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Kosch TA, Torres-Sánchez M, Liedtke HC, Summers K, Yun MH, Crawford AJ, Maddock ST, Ahammed MS, Araújo VLN, Bertola LV, Bucciarelli G, Carné A, Carneiro CM, Chan KO, Chen Y, Crottini A, da Silva JM, Denton RD, Dittrich C, Themudo GE, Farquharson KA, Forsdick NJ, Gilbert E, Jing C, Katzenback BA, Kotharambath R, Levis NA, Márquez R, Mazepa G, Mulder KP, Müller H, O’Connell MJ, Orozco-terWengel P, Palomar G, Petzold A, Pfennig DW, Pfennig KS, Reichert MS, Robert J, Scherz MD, Siu-Ting K, Snead AA, Stöck M, Stuckert AMM, Stynoski JL, Tarvin RD, Valero KCW. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601086. [PMID: 39005434 PMCID: PMC11244923 DOI: 10.1101/2024.06.27.601086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.
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Affiliation(s)
- Tiffany A. Kosch
- One Health Research Group, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Werribee, Victoria, Australia
| | - María Torres-Sánchez
- Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Kyle Summers
- Biology Department, East Carolina University, Greenville, NC, USA 27858
| | - Maximina H. Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrew J. Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
- Museo de Historia Natural C.J. Marinkelle, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Simon T. Maddock
- School of Natural and Environmental Sciences, Newcastle University, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Seychelles
| | | | - Victor L. N. Araújo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Lorenzo V. Bertola
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, QLD 4810, Australia
| | - Gary Bucciarelli
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, USA
| | - Albert Carné
- Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Céline M. Carneiro
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kin O. Chan
- University of Kansas Biodiversity Institute and Natural History Museum, Lawrence, Kansas 66045, USA
| | - Ying Chen
- Biology Department, Queen’s University, Ontario, Canada
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169– 007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jessica M. da Silva
- Evolutionary Genomics and Wildlife Management, Foundatonal Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute, Newlands 7735, Cape Town, South Africa
- Centre for Evolutionary Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa
| | - Robert D. Denton
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Carolin Dittrich
- Rojas Lab, Konrad-Lorenz-Institute of Ethology, Department of Life Science, University of Veterinary Medicine, Vienna, Austria
| | - Gonçalo Espregueira Themudo
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos, Portugal
| | - Katherine A. Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Edward Gilbert
- School of Natural Sciences, The University of Hull, Hull, HU6 7RX, United Kingdom
- Energy and Environment Institute, The University of Hull, Hull, HU6 7RX, United Kingdom
| | - Che Jing
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | | | - Ramachandran Kotharambath
- Herpetology Lab, Dept. of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, 671320, India
| | - Nicholas A. Levis
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Roberto Márquez
- Department of Biological Sciences, Virginia Tech. Blacksburg, VA 24060, USA
| | - Glib Mazepa
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Switzerland
- Department of Ecology and Genetics, Evolutionary Biology, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Kevin P. Mulder
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Hendrik Müller
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, D-06108 Halle (Saale), Germany
| | - Mary J. O’Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Museum Avenue, CF10 3AX Cardiff, United Kingdom
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology; Faculty of Biological Sciences; Complutense University of Madrid, Madrid, Spain
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Alice Petzold
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str.24-25, 14476 Potsdam, Germany
| | - David W. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karin S. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael S. Reichert
- Department of Integrative Biology, Oklahoma State University, Stillwater OK, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Karen Siu-Ting
- School of Biological Sciences, Queen’s University Belfast, Belfast, BT7 1NN, Northern Ireland, United Kingdom
- Instituto Peruano de Herpetología, Ca. Augusto Salazar Bondy 136, Surco, Lima, Peru
- Herpetology Lab, The Natural History Museum, London, United Kingdom
| | - Anthony A Snead
- Department of Biology, New York University, New York, NY, USA
| | - Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany
| | - Adam M. M. Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204, USA
| | | | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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Mulder KP, Alarcón-Ríos L, Nicieza AG, Fleischer RC, Bell RC, Velo-Antón G. Independent evolutionary transitions to pueriparity across multiple timescales in the viviparous genus Salamandra. Mol Phylogenet Evol 2021; 167:107347. [PMID: 34763070 DOI: 10.1016/j.ympev.2021.107347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023]
Abstract
The ability to bear live offspring, viviparity, has evolved multiple times across the tree of life and is a remarkable adaptation with profound life-history and ecological implications. Within amphibians the ancestral reproductive mode is oviparity followed by a larval life stage, but viviparity has evolved independently in all three amphibian orders. Two types of viviparous reproduction can be distinguished in amphibians; larviparity and pueriparity. Larviparous amphibians deliver larvae into nearby ponds and streams, while pueriparous amphibians deliver fully developed juveniles and thus do not require waterbodies for reproduction. Among amphibians, the salamander genus Salamandra is remarkable as it exhibits both inter- and intraspecific variation in the occurrence of larviparity and pueriparity. While the evolutionary relationships among Salamandra lineages have been the focus of several recent studies, our understanding of how often and when transitions between modes occurred is still incomplete. Furthermore, in species with intraspecific variation, the reproductive mode of a given population can only be confirmed by direct observation of births and thus the prevalence of pueriparous populations is also incompletely documented. We used sequence capture to obtain 1,326 loci from 94 individuals from across the geographic range of the genus, focusing on potential reproductive mode transition zones. We also report additional direct observations of pueriparous births for 20 new locations and multiple lineages. We identify at least five independent transitions from the ancestral mode of larviparity to pueriparity among and within species, occurring at different evolutionary timescales ranging from the Pliocene to the Holocene. Four of these transitions occurred within species. Based on a distinct set of markers and analyses, we also confirm previous findings of introgression between species and the need for taxonomic revisions in the genus. We discuss the implications of our findings with respect to the evolution of this complex trait, and the potential of using five independent convergent transitions for further studies on the ecological context in which pueriparity evolves and the genetic architecture of this specialized reproductive mode.
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Affiliation(s)
- Kevin P Mulder
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC 20560, USA; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
| | - Lucía Alarcón-Ríos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo UO, Oviedo, Spain
| | - Alfredo G Nicieza
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo UO, Oviedo, Spain; Biodiversity Research Institute (IMIB), University of Oviedo-Principality of Asturias-CSIC, 33600 Mieres, Spain
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC 20560, USA; Herpetology Department, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Guillermo Velo-Antón
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Universidade de Vigo, Grupo GEA, Departamento de Ecoloxía e Bioloxía Animal, Vigo, Spain.
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Tao Y, Chen B, Kang M, Liu Y, Wang J. Genome-Wide Evidence for Complex Hybridization and Demographic History in a Group of Cycas From China. Front Genet 2021; 12:717200. [PMID: 34527022 PMCID: PMC8435751 DOI: 10.3389/fgene.2021.717200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022] Open
Abstract
Cycads represent one of the most ancestral living seed plants as well as one of the most threatened plant groups in the world. South China is a major center and potential origin of Cycas, the most rapidly diversified lineage of cycads. However, genomic-wide diversity of Cycas remains poorly understood due to the challenge of generating genomic markers associated with their inherent large genomes. Here, we perform a comprehensive conservation genomic study based on restriction-site associated DNA sequencing (RADseq) data in six representative species of Cycas in South China. Consistently low genetic diversity and strong genetic differentiation were detected across species. Both phylogenetic inference and genetic structure analysis via several methods revealed generally congruent groups among the six Cycas species. The analysis with ADMIXTURE showed low mixing of genetic composition among species, while individuals of C. dolichophylla exhibited substantial genetic admixture with C. bifida, C. changjiangensis, and C. balansae. Furthermore, the results from Treemix, f4-statistic, and ABBA-BABA test were generally consistent and revealed the complex patterns of interspecific gene flow. Relatively strong signals of hybridization were detected between C. dolichophylla and C. szechuanensis, and the ancestor of C. taiwaniana and C. changjiangensis. Distinct patterns of demographic history were inferred for these species by Stairway Plot, and our results suggested that both climate fluctuation and frequent geological activities during the late Pleistocene exerted deep impacts on the population dynamics of these species in South China. Finally, we explore the practical implications of our findings for the development of conservation strategies in Cycas. The present study demonstrates the efficiency of RADseq for conservation genomic studies on non-model species with large and complex genomes. Given the great significance of cycads as a radical transition in the evolution of plant biodiversity, our study provides important insights into the mechanisms of diversification in such recently radiated living fossil taxa.
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Affiliation(s)
- Yueqi Tao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bin Chen
- Shanghai Chenshan Botanical Garden, Shanghai, China.,Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Yongbo Liu
- State Environment Protection Key Laboratory of Regional Ecological Process and Functional Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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