1
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White OW, Biswas MK, Abebe WM, Dussert Y, Kebede F, Nichols RA, Buggs RJA, Demissew S, Woldeyes F, Papadopulos AST, Schwarzacher T, Heslop-Harrison PJS, Wilkin P, Borrell JS. Maintenance and expansion of genetic and trait variation following domestication in a clonal crop. Mol Ecol 2023. [PMID: 37264989 DOI: 10.1111/mec.17033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/24/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterize the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and a principal starch staple for 20 million Ethiopians. Wild enset reproduction occurs strictly by sexual outcrossing, but for cultivation, it is propagated clonally and associated with diversification and specialization into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested an accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by the amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages, we found a significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. The development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.
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Affiliation(s)
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Yann Dussert
- CNRS, Université de Poitiers, EBI, Poitiers, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Firew Kebede
- Department of Biology, Hawassa University, Hawassa, Ethiopia
| | - Richard A Nichols
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Richard J A Buggs
- Royal Botanic Gardens Kew, Richmond, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sebsebe Demissew
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Pat J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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2
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Brekke TD, Papadopulos AST, Julià E, Fornas O, Fu B, Yang F, de la Fuente R, Page J, Baril T, Hayward A, Mulley JF. A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome. Mol Biol Evol 2023:7162499. [PMID: 37183864 DOI: 10.1093/molbev/msad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/23/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023] Open
Abstract
Chromosome-scale genome assemblies based on ultra-long read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation in genome features such as heterochromatin, GC content, recombination rate, and gene content. We present here a new chromosome-scale genome of the Mongolian gerbil (Meriones unguiculatus) which includes the complete sequence of all centromeres. Gerbils are thus the one of the first vertebrates to have their centromeres completely sequenced. Gerbil centromeres are composed of four different repeats of length 6pb, 37 bp, 127 bp, or 1747bp which occur in simple alternating arrays and span 1-6Mb. Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intra-arm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150 kb) repeated sequences. In addition to characterizing centromeres, our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data, and highlight novel patterns involved in the evolution of chromosomes.
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Affiliation(s)
- Thomas D Brekke
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, United Kingdom
| | | | - Eva Julià
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Oscar Fornas
- Pompeu Fabra University (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Beiyuan Fu
- Cambridge Epigenetix, The Trinity Building, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | | | - Roberto de la Fuente
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland
| | - Jesus Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Tobias Baril
- University of Exeter, Penryn Campus, Cornwall, TR10 9FE, United Kingdom
| | - Alexander Hayward
- University of Exeter, Penryn Campus, Cornwall, TR10 9FE, United Kingdom
| | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, United Kingdom
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3
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Osborne OG, Dobreva MP, Papadopulos AST, de Moura MSB, Brunello AT, de Queiroz LP, Pennington RT, Lloyd J, Savolainen V. Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing. New Phytol 2023; 238:1305-1317. [PMID: 36444527 DOI: 10.1111/nph.18645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.
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Affiliation(s)
- Owen G Osborne
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Mariya P Dobreva
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
| | - Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Magna S B de Moura
- Empresa Brasileira de Pesquisa Agropecuária, 56302-970, Petrolina, PE, Brazil
| | - Alexandre T Brunello
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Monte Alegre, 14040-901, Ribeirão Preto, SP, Brazil
| | - Luciano P de Queiroz
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, 44036-900, Feira de Santana, BA, Brazil
| | - R Toby Pennington
- Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, UK
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Jon Lloyd
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Vincent Savolainen
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
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4
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Wood DP, Holmberg JA, Osborne OG, Helmstetter AJ, Dunning LT, Ellison AR, Smith RJ, Lighten J, Papadopulos AST. Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora. Nat Ecol Evol 2023; 7:414-423. [PMID: 36702857 PMCID: PMC9998271 DOI: 10.1038/s41559-022-01975-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/12/2022] [Indexed: 01/27/2023]
Abstract
Phenotypic plasticity in ancestral populations is hypothesized to facilitate adaptation, but evidence is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel adaptive changes has not been explored. The most general finding is that ancestral responses to a new environment are reversed following adaptation (known as reversion). We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared with zinc-sensitive plants. We show that ancestral plasticity that moves expression closer to the optimum value in the new environment influences the evolution of gene expression among genes that are likely to be involved in adaptation and increases the chance that genes are recruited repeatedly during adaptation. However, despite convergence in gene expression levels between independently adapted lineages, ancestral plasticity does not influence how similar expression values of adaptive genes become. Surprisingly, we also observed that ancestral plasticity that increases fitness often becomes genetically determined and fixed, that is, genetically assimilated. These results emphasize the important role of ancestral plasticity in parallel adaptation.
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Affiliation(s)
- Daniel P Wood
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | - Jon A Holmberg
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | - Andrew J Helmstetter
- Fondation pour la Recherche sur la Biodiversité - Centre for the Synthesis and Analysis of Biodiversity, Institut Bouisson Bertrand, Montpellier, France
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, Sheffield, UK
| | - Amy R Ellison
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | | | - Jackie Lighten
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK.
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5
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Antonelli A, Smith RJ, Perrigo AL, Crottini A, Hackel J, Testo W, Farooq H, Torres Jiménez MF, Andela N, Andermann T, Andriamanohera AM, Andriambololonera S, Bachman SP, Bacon CD, Baker WJ, Belluardo F, Birkinshaw C, Borrell JS, Cable S, Canales NA, Carrillo JD, Clegg R, Clubbe C, Cooke RSC, Damasco G, Dhanda S, Edler D, Faurby S, de Lima Ferreira P, Fisher BL, Forest F, Gardiner LM, Goodman SM, Grace OM, Guedes TB, Henniges MC, Hill R, Lehmann CER, Lowry PP, Marline L, Matos-Maraví P, Moat J, Neves B, Nogueira MGC, Onstein RE, Papadopulos AST, Perez-Escobar OA, Phelps LN, Phillipson PB, Pironon S, Przelomska NAS, Rabarimanarivo M, Rabehevitra D, Raharimampionona J, Rajaonah MT, Rajaonary F, Rajaovelona LR, Rakotoarinivo M, Rakotoarisoa AA, Rakotoarisoa SE, Rakotomalala HN, Rakotonasolo F, Ralaiveloarisoa BA, Ramirez-Herranz M, Randriamamonjy JEN, Randriamboavonjy T, Randrianasolo V, Rasolohery A, Ratsifandrihamanana AN, Ravololomanana N, Razafiniary V, Razanajatovo H, Razanatsoa E, Rivers M, Sayol F, Silvestro D, Vorontsova MS, Walker K, Walker BE, Wilkin P, Williams J, Ziegler T, Zizka A, Ralimanana H. Madagascar’s extraordinary biodiversity: Evolution, distribution, and use. Science 2022; 378:eabf0869. [DOI: 10.1126/science.abf0869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
| | - Rhian J. Smith
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Allison L. Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Weston Testo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Field Museum of Natural History, Chicago, Illinois, USA
| | - Harith Farooq
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique
| | - Maria F. Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Niels Andela
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, UK
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | | | - Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Chris Birkinshaw
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
- Missouri Botanical Garden, St. Louis, Missouri, USA
| | | | - Stuart Cable
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nataly A. Canales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Juan D. Carrillo
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CR2P, Muséum National d’Histoire Naturelle, Paris, France
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Rosie Clegg
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Geography, University of Exeter, Exeter, Devon, UK
| | - Colin Clubbe
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Robert S. C. Cooke
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- UK Centre for Ecology and Hydrology, Wallingford, UK
| | - Gabriel Damasco
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sonia Dhanda
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Daniel Edler
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Paola de Lima Ferreira
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Brian L. Fisher
- California Academy of Sciences, San Francisco, California, USA
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Lauren M. Gardiner
- Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, Illinois, USA
- Association Vahatra, Antananarivo, Madagascar
| | | | - Thaís B. Guedes
- Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, Campinas, São Paulo, Brazil
| | - Marie C. Henniges
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rowena Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Caroline E. R. Lehmann
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, Missouri, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Lovanomenjanahary Marline
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
- Association Vahatra, Antananarivo, Madagascar
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Justin Moat
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Beatriz Neves
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus G. C. Nogueira
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renske E. Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR Leiden, the Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Leanne N. Phelps
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Peter B. Phillipson
- Missouri Botanical Garden, St. Louis, Missouri, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | | | - David Rabehevitra
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Mamy Tiana Rajaonah
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Fano Rajaonary
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
| | - Landy R. Rajaovelona
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Mijoro Rakotoarinivo
- Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar
| | - Amédée A. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Solofo E. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Herizo N. Rakotomalala
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Myriam Ramirez-Herranz
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile
- Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile
| | | | | | - Vonona Randrianasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | | | - Velosoa Razafiniary
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Henintsoa Razanajatovo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Estelle Razanatsoa
- Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa
| | - Malin Rivers
- Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK
| | - Ferran Sayol
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | | | - Kim Walker
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Royal Holloway, University of London, Egham, Surrey, UK
| | | | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Hélène Ralimanana
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
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6
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Ralimanana H, Perrigo AL, Smith RJ, Borrell JS, Faurby S, Rajaonah MT, Randriamboavonjy T, Vorontsova MS, Cooke RSC, Phelps LN, Sayol F, Andela N, Andermann T, Andriamanohera AM, Andriambololonera S, Bachman SP, Bacon CD, Baker WJ, Belluardo F, Birkinshaw C, Cable S, Canales NA, Carrillo JD, Clegg R, Clubbe C, Crottini A, Damasco G, Dhanda S, Edler D, Farooq H, de Lima Ferreira P, Fisher BL, Forest F, Gardiner LM, Goodman SM, Grace OM, Guedes TB, Hackel J, Henniges MC, Hill R, Lehmann CER, Lowry PP, Marline L, Matos-Maraví P, Moat J, Neves B, Nogueira MGC, Onstein RE, Papadopulos AST, Perez-Escobar OA, Phillipson PB, Pironon S, Przelomska NAS, Rabarimanarivo M, Rabehevitra D, Raharimampionona J, Rajaonary F, Rajaovelona LR, Rakotoarinivo M, Rakotoarisoa AA, Rakotoarisoa SE, Rakotomalala HN, Rakotonasolo F, Ralaiveloarisoa BA, Ramirez-Herranz M, Randriamamonjy JEN, Randrianasolo V, Rasolohery A, Ratsifandrihamanana AN, Ravololomanana N, Razafiniary V, Razanajatovo H, Razanatsoa E, Rivers M, Silvestro D, Testo W, Torres Jiménez MF, Walker K, Walker BE, Wilkin P, Williams J, Ziegler T, Zizka A, Antonelli A. Madagascar’s extraordinary biodiversity: Threats and opportunities. Science 2022; 378:eadf1466. [DOI: 10.1126/science.adf1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.
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Affiliation(s)
- Hélène Ralimanana
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Allison L. Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Rhian J. Smith
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mamy Tiana Rajaonah
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | - Robert S. C. Cooke
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- UK Centre for Ecology and Hydrology, Wallingford, UK
| | - Leanne N. Phelps
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Ferran Sayol
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Niels Andela
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, UK
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | | | - Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Chris Birkinshaw
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Stuart Cable
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nataly A. Canales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Juan D. Carrillo
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CR2P, Muséum National d’Histoire Naturelle, Paris, France
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Rosie Clegg
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Geography, University of Exeter, Exeter, Devon, UK
| | - Colin Clubbe
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Gabriel Damasco
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sonia Dhanda
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Daniel Edler
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Harith Farooq
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique
| | - Paola de Lima Ferreira
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Lauren M. Gardiner
- Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Steven M. Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, IL, USA
| | | | - Thaís B. Guedes
- Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, Campinas, São Paulo, Brazil
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Marie C. Henniges
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rowena Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Caroline E. R. Lehmann
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, MO, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Lovanomenjanahary Marline
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Association Vahatra, Antananarivo, Madagascar
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Justin Moat
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Beatriz Neves
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus G. C. Nogueira
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renske E. Onstein
- Naturalis Biodiversity Center, Leiden, Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Peter B. Phillipson
- Missouri Botanical Garden, St. Louis, MO, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | | | - David Rabehevitra
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Fano Rajaonary
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
| | - Landy R. Rajaovelona
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Mijoro Rakotoarinivo
- Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar
| | - Amédée A. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Solofo E. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Herizo N. Rakotomalala
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Myriam Ramirez-Herranz
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile
- Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile
| | | | - Vonona Randrianasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | | | - Velosoa Razafiniary
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Henintsoa Razanajatovo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Estelle Razanatsoa
- Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa
| | - Malin Rivers
- Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Weston Testo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Field Museum of Natural History, Chicago, IL, USA
| | - Maria F. Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Kim Walker
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Royal Holloway, University of London, Egham, Surrey, UK
| | | | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biology, University of Oxford, Oxford, UK
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7
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Dunning LT, Olofsson JK, Papadopulos AST, Hibdige SGS, Hidalgo O, Leitch IJ, Baleeiro PC, Ntshangase S, Barker N, Jobson RW. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Mol Ecol 2022; 31:5846-5860. [PMID: 36089907 PMCID: PMC9828686 DOI: 10.1111/mec.16691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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Affiliation(s)
- Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Jill K. Olofsson
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Samuel G. S. Hibdige
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Oriane Hidalgo
- Royal Botanic GardensSurreyUK,Institut Botànic de Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelonaSpain
| | | | - Paulo C. Baleeiro
- Department of Biological ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | | | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaHatfieldSouth Africa
| | - Richard W. Jobson
- National Herbarium of New South Wales, Australian Institute of Botanical ScienceSydneyNew South WalesAustralia
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8
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Helmstetter AJ, Cable S, Rakotonasolo F, Rabarijaona R, Rakotoarinivo M, Eiserhardt WL, Baker WJ, Papadopulos AST. The demographic history of Madagascan micro-endemics: have rare species always been rare? Proc Biol Sci 2021; 288:20210957. [PMID: 34547905 PMCID: PMC8456134 DOI: 10.1098/rspb.2021.0957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/25/2021] [Indexed: 01/25/2023] Open
Abstract
Extinction has increased as human activities impact ecosystems, yet relatively few species have conservation assessments. Novel approaches are needed to highlight threatened species that are currently data-deficient. Many Madagascan plant species have extremely narrow ranges, but this may not have always been the case-it is unclear how the island's diverse flora evolved. To assess this, we generated restriction-site associated DNA sequence data for 10 Madagascan plant species, estimated effective population size (Ne) for each species and compared this to census (Nc) sizes. In each case, Ne was an order of magnitude larger than Nc-signifying rapid, recent population decline. We then estimated species' demographic history, tracking changes in Ne over time. We show that it is possible to predict extinction risk, particularly in the most threatened species. Furthermore, simulations showed that our approach has the power to detect population decline during the Anthropocene. Our analyses reveal that Madagascar's micro-endemics were not always rare, having experienced a rapid decline in their recent history. This casts further uncertainty over the processes that generated Madagascar's exceptional biodiversity. Our approach targets data-deficient species in need of conservation assessment, particularly in regions where human modification of the environment has been rapid.
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Affiliation(s)
- Andrew J. Helmstetter
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, 911 Avenue Agropolis, BP 64501, Montpellier 34394, France
| | - Stuart Cable
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Kew Madagascar Conservation Centre, Lot II J 131 B Ambodivoanjo, Ivandry, Antananarivo 101, Madagascar
| | - Franck Rakotonasolo
- Kew Madagascar Conservation Centre, Lot II J 131 B Ambodivoanjo, Ivandry, Antananarivo 101, Madagascar
| | - Romer Rabarijaona
- Kew Madagascar Conservation Centre, Lot II J 131 B Ambodivoanjo, Ivandry, Antananarivo 101, Madagascar
| | - Mijoro Rakotoarinivo
- Mention Biologie et Ecologie Végétales, Faculté des Sciences, Université d'Antananarivo, Antananarivo BP 906101, Madagascar
| | - Wolf L. Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Alexander S. T. Papadopulos
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
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9
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Papadopulos AST, Helmstetter AJ, Osborne OG, Comeault AA, Wood DP, Straw EA, Mason L, Fay MF, Parker J, Dunning LT, Foote AD, Smith RJ, Lighten J. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution. Mol Biol Evol 2021; 38:3724-3736. [PMID: 33950261 PMCID: PMC8382892 DOI: 10.1093/molbev/msab141] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.
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Affiliation(s)
- Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Andrew J Helmstetter
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- FRB-CESAB, Institut Bouisson Bertrand, Rue de l'École de Médecine, Montpellier, France
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Aaron A Comeault
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Daniel P Wood
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Edward A Straw
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School for Life Sciences and the Environment, Royal Holloway University of London, Egham, United Kingdom
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Joe Parker
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Biofilms Innovation Centre, Department of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Department of Natural History, Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
| | - Rhian J Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jackie Lighten
- Biosciences, University of Exeter, Exeter, United Kingdom
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10
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Pérez-Escobar OA, Bellot S, Przelomska NAS, Flowers JM, Nesbitt M, Ryan P, Gutaker RM, Gros-Balthazard M, Wells T, Kuhnhäuser BG, Schley R, Bogarín D, Dodsworth S, Diaz R, Lehmann M, Petoe P, Eiserhardt WL, Preick M, Hofreiter M, Hajdas I, Purugganan M, Antonelli A, Gravendeel B, Leitch IJ, Torres Jimenez MF, Papadopulos AST, Chomicki G, Renner SS, Baker WJ. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Mol Biol Evol 2021; 38:4475-4492. [PMID: 34191029 PMCID: PMC8476131 DOI: 10.1093/molbev/msab188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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Affiliation(s)
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Mark Nesbitt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Philippa Ryan
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Muriel Gros-Balthazard
- French National Research Institute for Sustainable Development, Montpellier, BP 64501 - 34394 Cedex 5, France
| | - Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, San José, 302-7050, Costa Rica
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Rudy Diaz
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Peter Petoe
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Michaela Preick
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Irka Hajdas
- Department of Earth Sciences, ETH Zurich, 8092, Switzerland
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK.,Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Maria Fernanda Torres Jimenez
- Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Bangor LL57 2UW, UK
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
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11
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Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas A, Marques‐Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. Inference of natural selection from ancient DNA. Evol Lett 2020; 4:94-108. [PMID: 32313686 PMCID: PMC7156104 DOI: 10.1002/evl3.165] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/13/2020] [Accepted: 02/02/2020] [Indexed: 01/01/2023] Open
Abstract
Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
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Affiliation(s)
- Marianne Dehasque
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - María C. Ávila‐Arcos
- International Laboratory for Human Genome Research (LIIGH)UNAM JuriquillaQueretaro76230Mexico
| | - David Díez‐del‐Molino
- Centre for Palaeogenetics10691StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park CampusImperial College LondonAscotSL5 7PYUnited Kingdom
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Science for Life LaboratoryUppsala University75236UppsalaSweden
| | | | - Anna‐Sapfo Malaspinas
- Department of Computational BiologyUniversity of Lausanne1015LausanneSwitzerland
- SIB Swiss Institute of Bioinformatics1015LausanneSwitzerland
| | - Tomas Marques‐Bonet
- Institut de Biologia Evolutiva(CSIC‐Universitat Pompeu Fabra), Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain
- National Centre for Genomic Analysis—Centre for Genomic RegulationBarcelona Institute of Science and Technology08028BarcelonaSpain
- Institucio Catalana de Recerca i Estudis Avançats08010BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Michael D. Martin
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Gemma G. R. Murray
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB2 1TNUnited Kingdom
| | - Alexander S. T. Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
| | | | - Daniel Wegmann
- Department of BiologyUniversité de Fribourg1700FribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Love Dalén
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
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12
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Wong ELY, Nevado B, Osborne OG, Papadopulos AST, Bridle JR, Hiscock SJ, Filatov DA. Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna. Mol Ecol 2019; 29:394-412. [PMID: 31793091 DOI: 10.1111/mec.15319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022]
Abstract
Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.
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Affiliation(s)
- Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, UK
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13
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Papadopulos AST, Igea J, Smith TP, Hutton I, Baker WJ, Butlin RK, Savolainen V. Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of
Howea
in the face of high gene flow. Evolution 2019; 73:1996-2002. [DOI: 10.1111/evo.13813] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/04/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Alexander S. T. Papadopulos
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Molecular Ecology and Fisheries Genetics LaboratoryEnvironment Centre WalesSchool of Natural SciencesBangor University Bangor LL57 2UW United Kingdom
| | - Javier Igea
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Department of Plant SciencesUniversity of Cambridge Cambridge CB2 3EA United Kingdom
| | - Thomas P. Smith
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
| | - Ian Hutton
- Lord Howe Island Museum Lord Howe Island New South Wales Australia
| | | | - Roger K. Butlin
- Department of Animal and Plant SciencesUniversity of Sheffield Sheffield S10 2TN United Kingdom
- Department of Marine SciencesUniversity of Gothenburg Gothenburg SE‐405 30 Sweden
| | - Vincent Savolainen
- Department of Life SciencesSilwood Park CampusImperial College London Ascot SL5 7PY United Kingdom
- Royal Botanic Gardens, Kew Richmond TW9 3AB United Kingdom
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14
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Papadopulos AST, Igea J, Dunning LT, Osborne OG, Quan X, Pellicer J, Turnbull C, Hutton I, Baker WJ, Butlin RK, Savolainen V. Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea. Evolution 2019; 73:1986-1995. [PMID: 31298414 DOI: 10.1111/evo.13796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022]
Abstract
Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction site-associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, four of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
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Affiliation(s)
- Alexander S T Papadopulos
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University, Bangor, LL57 2UW, United Kingdom
| | - Javier Igea
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Luke T Dunning
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Owen G Osborne
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
| | - Xueping Quan
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, United Kingdom
| | - Colin Turnbull
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom
| | - Ian Hutton
- Lord Howe Island Museum, Lord Howe Island, NSW, 2898, Australia
| | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Department of Marine Sciences, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.,Royal Botanic Gardens, Kew, Richmond, TW9 3AB, United Kingdom
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15
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Lighten J, Papadopulos AST, Mohammed RS, Ward BJ, G Paterson I, Baillie L, Bradbury IR, Hendry AP, Bentzen P, van Oosterhout C. Evolutionary genetics of immunological supertypes reveals two faces of the Red Queen. Nat Commun 2017; 8:1294. [PMID: 29101318 PMCID: PMC5670221 DOI: 10.1038/s41467-017-01183-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/23/2017] [Indexed: 11/09/2022] Open
Abstract
Red Queen host-parasite co-evolution can drive adaptations of immune genes by positive selection that erodes genetic variation (Red Queen arms race) or results in a balanced polymorphism (Red Queen dynamics) and long-term preservation of genetic variation (trans-species polymorphism). These two Red Queen processes are opposite extremes of the co-evolutionary spectrum. Here we show that both Red Queen processes can operate simultaneously by analysing the major histocompatibility complex (MHC) in guppies (Poecilia reticulata and P. obscura) and swamp guppies (Micropoecilia picta). Sub-functionalisation of MHC alleles into 'supertypes' explains how polymorphisms persist during rapid host-parasite co-evolution. Simulations show the maintenance of supertypes as balanced polymorphisms, consistent with Red Queen dynamics, whereas alleles within supertypes are subject to positive selection in a Red Queen arms race. Building on the divergent allele advantage hypothesis, we show that functional aspects of allelic diversity help to elucidate the evolution of polymorphic genes involved in Red Queen co-evolution.
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Affiliation(s)
- Jackie Lighten
- School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Ryan S Mohammed
- Department of Life Sciences, The University of the West Indies, St Augustine, Trinidad and Tobago
| | - Ben J Ward
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK
| | - Ian G Paterson
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2
| | - Lyndsey Baillie
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Ian R Bradbury
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2.,Science Branch, Department of Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, NL, Canada, A1C 5X1
| | - Andrew P Hendry
- McGill University, 859 Sherbrooke Street West, Montreal, QC, Canada, H3A 0C4.,Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, QC, Canada, H3A 0C4
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
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16
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Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST. Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep 2017; 7:8345. [PMID: 28827531 PMCID: PMC5566789 DOI: 10.1038/s41598-017-08461-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/12/2017] [Indexed: 01/04/2023] Open
Abstract
Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.) has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification and phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, “al fresco” laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible.
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Affiliation(s)
- Joe Parker
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB.
| | | | - Dion Devey
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB
| | - Tim Wilkinson
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB
| | - Alexander S T Papadopulos
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK, TW9 3AB. .,Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University, Bangor, UK, LL57 2UW.
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17
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Hipperson H, Dunning LT, Baker WJ, Butlin RK, Hutton I, Papadopulos AST, Smadja CM, Wilson TC, Devaux C, Savolainen V. Ecological speciation in sympatric palms: 2. Pre- and post-zygotic isolation. J Evol Biol 2016; 29:2143-2156. [PMID: 27374779 PMCID: PMC5096058 DOI: 10.1111/jeb.12933] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 01/22/2023]
Abstract
We evaluated reproductive isolation in two species of palms (Howea) that have evolved sympatrically on Lord Howe Island (LHI, Australia). We estimated the strength of some pre- and post-zygotic mechanisms in maintaining current species boundaries. We found that flowering time displacement between species is consistent across in and ex situ common gardens and is thus partly genetically determined. On LHI, pre-zygotic isolation due solely to flowering displacement was 97% for Howea belmoreana and 80% for H. forsteriana; this asymmetry results from H. forsteriana flowering earlier than H. belmoreana and being protandrous. As expected, only a few hybrids (here confirmed by genotyping) at both juvenile and adult stages could be detected in two sites on LHI, in which the two species grow intermingled (the Far Flats) or adjacently (Transit Hill). Yet, the distribution of hybrids was different between sites. At Transit Hill, we found no hybrid adult trees, but 13.5% of younger palms examined there were of late hybrid classes. In contrast, we found four hybrid adult trees, mostly of late hybrid classes, and only one juvenile F1 hybrid in the Far Flats. This pattern indicates that selection acts against hybrids between the juvenile and adult stages. An in situ reciprocal seed transplant between volcanic and calcareous soils also shows that early fitness components (up to 36 months) were affected by species and soil. These results are indicative of divergent selection in reproductive isolation, although it does not solely explain the current distribution of the two species on LHI.
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Affiliation(s)
- H Hipperson
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
| | - L T Dunning
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
| | - W J Baker
- Royal Botanic Gardens, Kew, Richmond, UK
| | - R K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Sven Lovén Centre for Marine Sciences, Tjärnö, University of Gothenburg, Stromstäd, Sweden
| | - I Hutton
- Lord Howe Island Museum, Lord Howe Island, NSW, Australia
| | - A S T Papadopulos
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
- Royal Botanic Gardens, Kew, Richmond, UK
| | - C M Smadja
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
| | - T C Wilson
- Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | | | - V Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK.
- Royal Botanic Gardens, Kew, Richmond, UK.
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18
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Dunning LT, Hipperson H, Baker WJ, Butlin RK, Devaux C, Hutton I, Igea J, Papadopulos AST, Quan X, Smadja CM, Turnbull CGN, Savolainen V. Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy. J Evol Biol 2016; 29:1472-87. [PMID: 27177130 PMCID: PMC6680112 DOI: 10.1111/jeb.12895] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 05/04/2016] [Accepted: 05/11/2016] [Indexed: 02/02/2023]
Abstract
Ecological speciation requires divergent selection, reproductive isolation and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil types and have displaced flowering times, representing an ideal candidate for ecological speciation. We generated large amounts of RNA‐Seq data from multiple individuals and tissue types collected on the island from each of the two species. We found that differentially expressed loci as well as those with divergent coding sequences between Howea species were associated with known ecological and phenotypic differences, including response to salinity, drought, pH and flowering time. From these loci, we identified potential ‘ecological speciation genes’ and further validate their effect on flowering time by knocking out orthologous loci in a model plant species. Finally, we put forward six plausible ecological speciation loci, providing support for the hypothesis that pleiotropy could help to overcome the antagonism between selection and recombination during speciation with gene flow.
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Affiliation(s)
- L T Dunning
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - H Hipperson
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - W J Baker
- Royal Botanic Gardens, Kew, Richmond, UK
| | - R K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Sven Lovén Centre for Marine Sciences, Tjärnö, University of Gothenburg, Stromstäd, Sweden
| | - C Devaux
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - I Hutton
- Lord Howe Island Museum, Lord Howe Island, NSW, Australia
| | - J Igea
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - A S T Papadopulos
- Department of Life Sciences, Imperial College London, Ascot, UK.,Royal Botanic Gardens, Kew, Richmond, UK
| | - X Quan
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - C M Smadja
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - C G N Turnbull
- Department of Life Sciences, Imperial College London, London, UK
| | - V Savolainen
- Department of Life Sciences, Imperial College London, Ascot, UK.,Royal Botanic Gardens, Kew, Richmond, UK
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19
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Filatov DA, Osborne OG, Papadopulos AST. Demographic history of speciation in a Senecio altitudinal hybrid zone on Mt. Etna. Mol Ecol 2016; 25:2467-81. [PMID: 26994342 DOI: 10.1111/mec.13618] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 01/16/2023]
Abstract
Hybrid zones typically form as a result of species coming into secondary contact, but can also be established in situ as an ecotonal hybrid zone, a situation which has been reported far less frequently. An altitudinal hybrid zone on Mount Etna between two ragwort species (the low elevation Senecio chrysanthemifolius and high elevation S. aethnensis) could potentially represent either of these possibilities. However, a scenario of secondary contact vs. speciation with gene flow has not been explicitly tested. Here, we test these alternatives and demonstrate that the data do not support secondary contact. Furthermore, we report that the previous analyses of speciation history of these species were based on admixed populations, which has led to inflated estimates of ongoing, interspecific gene flow. Our new analyses, based on 'pure' S. aethnensis and S. chrysanthemifolius populations, reveal gene exchange of less than one effective migrant per generation, a level low enough to allow the species to accumulate neutral, genomewide differences. Overall, our results are consistent with a scenario of speciation with gene flow and a divergence time which coincides with the rise of Mt. Etna to altitudes above 2000 m (~150 KY). Further work to quantify the role of adaptation to contrasting environments of high and low altitudes will be needed to support the scenario of recent ecological speciation in this system.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Alexander S T Papadopulos
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.,Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
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20
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Papadopulos AST, Kaye M, Devaux C, Hipperson H, Lighten J, Dunning LT, Hutton I, Baker WJ, Butlin RK, Savolainen V. Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0342. [PMID: 24958917 PMCID: PMC4071517 DOI: 10.1098/rstb.2013.0342] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.
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Affiliation(s)
- Alexander S T Papadopulos
- Grand Challenges in Ecosystem and the Environment Initiative, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Maria Kaye
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Céline Devaux
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554, 34095 Montpellier, France
| | - Helen Hipperson
- Grand Challenges in Ecosystem and the Environment Initiative, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Jackie Lighten
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Luke T Dunning
- Grand Challenges in Ecosystem and the Environment Initiative, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Ian Hutton
- Lord Howe Island Museum, Lord Howe Island, PO Box 157, New South Wales 2898, Australia
| | | | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Vincent Savolainen
- Grand Challenges in Ecosystem and the Environment Initiative, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
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Igea J, Bogarín D, Papadopulos AST, Savolainen V. A comparative analysis of island floras challenges taxonomy-based biogeographical models of speciation. Evolution 2015; 69:482-91. [PMID: 25522772 PMCID: PMC6681140 DOI: 10.1111/evo.12587] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/28/2014] [Indexed: 11/30/2022]
Abstract
Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy‐based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation.
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Affiliation(s)
- Javier Igea
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, United Kingdom
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22
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Valente LM, Britton AW, Powell MP, Papadopulos AST, Burgoyne PM, Savolainen V. Correlates of hyperdiversity in southern African ice plants (Aizoaceae). Bot J Linn Soc 2014; 174:110-129. [PMID: 25821244 PMCID: PMC4373134 DOI: 10.1111/boj.12117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 05/27/2013] [Accepted: 08/24/2013] [Indexed: 05/29/2023]
Abstract
The exceptionally high plant diversity of the Greater Cape Floristic Region (GCFR) comprises a combination of ancient lineages and young radiations. A previous phylogenetic study of Aizoaceae subfamily Ruschioideae dated the radiation of this clade of > 1500 species in the GCFR to 3.8-8.7 Mya, establishing it as a flagship example of a diversification event triggered by the onset of a summer-arid climate in the region. However, a more recent analysis found an older age for the Ruschioideae lineage (17 Mya), suggesting that the group may in fact have originated much before the aridification of the region 10-15 Mya. Here, we reassess the tempo of radiation of ice plants by using the most complete generic-level phylogenetic tree for Aizoaceae to date, a revised calibration age and a new dating method. Our estimates of the age of the clade are even younger than initially thought (stem age 1.13-6.49 Mya), supporting the hypothesis that the radiation post-dates the establishment of an arid environment in the GCFR and firmly placing the radiation among the fastest in angiosperms (diversification rate of 4.4 species per million years). We also statistically examine environmental and morphological correlates of richness in ice plants and find that diversity is strongly linked with precipitation, temperature, topographic complexity and the evolution of highly succulent leaves and wide-band tracheids.
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Affiliation(s)
- Luis M Valente
- Imperial College LondonSilwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Adam W Britton
- Imperial College LondonSilwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Martyn P Powell
- Imperial College LondonSilwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | | | - Priscilla M Burgoyne
- South African National Biodiversity InstitutePrivate Bag X101, Pretoria, 0001, South Africa
| | - Vincent Savolainen
- Imperial College LondonSilwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
- Jodrell Laboratory, Royal Botanic GardensKew, Richmond, Surrey, TW9 3DS, UK
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23
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Papadopulos AST, Powell MP, Pupulin F, Warner J, Hawkins JA, Salamin N, Chittka L, Williams NH, Whitten WM, Loader D, Valente LM, Chase MW, Savolainen V. Convergent evolution of floral signals underlies the success of Neotropical orchids. Proc Biol Sci 2013; 280:20130960. [PMID: 23804617 PMCID: PMC3712443 DOI: 10.1098/rspb.2013.0960] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The great majority of plant species in the tropics require animals to achieve pollination, but the exact role of floral signals in attraction of animal pollinators is often debated. Many plants provide a floral reward to attract a guild of pollinators, and it has been proposed that floral signals of non-rewarding species may converge on those of rewarding species to exploit the relationship of the latter with their pollinators. In the orchid family (Orchidaceae), pollination is almost universally animal-mediated, but a third of species provide no floral reward, which suggests that deceptive pollination mechanisms are prevalent. Here, we examine floral colour and shape convergence in Neotropical plant communities, focusing on certain food-deceptive Oncidiinae orchids (e.g. Trichocentrum ascendens and Oncidium nebulosum) and rewarding species of Malpighiaceae. We show that the species from these two distantly related families are often more similar in floral colour and shape than expected by chance and propose that a system of multifarious floral mimicry—a form of Batesian mimicry that involves multiple models and is more complex than a simple one model–one mimic system—operates in these orchids. The same mimetic pollination system has evolved at least 14 times within the species-rich Oncidiinae throughout the Neotropics. These results help explain the extraordinary diversification of Neotropical orchids and highlight the complexity of plant–animal interactions.
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Papadopulos AST, Price Z, Devaux C, Hipperson H, Smadja CM, Hutton I, Baker WJ, Butlin RK, Savolainen V. A comparative analysis of the mechanisms underlying speciation on Lord Howe Island. J Evol Biol 2013; 26:733-45. [PMID: 23320532 DOI: 10.1111/jeb.12071] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 11/29/2022]
Abstract
On Lord Howe Island, speciation is thought to have taken place in situ in a diverse array of distantly related plant taxa (Metrosideros, Howea and Coprosma; Proc. Natl Acad. Sci. USA 108, 2011, 13188). We now investigate whether the speciation processes were driven by divergent natural selection in each genus by examining the extent of ecological and genetic divergence. We present new and extensive, ecological and genetic data for all three genera. Consistent with ecologically driven speciation, outlier loci were detected using genome scan methods. This mechanism is supported by individual-based analyses of genotype-environment correlations within species, demonstrating that local adaptation is currently widespread on the island. Genetic analyses show that prezygotic isolating barriers within species are currently insufficiently strong to allow further population differentiation. Interspecific hybridization was found in both Howea and Coprosma, and species distribution modelling indicates that competitive exclusion may result in selection against admixed individuals. Colonization of new niches, partly fuelled by the rapid generation of new adaptive genotypes via hybridization, appears to have resulted in the adaptive radiation in Coprosma - supporting the 'Syngameon hypothesis'.
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Fiz-Palacios O, Vargas P, Vila R, Papadopulos AST, Aldasoro JJ. The uneven phylogeny and biogeography of Erodium (Geraniaceae): radiations in the Mediterranean and recent recurrent intercontinental colonization. Ann Bot 2010; 106:871-84. [PMID: 20858592 PMCID: PMC2990656 DOI: 10.1093/aob/mcq184] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The genus Erodium is a common feature of Mediterranean-type climates throughout the world, but the Mediterranean Basin has significantly higher diversity than other areas. The aim here is to reveal the biogeographical history of the genus and the causes behind the evolution of the uneven distribution. METHODS Seventy-eight new nrITS sequences were incorporated with existing plastid data to explore the phylogenetic relationships and biogeography of Erodium using several reconstruction methods. Divergence times for major clades were calculated and contrasted with other previously published information. Furthermore, topological and temporal diversification rate shift analyses were employed using these data. KEY RESULTS Phylogenetic relationships among species are widely congruent with previous plastid reconstructions, which refute the classical taxonomical classification. Biogeographical reconstructions point to Asia as the ancestral area of Erodium, arising approx. 18 MYA. Four incidences of intercontinental dispersal from the Mediterranean Basin to similar climates are demonstrated. Increases in diversification were present in two independent Erodium lineages concurrently. Two bursts of diversification (3 MYA and 0·69 MYA) were detected only in the Mediterranean flora. CONCLUSIONS Two lineages diverged early in the evolution of the genus Erodium: (1) subgenus Erodium plus subgenus Barbata subsection Absinthioidea and (2) the remainder of subgenus Barbata. Dispersal across major water bodies, although uncommon, has had a major influence on the distribution of this genus and is likely to have played as significant role as in other, more easily dispersed, genera. Establishment of Mediterranean climates has facilitated the spread of the genus and been crucial in its diversification. Two, independent, rapid radiations in response to the onset of drought and glacial climate change indicate putative adaptive radiations in the genus.
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Affiliation(s)
- Omar Fiz-Palacios
- Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain.
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