a global public health problem that requires the development of new bioactive compounds. In this context, metabolomic analyses can expedite the research of fungal metabolites as a valuable resource. OBJECTIVES To investigate the metabolic profiles and isolate antibacterial compounds from micromycetes associated with Mexican cloud forest ants by utilizing network analysis of their chemical and bioactivity data. MATERIAL AND METHODS 248 fungal strains isolated from six ant's species, soil of their anthills, and soil of the surroundings were evaluated for their in vitro inhibition growth of extensively drug-resistant Acinetobacter baumannii and hypervirulent Klebsiella pneumoniae; subsequently, their metabolites were dereplicated and analyzed by molecular networking and compound activity mapping from spectrometric data. Prioritization of some fungi for isolation of their major constituents was performed, and their structures were established by spectroscopic and spectrometric analysis and their bioactivity determined. RESULTS From the fungal collection, 15 secondary metabolites (1-15) were dereplicated, and 10 compounds (16-25), including the new (E)-tridec-7-ene-3,5,6,10-tetraol (25), were isolated from Ascomycetes of Trichoderma, Cladosporium, and Clonostachys genera. Compounds 16-18 stood out for being bioactive. This study is the first report of antibacterial activity against A. baumannii for the tricyclic pyridin-2-ones deoxy-PF1140 (16) and PF1140 (17), with minimum inhibitory concentration of 50 μg/mL. CONCLUSION Network analysis and dereplication proved effective in bioprospecting for antibacterial compounds, offering valuable insights into the chemical diversity of cloud forest soil fungi and their potential applications. Moreover, this study broadens the knowledge of fungal secondary metabolites linked to leafcutter, fire, and warrior ants.
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Affiliation(s)
- Ángel S Aguilar-Colorado
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior, Ciudad de México, Mexico
| | - Jesús Morales-Jiménez
- Departamento El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Ciudad de México, Mexico
| | - José Rivera-Chávez
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior, Ciudad de México, Mexico
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Mayorga-Martino V, Mansurova M, Calla-Quispe E, Ibáñez AJ. Unlocking the Secrets of Insects: The Role of Mass Spectrometry to Understand the Life of Insects. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39679754 DOI: 10.1002/mas.21922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 11/14/2024] [Accepted: 11/27/2024] [Indexed: 12/17/2024]
Abstract
Chemical signaling is crucial during the insect lifespan, significantly affecting their survival, reproduction, and ecological interactions. Unfortunately, most chemical signals insects use are impossible for humans to perceive directly. Hence, mass spectrometry has become a vital tool by offering vital insight into the underlying chemical and biochemical processes in various variety of insect activities, such as communication, mate recognition, mating behavior, and adaptation (defense/attack mechanisms), among others. Here, we review different mass spectrometry-based strategies used to gain a deeper understanding of the chemicals involved in shaping the complex behaviors among insects and mass spectrometry-based research in insects that have direct impact in global economic activities.
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Affiliation(s)
- Vanessa Mayorga-Martino
- Institute for Omics Sciences and Applied Biotechnology (ICOBA PUCP), Pontificia Universidad Católica del Perú, Lima, Peru
- Science Department, Pontificia Universidad Católica del Perú, San Miguel, Lima, Peru
| | - Madina Mansurova
- Institute for Omics Sciences and Applied Biotechnology (ICOBA PUCP), Pontificia Universidad Católica del Perú, Lima, Peru
- Science Department, Pontificia Universidad Católica del Perú, San Miguel, Lima, Peru
| | - Erika Calla-Quispe
- Institute for Omics Sciences and Applied Biotechnology (ICOBA PUCP), Pontificia Universidad Católica del Perú, Lima, Peru
| | - Alfredo J Ibáñez
- Institute for Omics Sciences and Applied Biotechnology (ICOBA PUCP), Pontificia Universidad Católica del Perú, Lima, Peru
- Science Department, Pontificia Universidad Católica del Perú, San Miguel, Lima, Peru
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6
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Dabas R, Koh A, Carling D, Kamaly N, Brown AEX. Redox-Responsive Polymeric Nanogels as Efficient mRNA Delivery Vehicles in Caenorhabditis elegans. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001428. [PMID: 39726755 PMCID: PMC11669991 DOI: 10.17912/micropub.biology.001428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 12/06/2024] [Accepted: 12/06/2024] [Indexed: 12/28/2024]
Abstract
Efficient delivery of sensitive nucleic acid payloads, including mRNA, in Caenorhabditis elegans remains challenging, especially with traditional, labor-intensive transgenesis methods. We addressed these challenges using polymeric nanogels (NGs) as an advanced platform for mRNA delivery in C. elegans . These polymeric delivery vehicles can be engineered to suit desired applications owing to their chemical versatility, resulting from the ability to conjugate multiple functional groups onto the same backbone. Here, we validate the in vivo RNA delivery potential of redox-responsive NGs. The NGs showed up to 72.4 % RNA encapsulation and 6.61 % loading efficiencies and facilitated the controlled release of the mRNA payloads at intracellular concentrations of the reducing agent glutathione, where most of the RNA was released within 24 hours. As a proof of concept, we successfully delivered green fluorescent protein (GFP)-expressing mRNA using NGs in C. elegans for the first time. Physicochemical characterization revealed uniform NG size and charge, and fluorescence microscopy confirmed GFP expression in the gut after 24 hours of treatment. Our findings show NGs' potential as an mRNA delivery system in C. elegans .
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Affiliation(s)
- Rupali Dabas
- MRC Laboratory of Medical Sciences, Institute of Clinical Sciences, London, England, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
| | - Alan Koh
- MRC Laboratory of Medical Sciences, Institute of Clinical Sciences, London, England, United Kingdom
| | - David Carling
- MRC Laboratory of Medical Sciences, Institute of Clinical Sciences, London, England, United Kingdom
| | - Nazila Kamaly
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, W12 0BZ London, United Kingdom
| | - André E. X. Brown
- MRC Laboratory of Medical Sciences, Institute of Clinical Sciences, London, England, United Kingdom
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7
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Woinarski JC, Braby MF, Gibb H, Harvey MS, Legge SM, Marsh JR, Moir ML, New TR, Rix MG, Murphy BP. This is the way the world ends; not with a bang but a whimper: Estimating the number and ongoing rate of extinctions of Australian non-marine invertebrates. CAMBRIDGE PRISMS. EXTINCTION 2024; 2:e23. [PMID: 40078797 PMCID: PMC11895748 DOI: 10.1017/ext.2024.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 10/14/2024] [Accepted: 10/23/2024] [Indexed: 03/14/2025]
Abstract
Biodiversity is in rapid decline, but the extent of loss is not well resolved for poorly known groups. We estimate the number of extinctions for Australian non-marine invertebrates since the European colonisation of the continent. Our analyses use a range of approaches, incorporate stated uncertainties and recognise explicit caveats. We use plausible bounds for the number of species, two approaches for estimating extinction rate, and Monte Carlo simulations to select combinations of projected distributions from these variables. We conclude that 9,111 (plausible bounds of 1,465 to 56,828) Australian species have become extinct over this 236-year period. These estimates dwarf the number of formally recognised extinctions of Australian invertebrates (10 species) and of the single invertebrate species listed as extinct under Australian legislation. We predict that 39-148 species will become extinct in 2024. This is inconsistent with a recent pledge by the Australian government to prevent all extinctions. This high rate of loss is largely a consequence of pervasive taxonomic biases in community concern and conservation investment. Those characteristics also make it challenging to reduce that rate of loss, as there is uncertainty about which invertebrate species are at the most risk. We outline conservation responses to reduce the likelihood of further extinctions.
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Affiliation(s)
- John C.Z. Woinarski
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT, Australia
| | - Michael F. Braby
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Australian National Insect Collection, Canberra, ACT, Australia
| | - Heloise Gibb
- Centre for Future Landscapes, La Trobe University, Bundoora, VIC, Australia
| | | | - Sarah M. Legge
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT, Australia
- Fenner School of Society and the Environment, The Australian National University, Canberra, ACT, Australia
| | - Jessica R. Marsh
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA, Australia
| | - Melinda L. Moir
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Tim R. New
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC, Australia
| | | | - Brett P. Murphy
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT, Australia
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Crowther TW, Rappuoli R, Corinaldesi C, Danovaro R, Donohue TJ, Huisman J, Stein LY, Timmis JK, Timmis K, Anderson MZ, Bakken LR, Baylis M, Behrenfeld MJ, Boyd PW, Brettell I, Cavicchioli R, Delavaux CS, Foreman CM, Jansson JK, Koskella B, Milligan-McClellan K, North JA, Peterson D, Pizza M, Ramos JL, Reay D, Remais JV, Rich VI, Ripple WJ, Singh BK, Smith GR, Stewart FJ, Sullivan MB, van den Hoogen J, van Oppen MJH, Webster NS, Zohner CM, van Galen LG. Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals. Cell 2024; 187:5195-5216. [PMID: 39303686 DOI: 10.1016/j.cell.2024.07.051] [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: 10/18/2023] [Revised: 07/05/2024] [Accepted: 07/27/2024] [Indexed: 09/22/2024]
Abstract
Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.
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Affiliation(s)
- Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland; Restor Eco AG, Zürich 8001, Switzerland.
| | - Rino Rappuoli
- Fondazione Biotecnopolo di Siena, Siena 53100, Italy.
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona 60131, Italy; National Biodiversity Future Center, Palermo 90133, Italy
| | - Roberto Danovaro
- National Biodiversity Future Center, Palermo 90133, Italy; Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Timothy J Donohue
- Wisconsin Energy Institute, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam 94240, the Netherlands
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - James Kenneth Timmis
- Institute of Political Science, University of Freiburg, Freiburg 79085, Germany; Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081, the Netherlands
| | - Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig 38106, Germany
| | - Matthew Z Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas 1433, Norway
| | - Matthew Baylis
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Cheshire, Neston CH64 7TE, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia
| | - Ian Brettell
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Camille S Delavaux
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Christine M Foreman
- Department of Chemical and Biological Engineering and Center for Biofilm Engineering, Montana State University, Bozeman, MT 59718, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kat Milligan-McClellan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Devin Peterson
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
| | - Mariagrazia Pizza
- Department of Life Sciences, CBRB Center, Imperial College, London SW7 2AZ, UK
| | - Juan L Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada 18008, Spain
| | - David Reay
- School of GeoSciences, The University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Virginia I Rich
- Center of Microbiome Science, Byrd Polar and Climate Research, and Microbiology Department, The Ohio State University, Columbus, OH 43214, USA
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5704, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Gabriel Reuben Smith
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Center of Microbiome Science, and EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Johan van den Hoogen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia; School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicole S Webster
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7004, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Constantin M Zohner
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland
| | - Laura G van Galen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich (Swiss Federal Institute of Technology), Zürich 8092, Switzerland; Society for the Protection of Underground Networks (SPUN), Dover, DE 19901, USA.
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Khdhiri M, Thomas E, de Smet C, Chandar P, Chandrakumar I, Davidson JM, Anderson P, Chorlton SD. refMLST: reference-based multilocus sequence typing enables universal bacterial typing. BMC Bioinformatics 2024; 25:280. [PMID: 39192191 DOI: 10.1186/s12859-024-05913-4] [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: 09/18/2023] [Accepted: 08/22/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Commonly used approaches for genomic investigation of bacterial outbreaks, including SNP and gene-by-gene approaches, are limited by the requirement for background genomes and curated allele schemes, respectively. As a result, they only work on a select subset of known organisms, and fail on novel or less studied pathogens. We introduce refMLST, a gene-by-gene approach using the reference genome of a bacterium to form a scalable, reproducible and robust method to perform outbreak investigation. RESULTS When applied to multiple outbreak causing bacteria including 1263 Salmonella enterica, 331 Yersinia enterocolitica and 6526 Campylobacter jejuni genomes, refMLST enabled consistent clustering, improved resolution, and faster processing in comparison to commonly used tools like chewieSnake. CONCLUSIONS refMLST is a novel multilocus sequence typing approach that is applicable to any bacterial species with a public reference genome, does not require a curated scheme, and automatically accounts for genetic recombination. AVAILABILITY AND IMPLEMENTATION refMLST is freely available for academic use at https://bugseq.com/academic .
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Affiliation(s)
| | - Ella Thomas
- California Polytechnic State University, San Luis Obispo, CA, USA
| | - Chanel de Smet
- California Polytechnic State University, San Luis Obispo, CA, USA
| | - Priyanka Chandar
- California Polytechnic State University, San Luis Obispo, CA, USA
| | | | - Jean M Davidson
- California Polytechnic State University, San Luis Obispo, CA, USA
| | - Paul Anderson
- California Polytechnic State University, San Luis Obispo, CA, USA
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10
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Harrison TA, Goto R, Li J, Ó Foighil D. Within-host adaptive speciation of commensal yoyo clams leads to ecological exclusion, not co-existence. PeerJ 2024; 12:e17753. [PMID: 39119103 PMCID: PMC11308998 DOI: 10.7717/peerj.17753] [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: 03/04/2024] [Accepted: 06/25/2024] [Indexed: 08/10/2024] Open
Abstract
Symbionts dominate planetary diversity and three primary symbiont diversification processes have been proposed: co-speciation with hosts, speciation by host-switching, and within-host speciation. The last mechanism is prevalent among members of an extraordinary marine symbiosis in the Indian River Lagoon, Florida, composed of a host mantis shrimp, Lysiosquilla scabricauda, and seven host-specific commensal vasconielline "yoyo" clams (Galeommatoidea) that collectively occupy two distinct niches: burrow-wall-attached, and host-attached/ectocommensal. This within-host symbiont radiation provides a natural experiment to test how symbiont coexistence patterns are regulated in a common ancestral habitat. The competitive exclusion principle predicts that sister taxa produced by adaptive speciation (with distinct morphologies and within-burrow niches) are most likely to coexist whereas the neutral theory predicts no difference among adaptive and non-adaptive sister taxa co-occurrence. To test these predictions, we engaged in (1) field-censusing commensal species assemblages; (2) trophic niche analyses; (3) laboratory behavioral observations. Although predicted by both models, the field census found no mixed-niche commensal assemblages: multi-species burrows were exclusively composed of burrow-wall commensals. Their co-occurrence matched random assembly process expectations, but presence of the single ectocommensal species had a highly significant negative effect on recruitment of all burrow-wall commensal species (P < 0.001), including on its burrow-wall commensal sister species (P < 0.001). Our stable isotope data indicated that commensals are suspension feeders and that co-occurring burrow-wall commensals may exhibit trophic niche differentiation. The artificial burrow behavioral experiment yielded no evidence of spatial segregation among burrow-wall commensals, and it was terminated by a sudden breakdown of the host-commensal relationship resulting in a mass mortality of all commensals unattached to the host. This study system appears to contain two distinct, superimposed patterns of commensal distribution: (1) all burrow-wall commensal species; (2) the ectocommensal species. Burrow-wall commensals (the plesiomorphic condition) broadly adhere to neutral theory expectations of species assembly but the adaptive evolution of ectocommensalism has apparently led to ecological exclusion rather than coexistence, an inverse outcome of theoretical expectations. The ecological factors regulating the observed burrow-wall/ectocommensal exclusion are currently obscure but potentially include differential recruitment to host burrows and/or differential survival in "mixed" burrow assemblages, the latter potentially due to changes in host predatory behavior. Resampling host burrows during commensal recruitment peak periods and tracking burrow-wall commensal survival in host burrows with and without added ectocommensals could resolve this outstanding issue.
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Affiliation(s)
- Teal A. Harrison
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, United States of America
| | - Ryutaro Goto
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Shirahama, Wakayama, Japan
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology and Museum of Natural History, University of Colorado, Boulder, CO, United States of America
| | - Diarmaid Ó Foighil
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, United States of America
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11
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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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12
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Solano YJ, Kiser PD. Double-duty isomerases: a case study of isomerization-coupled enzymatic catalysis. Trends Biochem Sci 2024; 49:703-716. [PMID: 38760195 PMCID: PMC11780667 DOI: 10.1016/j.tibs.2024.04.007] [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: 02/15/2024] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Enzymes can usually be unambiguously assigned to one of seven classes specifying the basic chemistry of their catalyzed reactions. Less frequently, two or more reaction classes are catalyzed by a single enzyme within one active site. Two examples are an isomerohydrolase and an isomero-oxygenase that catalyze isomerization-coupled reactions crucial for production of vision-supporting 11-cis-retinoids. In these enzymes, isomerization is obligately paired and mechanistically intertwined with a second reaction class. A handful of other enzymes carrying out similarly coupled isomerization reactions have been described, some of which have been subjected to detailed structure-function analyses. Herein we review these rarefied enzymes, focusing on the mechanistic and structural basis of their reaction coupling with the goal of revealing catalytic commonalities.
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Affiliation(s)
- Yasmeen J Solano
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA 92697, USA
| | - Philip D Kiser
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA 92697, USA; Department of Clinical Pharmacy Practice, University of Irvine School of Pharmacy and Pharmaceutical Sciences, Irvine, CA 92697, USA; Department of Ophthalmology, Gavin Herbert Eye Institute - Center for Translational Vision Research, University of California Irvine School of Medicine, Irvine, CA 92697, USA; Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA.
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13
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Ilík V, Schwarz EM, Nosková E, Pafčo B. Hookworm genomics: dusk or dawn? Trends Parasitol 2024; 40:452-465. [PMID: 38677925 DOI: 10.1016/j.pt.2024.04.003] [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: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
Hookworms are parasites, closely related to the model nematode Caenorhabditis elegans, that are a major economic and health burden worldwide. Primarily three hookworm species (Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum) infect humans. Another 100 hookworm species from 19 genera infect primates, ruminants, and carnivores. Genetic data exist for only seven of these species. Genome sequences are available from only four of these species in two genera, leaving 96 others (particularly those parasitizing wildlife) without any genomic data. The most recent hookworm genomes were published 5 years ago, leaving the field in a dusk. However, assembling genomes from single hookworms may bring a new dawn. Here we summarize advances, challenges, and opportunities for studying these neglected but important parasitic nematodes.
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Affiliation(s)
- Vladislav Ilík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eva Nosková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
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14
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Matthews AE. Empirically tuned theory reveals why symbiont abundance 'mite' vary across hosts. J Anim Ecol 2024; 93:373-376. [PMID: 38351463 DOI: 10.1111/1365-2656.14057] [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: 01/18/2024] [Accepted: 01/28/2024] [Indexed: 04/04/2024]
Abstract
Research Highlight: del Mar Labrador, M., Serrano, D., Doña, J., Aguilera, E., Arroyo, J. L., Atiénzar, F., Barba, E., Bermejo, A., Blanco, G., Borràs, A., Calleja, J. A., Cantó, J. L., Cortés, V., de la Puente, J., de Palacio, D., Fernández-González, S., Figuerola, J., Frías, Ó., Fuertes-Marcos, B. Garamszegi, L. Z., Gordo, Ó., Gurpegui, M., Kovács, I., Martínez, J. L., Meléndez, L., Mestre, A., Møller, A. P., Monrós, J. S., Moreno-Opo, R., Navarro, C., Pap, P. L., Pérez-Tris, J., Piculo, R., Ponce, C., Proctor, H., Rodríguez, R., Sallent, Á., Senar, J., Tella, J. L., Vágási, C. I., Vögeli, M., & Jovani, R. (2023). Host space, not energy or symbiont size, constrains feather mite abundance across passerine bird species. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.14032. Symbionts represent crucial links between species in ecosystems. Consequently, understanding their patterns of abundance is a major goal in the study of symbioses. However, multiple biotic and abiotic factors may regulate symbionts, and disentangling the mechanisms that drive variation in their abundance across host species is challenging. One promising strategy to approach this challenge is to incorporate biologically relevant data into theoretical models. In a recent study, Labrador et al. (2023) used this strategy to investigate the poorly understood symbiosis between feather mites and their avian hosts. They integrate a remarkable amount of empirical data with models based on the metabolic theory of ecology to determine what factors limit feather mite abundance across European passerines. Their quantitative analyses indicate that the number of feather barbs limits mite abundance across host species, suggesting that mite populations are spatially, but not energetically, constrained. These findings not only reveal mechanisms that may drive the variation in feather mite abundances across hosts, but also advance our understanding of the ecology of interspecific interactions more generally.
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Affiliation(s)
- Alix E Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, Arkansas, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
- Department of Biology, Rhodes College, Memphis, Tennessee, USA
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15
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Del Mar Labrador M, Serrano D, Doña J, Aguilera E, Arroyo JL, Atiénzar F, Barba E, Bermejo A, Blanco G, Borràs A, Calleja JA, Cantó JL, Cortés V, De la Puente J, De Palacio D, Fernández-González S, Figuerola J, Frías Ó, Fuertes-Marcos B, Garamszegi LZ, Gordo Ó, Gurpegui M, Kovács I, Martínez JL, Meléndez L, Mestre A, Møller AP, Monrós JS, Moreno-Opo R, Navarro C, Pap PL, Pérez-Tris J, Piculo R, Ponce C, Proctor HC, Rodríguez R, Sallent Á, Senar JC, Tella JL, Vágási CI, Vögeli M, Jovani R. Host space, not energy or symbiont size, constrains feather mite abundance across passerine bird species. J Anim Ecol 2024; 93:393-405. [PMID: 38100230 DOI: 10.1111/1365-2656.14032] [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: 02/15/2023] [Accepted: 11/06/2023] [Indexed: 04/04/2024]
Abstract
Comprehending symbiont abundance among host species is a major ecological endeavour, and the metabolic theory of ecology has been proposed to understand what constrains symbiont populations. We parameterized metabolic theory equations to investigate how bird species' body size and the body size of their feather mites relate to mite abundance according to four potential energy (uropygial gland size) and space constraints (wing area, total length of barbs and number of feather barbs). Predictions were compared with the empirical scaling of feather mite abundance across 106 passerine bird species (26,604 individual birds sampled), using phylogenetic modelling and quantile regression. Feather mite abundance was strongly constrained by host space (number of feather barbs) but not by energy. Moreover, feather mite species' body size was unrelated to the body size of their host species. We discuss the implications of our results for our understanding of the bird-feather mite system and for symbiont abundance in general.
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Affiliation(s)
- María Del Mar Labrador
- Doñana Biological Station (CSIC), Seville, Spain
- SEO-Monticola Ornithological Group, Autonomous University of Madrid, Madrid, Spain
| | | | - Jorge Doña
- University of Illinois, Urbana, Illinois, USA
- University of Granada, Granada, Spain
| | | | | | | | | | - Ana Bermejo
- SEO-Monticola Ornithological Group, Autonomous University of Madrid, Madrid, Spain
| | | | - Antoni Borràs
- Museu de Ciències Naturals de Barcelona, Barcelona, Spain
| | - Juan A Calleja
- SEO-Monticola Ornithological Group, Autonomous University of Madrid, Madrid, Spain
- Autonomous University of Madrid, Madrid, Spain
| | | | | | - Javier De la Puente
- SEO-Monticola Ornithological Group, Autonomous University of Madrid, Madrid, Spain
| | - Diana De Palacio
- SEO-Monticola Ornithological Group, Autonomous University of Madrid, Madrid, Spain
| | | | | | | | | | - László Z Garamszegi
- Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - Óscar Gordo
- Doñana Biological Station (CSIC), Seville, Spain
| | - Míriam Gurpegui
- National Institute for Agricultural and Food Research and Technology (CSIC), Madrid, Spain
| | - István Kovács
- 'Milvus Group' Bird and Nature Protection Association, Târgu Mureş, Romania
| | | | - Leandro Meléndez
- Biodiversity Research Institute (Univ. of Oviedo-CSIC-Princ. Asturias), Mieres, Spain
| | | | | | | | - Rubén Moreno-Opo
- SEO-Monticola Ornithological Group, Autonomous University of Madrid, Madrid, Spain
| | | | - Péter L Pap
- Babeş-Bolyai University, Cluj-Napoca, Romania
- University of Debrecen, Debrecen, Hungary
| | | | | | - Carlos Ponce
- SEO-Monticola Ornithological Group, Autonomous University of Madrid, Madrid, Spain
| | | | | | - Ángel Sallent
- Naturalists Association of Southeast (ANSE), Murcia, Spain
| | | | - José L Tella
- Doñana Biological Station (CSIC), Seville, Spain
| | | | | | - Roger Jovani
- Doñana Biological Station (CSIC), Seville, Spain
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16
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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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17
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Schaible MJ, Szeinbaum N, Bozdag GO, Chou L, Grefenstette N, Colón-Santos S, Rodriguez LE, Styczinski MJ, Thweatt JL, Todd ZR, Vázquez-Salazar A, Adams A, Araújo MN, Altair T, Borges S, Burton D, Campillo-Balderas JA, Cangi EM, Caro T, Catalano E, Chen K, Conlin PL, Cooper ZS, Fisher TM, Fos SM, Garcia A, Glaser DM, Harman CE, Hermis NY, Hooks M, Johnson-Finn K, Lehmer O, Hernández-Morales R, Hughson KHG, Jácome R, Jia TZ, Marlow JJ, McKaig J, Mierzejewski V, Muñoz-Velasco I, Nural C, Oliver GC, Penev PI, Raj CG, Roche TP, Sabuda MC, Schaible GA, Sevgen S, Sinhadc P, Steller LH, Stelmach K, Tarnas J, Tavares F, Trubl G, Vidaurri M, Vincent L, Weber JM, Weng MM, Wilpiszeki RL, Young A. Chapter 1: The Astrobiology Primer 3.0. ASTROBIOLOGY 2024; 24:S4-S39. [PMID: 38498816 DOI: 10.1089/ast.2021.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.
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Affiliation(s)
- Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Georgetown University, Washington DC, USA
| | - Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M J Styczinski
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- University of Washington, Seattle, Washington, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA
| | | | - Dana Burton
- Department of Anthropology, George Washington University, Washington DC, USA
| | | | - Eryn M Cangi
- Laboratory for Atmospheric and Space Physics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Enrico Catalano
- Sant'Anna School of Advanced Studies, The BioRobotics Institute, Pisa, Italy
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Z S Cooper
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, USA
| | - D M Glaser
- Arizona State University, Tempe, Arizona, USA
| | - Chester E Harman
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada, Spain
| | - M Hooks
- NASA Johnson Space Center, Houston, Texas, USA
| | - K Johnson-Finn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Owen Lehmer
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kynan H G Hughson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tony Z Jia
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jordan McKaig
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Veronica Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chinmayee Govinda Raj
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Serhat Sevgen
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Kamil Stelmach
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - J Tarnas
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Frank Tavares
- Space Enabled Research Group, MIT Media Lab, Cambridge, Massachusetts, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Monica Vidaurri
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | - Amber Young
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Northern Arizona University, Flagstaff, Arizona, USA
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18
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Shaw S, Cohn IS, Baptista RP, Xia G, Melillo B, Agyabeng-Dadzie F, Kissinger JC, Striepen B. Genetic crosses within and between species of Cryptosporidium. Proc Natl Acad Sci U S A 2024; 121:e2313210120. [PMID: 38147547 PMCID: PMC10769859 DOI: 10.1073/pnas.2313210120] [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] [Accepted: 11/12/2023] [Indexed: 12/28/2023] Open
Abstract
Parasites and their hosts are engaged in reciprocal coevolution that balances competing mechanisms of virulence, resistance, and evasion. This often leads to host specificity, but genomic reassortment between different strains can enable parasites to jump host barriers and conquer new niches. In the apicomplexan parasite Cryptosporidium, genetic exchange has been hypothesized to play a prominent role in adaptation to humans. The sexual lifecycle of the parasite provides a potential mechanism for such exchange; however, the boundaries of Cryptosporidium sex are currently undefined. To explore this experimentally, we established a model for genetic crosses. Drug resistance was engineered using a mutated phenylalanyl tRNA synthetase gene and marking strains with this and the previously used Neo transgene enabled selection of recombinant progeny. This is highly efficient, and genomic recombination is evident and can be continuously monitored in real time by drug resistance, flow cytometry, and PCR mapping. Using this approach, multiple loci can now be modified with ease. We demonstrate that essential genes can be ablated by crossing a Cre recombinase driver strain with floxed strains. We further find that genetic crosses are also feasible between species. Crossing Cryptosporidium parvum, a parasite of cattle and humans, and Cryptosporidium tyzzeri a mouse parasite resulted in progeny with a recombinant genome derived from both species that continues to vigorously replicate sexually. These experiments have important fundamental and translational implications for the evolution of Cryptosporidium and open the door to reverse- and forward-genetic analysis of parasite biology and host specificity.
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Affiliation(s)
- Sebastian Shaw
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ian S. Cohn
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Rodrigo P. Baptista
- Department of Medicine, Houston Methodist Research Institute, Houston, TX77030
| | - Guoqin Xia
- Department of Chemistry, Scripps Research, La Jolla, CA92037
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA92037
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA02142
| | | | - Jessica C. Kissinger
- Department of Genetics, University of Georgia, Athens, GA30602
- Center for Tropical and Emerging Global Diseases and Institute of Bioinformatics, University of Georgia, Athens, GA30602
| | - Boris Striepen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA19104
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19
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Wiens JJ, Zelinka J. How many species will Earth lose to climate change? GLOBAL CHANGE BIOLOGY 2024; 30:e17125. [PMID: 38273487 DOI: 10.1111/gcb.17125] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 01/27/2024]
Abstract
Climate change may be an important threat to global biodiversity, potentially leading to the extinction of numerous species. But how many? There have been various attempts to answer this question, sometimes yielding strikingly different estimates. Here, we review these estimates, assess their disagreements and methodology, and explore how we might reach better estimates. Large-scale studies have estimated the extinction of ~1% of sampled species up to ~70%, even when using the same approach (species distribution models; SDMs). Nevertheless, worst-case estimates often converge near 20%-30% species loss, and many differences shrink when using similar assumptions. We perform a new review of recent SDM studies, which show ~17% loss of species to climate change under worst-case scenarios. However, this review shows that many SDM studies are biased by excluding the most vulnerable species (those known from few localities), which may lead to underestimating global species loss. Conversely, our analyses of recent climate change responses show that a fundamental assumption of SDM studies, that species' climatic niches do not change over time, may be frequently violated. For example, we find mean rates of positive thermal niche change across species of ~0.02°C/year. Yet, these rates may still be slower than projected climate change by ~3-4 fold. Finally, we explore how global extinction levels can be estimated by combining group-specific estimates of species loss with recent group-specific projections of global species richness (including cryptic insect species). These preliminary estimates tentatively forecast climate-related extinction of 14%-32% of macroscopic species in the next ~50 years, potentially including 3-6 million (or more) animal and plant species, even under intermediate climate change scenarios.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Joseph Zelinka
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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20
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Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [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: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
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Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
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21
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Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [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: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
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22
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Wiens JJ. How many species are there on Earth? Progress and problems. PLoS Biol 2023; 21:e3002388. [PMID: 37983223 PMCID: PMC10659151 DOI: 10.1371/journal.pbio.3002388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
How many species exist on Earth? Projections range from millions to trillions. A 2011 paper in PLOS Biology provided a comprehensive estimate of 9 million.
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Affiliation(s)
- John J. Wiens
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona, United States of America
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23
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Fanfarillo E, Angiolini C, Tordoni E, Bacaro G, Bazzato E, Castaldini M, Cucu MA, Grattacaso M, Loppi S, Marignani M, Mocali S, Muggia L, Salerni E, Maccherini S. Arable plant communities as a surrogate of crop rhizosphere microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165141. [PMID: 37379915 DOI: 10.1016/j.scitotenv.2023.165141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 06/30/2023]
Abstract
Soil microbiota is a crucial component of agroecosystem biodiversity, enhancing plant growth and providing important services in agriculture. However, its characterization is demanding and relatively expensive. In this study, we evaluated whether arable plant communities can be used as a surrogate of bacterial and fungal communities of the rhizosphere of Elephant Garlic (Allium ampeloprasum L.), a traditional crop plant of central Italy. We sampled plant, bacterial, and fungal communities, i.e., the groups of such organisms co-existing in space and time, in 24 plots located in eight fields and four farms. At the plot level, no correlations in species richness emerged, while the composition of plant communities was correlated with that of both bacterial and fungal communities. As regards plants and bacteria, such correlation was mainly driven by similar responses to geographic and environmental factors, while fungal communities seemed to be correlated in species composition with both plants and bacteria due to biotic interactions. All the correlations in species composition were unaffected by the number of fertilizer and herbicide applications, i.e., agricultural intensity. Besides correlations, we detected a predictive relationship of plant community composition towards fungal community composition. Our results highlight the potential of arable plant communities to be used as a surrogate of crop rhizosphere microbial communities in agroecosystems.
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Affiliation(s)
- Emanuele Fanfarillo
- Department of Life Sciences, University of Siena, Siena, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy.
| | - Claudia Angiolini
- Department of Life Sciences, University of Siena, Siena, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy; BAT Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Naples, Italy
| | - Enrico Tordoni
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Giovanni Bacaro
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Erika Bazzato
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy; Department of Agricultural Sciences, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | | | - Maria A Cucu
- CREA - Research Center for Agriculture and Environment, Florence, Italy
| | | | - Stefano Loppi
- Department of Life Sciences, University of Siena, Siena, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy; BAT Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Naples, Italy
| | - Michela Marignani
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Stefano Mocali
- CREA - Research Center for Agriculture and Environment, Florence, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Elena Salerni
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Simona Maccherini
- Department of Life Sciences, University of Siena, Siena, Italy; NBFC, National Biodiversity Future Center, Palermo, Italy; BAT Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Naples, Italy
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24
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Matthews AE, Boves TJ, Percy KL, Schelsky WM, Wijeratne AJ. Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host-Symbiont Coevolution. Life (Basel) 2023; 13:2054. [PMID: 37895435 PMCID: PMC10608719 DOI: 10.3390/life13102054] [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: 06/29/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host-symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host-symbiont coevolution at multiple evolutionary scales.
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Affiliation(s)
- Alix E. Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, AR 72401, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
| | - Than J. Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
| | - Katie L. Percy
- Audubon Delta, National Audubon Society, Baton Rouge, LA 70808, USA;
- United States Department of Agriculture, Natural Resources Conservation Service, Addis, LA 70710, USA
| | - Wendy M. Schelsky
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, Champaign, IL 61801, USA;
- Prairie Research Institute, Illinois Natural History Survey, University of Illinois, Urbana-Champaign, Champaign, IL 61820, USA
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
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25
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Hartebrodt L, Wilson S, Costello MJ. Progress in the discovery of isopods (Crustacea: Peracarida)-is the description rate slowing down? PeerJ 2023; 11:e15984. [PMID: 37692117 PMCID: PMC10484202 DOI: 10.7717/peerj.15984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Taxonomic species are the best standardised metric of biodiversity. Therefore, there is broad scientific and public interest in how many species have already been named and how many more may exist. Crustaceans comprise about 6% of all named animal species and isopods about 15% of all crustaceans. Here, we review progress in the naming of isopods in relation to the number of people describing new species and estimate how many more species may yet be named by 2050 and 2100, respectively. In over two and a half centuries of discovery, 10,687 isopod species in 1,557 genera and 141 families have been described by 755 first authors. The number of authors has increased over time, especially since the 1950s, indicating increasing effort in the description of new species. Despite that the average number of species described per first author has declined since the 1910s, and the description rate has slowed down over the recent decades. Authors' publication lifetimes did not change considerably over time, and there was a distinct shift towards multi-authored publications in recent decades. Estimates from a non-homogeneous renewal process model predict that an additional 660 isopod species will be described by 2100, assuming that the rate of description continues at its current pace.
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Affiliation(s)
- Lena Hartebrodt
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Simon Wilson
- School of Computer Science and Statistics, University of Dublin, Trinity College, Dublin, Ireland
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26
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Lee YC, Ke HM, Liu YC, Lee HH, Wang MC, Tseng YC, Kikuchi T, Tsai IJ. Single-worm long-read sequencing reveals genome diversity in free-living nematodes. Nucleic Acids Res 2023; 51:8035-8047. [PMID: 37526286 PMCID: PMC10450198 DOI: 10.1093/nar/gkad647] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
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Affiliation(s)
- Yi-Chien Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Min-Chen Wang
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Yung-Che Tseng
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
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27
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Matthews AE, Wijeratne AJ, Sweet AD, Hernandes FA, Toews DPL, Boves TJ. Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity. Syst Biol 2023; 72:802-819. [PMID: 36960591 DOI: 10.1093/sysbio/syad014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/08/2023] [Accepted: 03/21/2023] [Indexed: 03/25/2023] Open
Abstract
A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].
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Affiliation(s)
- Alix E Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, AR, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Asela J Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Fabio A Hernandes
- Department of Ecology and Zoology, CCB/ECZ, Federal University of Santa Catarina (UFSC), Trindade, Florianópolis, Santa Catarina, Brazil
| | - David P L Toews
- Department of Biology, Pennsylvania State University, State College, PA, USA
| | - Than J Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
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28
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Orr MC, Hughes AC, Carvajal OT, Ferrari RR, Luo A, Rajaei H, Ron SR, Warrit N, Zamani A, Zhang YM, Zhu CD. Inclusive and productive ways forward needed for species-naming conventions. Nat Ecol Evol 2023; 7:1168-1169. [PMID: 37337001 DOI: 10.1038/s41559-023-02103-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Affiliation(s)
- Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany.
| | - Alice C Hughes
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Omar Torres Carvajal
- Pontifical Catholic University of Ecuador, School of Biology, Museum of Zoology, Quito, Ecuador
| | - Rafael R Ferrari
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Environmental Science Training Center, Federal University of Southern Bahia, Porto Seguro, Brazil
| | - Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hossein Rajaei
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Santiago R Ron
- Pontifical Catholic University of Ecuador, School of Biology, Museum of Zoology, Quito, Ecuador
| | - Natapot Warrit
- Center of Excellence in Entomology and Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Alireza Zamani
- Zoological Museum, Biodiversity Unit, Faculty of Science, University of Turku, Turku, Finland
| | | | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Rheindt FE, Bouchard P, Pyle RL, Welter-Schultes F, Aescht E, Ahyong ST, Ballerio A, Bourgoin T, Ceríaco LMP, Dmitriev D, Evenhuis N, Grygier MJ, Harvey MS, Kottelat M, Kluge N, Krell FT, Kojima JI, Kullander SO, Lucinda P, Lyal CHC, Scioscia CL, Whitmore D, Yanega D, Zhang ZQ, Zhou HZ, Pape T. Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice. PLoS Biol 2023; 21:e3002251. [PMID: 37607211 PMCID: PMC10443861 DOI: 10.1371/journal.pbio.3002251] [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: 08/24/2023] Open
Abstract
Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of "species diagnosis" in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.
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Affiliation(s)
- Frank E. Rheindt
- National University of Singapore, Department of Biological Sciences, Singapore
| | - Patrice Bouchard
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Richard L. Pyle
- Department of Natural Sciences, Bernice Pauahi Bishop Museum, Honolulu, Hawaii, United States of America
| | - Francisco Welter-Schultes
- Abteilung Evolution und Biodiversität der Tiere und Zoologisches Museum, Universität Göttingen, Göttingen, Germany
| | - Erna Aescht
- Biology Centre of the Upper Austrian Museum, Linz, Austria
| | - Shane T. Ahyong
- Australian Museum, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | | | - Thierry Bourgoin
- Institut Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-Sorbonne Université-EPHE- Université des Antilles, Museum National d’Histoire Naturelle, Paris, France
| | - Luis M. P. Ceríaco
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dmitry Dmitriev
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Neal Evenhuis
- Department of Natural Sciences, Bernice Pauahi Bishop Museum, Honolulu, Hawaii, United States of America
| | - Mark J. Grygier
- National Museum of Marine Biology and Aquarium, Checheng, Taiwan
| | - Mark S. Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Welshpool DC, Australia
| | | | - Nikita Kluge
- Department of Entomology, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Frank-T. Krell
- Denver Museum of Nature and Science, Denver, Colorado, United States of America
| | - Jun-ichi Kojima
- Natural History Laboratory, Faculty of Science, Ibaraki University, Mito, Japan
| | - Sven O. Kullander
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Paulo Lucinda
- Laboratório de Ictiologia Sistemática, Universidade Federal do Tocantins, Tocantins, Brazil
| | | | - Cristina Luisa Scioscia
- Arachnology Division, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, Buenos Aires, Argentina
| | - Daniel Whitmore
- Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Douglas Yanega
- Department of Entomology, University of California, Riverside, Riverside, California, United States of America
| | - Zhi-Qiang Zhang
- Manaaki Whenua–Landcare Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Hong-Zhang Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Thomas Pape
- Zoological Museum, Natural History Museum of Denmark, Copenhagen, Denmark
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30
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Fishman FJ, Lennon JT. Macroevolutionary constraints on global microbial diversity. Ecol Evol 2023; 13:e10403. [PMID: 37560179 PMCID: PMC10408003 DOI: 10.1002/ece3.10403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Biologists have long sought to quantify the number of species on Earth. Often missing from these efforts is the contribution of microorganisms, the smallest but most abundant form of life on the planet. Despite recent large-scale sampling efforts, estimates of global microbial diversity span many orders of magnitude. It is important to consider how speciation and extinction over the last 4 billion years constrain inventories of biodiversity. We parameterized macroevolutionary models based on birth-death processes that assume constant and universal speciation and extinction rates. The models reveal that richness beyond 1012 species is feasible and in agreement with empirical predictions. Additional simulations suggest that mass extinction events do not place hard limits on modern-day microbial diversity. Together, our study provides independent support for a massive global-scale microbiome while shedding light on the upper limits of life on Earth.
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Affiliation(s)
- Ford J. Fishman
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
| | - Jay T. Lennon
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
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31
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Botero-Cañola S, Gardner SL. Tapping into natural history collections to assess latitudinal gradients of parasite diversity. Parasitology 2023; 150:723-733. [PMID: 37157058 PMCID: PMC10410379 DOI: 10.1017/s0031182023000458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/22/2023] [Accepted: 04/22/2023] [Indexed: 05/10/2023]
Abstract
Parasites are key components of the biosphere not only due to their huge diversity, but also because they exert important influences on ecological processes. Nevertheless, we lack an understanding of the biogeographical patterns of parasite diversity. Here, we tap into the potential of biodiversity collections for understanding parasite biogeography. We assess species richness of supracommunities of helminth parasites infecting mammal assemblages in the Nearctic, and describe its relation to latitude, climate, host diversity, and land area. We compiled data from parasitology collections and assessed parasite diversity in Nearctic ecoregions for the entire parasite supracommunity of mammals in each ecoregion, as well as separately from carnivores and rodents to explore the effect of host taxonomic resolution on observed patterns. For carnivores, we found evidence of a negative latitudinal gradient, while parasites of rodents displayed no clear pattern. We found that parasite diversity was positively correlated with mean annual temperature and negatively correlated with seasonal precipitation. Parasite richness shows a diversity peak at intermediate host richness values and in carnivores correlates with temperature and seasonal precipitation. Rodent parasite diversity did not correlate with explored factors. Other researchers are encouraged to use parasitology collections to continue exploring patterns of parasite biogeography and macroecology.
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Affiliation(s)
- Sebastian Botero-Cañola
- H.W. Manter Laboratory of Parasitology, University of Nebraska State Museum, University of Nebraska - Lincoln, Lincoln, NE, USA
- Wisely Lab, University of Florida, Gainesville, FL, USA
| | - Scott L. Gardner
- H.W. Manter Laboratory of Parasitology, University of Nebraska State Museum, University of Nebraska - Lincoln, Lincoln, NE, USA
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32
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Mercado-Díaz JA, Lücking R, Moncada B, C St E Campbell K, Delnatte C, Familia L, Falcón-Hidalgo B, Motito-Marín A, Rivera-Queralta Y, Widhelm TJ, Thorsten Lumbsch H. Species assemblages of insular Caribbean Sticta (lichenized Ascomycota: Peltigerales) over ecological and evolutionary time scales. Mol Phylogenet Evol 2023:107830. [PMID: 37247703 DOI: 10.1016/j.ympev.2023.107830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/28/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Phylogenetic approaches to macroevolution have provided unique insight into evolutionary relationships, ancestral ranges, and diversification patterns for many taxa. Similar frameworks have also been developed to assess how environmental and/or spatial variables shape species diversity and distribution patterns at different spatial/temporal scales, but studies implementing these are still scarce for many groups, including lichens. Here, we combine phylogeny-based ancestral range reconstruction and diversification analysis with community phylogenetics to reconstruct evolutionary origins and assess patterns of taxonomic and phylogenetic relatedness between island communities of the lichenized fungal genus Sticta in the Caribbean. Sampling was carried out in the Greater Antilles (Cuba, Jamaica, Dominican Republic, and Puerto Rico) and Lesser Antilles (Dominica, Guadeloupe, and Martinique). Data for six molecular loci were obtained for 64 candidate Caribbean species and used to perform both macroevolutionary phylogenetics, which also included worldwide taxa, and phylobetadiversity analyses, which emphasized island-level communities. Our work uncovered high levels of island endemism (∼59%) in Caribbean Sticta. We estimate initial colonization of the region occurred about 19 Mya from a South American ancestor. Reverse migration events by Caribbean lineages to South America were also inferred. We found no evidence for increased diversification rates associated with range expansion into the Caribbean. Taxonomic and phylogenetic turnover between island-level communities was most strongly correlated with environmental variation rather than with geographic distance. We observed less dissimilarity among communities from the Dominican Republic and Jamaica than between these islands and the Lesser Antilles/Puerto Rico. High levels of hidden diversity and endemism in Caribbean Sticta reaffirm that islands are crucial for the maintenance of global biodiversity of lichenized fungi. Altogether, our findings suggest that strong evolutionary links exist between Caribbean and South American biotas but at regional scales, species assemblages exhibit complex taxonomic and phylogenetic relationships that are determined by local environments and shared evolutionary histories.
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Affiliation(s)
- Joel A Mercado-Díaz
- Committee on Evolutionary Biology, University of Chicago 1025 E. 57th Street, Chicago, Illinois 60637, U.S.A; Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, U.S.A.
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Königin-Luise-Straße 6-8, 14195 Berlin, Germany.
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia.
| | - Keron C St E Campbell
- Natural History Museum of Jamaica, Institute of Jamaica, 10-16 East Street, Kingston, Jamaica.
| | - Cesar Delnatte
- Biotope Amazonie, 3 rue Mezin Gildon, F-97354 Rémire-Montjoly, Guyane française.
| | - Lemuel Familia
- Departamento de Vida Silvestre, Ministerio de Medio Ambiente y Recursos Naturales, Avenida Cayetano Germosén esq. Avenida Gregorio Luperón, Ensanche El Pedregal, Santo Domingo, República Dominicana.
| | - Banessa Falcón-Hidalgo
- Jardín Botánico Nacional, Universidad de La Habana, Carretera "El Rocío" km 3.5, Calabazar, Boyeros, La Habana, Cuba.
| | - Angel Motito-Marín
- Departamento de Biología Vegetal, Centro Oriental de Ecosistemas y Biodiversidad (BioEco), Código Postal 90100, José A. Saco 601, Esquina Barnada, Santiago de Cuba, Cuba.
| | - Yoira Rivera-Queralta
- Departamento de Biología Vegetal, Centro Oriental de Ecosistemas y Biodiversidad (BioEco), Código Postal 90100, José A. Saco 601, Esquina Barnada, Santiago de Cuba, Cuba.
| | - Todd J Widhelm
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, U.S.A.
| | - H Thorsten Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, U.S.A.
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33
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Reimer JD, Gösser F. Can environmental DNA unlock the mysteries of biodiversity on coral reefs? Proc Biol Sci 2023; 290:20230605. [PMID: 37161320 PMCID: PMC10170188 DOI: 10.1098/rspb.2023.0605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Affiliation(s)
- James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Fabian Gösser
- Molecular Invertebrate Systematics and Ecology Laboratory, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
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34
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Zhang H, Chen W. Automated recognition and analysis of body bending behavior in C. elegans. BMC Bioinformatics 2023; 24:175. [PMID: 37118676 PMCID: PMC10148436 DOI: 10.1186/s12859-023-05307-y] [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: 01/27/2023] [Accepted: 04/26/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Locomotion behaviors of Caenorhabditis elegans play an important role in drug activity screening, anti-aging research, and toxicological assessment. Previous studies have provided important insights into drug activity screening, anti-aging, and toxicological research by manually counting the number of body bends. However, manual counting is often low-throughput and takes a lot of time and manpower. And it is easy to cause artificial bias and error in counting results. RESULTS In this paper, an algorithm is proposed for automatic counting and analysis of the body bending behavior of nematodes. First of all, the numerical coordinate regression method with convolutional neural network is used to obtain the head and tail coordinates. Next, curvature-based feature point extraction algorithm is used to calculate the feature points of the nematode centerline. Then the maximum distance between the peak point and the straight line between the pharynx and the tail is calculated. The number of body bends is counted according to the change in the maximum distance per frame. CONCLUSION Experiments are performed to prove the effectiveness of the proposed algorithm. The accuracy of head coordinate prediction is 0.993, and the accuracy of tail coordinate prediction is 0.990. The Pearson correlation coefficient between the results of the automatic count and manual count of the number of body bends is 0.998 and the mean absolute error is 1.931. Different strains of nematodes are selected to analyze differences in body bending behavior, demonstrating a relationship between nematode vitality and lifespan. The code is freely available at https://github.com/hthana/Body-Bend-Count .
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Affiliation(s)
- Hui Zhang
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China
- School of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Weiyang Chen
- School of Cyber Science and Engineering, Qufu Normal University, Qufu, China.
- School of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
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35
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Du X, Gu S, Zhang Z, Li S, Zhou Y, Zhang Z, Zhang Q, Wang L, Ju Z, Yan C, Li T, Wang D, Yang X, Peng X, Deng Y. Spatial distribution patterns across multiple microbial taxonomic groups. ENVIRONMENTAL RESEARCH 2023; 223:115470. [PMID: 36775088 DOI: 10.1016/j.envres.2023.115470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R2 = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.
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Affiliation(s)
- Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Zheng Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yuqi Zhou
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhaojing Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Qi Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Linlin Wang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhicheng Ju
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengliang Yan
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
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36
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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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Microsporidians (Microsporidia) parasitic on mosquitoes (Culicidae) in central Europe are often multi-host species. J Invertebr Pathol 2023; 197:107873. [PMID: 36577478 DOI: 10.1016/j.jip.2022.107873] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Microsporidians (Microsporidia) are a diverse group of obligate and intracellular parasites of eukaryotes. There is evidence that the real species diversity in the phylum could be greatly underestimated, especially for microsporidians parasitic on invertebrates. Mosquitoes (Culicidae) are among very important microsporidian host groups. However, to date, no extensive survey on the prevalence of microsporidians in European mosquitoes has been performed. Here, we used mosquitoes collected in west-central Poland and a metabarcoding approach to examine the prevalence and diversity of microsporidian species among European mosquitoes. We found that up to one-third of mosquitoes in Europe may be infected with at least 13 microsporidian species belonging to the genera Amblyospora, Hazardia, Encephalitozoon, Enterocytospora, and Nosema and the holding genus Microsporidium. The lack of a difference in microsporidian prevalence between mosquito sexes implies that other factors, e.g., temperature or humidity, affect microsporidian occurrence in adult mosquitoes. Each microsporidian species was found in at least three mosquito species, which suggests that these microsporidians are polyxenic rather than monoxenic parasites. The co-occurrence of at least two different microsporidian species was found in 3.6% of host individuals. The abundance of microsporidian DNA sequences suggests interactions between co-occurring parasites; however, these results should be confirmed by microscopic and quantitative methods. In addition, further histological research is required to describe Microsporidium sp. PL01 or match its DNA to that of an already described species.
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38
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Farooq H, Antonelli A, Faurby S. A call for improving the Key Biodiversity Areas framework. Perspect Ecol Conserv 2023. [DOI: 10.1016/j.pecon.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
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39
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Hu Q, Qian R, Zhang Y, Ma X, Ye Y, Zhang X, Lin L, Liu H, Zheng J. Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China. Sci Rep 2023; 13:1356. [PMID: 36693990 PMCID: PMC9873718 DOI: 10.1038/s41598-023-28432-3] [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: 08/25/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Sphaeropteris lepifera is a tree fern in the Cyatheaceae, a family that has played an important role in the evolution of plant systems. This study aimed to analyze the complete chloroplast genome of S. lepifera and compared it with previously published chloroplast genomes Cyatheaceae family. The chloroplast genome of S. lepifera comprised 162,114 bp, consisting of a large single copy (LSC) region of 86,327 bp, a small single copy (SSC) region of 27,731 bp and a pair of inverted repeats (IRa and IRb) of 24,028 bp each. The chloroplast genome encoded 129 genes, comprising 32 transfer RNAs, 8 ribosomal RNAs, and 89 protein-coding genes. Comparison of the genomes of 7 Cyatheaceae plants showed that the chloroplast genome of S. lepifera was missing the gene trnV-UAC. Expansion of the SSC region led to the difference in the chloroplast genome size of S. lepifera. Eight genes, atpI, ccsA, petA, psaB, rpl16, rpoA, rpoC1, and ycf2 have high nucleic acid diversity and can be regarded as potential molecular markers. The genes trnG-trnR and atpB were suitable for DNA barcodes between different communities of S. lepifera. The S. lepifera groups in Zhejiang Province probably diffused from Pingtan and Ningde, Fujian. The results will provide a basis for species identification, biological studies, and endangerment mechanism of S. lepifera.
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Affiliation(s)
- Qingdi Hu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Renjuan Qian
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Yanjun Zhang
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang, China
| | - Xiaohua Ma
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Youju Ye
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Xule Zhang
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Lin Lin
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Hongjian Liu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Jian Zheng
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China.
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Bromham L. Language endangerment: Using analytical methods from conservation biology to illuminate loss of linguistic diversity. CAMBRIDGE PRISMS. EXTINCTION 2023; 1:e3. [PMID: 40078691 PMCID: PMC11895721 DOI: 10.1017/ext.2022.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/17/2022] [Accepted: 12/13/2022] [Indexed: 03/14/2025]
Abstract
Language diversity is under threat, with between a third to a half of all languages considered endangered, and predicted rates of loss equivalent to one language per month for the rest of the century. Rather than reviewing the extensive body of linguistic research on endangered languages, this review focuses specifically on the interdisciplinary transfer of methods developed in conservation biology, macroecology and macroevolution to the study of language endangerment and loss. While the causes of language endangerment and loss are different to those for species, studying patterns of diversity of species and languages involves similar analytical challenges, associated with testing hypotheses and identifying causal relationships. Solutions developed in biology can be adapted to illuminate patterns in language endangerment, such as statistical methods that explicitly model phylogenetic nonindependence, spatial autocorrelation and covariation between variables, which may otherwise derail the search for meaningful predictors of language endangerment. However, other tools from conservation biology may be much less use in understanding or predicting language endangerment, such as metrics based on International Union for Conservation of Nature (IUCN) criteria, population viability analysis or niche modelling. This review highlights both the similarities and the differences in approaches to understanding the concurrent crises in loss of both linguistic diversity and biodiversity.
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Affiliation(s)
- Lindell Bromham
- Macroevolution and Macroecology Group, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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Hietaranta E, Juottonen H, Kytöviita MM. Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems. Oecologia 2023; 201:59-72. [PMID: 36434466 DOI: 10.1007/s00442-022-05285-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 11/07/2022] [Indexed: 11/26/2022]
Abstract
Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant-pollinator-microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant-pollinator-microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.
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Affiliation(s)
- Elsi Hietaranta
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland.
| | - Heli Juottonen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Minna-Maarit Kytöviita
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
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Devkota S, Fang W, Arunachalam K, Phyo KMM, Shakya B. Systematic review of fungi, their diversity and role in ecosystem services from the Far Eastern Himalayan Landscape (FHL). Heliyon 2023; 9:e12756. [PMID: 36685357 PMCID: PMC9850047 DOI: 10.1016/j.heliyon.2022.e12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Fungi are morphologically and ecologically diverse kingdom but less explored in the global perspective. This systematic review of mainly higher fungi (mushrooms) and lichenized fungi (lichens) was aimed to convey comprehensive knowledge on these understudied taxa, especially considering diversity, research trends, taxonomic/geographic knowledge gaps, and their contribution to ecosystem services. We investigated literature from the Far Eastern Himalayas and adjacent areas. We followed the PRISM (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework for the evidence synthesis and reporting. Search strings were used to explore literature both in English and Chinese databases. Publications were validated examining the title, locality, abstract and full text. We included 75 eligible studies after screening 12,872 publications. The result on species diversity extrapolated from literature was consolidated as a species checklist and published on the Global Biodiversity Information Facility (GBIF) portal. This review demonstrates a significant shortage of research work on fungi, and a lack of quantitative data on diversity, ecology, and ecosystem services. Mycological inventories with multidisciplinary perspectives are urgent in the Landscape to better understand the importance of fungi in conservation and sustainable development science. This review is especially useful when global environmental and climate concerns are focused on the use of nature-based solutions, and fungi as integral part of all ecological processes, could play important role in enhancing ecosystem services and therefore benefits coming to people as natural solutions.
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Affiliation(s)
- Shiva Devkota
- Global Institute for Interdisciplinary Studies (GIIS), Kathmandu, GPO Box 3226, Nepal
- Himalayan Climate and Science Institute (HCSI), Washington DC, USA
| | - Wei Fang
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany (KIB), Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Karuppusamy Arunachalam
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany (KIB), Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | | | - Bandana Shakya
- Centre for Integrated Mountain Development (ICIMOD), Khumaltar, Lalitpur, 44700, GPO Box 3226, Nepal
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Affiliation(s)
- Mads Albertsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
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Rawat DS, Satish Chandra, Chaturvedi P. Threatened flora of Uttarakhand: an update. JOURNAL OF THREATENED TAXA 2022. [DOI: 10.11609/jott.6330.14.12.22309-22328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Encompassing 1.69% land area of India, Uttarakhand State sustains more than 25% species of flowering plants of India reflecting richness of flora. Large numbers of species in the state are threatened and several sources have come up with their own lists of threatened species using different threat categories leading to ambiguity. This communication attempts to compile a complete list of threatened Angiosperm species from eleven authentic sources with updated nomenclature, systematic position, original sources, threat assessment, elevational and global distribution. A total of 290 species belonging to 176 genera, 63 families, and 29 orders are listed which represent about 6% of the total flora. Elevational distribution of species shows that the 2–3 km elevation zone harbors more than half of the threatened flora (52.14%) and more than 44% endemic species despite the fact that maximum species richness is known in the 1–2 km elevation zone. Perusal of literature shows that selection of species for micropropagation is skewed towards medicinal plants rather than only threat status of a species. A disparity exists in two important sources (IUCN Red List 2020–21 and Indian Red Data Book) listing threatened taxa with only six species common to both. Eight additional species in IUCN Red List 2020–21 and 49 additional species in Indian Red Data Book are not included and vice versa. 267 species listed as threatened in various sources are not even evaluated by recent IUCN Redlist guidelines and thus warrant their immediate assessment to understand their correct present status in nature.
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Martinez-Rabert E, van Amstel C, Smith C, Sloan WT, Gonzalez-Cabaleiro R. Environmental and ecological controls of the spatial distribution of microbial populations in aggregates. PLoS Comput Biol 2022; 18:e1010807. [PMID: 36534694 PMCID: PMC9810174 DOI: 10.1371/journal.pcbi.1010807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/03/2023] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
In microbial communities, the ecological interactions between species of different populations are responsible for the spatial distributions observed in aggregates (granules, biofilms or flocs). To explore the underlying mechanisms that control these processes, we have developed a mathematical modelling framework able to describe, label and quantify defined spatial structures that arise from microbial and environmental interactions in communities. An artificial system of three populations collaborating or competing in an aggregate is simulated using individual-based modelling under different environmental conditions. In this study, neutralism, competition, commensalism and concurrence of commensalism and competition have been considered. We were able to identify interspecific segregation of communities that appears in competitive environments (columned stratification), and a layered distribution of populations that emerges in commensal (layered stratification). When different ecological interactions were considered in the same aggregate, the resultant spatial distribution was identified as the one controlled by the most limiting substrate. A theoretical modulus was defined, with which we were able to quantify the effect of environmental conditions and ecological interactions to predict the most probable spatial distribution. The specific microbial patterns observed in our results allowed us to identify the optimal spatial organizations for bacteria to thrive when building a microbial community and how this permitted co-existence of populations at different growth rates. Our model reveals that although ecological relationships between different species dictate the distribution of bacteria, the environment controls the final spatial distribution of the community.
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Affiliation(s)
- Eloi Martinez-Rabert
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Advanced Research Centre, Glasgow, United Kingdom
- * E-mail:
| | - Chiel van Amstel
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Cindy Smith
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Advanced Research Centre, Glasgow, United Kingdom
| | - William T. Sloan
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Advanced Research Centre, Glasgow, United Kingdom
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Tessler M, Galen SC, DeSalle R, Schierwater B. Let’s end taxonomic blank slates with molecular morphology. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many known evolutionary lineages have yet to be described formally due to a lack of traditional morphological characters. This is true for genetically distinctive groups within the amoeboid Placozoa animals, the protists in ponds, and the bacteria that cover nearly everything. These taxonomic tabula rasae, or blank slates, are problematic; without names, communication is hampered and other scientific progress is slowed. We suggest that the morphology of molecules be used to help alleviate this issue. Molecules, such as proteins, have structure. Proteins are even visualizable with X-ray crystallography, albeit more easily detected by and easier to work with using genomic sequencing. Given their structured nature, we believe they should not be considered as anything less than traditional morphology. Protein-coding gene content (presence/absence) can also be used easily with genomic sequences, and is a convenient binary character set. With molecular morphology, we believe that each taxonomic tabula rasa can be solved.
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Wells K, Flynn R. Managing host-parasite interactions in humans and wildlife in times of global change. Parasitol Res 2022; 121:3063-3071. [PMID: 36066742 PMCID: PMC9446624 DOI: 10.1007/s00436-022-07649-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
Global change in the Anthropocene has modified the environment of almost any species on earth, be it through climate change, habitat modifications, pollution, human intervention in the form of mass drug administration (MDA), or vaccination. This can have far-reaching consequences on all organisational levels of life, including eco-physiological stress at the cell and organism level, individual fitness and behaviour, population viability, species interactions and biodiversity. Host-parasite interactions often require highly adapted strategies by the parasite to survive and reproduce within the host environment and ensure efficient transmission among hosts. Yet, our understanding of the system-level outcomes of the intricate interplay of within host survival and among host parasite spread is in its infancy. We shed light on how global change affects host-parasite interactions at different organisational levels and address challenges and opportunities to work towards better-informed management of parasite control. We argue that global change affects host-parasite interactions in wildlife inhabiting natural environments rather differently than in humans and invasive species that benefit from anthropogenic environments as habitat and more deliberate rather than erratic exposure to therapeutic drugs and other control efforts.
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Affiliation(s)
- Konstans Wells
- Department of Biosciences, Swansea University, Swansea, SA28PP, UK.
| | - Robin Flynn
- Graduate Studies Office, South East Technological University, Cork Road Campus, Waterford, X91 K0EK, Ireland
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Measuring the Impact of Conservation: The Growing Importance of Monitoring Fauna, Flora and Funga. DIVERSITY 2022. [DOI: 10.3390/d14100824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Many stakeholders, from governments to civil society to businesses, lack the data they need to make informed decisions on biodiversity, jeopardising efforts to conserve, restore and sustainably manage nature. Here we review the importance of enhancing biodiversity monitoring, assess the challenges involved and identify potential solutions. Capacity for biodiversity monitoring needs to be enhanced urgently, especially in poorer, high-biodiversity countries where data gaps are disproportionately high. Modern tools and technologies, including remote sensing, bioacoustics and environmental DNA, should be used at larger scales to fill taxonomic and geographic data gaps, especially in the tropics, in marine and freshwater biomes, and for plants, fungi and invertebrates. Stakeholders need to follow best monitoring practices, adopting appropriate indicators and using counterfactual approaches to measure and attribute outcomes and impacts. Data should be made openly and freely available. Companies need to invest in collecting the data required to enhance sustainability in their operations and supply chains. With governments soon to commit to the post-2020 global biodiversity framework, the time is right to make a concerted push on monitoring. However, action at scale is needed now if we are to enhance results-based management adequately to conserve the biodiversity and ecosystem services we all depend on.
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Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks. Proc Natl Acad Sci U S A 2022; 119:e2122636119. [PMID: 36018838 PMCID: PMC9436379 DOI: 10.1073/pnas.2122636119] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taxonomic classification, that is, the assignment to biological clades with shared ancestry, is a common task in genetics, mainly based on a genome similarity search of large genome databases. The classification quality depends heavily on the database, since representative relatives must be present. Many genomic sequences cannot be classified at all or only with a high misclassification rate. Here we present BERTax, a deep neural network program based on natural language processing to precisely classify the superkingdom and phylum of DNA sequences taxonomically without the need for a known representative relative from a database. We show BERTax to be at least on par with the state-of-the-art approaches when taxonomically similar species are part of the training data. For novel organisms, however, BERTax clearly outperforms any existing approach. Finally, we show that BERTax can also be combined with database approaches to further increase the prediction quality in almost all cases. Since BERTax is not based on similar entries in databases, it allows precise taxonomic classification of a broader range of genomic sequences, thus increasing the overall information gain.
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50
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Ward AKG, Bagley RK, Egan SP, Hood GR, Ott JR, Prior KM, Sheikh SI, Weinersmith KL, Zhang L, Zhang YM, Forbes AA. Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both. Evolution 2022; 76:1849-1867. [PMID: 35819249 PMCID: PMC9541853 DOI: 10.1111/evo.14562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 01/22/2023]
Abstract
Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ∼1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae-primarily the oaks (genus Quercus; ∼435 sp.). The association of oak gall wasps with oaks is ancient (∼50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified the strong signal of host plant shifting among oak gall wasps that has been found in other phytophagous insect systems. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich. We collected 86 species of Nearctic oak gall wasps from most of the major clades of Nearctic oaks and sequenced >1000 Ultraconserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic wasp clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Although formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.
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Affiliation(s)
| | - Robin K. Bagley
- Department of BiologyUniversity of IowaIowa CityIowa52245
- Department of Evolution, Ecology, and Organismal BiologyThe Ohio State UniversityLimaOhio45804
| | - Scott P. Egan
- Department of BioSciencesRice UniversityHoustonTexas77005
| | - Glen Ray Hood
- Department of BioSciencesRice UniversityHoustonTexas77005
- Department of Biological ScienceWayne State UniversityDetroitMichigan48202
| | - James R. Ott
- Department of BiologyTexas State UniversitySan MarcosTexas78666
| | - Kirsten M. Prior
- Department of Biological SciencesBinghamton UniversityBinghamtonNew York13902
| | - Sofia I. Sheikh
- Department of BiologyUniversity of IowaIowa CityIowa52245
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinois60637
| | | | - Linyi Zhang
- Department of BioSciencesRice UniversityHoustonTexas77005
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM5S 3B2Canada
| | - Y. Miles Zhang
- Systematic Entomology Laboratory, USDA‐ARSc/o National Museum of Natural HistoryWashingtonD.C.20560
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