1
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Song S, Chen H, Zhang Y, Zhu X, Irwin DM, He K, Liu Y. Unique myoglobin adaptation to endothermy and flight since the origin of birds. Integr Zool 2024. [PMID: 39048923 DOI: 10.1111/1749-4877.12870] [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] [Indexed: 07/27/2024]
Abstract
Myoglobin (Mb) mediates oxygen diffusion and storage in muscle tissue and thus is important for the energy utilization and activity of animals. Birds generally have a high body temperature, and most species also possess the capability of powered flight. Both of these require high levels of aerobic metabolism. Within endothermic mammals, bats also independently evolved flight. Although the functional evolution of myoglobins in deep-diving amniote vertebrates has been well-studied, the functional evolution of myoglobin since the origins of both birds and bats is unclear. Here, with Mb-coding sequences from >200 extant amniote species, we reconstructed ancestral sequences to estimate the functional properties of myoglobin through amniote evolution. A dramatic change in net surface charge on myoglobin occurred during the origin of Aves, which might have been driven by positively selected amino acid substitutions that occurred on the lineage leading to all birds. However, in bats, no change in net surface charge occurred and instead, the Mb genes show evidence of strong purifying selection. The increased net surface charge on bird myoglobins implies an adaptation to flight-related endothermic and higher body temperatures, possibly by reducing harmful protein aggregations. Different from the findings of net surface charge, myoglobins of extant birds show lower stability compared with other amniotes, which probably accelerates the rate of oxygen utilization in muscles. In bats and other mammals, higher stability of Mb may be an alternative pathway for adaptation to endothermy, indicating divergent evolution of myoglobin in birds and bats.
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Affiliation(s)
- Shengjing Song
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Heye Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Yu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Xiaojia Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Kai He
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
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2
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Guedes JJM, Diniz-Filho JAF, Moura MR. Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates. Biol Lett 2024; 20:20240216. [PMID: 39046287 PMCID: PMC11268159 DOI: 10.1098/rsbl.2024.0216] [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: 04/19/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Most described species have not been explicitly included in phylogenetic trees-a problem named the Darwinian shortfall-owing to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group in which at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Future efforts should prioritize phylogenetic research on organisms that are narrow-ranged, small-bodied and underrepresented in scientific collections, such as fossorial species. Addressing the Darwinian shortfall will be imperative for advancing our understanding of evolutionary drivers shaping biodiversity patterns and implementing comprehensive conservation strategies.
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Affiliation(s)
- Jhonny J. M. Guedes
- Departamento de Ecologia, Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de Goiás—Campus Samambaia, Goiânia, GO74690-900, Brazil
| | - José Alexandre F. Diniz-Filho
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás — Campus Samambaia, Goiânia, GO74690-900, Brazil
| | - Mario R. Moura
- Departamento de Biologia Animal, Universidade Federal de Campinas, Campinas, SP13083-970, Brazil
- Departamento de Biociências, Universidade Federal da Paraíba, Areia, PB58397-000, Brazil
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3
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Moura MR, Ceron K, Guedes JJM, Chen-Zhao R, Sica YV, Hart J, Dorman W, Portmann JM, González-del-Pliego P, Ranipeta A, Catenazzi A, Werneck FP, Toledo LF, Upham NS, Tonini JFR, Colston TJ, Guralnick R, Bowie RCK, Pyron RA, Jetz W. A phylogeny-informed characterisation of global tetrapod traits addresses data gaps and biases. PLoS Biol 2024; 22:e3002658. [PMID: 38991106 PMCID: PMC11239118 DOI: 10.1371/journal.pbio.3002658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/03/2024] [Indexed: 07/13/2024] Open
Abstract
Tetrapods (amphibians, reptiles, birds, and mammals) are model systems for global biodiversity science, but continuing data gaps, limited data standardisation, and ongoing flux in taxonomic nomenclature constrain integrative research on this group and potentially cause biased inference. We combined and harmonised taxonomic, spatial, phylogenetic, and attribute data with phylogeny-based multiple imputation to provide a comprehensive data resource (TetrapodTraits 1.0.0) that includes values, predictions, and sources for body size, activity time, micro- and macrohabitat, ecosystem, threat status, biogeography, insularity, environmental preferences, and human influence, for all 33,281 tetrapod species covered in recent fully sampled phylogenies. We assess gaps and biases across taxa and space, finding that shared data missing in attribute values increased with taxon-level completeness and richness across clades. Prediction of missing attribute values using multiple imputation revealed substantial changes in estimated macroecological patterns. These results highlight biases incurred by nonrandom missingness and strategies to best address them. While there is an obvious need for further data collection and updates, our phylogeny-informed database of tetrapod traits can support a more comprehensive representation of tetrapod species and their attributes in ecology, evolution, and conservation research.
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Affiliation(s)
- Mario R. Moura
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Departamento de Biociências, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Karoline Ceron
- Departamento de Biologia, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Jhonny J. M. Guedes
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Rosana Chen-Zhao
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Yanina V. Sica
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Julie Hart
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
- New York Natural Heritage Program, State University of New York College of Environmental Science and Forestry, Albany, New York, United States of America
| | - Wendy Dorman
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
- Department of Natural Resources and Environmental Sciences (NRES), University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Julia M. Portmann
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Pamela González-del-Pliego
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
- Rui Nabeiro Biodiversity Chair, MED Institute, Universidade de Évora, Évora, Portugal
| | - Ajay Ranipeta
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Alessandro Catenazzi
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
| | - Fernanda P. Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus Amazonas, Brazil
| | - Luís Felipe Toledo
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Nathan S. Upham
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - João F. R. Tonini
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Timothy J. Colston
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - R. Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington DC, United States of America
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
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4
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Gvoždík V, Dolinay M, Zassi-Boulou AG, Lemmon AR, Lemmon EM, Procházka M. Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans. Biol Lett 2024; 20:20230448. [PMID: 38716586 PMCID: PMC11135362 DOI: 10.1098/rsbl.2023.0448] [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: 09/25/2023] [Revised: 12/18/2023] [Accepted: 03/04/2024] [Indexed: 05/31/2024] Open
Abstract
Recent molecular taxonomic advancements have expanded our understanding of crocodylian diversity, revealing the existence of previously overlooked species, including the Congo dwarf crocodile (Osteolaemus osborni) in the central Congo Basin rainforests. This study explores the genomic divergence between O. osborni and its better-known relative, the true dwarf crocodile (Osteolaemus tetraspis), shedding light on their evolutionary history. Field research conducted in the northwestern Republic of the Congo uncovered a locality where both species coexist in sympatry/syntopy. Genomic analysis of sympatric individuals reveals a level of divergence comparable to that between ecologically similar South American dwarf caimans (Paleosuchus palpebrosus and Paleosuchus trigonatus), suggesting parallel speciation in the Afrotropics and Neotropics during the Middle to Late Miocene, 10-12 Ma. Comparison of the sympatric and allopatric dwarf crocodiles indicates no gene flow between the analysed sympatric individuals of O. osborni and O. tetraspis. However, a larger sample will be required to answer the question of whether or to what extent these species hybridize. This study emphasizes the need for further research on the biology and conservation status of the Congo dwarf crocodile, highlighting its significance in the unique biodiversity of the Congolian rainforests and thus its potential as a flagship species.
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Affiliation(s)
- Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Matej Dolinay
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Ange-Ghislain Zassi-Boulou
- Department of Biology, National Institute for Research in Exact and Natural Sciences (IRSEN), Brazzaville, Republic of the Congo
| | - Alan R. Lemmon
- Department of Scientific Computing, Dirac Science Library, Florida State University, Tallahassee, FL, USA
| | - Emily M. Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
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5
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Gumbs R, Scott O, Bates R, Böhm M, Forest F, Gray CL, Hoffmann M, Kane D, Low C, Pearse WD, Pipins S, Tapley B, Turvey ST, Jetz W, Owen NR, Rosindell J. Global conservation status of the jawed vertebrate Tree of Life. Nat Commun 2024; 15:1101. [PMID: 38424441 PMCID: PMC10904806 DOI: 10.1038/s41467-024-45119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024] Open
Abstract
Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86-150 billion years (11-19%) of jawed vertebrate evolutionary history over the next 50-500 years. Second, we rank jawed vertebrate species by their EDGE scores to identify the highest priorities for species-focused conservation of evolutionary history, finding that chondrichthyans, ray-finned fish and testudines rank highest of all jawed vertebrates. Third, we assess the conservation status of jawed vertebrate families. We found that species within monotypic families are more likely to be threatened and more likely to be in decline than other species. We provide a baseline for the status of families at risk of extinction to catalyse conservation action. This work continues a trend of highlighting neglected groups-such as testudines, crocodylians, amphibians and chondrichthyans-as conservation priorities from a phylogenetic perspective.
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Affiliation(s)
- Rikki Gumbs
- Zoological Society of London, London, NW1 4RY, UK.
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, London, SW7 2AZ, UK.
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK.
| | - Oenone Scott
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Ryan Bates
- Zoological Society of London, London, NW1 4RY, UK
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - Monika Böhm
- Global Center for Species Survival, Indianapolis Zoological Society, Indianapolis, IN, 46222, USA
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | | | | | - Daniel Kane
- Zoological Society of London, London, NW1 4RY, UK
| | - Christopher Low
- Department of Genetics, Evolution and Environment, Centre for Biodiversity and Environment Research, University College London, London, WC1E 6BT, UK
| | - William D Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - Sebastian Pipins
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, London, SW7 2AZ, UK
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- On the Edge, London, SW3 2JJ, UK
| | | | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, London, NW1 4RY, UK
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT, 06511, USA
| | | | - James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
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6
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Gumbs R, Chaudhary A, Daru BH, Faith DP, Forest F, Gray CL, Kowalska A, Lee WS, Pellens R, Pipins S, Pollock LJ, Rosindell J, Scherson RA, Owen NR. Indicators to monitor the status of the tree of life. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14138. [PMID: 37377164 DOI: 10.1111/cobi.14138] [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: 10/04/2022] [Revised: 02/21/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Following the failure to fully achieve any of the 20 Aichi biodiversity targets, the future of biodiversity rests in the balance. The Convention on Biological Diversity's Kunming-Montreal Global Biodiversity Framework (GBF) presents the opportunity to preserve nature's contributions to people (NCPs) for current and future generations by conserving biodiversity and averting extinctions. There is a need to safeguard the tree of life-the unique and shared evolutionary history of life on Earth-to maintain the benefits it bestows into the future. Two indicators have been adopted within the GBF to monitor progress toward safeguarding the tree of life: the phylogenetic diversity (PD) indicator and the evolutionarily distinct and globally endangered (EDGE) index. We applied both to the world's mammals, birds, and cycads to show their utility at the global and national scale. The PD indicator can be used to monitor the overall conservation status of large parts of the evolutionary tree of life, a measure of biodiversity's capacity to maintain NCPs for future generations. The EDGE index is used to monitor the performance of efforts to conserve the most distinctive species. The risk to PD of birds, cycads, and mammals increased, and mammals exhibited the greatest relative increase in threatened PD over time. These trends appeared robust to the choice of extinction risk weighting. EDGE species had predominantly worsening extinction risk. A greater proportion of EDGE mammals (12%) had increased extinction risk compared with threatened mammals in general (7%). By strengthening commitments to safeguarding the tree of life, biodiversity loss can be reduced and thus nature's capacity to provide benefits to humanity now and in the future can be preserved.
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Affiliation(s)
- Rikki Gumbs
- EDGE of Existence Programme, Zoological Society of London, London, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
- IUCN SSC Phylogenetic Diversity Task Force, London, UK
| | - Abhishek Chaudhary
- Department of Civil Engineering, Indian Institute of Technology (IIT) Kanpur, Kanpur, India
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Daniel P Faith
- The Australian Museum Research Institute, The Australian Museum, Sydney, New South Wales, Australia
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Claudia L Gray
- EDGE of Existence Programme, Zoological Society of London, London, UK
| | | | - Who-Seung Lee
- Environmental Assessment Group, Korea Environment Institute, Sejong, Republic of Korea
| | - Roseli Pellens
- Institut de Systématique, Evolution, et Biodiversité (Muséum National d'Histoire Naturelle, Centre National pour la Recherche Scientifique, Sorbonne Université, Ecole Pratique de Hautes Etudes, Université des Antilles), Paris, France
| | - Sebastian Pipins
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Laura J Pollock
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
| | - Rosa A Scherson
- Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Nisha R Owen
- IUCN SSC Phylogenetic Diversity Task Force, London, UK
- On the EDGE Conservation, Chelsea, UK
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7
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Liang D, Giam X, Hu S, Ma L, Wilcove DS. Assessing the illegal hunting of native wildlife in China. Nature 2023; 623:100-105. [PMID: 37880359 DOI: 10.1038/s41586-023-06625-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/08/2023] [Indexed: 10/27/2023]
Abstract
Illegal harvesting and trading of wildlife have become major threats to global biodiversity and public health1-3. Although China is widely recognized as an important destination for wildlife illegally obtained abroad4, little attention has been given to illegal hunting within its borders. Here we extracted 9,256 convictions for illegal hunting from a nationwide database of trial verdicts in China spanning January 2014 to March 2020. These convictions involved illegal hunting of 21% (n = 673) of China's amphibian, reptile, bird and mammal species, including 25% of imperilled species in these groups. Sample-based extrapolation indicates that many more species were taken illegally during this period. Larger body mass and range size (for all groups), and proximity to urban markets (for amphibians and birds) increase the probability of a species appearing in the convictions database. Convictions pertained overwhelmingly to illegal hunting for commercial purposes and involved all major habitats across China. A small number of convictions represented most of the animals taken, indicating the existence of large commercial poaching operations. Prefectures closer to urban markets show higher densities of convictions and more individual animals taken. Our results suggest that illegal hunting is a major, overlooked threat to biodiversity throughout China.
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Affiliation(s)
- Dan Liang
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
| | - Xingli Giam
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, TN, USA
| | - Sifan Hu
- School of Ecology, Sun Yat-sen University, Shenzhen, China
- State Key Laboratory of Biological Control, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Liang Ma
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - David S Wilcove
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
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8
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Sales-Oliveira V, Altmanová M, Gvoždík V, Kretschmer R, Ezaz T, Liehr T, Padutsch N, Badjedjea G, Utsunomia R, Tanomtong A, Cioffi M. Cross-species chromosome painting and repetitive DNA mapping illuminate the karyotype evolution in true crocodiles (Crocodylidae). Chromosoma 2023; 132:289-303. [PMID: 37493806 DOI: 10.1007/s00412-023-00806-6] [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: 04/17/2023] [Revised: 05/23/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Crocodilians have maintained very similar karyotype structures and diploid chromosome numbers for around 100 million years, with only minor variations in collinearity. Why this karyotype structure has largely stayed unaltered for so long is unclear. In this study, we analyzed the karyotypes of six species belonging to the genera Crocodylus and Osteolaemus (Crocodylidae, true crocodiles), among which the Congolian endemic O. osborni was included and investigated. We utilized various techniques (differential staining, fluorescence in situ hybridization with repetitive DNA and rDNA probes, whole chromosome painting, and comparative genomic hybridization) to better understand how crocodile chromosomes evolved. We studied representatives of three of the four main diploid chromosome numbers found in crocodiles (2n = 30/32/38). Our data provided new information about the species studied, including the identification of four major chromosomal rearrangements that occurred during the karyotype diversification process in crocodiles. These changes led to the current diploid chromosome numbers of 2n = 30 (fusion) and 2n = 38 (fissions), derived from the ancestral state of 2n = 32. The conserved cytogenetic tendency in crocodilians, where extant species keep near-ancestral state, contrasts with the more dynamic karyotype evolution seen in other major reptile groups.
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Affiliation(s)
- Vanessa Sales-Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand
| | - Marcelo Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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9
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Weil SS, Gallien L, Nicolaï MPJ, Lavergne S, Börger L, Allen WL. Body size and life history shape the historical biogeography of tetrapods. Nat Ecol Evol 2023; 7:1467-1479. [PMID: 37604875 PMCID: PMC10482685 DOI: 10.1038/s41559-023-02150-5] [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: 01/17/2023] [Accepted: 07/04/2023] [Indexed: 08/23/2023]
Abstract
Dispersal across biogeographic barriers is a key process determining global patterns of biodiversity as it allows lineages to colonize and diversify in new realms. Here we demonstrate that past biogeographic dispersal events often depended on species' traits, by analysing 7,009 tetrapod species in 56 clades. Biogeographic models incorporating body size or life history accrued more statistical support than trait-independent models in 91% of clades. In these clades, dispersal rates increased by 28-32% for lineages with traits favouring successful biogeographic dispersal. Differences between clades in the effect magnitude of life history on dispersal rates are linked to the strength and type of biogeographic barriers and intra-clade trait variability. In many cases, large body sizes and fast life histories facilitate dispersal success. However, species with small bodies and/or slow life histories, or those with average traits, have an advantage in a minority of clades. Body size-dispersal relationships were related to a clade's average body size and life history strategy. These results provide important new insight into how traits have shaped the historical biogeography of tetrapod lineages and may impact present-day and future biogeographic dispersal.
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Affiliation(s)
- Sarah-Sophie Weil
- CNRS, Laboratoire d'Ecologie Alpine, University Savoie Mont Blanc, University Grenoble Alpes, Grenoble, France.
- Department of Biosciences, Swansea University, Swansea, UK.
| | - Laure Gallien
- CNRS, Laboratoire d'Ecologie Alpine, University Savoie Mont Blanc, University Grenoble Alpes, Grenoble, France
| | - Michaël P J Nicolaï
- Biology Department, Evolution and Optics of Nanostructures Group, Ghent University, Ghent, Belgium
| | - Sébastien Lavergne
- CNRS, Laboratoire d'Ecologie Alpine, University Savoie Mont Blanc, University Grenoble Alpes, Grenoble, France
| | - Luca Börger
- Department of Biosciences, Swansea University, Swansea, UK
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10
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Rodríguez-Caro RC, Graciá E, Blomberg SP, Cayuela H, Grace M, Carmona CP, Pérez-Mendoza HA, Giménez A, Salguero-Gómez R. Anthropogenic impacts on threatened species erode functional diversity in chelonians and crocodilians. Nat Commun 2023; 14:1542. [PMID: 36977697 PMCID: PMC10050202 DOI: 10.1038/s41467-023-37089-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
The Anthropocene is tightly associated with a drastic loss of species worldwide and the disappearance of their key ecosystem functions. The orders Testudines (turtles and tortoises) and Crocodilia (crocodiles, alligators, and gharials) contain numerous threatened, long-lived species for which the functional diversity and potential erosion by anthropogenic impacts remains unknown. Here, we examine 259 (69%) of the existing 375 species of Testudines and Crocodilia, quantifying their life history strategies (i.e., trade-offs in survival, development, and reproduction) from open-access data on demography, ancestry, and threats. We find that the loss of functional diversity in simulated extinction scenarios of threatened species is greater than expected by chance. Moreover, the effects of unsustainable local consumption, diseases, and pollution are associated with life history strategies. In contrast, climate change, habitat disturbance, and global trade affect species independent of their life history strategy. Importantly, the loss of functional diversity for threatened species by habitat degradation is twice that for all other threats. Our findings highlight the importance of conservation programmes focused on preserving the functional diversity of life history strategies jointly with the phylogenetic representativity of these highly threatened groups.
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Affiliation(s)
- R C Rodríguez-Caro
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- Departamento de Biología Aplicada, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain.
- Departamento de Ecología, Universidad de Alicante, San Vicent del Raspeig, 03690, Alicante, Spain.
| | - E Graciá
- Departamento de Biología Aplicada, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Universidad Miguel Hernández, 03312, Orihuela, Spain
| | - S P Blomberg
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - H Cayuela
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, F-769622, Villeurbanne, France
| | - M Grace
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - C P Carmona
- Institute of Ecology and Earth Sciences, University of Tartu, 50409, Tartu, Estonia
| | - H A Pérez-Mendoza
- Facultad de Estudios Superiores Iztacala, Universidad Autónoma de México, 54090, Tlalnepantla, México
| | - A Giménez
- Departamento de Biología Aplicada, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Universidad Miguel Hernández, 03312, Orihuela, Spain
| | - R Salguero-Gómez
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- Max Plank Institute for Demographic Research, Konrad-Zuße Straße 1, 18057, Rostock, Germany.
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11
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Lourenço-de-Moraes R, Campos FS, Cabral P, Silva-Soares T, Nobrega YC, Covre AC, França FGR. Global conservation prioritization areas in three dimensions of crocodilian diversity. Sci Rep 2023; 13:2568. [PMID: 36781891 PMCID: PMC9925794 DOI: 10.1038/s41598-023-28413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
Crocodilians are a taxonomic group of large predators with important ecological and evolutionary benefits for ecosystem functioning in the face of global change. Anthropogenic actions affect negatively crocodilians' survival and more than half of the species are threatened with extinction worldwide. Here, we map and explore three dimensions of crocodilian diversity on a global scale. To highlight the ecological importance of crocodilians, we correlate the spatial distribution of species with the ecosystem services of nutrient retention in the world. We calculate the effectiveness of global protected networks in safeguarding crocodilian species and provide three prioritization models for conservation planning. Our results show the main hotspots of ecological and evolutionary values are in southern North, Central and South America, west-central Africa, northeastern India, and southeastern Asia. African species have the highest correlation to nutrient retention patterns. Twenty-five percent of the world's crocodilian species are not significantly represented in the existing protected area networks. The most alarming cases are reported in northeastern India, eastern China, and west-central Africa, which include threatened species with low or non-significant representation in the protected area networks. Our highest conservation prioritization model targets southern North America, east-central Central America, northern South America, west-central Africa, northeastern India, eastern China, southern Laos, Cambodia, and some points in southeastern Asia. Our research provides a global prioritization scheme to protect multiple dimensions of crocodilian diversity for achieving effective conservation outcomes.
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Affiliation(s)
- Ricardo Lourenço-de-Moraes
- Programa de Pós-graduação em Ecologia e Monitoramento Ambiental (PPGEMA), Universidade Federal da Paraíba, Rio Tinto, PB, 58297-000, Brazil.
| | - Felipe S Campos
- NOVA Information Management School (NOVA IMS), Universidade Nova de Lisboa, Campus de Campolide, 1070-312, Lisbon, Portugal.
- Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Catalunya, Spain.
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), 08193, Cerdanyola del Vallès, Catalunya, Spain.
| | - Pedro Cabral
- NOVA Information Management School (NOVA IMS), Universidade Nova de Lisboa, Campus de Campolide, 1070-312, Lisbon, Portugal
| | - Thiago Silva-Soares
- Herpeto Capixaba project, Instituto Biodiversidade Neotropical, Nova Guarapari, Guarapari, ES, 29206-400, Brazil
- Museu de História Natural do Sul do Estado do Espírito Santo, Universidade Federal do Espírito Santo, Jerônimo Monteiro, ES, 29550-000, Brazil
| | - Yhuri C Nobrega
- Projeto Caiman, Instituto Marcos Daniel, Vitória, ES, 29055-290, Brazil
- Departamento de Medicina Veterinária, Centro Universitário FAESA, Vitória, ES, 29053-360, Brazil
| | - Amanda C Covre
- Programa de Pós-graduacão em Ecologia de Ambientes Aquáticos Continentais (PEA), Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Frederico G R França
- Programa de Pós-graduação em Ecologia e Monitoramento Ambiental (PPGEMA), Universidade Federal da Paraíba, Rio Tinto, PB, 58297-000, Brazil
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12
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Gumbs R, Gray CL, Böhm M, Burfield IJ, Couchman OR, Faith DP, Forest F, Hoffmann M, Isaac NJB, Jetz W, Mace GM, Mooers AO, Safi K, Scott O, Steel M, Tucker CM, Pearse WD, Owen NR, Rosindell J. The EDGE2 protocol: Advancing the prioritisation of Evolutionarily Distinct and Globally Endangered species for practical conservation action. PLoS Biol 2023; 21:e3001991. [PMID: 36854036 PMCID: PMC9974121 DOI: 10.1371/journal.pbio.3001991] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there have been important research advances since 2007, they have not been adopted in practice because of a lack of consensus in the conservation community. Here, building from an interdisciplinary workshop to update the existing EDGE approach, we present an "EDGE2" protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritising species conservation efforts. Key advances include methods for dealing with uncertainty and accounting for the extinction risk of closely related species. We describe EDGE2 in terms of distinct components to facilitate future revisions to its constituent parts without needing to reconsider the whole. We illustrate EDGE2 by applying it to the world's mammals. As we approach a crossroads for global biodiversity policy, this Consensus View shows how collaboration between academic and applied conservation biologists can guide effective and practical priority-setting to conserve biodiversity.
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Affiliation(s)
- Rikki Gumbs
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
- IUCN SSC Phylogenetic Diversity Task Force, London, United Kingdom
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, South Kensington, London, United Kingdom
- * E-mail:
| | - Claudia L. Gray
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Monika Böhm
- Institute of Zoology, Zoological Society of London, Regent’s Park, London, United Kingdom
- Global Center for Species Survival, Indianapolis Zoological Society, Indianapolis, Indiana, United States of America
| | - Ian J. Burfield
- BirdLife International, David Attenborough Building, Cambridge, United Kingdom
| | - Olivia R. Couchman
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Daniel P. Faith
- School of Philosophical and Historical Inquiry, The University of Sydney, Sydney, Australia
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Michael Hoffmann
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Nick J. B. Isaac
- UK Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, United Kingdom
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Georgina M. Mace
- Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Arne O. Mooers
- Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Kamran Safi
- Max-Planck Institute of Animal Behavior, Department of Migration, Radolfzell, Germany
- University of Konstanz, Department of Biology, Konstanz, Germany
| | - Oenone Scott
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Caroline M. Tucker
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - William D. Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Nisha R. Owen
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
- IUCN SSC Phylogenetic Diversity Task Force, London, United Kingdom
- On the EDGE Conservation, London, United Kingdom
| | - James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
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13
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Cunha FA, Sampaio I, Carneiro J, Vogt RC, Mittermeier RA, Rhodin AG, Andrade MC. A New South American Freshwater Turtle of the Genus Mesoclemmys from the Brazilian Amazon (Testudines: Pleurodira: Chelidae). CHELONIAN CONSERVATION AND BIOLOGY 2022. [DOI: 10.2744/ccb-1524.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Fábio A.G. Cunha
- Programa de Pós-Graduação em Ecologia Aquática e Pesca/PPGEAP, Núcleo de Ecologia Aquática e Pesca da Amazônia, Universidade Federal do Pará/UFPA, Campus Universitário do Guamá, Rua Augusto Corrêa, 01, Cep.: 66.075-110, Belém, Pará, Brazil [; andrade
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará/UFPA, Campus Bragança, Alameda Leandro Ribeiro, Cep.: 68.600-000, Bragança, Pará, Brazil [; ]
| | - Jeferson Carneiro
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará/UFPA, Campus Bragança, Alameda Leandro Ribeiro, Cep.: 68.600-000, Bragança, Pará, Brazil [; ]
| | - Richard C. Vogt
- Coordenação de Biodiversidade/CBIO, Instituto Nacional de Pesquisa da Amazônia/INPA, Av. André Araújo, 2936, Cep.: 69.067-375, Manaus, Amazonas, Brazil
| | | | - Anders G.J. Rhodin
- Chelonian Research Foundation, 564 Chittenden Drive, Arlington, Vermont 05250 USA []
| | - Marcelo C. Andrade
- Programa de Pós-Graduação em Ecologia Aquática e Pesca/PPGEAP, Núcleo de Ecologia Aquática e Pesca da Amazônia, Universidade Federal do Pará/UFPA, Campus Universitário do Guamá, Rua Augusto Corrêa, 01, Cep.: 66.075-110, Belém, Pará, Brazil [; andrade
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14
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Patterns and Trends in the Publication of Natural History Notes in Herpetology Journals Over the Past Decade. J HERPETOL 2022. [DOI: 10.1670/20-066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Griffith P, Lang JW, Turvey ST, Gumbs R. Using functional traits to identify conservation priorities for the world's crocodylians. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Phoebe Griffith
- Institute of Zoology Zoological Society of London London UK
- Wildlife Conservation Research Unit The Recanati‐Kaplan Centre, Department of Zoology, University of Oxford Oxford UK
| | - Jeffrey W. Lang
- Gharial Ecology Project Madras Crocodile Bank Trust Mamallapuram Tamil Nadu India
| | | | - Rikki Gumbs
- EDGE of Existence Programme Conservation and Policy, Zoological Society of London London UK
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16
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Skeels A, Bach W, Hagen O, Jetz W, Pellissier L. Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations. Syst Biol 2022:6637530. [PMID: 35809070 DOI: 10.1093/sysbio/syac048] [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: 10/08/2021] [Revised: 06/21/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - W Bach
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - O Hagen
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.,Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
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17
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Reinke BA, Cayuela H, Janzen FJ, Lemaître JF, Gaillard JM, Lawing AM, Iverson JB, Christiansen DG, Martínez-Solano I, Sánchez-Montes G, Gutiérrez-Rodríguez J, Rose FL, Nelson N, Keall S, Crivelli AJ, Nazirides T, Grimm-Seyfarth A, Henle K, Mori E, Guiller G, Homan R, Olivier A, Muths E, Hossack BR, Bonnet X, Pilliod DS, Lettink M, Whitaker T, Schmidt BR, Gardner MG, Cheylan M, Poitevin F, Golubović A, Tomović L, Arsovski D, Griffiths RA, Arntzen JW, Baron JP, Le Galliard JF, Tully T, Luiselli L, Capula M, Rugiero L, McCaffery R, Eby LA, Briggs-Gonzalez V, Mazzotti F, Pearson D, Lambert BA, Green DM, Jreidini N, Angelini C, Pyke G, Thirion JM, Joly P, Léna JP, Tucker AD, Limpus C, Priol P, Besnard A, Bernard P, Stanford K, King R, Garwood J, Bosch J, Souza FL, Bertoluci J, Famelli S, Grossenbacher K, Lenzi O, Matthews K, Boitaud S, Olson DH, Jessop TS, Gillespie GR, Clobert J, Richard M, Valenzuela-Sánchez A, Fellers GM, Kleeman PM, Halstead BJ, Grant EHC, Byrne PG, Frétey T, Le Garff B, Levionnois P, Maerz JC, Pichenot J, Olgun K, Üzüm N, Avcı A, Miaud C, Elmberg J, Brown GP, Shine R, Bendik NF, O'Donnell L, Davis CL, Lannoo MJ, Stiles RM, Cox RM, Reedy AM, Warner DA, Bonnaire E, Grayson K, Ramos-Targarona R, Baskale E, Muñoz D, Measey J, de Villiers FA, Selman W, Ronget V, Bronikowski AM, Miller DAW. Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity. Science 2022; 376:1459-1466. [PMID: 35737773 DOI: 10.1126/science.abm0151] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.
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Affiliation(s)
- Beth A Reinke
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
- Department of Ecosystem Science and Management, Pennsylvania State University, State College, PA, USA
| | - Hugo Cayuela
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Fredric J Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | | | - Jean-Michel Gaillard
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - A Michelle Lawing
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - John B Iverson
- Department of Biology, Earlham College, Richmond, IN, USA
| | - Ditte G Christiansen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Iñigo Martínez-Solano
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Gregorio Sánchez-Montes
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Jorge Gutiérrez-Rodríguez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Francis L Rose
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Nicola Nelson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Susan Keall
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Alain J Crivelli
- Research Institute for the Conservation of Mediterranean Wetlands, Tour du Valat, Arles, France
| | | | - Annegret Grimm-Seyfarth
- Department Conservation Biology and Social-Ecological Systems, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Klaus Henle
- Department Conservation Biology and Social-Ecological Systems, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Emiliano Mori
- Consiglio Nazionale delle Ricerche, Istituto di Ricerca sugli Ecosistemi Terrestri, Sesto Fiorentino, Italy
| | | | - Rebecca Homan
- Biology Department, Denison University, Granville, OH, USA
| | - Anthony Olivier
- Research Institute for the Conservation of Mediterranean Wetlands, Tour du Valat, Arles, France
| | - Erin Muths
- US Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - Blake R Hossack
- US Geological Survey, Northern Rocky Mountain Science Center, Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Xavier Bonnet
- Centre d'Etudes Biologiques de Chizé, CNRS UMR 7372 - Université de La Rochelle, Villiers-en-Bois, France
| | - David S Pilliod
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | | | | | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Info Fauna Karch, Neuchâtel, Switzerland
| | - Michael G Gardner
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - Marc Cheylan
- PSL Research University, Université de Montpellier, Université Paul-Valéry, Montpellier, France
| | - Françoise Poitevin
- PSL Research University, Université de Montpellier, Université Paul-Valéry, Montpellier, France
| | - Ana Golubović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ljiljana Tomović
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Richard A Griffiths
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
| | | | - Jean-Pierre Baron
- Ecole normale supérieure, PSL University, Département de biologie, CNRS, UMS 3194, Centre de recherche en écologie expérimentale et prédictive (CEREEP-Ecotron IleDeFrance), Saint-Pierre-lès-Nemours, France
| | - Jean-François Le Galliard
- Ecole normale supérieure, PSL University, Département de biologie, CNRS, UMS 3194, Centre de recherche en écologie expérimentale et prédictive (CEREEP-Ecotron IleDeFrance), Saint-Pierre-lès-Nemours, France
- Sorbonne Université, CNRS, INRA, UPEC, IRD, Institute of Ecology and Environmental Sciences, iEES-Paris, Paris, France
| | - Thomas Tully
- Sorbonne Université, CNRS, INRA, UPEC, IRD, Institute of Ecology and Environmental Sciences, iEES-Paris, Paris, France
| | - Luca Luiselli
- Institute for Development, Ecology, Conservation and Cooperation, Rome, Italy
- Department of Animal and Applied Biology, Rivers State University of Science and Technology, Port Harcourt, Nigeria
- Department of Zoology, University of Lomé, Lomé, Togo
| | | | - Lorenzo Rugiero
- Institute for Development, Ecology, Conservation and Cooperation, Rome, Italy
| | - Rebecca McCaffery
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Port Angeles, WA, USA
| | - Lisa A Eby
- Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Venetia Briggs-Gonzalez
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, USA
| | - Frank Mazzotti
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, USA
| | - David Pearson
- Department of Biodiversity, Conservation and Attractions, Wanneroo, WA, Australia
| | - Brad A Lambert
- Colorado Natural Heritage Program, Colorado State University, Fort Collins, CO, USA
| | - David M Green
- Redpath Museum, McGill University, Montreal, QC, Canada
| | | | | | - Graham Pyke
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, CN, Kunming, PR China
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Pierre Joly
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, France
| | - Jean-Paul Léna
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, France
| | - Anton D Tucker
- Department of Biodiversity, Conservation and Attractions, Parks and Wildlife Service-Marine Science Program, Kensington, WA, Australia
| | - Col Limpus
- Threatened Species Operations, Queensland Department of Environment and Science, Ecosciences Precinct, Dutton Park, QLD, Australia
| | | | - Aurélien Besnard
- CNRS, EPHE, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, PSL Research University, Montpelier, France
| | - Pauline Bernard
- Conservatoire d'espaces naturels d'Occitanie, Montpellier, France
| | - Kristin Stanford
- Ohio Sea Grant and Stone Laboratory, The Ohio State University, Put-In-Bay, OH, USA
| | - Richard King
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Justin Garwood
- California Department of Fish and Wildlife, Arcata, CA, USA
| | - Jaime Bosch
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- IMIB-Biodiversity Research Unit, University of Oviedo-Principality of Asturias, Mieres, Spain
- Centro de Investigación, Seguimiento y Evaluación, Sierra de Guadarrama National Park, Rascafría, Spain
| | - Franco L Souza
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Jaime Bertoluci
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, São Paulo, Brazil
| | - Shirley Famelli
- School of Science, RMIT University, Melbourne, VIC, Australia
- Environmental Research Institute, North Highland College, University of the Highlands and Islands, Thurso, Scotland, UK
| | | | - Omar Lenzi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Kathleen Matthews
- USDA Forest Service (Retired), Pacific Southwest Research Station, Albany, CA, USA
| | - Sylvain Boitaud
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Deanna H Olson
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR, USA
| | - Tim S Jessop
- Centre for Integrative Ecology, Deakin University, Waurn Ponds, Geelong, VIC, Australia
| | - Graeme R Gillespie
- Department of Environment and Natural Resources, Palmerston, NT, Australia
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS-UMR532, Saint Girons, France
| | - Murielle Richard
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS-UMR532, Saint Girons, France
| | - Andrés Valenzuela-Sánchez
- Instituto de Conservación, Biodiversidad y Territorio, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia, Chile
- ONG Ranita de Darwin, Valdivia, Chile
| | - Gary M Fellers
- US Geological Survey, Western Ecological Research Center, Point Reyes National Seashore, Point Reyes, CA, USA
| | - Patrick M Kleeman
- US Geological Survey, Western Ecological Research Center, Point Reyes National Seashore, Point Reyes, CA, USA
| | - Brian J Halstead
- US Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Evan H Campbell Grant
- US Geological Survey Eastern Ecological Research Center (formerly Patuxent Wildlife Research Center), S.O. Conte Anadromous Fish Research Center, Turners Falls, MA, USA
| | - Phillip G Byrne
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | | | | | | | - John C Maerz
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | - Julian Pichenot
- Université de Reims Champagne-Ardenne, Centre de Recherche et de Formation en Eco-éthologie, URCA-CERFE, Boult-aux-Bois, France
| | - Kurtuluş Olgun
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - Nazan Üzüm
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - Aziz Avcı
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - Claude Miaud
- PSL Research University, Université de Montpellier, Université Paul-Valéry, Montpellier, France
| | - Johan Elmberg
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
| | - Gregory P Brown
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Nathan F Bendik
- Watershed Protection Department, City of Austin, Austin, TX, USA
| | - Lisa O'Donnell
- Balcones Canyonlands Preserve, City of Austin, Austin, TX, USA
| | | | | | | | - Robert M Cox
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Aaron M Reedy
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Daniel A Warner
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Eric Bonnaire
- Office National des Forêts, Agence de Meurthe-et-Moselle, Nancy, France
| | - Kristine Grayson
- Department of Biology, University of Richmond, Richmond, VA, USA
| | | | - Eyup Baskale
- Department of Biology, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - David Muñoz
- Department of Ecosystem Science and Management, Pennsylvania State University, State College, PA, USA
| | - John Measey
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - F Andre de Villiers
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Will Selman
- Department of Biology, Millsaps College, Jackson, MS, USA
| | - Victor Ronget
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
| | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - David A W Miller
- Department of Ecosystem Science and Management, Pennsylvania State University, State College, PA, USA
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18
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Caetano GHDO, Chapple DG, Grenyer R, Raz T, Rosenblatt J, Tingley R, Böhm M, Meiri S, Roll U. Automated assessment reveals that the extinction risk of reptiles is widely underestimated across space and phylogeny. PLoS Biol 2022; 20:e3001544. [PMID: 35617356 PMCID: PMC9135251 DOI: 10.1371/journal.pbio.3001544] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
The Red List of Threatened Species, published by the International Union for Conservation of Nature (IUCN), is a crucial tool for conservation decision-making. However, despite substantial effort, numerous species remain unassessed or have insufficient data available to be assigned a Red List extinction risk category. Moreover, the Red Listing process is subject to various sources of uncertainty and bias. The development of robust automated assessment methods could serve as an efficient and highly useful tool to accelerate the assessment process and offer provisional assessments. Here, we aimed to (1) present a machine learning–based automated extinction risk assessment method that can be used on less known species; (2) offer provisional assessments for all reptiles—the only major tetrapod group without a comprehensive Red List assessment; and (3) evaluate potential effects of human decision biases on the outcome of assessments. We use the method presented here to assess 4,369 reptile species that are currently unassessed or classified as Data Deficient by the IUCN. The models used in our predictions were 90% accurate in classifying species as threatened/nonthreatened, and 84% accurate in predicting specific extinction risk categories. Unassessed and Data Deficient reptiles were considerably more likely to be threatened than assessed species, adding to mounting evidence that these species warrant more conservation attention. The overall proportion of threatened species greatly increased when we included our provisional assessments. Assessor identities strongly affected prediction outcomes, suggesting that assessor effects need to be carefully considered in extinction risk assessments. Regions and taxa we identified as likely to be more threatened should be given increased attention in new assessments and conservation planning. Lastly, the method we present here can be easily implemented to help bridge the assessment gap for other less known taxa.
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Affiliation(s)
- Gabriel Henrique de Oliveira Caetano
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - David G. Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Richard Grenyer
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Tal Raz
- School of Zoology and Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | | | - Reid Tingley
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Monika Böhm
- Institute of Zoology, Zoological Society of London, London, United Kingdom
- Global Center for Species Survival, Indianapolis Zoological Society, Indianapolis, Indiana, United States of America
| | - Shai Meiri
- School of Zoology and Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Uri Roll
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- * E-mail:
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19
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Cox N, Young BE, Bowles P, Fernandez M, Marin J, Rapacciuolo G, Böhm M, Brooks TM, Hedges SB, Hilton-Taylor C, Hoffmann M, Jenkins RKB, Tognelli MF, Alexander GJ, Allison A, Ananjeva NB, Auliya M, Avila LJ, Chapple DG, Cisneros-Heredia DF, Cogger HG, Colli GR, de Silva A, Eisemberg CC, Els J, Fong G A, Grant TD, Hitchmough RA, Iskandar DT, Kidera N, Martins M, Meiri S, Mitchell NJ, Molur S, Nogueira CDC, Ortiz JC, Penner J, Rhodin AGJ, Rivas GA, Rödel MO, Roll U, Sanders KL, Santos-Barrera G, Shea GM, Spawls S, Stuart BL, Tolley KA, Trape JF, Vidal MA, Wagner P, Wallace BP, Xie Y. A global reptile assessment highlights shared conservation needs of tetrapods. Nature 2022; 605:285-290. [PMID: 35477765 PMCID: PMC9095493 DOI: 10.1038/s41586-022-04664-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Comprehensive assessments of species’ extinction risks have documented the extinction crisis1 and underpinned strategies for reducing those risks2. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction3. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods4–7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs6. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles. An extinction-risk assessment of reptiles shows that at least 21.1% of species are threatened by factors such as agriculture, logging, urban development and invasive species, and that efforts to protect birds, mammals and amphibians probably also benefit many reptiles.
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Affiliation(s)
- Neil Cox
- Biodiversity Assessment Unit, IUCN-Conservation International, Washington, DC, USA
| | | | - Philip Bowles
- Biodiversity Assessment Unit, IUCN-Conservation International, Washington, DC, USA
| | - Miguel Fernandez
- NatureServe, Arlington, VA, USA.,Smithsonian-Mason School of Conservation and Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA.,Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Julie Marin
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
| | - Giovanni Rapacciuolo
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Monika Böhm
- Institute of Zoology, Zoological Society of London, London, UK
| | - Thomas M Brooks
- IUCN, Gland, Switzerland.,World Agroforestry Center (ICRAF), University of The Philippines, Los Baños, The Philippines.,Institute for Marine & Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - S Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, PA, USA
| | - Craig Hilton-Taylor
- Science & Data Centre: Biodiversity Assessment & Knowledge Team, IUCN, Cambridge, UK
| | - Michael Hoffmann
- Conservation and Policy, Zoological Society of London, London, UK
| | - Richard K B Jenkins
- Science & Data Centre: Biodiversity Assessment & Knowledge Team, IUCN, Cambridge, UK
| | - Marcelo F Tognelli
- Biodiversity Assessment Unit, IUCN-Conservation International, Washington, DC, USA
| | - Graham J Alexander
- Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Natalia B Ananjeva
- Department of Herpetology, Zoological Institute, St Petersburg, Russian Federation
| | - Mark Auliya
- Department of Herpetology, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Luciano Javier Avila
- Grupo Herpetología Patagónica (GHP-LASIBIBE), Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Puerto Madryn, Argentina
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Diego F Cisneros-Heredia
- Colegio de Ciencias Biológicas y Ambientales, Museo de Zoología, Instituto de Biodiversidad Tropical iBIOTROP, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Instituto Nacional de Biodiversidad, Quito, Ecuador
| | - Harold G Cogger
- Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Anslem de Silva
- South Asia Regional Office, Crocodile Specialist Group, Gampols, Sri Lanka
| | | | - Johannes Els
- Environment and Protected Areas Authority, Government of Sharjah, Sharjah, United Arab Emirates
| | - Ansel Fong G
- Centro Oriental de Ecosistemas y Biodiversidad (BIOECO), Museo de Historia Natural "Tomás Romay", Santiago de Cuba, Cuba
| | - Tandora D Grant
- Conservation Science & Wildlife Health, San Diego Zoo Wildlife Alliance, San Diego, CA, USA
| | | | | | - Noriko Kidera
- Department of Biosphere-Geosphere Science, Okayama University of Science, Okayama, Japan.,National Institute for Environmental Studies, Tsukuba, Japan
| | - Marcio Martins
- Departamento de Ecologia, Universidade de São Paulo, São Paulo, Brazil
| | - Shai Meiri
- School of Zoology & the Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Nicola J Mitchell
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | | | | | - Juan Carlos Ortiz
- Departamento de Zoología, Universidad de Concepción, Concepción, Chile
| | - Johannes Penner
- Chair of Wildlife Ecology and Management, University of Freiburg, Freiburg, Germany.,Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Gilson A Rivas
- Museo de Biología, Universidad del Zulia, Maracaibo, Venezuela
| | - Mark-Oliver Rödel
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Uri Roll
- Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Kate L Sanders
- University of Adelaide, Adelaide, South Australia, Australia
| | | | - Glenn M Shea
- Australian Museum Research Institute, Sydney, New South Wales, Australia.,Sydney School of Veterinary Science B01, University of Sydney, Sydney, New South Wales, Australia
| | | | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Krystal A Tolley
- Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa.,South African National Biodiversity Institute, Cape Town, South Africa
| | | | - Marcela A Vidal
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
| | | | | | - Yan Xie
- Chinese Academy of Sciences, Beijing, China
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20
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Gable SM, Byars MI, Literman R, Tollis M. A Genomic Perspective on the Evolutionary Diversification of Turtles. Syst Biol 2022; 71:1331-1347. [DOI: 10.1093/sysbio/syac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
| | - Robert Literman
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingstown, RI, 0288, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
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21
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Cunha FA, Sampaio I, Carneiro J, Vogt RC. A New Species of Amazon Freshwater Toad-Headed Turtle in the Genus Mesoclemmys (Testudines: Pleurodira: Chelidae) from Brazil. CHELONIAN CONSERVATION AND BIOLOGY 2021. [DOI: 10.2744/ccb-1448.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fábio A.G. Cunha
- Programa de Pós-Graduação em Ecologia Aquática e Pesca/PPGEAP, Universidade Federal do Pará/UFPA, Campus Universitário do Guamá, Rua Augusto Corrêa, 01, Cep.: 66.075-110, Belém, PA, Brasil []
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará/UFPA, Campus Bragança, Alameda Leandro Ribeiro, Cep.: 68.600-000, Bragança, PA, Brasil [; ]
| | - Jeferson Carneiro
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará/UFPA, Campus Bragança, Alameda Leandro Ribeiro, Cep.: 68.600-000, Bragança, PA, Brasil [; ]
| | - Richard C. Vogt
- Coordenação de Biodiversidade/CBIO, Instituto Nacional de Pesquisa da Amazônia/INPA, Av. André Araújo, 2936, Cep.: 69.067-375, Manaus, AM, Brasil
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22
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Glaberman S, Bulls SE, Vazquez JM, Chiari Y, Lynch VJ. Concurrent evolution of anti-aging gene duplications and cellular phenotypes in long-lived turtles. Genome Biol Evol 2021; 13:6430984. [PMID: 34792580 PMCID: PMC8688777 DOI: 10.1093/gbe/evab244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
There are many costs associated with increased body size and longevity in animals, including the accumulation of genotoxic and cytotoxic damage that comes with having more cells and living longer. Yet, some species have overcome these barriers and have evolved remarkably large body sizes and long lifespans, sometimes within a narrow window of evolutionary time. Here, we demonstrate through phylogenetic comparative analysis that multiple turtle lineages, including Galapagos giant tortoises, concurrently evolved large bodies, long lifespans, and reduced cancer risk. We also show through comparative genomic analysis that Galapagos giant tortoises have gene duplications related to longevity and tumor suppression. To examine the molecular basis underlying increased body size and lifespan in turtles, we treated cell lines from multiple species, including Galapagos giant tortoises, with drugs that induce different types of cytotoxic stress. Our results indicate that turtle cells, in general, are resistant to oxidative stress related to aging, whereas Galapagos giant tortoise cells, specifically, are sensitive to endoplasmic reticulum stress, which may give this species an ability to mitigate the effects of cellular stress associated with increased body size and longevity.
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Affiliation(s)
- Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA.,Department of Biology, University of South Alabama, Mobile, AL, USA
| | | | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, Buffalo, NY, USA
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23
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Greenberg DA, Pyron RA, Johnson LGW, Upham NS, Jetz W, Mooers AØ. Evolutionary legacies in contemporary tetrapod imperilment. Ecol Lett 2021; 24:2464-2476. [PMID: 34510687 DOI: 10.1111/ele.13868] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/12/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns - but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.
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Affiliation(s)
- Dan A Greenberg
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - R Alexander Pyron
- Department of Biological Sciences, George Washington University, Washington, District of Columbia, USA
| | - Liam G W Johnson
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Nathan S Upham
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
| | - Arne Ø Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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24
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Rio JP, Mannion PD. Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem. PeerJ 2021; 9:e12094. [PMID: 34567843 PMCID: PMC8428266 DOI: 10.7717/peerj.12094] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/09/2021] [Indexed: 12/16/2022] Open
Abstract
First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.
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Affiliation(s)
- Jonathan P. Rio
- Department of Earth Science and Engineering, Imperial College London, London, United Kingdom
| | - Philip D. Mannion
- Department of Earth Sciences, University College London, London, United Kingdom
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Ascarrunz E, Claude J, Joyce WG. The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters. PeerJ 2021; 9:e11805. [PMID: 34430073 PMCID: PMC8349520 DOI: 10.7717/peerj.11805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/27/2021] [Indexed: 11/30/2022] Open
Abstract
The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as "Ocadia" kehreri and "Ocadia" messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.
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Affiliation(s)
- Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Julien Claude
- Institut des Sciences de l’Évolution de Montpellier, UMR UM/CNRS/IRD/EPHE, Montpellier, France
| | - Walter G. Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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Ibáñez A, Fritz U, Auer M, Martínez-Silvestre A, Praschag P, Załugowicz E, Podkowa D, Pabijan M. Evolutionary history of mental glands in turtles reveals a single origin in an aquatic ancestor and recurrent losses independent of macrohabitat. Sci Rep 2021; 11:10396. [PMID: 34001926 PMCID: PMC8129087 DOI: 10.1038/s41598-021-89520-w] [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: 01/28/2021] [Accepted: 04/21/2021] [Indexed: 02/03/2023] Open
Abstract
Despite the relevance of chemical communication in vertebrates, comparative examinations of macroevolutionary trends in chemical signaling systems are scarce. Many turtle and tortoise species are reliant on chemical signals to communicate in aquatic and terrestrial macrohabitats, and many of these species possess specialized integumentary organs, termed mental glands (MGs), involved in the production of chemosignals. We inferred the evolutionary history of MGs and tested the impact of macrohabitat on their evolution. Inference of ancestral states along a time-calibrated phylogeny revealed a single origin in the ancestor of the subclade Testudinoidea. Thus, MGs represent homologous structures in all descending lineages. We also inferred multiple independent losses of MGs in both terrestrial and aquatic clades. Although MGs first appeared in an aquatic turtle (the testudinoid ancestor), macrohabitat seems to have had little effect on MG presence or absence in descendants. Instead, we find clade-specific evolutionary trends, with some clades showing increased gland size and morphological complexity, whereas others exhibiting reduction or MG loss. In sister clades inhabiting similar ecological niches, contrasting patterns (loss vs. maintenance) may occur. We conclude that the multiple losses of MGs in turtle clades have not been influenced by macrohabitat and that other factors have affected MG evolution.
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Affiliation(s)
- Alejandro Ibáñez
- grid.5522.00000 0001 2162 9631Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, 30-387 Kraków, Poland ,grid.10789.370000 0000 9730 2769Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 90-237 Łódź, Poland
| | - Uwe Fritz
- grid.438154.f0000 0001 0944 0975Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany
| | - Markus Auer
- grid.438154.f0000 0001 0944 0975Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany
| | | | | | - Emilia Załugowicz
- grid.5522.00000 0001 2162 9631Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, 30-387 Kraków, Poland
| | - Dagmara Podkowa
- grid.5522.00000 0001 2162 9631Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, 30-387 Kraków, Poland
| | - Maciej Pabijan
- grid.5522.00000 0001 2162 9631Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, 30-387 Kraków, Poland
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Meiri S, Murali G, Zimin A, Shak L, Itescu Y, Caetano G, Roll U. Different solutions lead to similar life history traits across the great divides of the amniote tree of life. ACTA ACUST UNITED AC 2021; 28:3. [PMID: 33557958 PMCID: PMC7869468 DOI: 10.1186/s40709-021-00134-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023]
Abstract
Amniote vertebrates share a suite of extra-embryonic membranes that distinguish them from anamniotes. Other than that, however, their reproductive characteristics could not be more different. They differ in basic ectothermic vs endothermic physiology, in that two clades evolved powered flight, and one clade evolved a protective shell. In terms of reproductive strategies, some produce eggs and others give birth to live young, at various degrees of development. Crucially, endotherms provide lengthy parental care, including thermal and food provisioning—whereas ectotherms seldom do. These differences could be expected to manifest themselves in major differences between clades in quantitative reproductive traits. We review the reproductive characteristics, and the distributions of brood sizes, breeding frequencies, offspring sizes and their derivatives (yearly fecundity and biomass production rates) of the four major amniote clades (mammals, birds, turtles and squamates), and several major subclades (birds: Palaeognathae, Galloanserae, Neoaves; mammals: Metatheria and Eutheria). While there are differences between these clades in some of these traits, they generally show similar ranges, distribution shapes and central tendencies across birds, placental mammals and squamates. Marsupials and turtles, however, differ in having smaller offspring, a strategy which subsequently influences other traits.
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Affiliation(s)
- Shai Meiri
- School of Zoology, Tel Aviv University, 6997801, Tel Aviv, Israel. .,The Steinhardt Museum of Natural History, Tel Aviv University, 6997801, Tel Aviv, Israel.
| | - Gopal Murali
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Anna Zimin
- School of Zoology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Lior Shak
- School of Zoology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Yuval Itescu
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.,Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Gabriel Caetano
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Uri Roll
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
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Cytogenetic Analysis of the Asian Box Turtles of the Genus Cuora (Testudines, Geoemydidae). Genes (Basel) 2021; 12:genes12020156. [PMID: 33503936 PMCID: PMC7911423 DOI: 10.3390/genes12020156] [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: 12/27/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/18/2022] Open
Abstract
The Asian box turtle genus Cuora currently comprises 13 species with a wide distribution in Southeast Asia, including China and the islands of Indonesia and Philippines. The populations of these species are rapidly declining due to human pressure, including pollution, habitat loss, and harvesting for food consumption. Notably, the IUCN Red List identifies almost all species of the genus Cuora as Endangered (EN) or Critically Endangered (CR). In this study, we explore the karyotypes of 10 Cuora species with conventional (Giemsa staining, C-banding, karyogram reconstruction) and molecular cytogenetic methods (in situ hybridization with probes for rDNA loci and telomeric repeats). Our study reveals a diploid chromosome number of 2n = 52 chromosomes in all studied species, with karyotypes of similar chromosomal morphology. In all examined species, rDNA loci are detected at a single medium-sized chromosome pair and the telomeric repeats are restricted to the expected terminal position across all chromosomes. In contrast to a previous report, sex chromosomes are neither detected in Cuoragalbinifrons nor in any other species. Therefore, we assume that these turtles have either environmental sex determination or genotypic sex determination with poorly differentiated sex chromosomes. The conservation of genome organization could explain the numerous observed cases of interspecific hybridization both within the genus Cuora and across geoemydid turtles.
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The Amazonian Red Side-Necked Turtle Rhinemys rufipes (Spix, 1824) (Testudines, Chelidae) Has a GSD Sex-Determining Mechanism with an Ancient XY Sex Microchromosome System. Cells 2020; 9:cells9092088. [PMID: 32932633 PMCID: PMC7563702 DOI: 10.3390/cells9092088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023] Open
Abstract
The Amazonian red side-necked turtle Rhynemis rufipes is an endemic Amazonian Chelidae species that occurs in small streams throughout Colombia and Brazil river basins. Little is known about various biological aspects of this species, including its sex determination strategies. Among chelids, the greatest karyotype diversity is found in the Neotropical species, with several 2n configurations, including cases of triploidy. Here, we investigate the karyotype of Rhinemys rufipes by applying combined conventional and molecular cytogenetic procedures. This allowed us to discover a genetic sex-determining mechanism that shares an ancestral micro XY sex chromosome system. This ancient micro XY system recruited distinct repeat motifs before it diverged from several South America and Australasian species. We propose that such a system dates back to the earliest lineages of the chelid species before the split of South America and Australasian lineages.
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