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Dagallier LPMJ, Condamine FL, Couvreur TLP. Sequential diversification with Miocene extinction and Pliocene speciation linked to mountain uplift explains the diversity of the African rain forest clade Monodoreae (Annonaceae). ANNALS OF BOTANY 2024; 133:677-696. [PMID: 37659091 PMCID: PMC11082524 DOI: 10.1093/aob/mcad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND AND AIMS Throughout the Cenozoic, Africa underwent several climatic and geological changes impacting the evolution of tropical rain forests (TRFs). African TRFs are thought to have extended from east to west in a 'pan-African' TRF, followed by several events of fragmentation during drier climate periods. During the Miocene, climate cooling and mountain uplift led to the aridification of tropical Africa and open habitats expanded at the expense of TRFs, which probably experienced local extinctions. However, in plants, these drivers were previously inferred using limited taxonomic and molecular data. Here, we tested the impact of climate and geological changes on diversification within the diverse clade Monodoreae (Annonaceae) composed of 90 tree species restricted to African TRFs. METHODS We reconstructed a near-complete phylogenetic tree, based on 32 nuclear genes, and dated using relaxed clocks and fossil calibrations in a Bayesian framework. We inferred the biogeographical history and the diversification dynamics of the clade using multiple birth-death models. KEY RESULTS Monodoreae originated in East African TRFs ~25 million years ago (Ma) and expanded toward Central Africa during the Miocene. We inferred range contractions during the middle Miocene and document important connections between East and West African TRFs after 15-13 Ma. Our results indicated a sudden extinction event during the late Miocene, followed by an increase in speciation rates. Birth-death models suggested that African elevation change (orogeny) is positively linked to speciation in this clade. CONCLUSION East Africa is inferred as an important source of Monodoreae species, and possibly for African plant diversity in general. Our results support a 'sequential scenario of diversification' in which increased aridification triggered extinction of TRF species in Monodoreae. This was quickly followed by fragmentation of rain forests, subsequently enhancing lagged speciation resulting from vicariance and improved climate conditions. In contrast to previous ideas, the uplift of East Africa is shown to have played a positive role in Monodoreae diversification.
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Affiliation(s)
- Léo-Paul M J Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458, USA
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France
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2
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Cusack DF, Christoffersen B, Smith-Martin CM, Andersen KM, Cordeiro AL, Fleischer K, Wright SJ, Guerrero-Ramírez NR, Lugli LF, McCulloch LA, Sanchez-Julia M, Batterman SA, Dallstream C, Fortunel C, Toro L, Fuchslueger L, Wong MY, Yaffar D, Fisher JB, Arnaud M, Dietterich LH, Addo-Danso SD, Valverde-Barrantes OJ, Weemstra M, Ng JC, Norby RJ. Toward a coordinated understanding of hydro-biogeochemical root functions in tropical forests for application in vegetation models. THE NEW PHYTOLOGIST 2024; 242:351-371. [PMID: 38416367 DOI: 10.1111/nph.19561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest-climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine-root strategies for soil resource exploration, (2) coupling and trade-offs in fine-root water vs nutrient acquisition, and (3) aboveground-belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground-belowground hydro-nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.
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Affiliation(s)
- Daniela F Cusack
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Bradley Christoffersen
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Chris M Smith-Martin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Amanda L Cordeiro
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Katrin Fleischer
- Department Biogeochemical Signals, Max-Planck-Institute for Biogeochemistry, Hans-Knöll-Straße 10, Jena, 07745, Germany
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Nathaly R Guerrero-Ramírez
- Silviculture and Forest Ecology of Temperate Zones, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Gottingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Gottingen, 37077, Germany
| | - Laynara F Lugli
- School of Life Sciences, Technical University of Munich, Freising, 85354, Germany
| | - Lindsay A McCulloch
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
- National Center for Atmospheric Research, National Oceanographic and Atmospheric Agency, 1850 Table Mesa Dr., Boulder, CO, 80305, USA
| | - Mareli Sanchez-Julia
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Sarah A Batterman
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
- School of Geography, University of Leeds, Leeds, LS2 9JT, UK
| | - Caroline Dallstream
- Department of Biology, McGill University, 1205 Av. du Docteur-Penfield, Montreal, QC, H3A 1B1, Canada
| | - Claire Fortunel
- AMAP (Botanique et Modélisation de l'Architecture des Plantes et des Végétations), Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, 34398, France
| | - Laura Toro
- Yale Applied Science Synthesis Program, The Forest School at the Yale School of the Environment, Yale University, New Haven, CT, 06511, USA
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, 1030, Austria
| | - Michelle Y Wong
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Daniela Yaffar
- Functional Forest Ecology, Universität Hamburg, Barsbüttel, 22885, Germany
| | - Joshua B Fisher
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA, 92866, USA
| | - Marie Arnaud
- Institute of Ecology and Environmental Sciences (IEES), UMR 7618, CNRS-Sorbonne University-INRAE-UPEC-IRD, Paris, 75005, France
- School of Geography, Earth and Environmental Sciences & BIFOR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Lee H Dietterich
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, 39180, USA
- Department of Biology, Haverford College, Haverford, PA, 19003, USA
| | - Shalom D Addo-Danso
- Forests and Climate Change Division, CSIR-Forestry Research Institute of Ghana, P.O Box UP 63 KNUST, Kumasi, Ghana
| | - Oscar J Valverde-Barrantes
- Department of Biological Sciences, International Center for Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- Department of Biological Sciences, International Center for Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
| | - Jing Cheng Ng
- Nanyang Technological University, Singapore, 639798, Singapore
| | - Richard J Norby
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
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3
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Pérez-Escobar OA, Bogarín D, Przelomska NAS, Ackerman JD, Balbuena JA, Bellot S, Bühlmann RP, Cabrera B, Cano JA, Charitonidou M, Chomicki G, Clements MA, Cribb P, Fernández M, Flanagan NS, Gravendeel B, Hágsater E, Halley JM, Hu AQ, Jaramillo C, Mauad AV, Maurin O, Müntz R, Leitch IJ, Li L, Negrão R, Oses L, Phillips C, Rincon M, Salazar GA, Simpson L, Smidt E, Solano-Gomez R, Parra-Sánchez E, Tremblay RL, van den Berg C, Tamayo BSV, Zuluaga A, Zuntini AR, Chase MW, Fay MF, Condamine FL, Forest F, Nargar K, Renner SS, Baker WJ, Antonelli A. The origin and speciation of orchids. THE NEW PHYTOLOGIST 2024; 242:700-716. [PMID: 38382573 DOI: 10.1111/nph.19580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024]
Abstract
Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.
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Affiliation(s)
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
- Naturalis Biodiversity Centre, Leiden, CR 2333, the Netherlands
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - James D Ackerman
- University of Puerto Rico - Rio Piedras, San Juan, PR, 00925-2537, USA
| | | | | | | | - Betsaida Cabrera
- Jardín Botánico Rafael Maria Moscoso, Santo Domingo, 21-9, Dominican Republic
| | | | | | | | - Mark A Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Melania Fernández
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Nicola S Flanagan
- Universidad Pontificia Javeriana, Seccional Cali, Cali, 760031, Colombia
| | | | | | | | - Ai-Qun Hu
- Singapore Botanic Gardens, 1 Cluny Road, Singapore, 257494, Singapore
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Apartado, Panama City, 0843-03092, Panama
| | | | | | - Robert Müntz
- Reserva Biológica Guaitil, Eisenstadt, 7000, Austria
| | | | - Lan Li
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Lizbeth Oses
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Charlotte Phillips
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Milton Rincon
- Jardín Botánico Jose Celestino Mutis, Bogota, 111071, Colombia
| | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
| | - Eric Smidt
- Universidade Federal do Paraná, Curitiba, 19031, Brazil
| | | | | | | | - Cassio van den Berg
- Universidade Estadual de Feira de Santana, Feira de Santana, 44036-900, Brazil
| | | | | | | | - Mark W Chase
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6102, Australia
| | | | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), Place Eugène Bataillon, Montpellier, 34000, France
| | | | - Katharina Nargar
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
- Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Gothenburg, 417 56, Sweden
- University of Gothenburg, Gothenburg, 417 56, Sweden
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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4
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Francisconi AF, Marroquín JAM, Cauz-Santos LA, van den Berg C, Martins KKM, Costa MF, Picanço-Rodrigues D, de Alencar LD, Zanello CA, Colombo CA, Hernández BGD, Amaral DT, Lopes MTG, Veasey EA, Zucchi MI. Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns. Sci Rep 2023; 13:20635. [PMID: 37996522 PMCID: PMC10667357 DOI: 10.1038/s41598-023-44631-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Jonathan Andre Morales Marroquín
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Luiz Augusto Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina S/N-Novo Horizonte, Feira de SantanaFeira de Santana, Bahia, CEP 44036-900, Brazil
| | - Kauanne Karolline Moreno Martins
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Marcones Ferreira Costa
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
- Universidade Federal do Piauí, BR-343 Km 3.5, Floriano, Piauí, CEP 64808-605, Brazil
| | - Doriane Picanço-Rodrigues
- Departamento de Biologia, Universidade Federal do Amazonas, Avenida Gen. Rodrigo Octávio Jordão Ramos, 3000-Coroado I-Campus Universitário-Senador Arthur Virgílio Filho-Setor Sul, Bloco H, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Luciano Delmodes de Alencar
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Cesar Augusto Zanello
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Carlos Augusto Colombo
- Instituto Agronômico, Av. Theodureto de Almeida Camargo, 1500, Campinas, São Paulo, CEP 13075-630, Brazil
| | | | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo, CEP 09040-040, Brazil
| | - Maria Teresa Gomes Lopes
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Avenida Rodrigo Otávio Ramos, 3000-Bairro Coroado, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11-Bairro São Dimas, Piracicaba, São Paulo, CEP 13418-900, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos Agronegócios (APTA), Polo Centro Sul, Rodovia SP 127 Km 30, CP 28, Piracicaba, São Paulo, CEP 13400-970, Brazil.
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Gopal A, Bharti DK, Page N, Dexter KG, Krishnamani R, Kumar A, Joshi J. Range restricted old and young lineages show the southern Western Ghats to be both a museum and a cradle of diversity for woody plants. Proc Biol Sci 2023; 290:20222513. [PMID: 37122248 PMCID: PMC10130714 DOI: 10.1098/rspb.2022.2513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
The Western Ghats (WG) mountain chain is a global biodiversity hotspot with high diversity and endemicity of woody plants. The latitudinal breadth of the WG offers an opportunity to determine the evolutionary drivers of latitudinal diversity patterns. We examined the spatial patterns of evolutionary diversity using complementary phylogenetic diversity and endemism measures. To examine if different regions of the WG serve as a museum or cradle of evolutionary diversity, we examined the distribution of 470 species based on distribution modelling and occurrence locations across the entire region. In accordance with the expectation, we found that the southern WG is both a museum and cradle of woody plant evolutionary diversity, as a higher proportion of both old and young evolutionary lineages are restricted to the southern WG. The diversity gradient is likely driven by high geo-climatic stability in the south and phylogenetic niche conservatism for moist and aseasonal sites. This is corroborated by persistent lineage nestedness at almost all evolutionary depths (10-135 million years), and a strong correlation of evolutionary diversity with drought seasonality, precipitation and topographic heterogeneity. Our results highlight the global value of the WG, demonstrating, in particular, the importance of protecting the southern WG-an engine of plant diversification and persistence.
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Affiliation(s)
- Abhishek Gopal
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - D K Bharti
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Kyle G Dexter
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Ajith Kumar
- Centre for Wildlife Studies, Bangalore, Karnataka, India
| | - Jahnavi Joshi
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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6
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Barahukwa A, Chapman CA, Namaganda M, Eilu G, Omeja PA, Lawes MJ. The effects of the invasive species,
Lantana camara
, on regeneration of an African rainforest. Afr J Ecol 2023. [DOI: 10.1111/aje.13133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Anke Barahukwa
- Department of Environmental Management Makerere University Kampala Uganda
| | - Colin A. Chapman
- Wilson Center Washington District of Columbia USA
- Department of Anthropology The George Washington University Washington District of Columbia USA
- School of Life Sciences University of KwaZulu‐Natal Scottsville, Pietermaritzburg South Africa
- Shaanxi Key Laboratory for Animal Conservation Northwest University Xi'an China
| | - Mary Namaganda
- Department of Plant Sciences, Microbiology and Biotechnology Makerere University Kampala Uganda
| | - Gerald Eilu
- Department of Forestry Biodiversity and Tourism, Makerere University Kampala Uganda
| | - Patrick A. Omeja
- Department of Forestry Biodiversity and Tourism, Makerere University Kampala Uganda
- Makerere University Biological Field Station Fort Portal Uganda
| | - Michael J. Lawes
- School of Life Sciences University of KwaZulu‐Natal Scottsville, Pietermaritzburg South Africa
- Institute of Biodiversity and Environmental Conservation (IBEC) Universiti Malaysia Sarawak Kota Samarahan Malaysia
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7
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Ringelberg JJ, Koenen EJ, Sauter B, Aebli A, Rando JG, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Miller JT, Simon MF, Jordão LS, Morales M, Bailey CD, Nageswara-Rao M, Nicholls JA, Loiseau O, Pennington RT, Dexter KG, Zimmermann NE, Hughes CE. Precipitation is the main axis of tropical plant phylogenetic turnover across space and time. SCIENCE ADVANCES 2023; 9:eade4954. [PMID: 36800419 PMCID: PMC10957106 DOI: 10.1126/sciadv.ade4954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Benjamin Sauter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Anahita Aebli
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Juliana G. Rando
- Programa de Pós Graduação em Ciências Ambientais, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Rua Prof. José Seabra de Lemos, 316, Bairro Recanto dos Pássaros, 47808-021 Barreiras-BA, Brazil
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, 96010-900 Capão do Leão-RS, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900 Feira de Santana-BA, Brazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia
- School of Biological, Earth and Environmental Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Joseph T. Miller
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e Biotecnologia, 70770-901 Brasília-DF, Brazil
| | - Lucas S. B. Jordão
- Programa de Pós-Graduação em Botânica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, 22460-030 Rua Pacheco Leão-RJ, Brazil
| | - Matías Morales
- Instituto de Recursos Biológicos, CIRN-CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía y Ciencias Agroalimentarias, Universidad de Morón, B1708JPD Morón, Buenos Aires, Argentina
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM 88001, USA
| | - Madhugiri Nageswara-Rao
- United States Department of Agriculture - Agricultural Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL 33158, USA
| | - James A. Nicholls
- Australian National Insect Collection, CSIRO, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Kyle G. Dexter
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Niklaus E. Zimmermann
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
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8
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Vasconcelos T. A trait-based approach to determining principles of plant biogeography. AMERICAN JOURNAL OF BOTANY 2023; 110:e16127. [PMID: 36648370 DOI: 10.1002/ajb2.16127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Lineage-specific traits determine how plants interact with their surrounding environment. Unrelated species may evolve similar phenotypic characteristics to tolerate, persist in, and invade environments with certain characteristics, resulting in some traits becoming relatively more common in certain types of habitats. Analyses of these general patterns of geographical trait distribution have led to the proposal of general principles to explain how plants diversify in space over time. Trait-environment correlation analyses quantify to what extent unrelated lineages have similar evolutionary responses to a given type of habitat. In this synthesis, I give a short historical overview on trait-environment correlation analyses, from some key observations from classic naturalists to modern approaches using trait evolution models, large phylogenies, and massive data sets of traits and distributions. I discuss some limitations of modern approaches, including the need for more realistic models, the lack of data from tropical areas, and the necessary focus on trait scoring that goes beyond macromorphology. Overcoming these limitations will allow the field to explore new questions related to trait lability and niche evolution and to better identify generalities and exceptions in how plants diversify in space over time.
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Affiliation(s)
- Thais Vasconcelos
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
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9
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Pelegrin JS, Cantalapiedra JL, Gamboa S, Menéndez I, Hernández Fernández M. Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biomes are climatically and biotically distinctive macroecological units that formed over geological time scales. Their features consolidate them as ‘evolutionary scenarios’, with their own diversification dynamics. Under the concept of phylogenetic niche conservatism, we assessed, for the first time, the evolution of biome occupation in birds. We aimed to analyse patterns of adaptation to different climatic regimes and the determinant factors for colonization of emerging biomes by clades from different ancestral biomes. In this work, we reconstructed the biome occupation history of two clades of birds (Galliformes and Falconiformes) under an integrative perspective through a comprehensive review of ecological, phylogenetic, palaeontological and biogeographical evidence. Our findings for both groups are consistent with a scenario of phylogenetic biome conservatism and highlight the importance of changes in climate during the Miocene in the adaptation and evolution of climatic niches. In particular, our results indicate high biome conservatism associated with biomes situated in some of the extremes of the global climate gradient (evergreen tropical rainforest, steppe and tundra) for both bird taxa. Finally, the historical dynamics of tropical seasonal biomes, such as tropical deciduous woodlands and savannas, appear to have played a preponderant role during the diversification processes of these bird lineages.
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Affiliation(s)
- Jonathan S Pelegrin
- Grupo de Investigación en Ecología y Conservación de la Biodiversidad (EcoBio), Área de Biología y Programa de Maestría en Educación Ambiental y Desarrollo Sostenible, Facultades de Ciencias Básicas y Educación, Universidad Santiago de Cali , Colombia
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle , Colombia
| | - Juan L Cantalapiedra
- GloCEE – Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, Universidad de Alcalá , 28805, Alcalá de Henares (Madrid ), Spain
| | - Sara Gamboa
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
| | - Iris Menéndez
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
| | - Manuel Hernández Fernández
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
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10
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Rickenback J, Pennington RT, Lehmann CER. Diversity in habit expands the environmental niche of
Ziziphus
(Rhamnaceae). Biotropica 2022. [DOI: 10.1111/btp.13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jess Rickenback
- School of Geosciences University of Edinburgh Edinburgh UK
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
| | - R. Toby Pennington
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
- College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Caroline E. R. Lehmann
- School of Geosciences University of Edinburgh Edinburgh UK
- Tropical Diversity Royal Botanic Garden Edinburgh Edinburgh UK
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11
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Morales-Marroquín JA, Solis Miranda R, Baldin Pinheiro J, Zucchi MI. Biodiversity Research in Central America: A Regional Comparison in Scientific Production Using Bibliometrics and Democracy Indicators. Front Res Metr Anal 2022; 7:898818. [PMID: 35910707 PMCID: PMC9329674 DOI: 10.3389/frma.2022.898818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Central America science production on biodiversity topics is important in planning future adaptive and conservation policies in a climate-related risk region that is considered a biodiversity hotspot but has the lowest Human Development Index of Latin America. Science production on biodiversity is related to geo-referenced species occurrence records, but the accessibility depends on political frameworks and science funding. This paper aims at foregrounding how the democratic shifts throughout the years have had an impact on science production on biodiversity research, and species records. For this exploration we developed a novel systematic scientometric analysis of science production on biodiversity topics, we used Bio-Dem (open-source software of biodiversity records and socio-political variables) and briefly analyzed the history—from 1980 to 2020—of Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, and Panama. With a data set of 16,304 documents, our analysis shows the significant discrepancies between the low science production of Central American Northern countries (Guatemala, El Salvador, Honduras, and Nicaragua), the prolific production from the Southern (Costa Rica and Panama), and how this relates to democratic stability. Scientific production tends to be more abundant when democratic conditions are guaranteed. The state capture phenomenon and colonial-rooted interactions worldwide have an effect on the conditions under which science is being produced in Central America. Democracy, science production, funding, and conservation are core elements that go hand in hand, and that need to be nourished in a region that struggles with the protection of life and extractive activities in a climate change scenario.
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Affiliation(s)
- Jonathan A. Morales-Marroquín
- Genetics and Molecular Biology Department, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Jonathan A. Morales-Marroquín
| | - Regina Solis Miranda
- School of Languages and Cultures, University of Sheffield, Sheffield, United Kingdom
| | - José Baldin Pinheiro
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Maria Imaculada Zucchi
- Genetics and Molecular Biology Department, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, Brazil
- Unidade Regional de Pesquisa e Desenvolvimento (APTA), Secretaria de Agricultura, São Paulo, Brazil
- Maria Imaculada Zucchi
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12
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Global variation in diversification rate and species richness are unlinked in plants. Proc Natl Acad Sci U S A 2022; 119:e2120662119. [PMID: 35767644 PMCID: PMC9271200 DOI: 10.1073/pnas.2120662119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.
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13
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Pinanga palms revisited 20 years on: what can changes in Pinanga species populations tell us about rainforest understory palm persistence? JOURNAL OF TROPICAL ECOLOGY 2022. [DOI: 10.1017/s0266467422000256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Borneo is the centre of diversity of the palm genus Pinanga. At least 13 understory species have been recorded in the Ulu Temburong National Park in Brunei, but little is known of their persistence. Changes in populations of Pinanga understory palms may be indicative of more widespread changes due to climate change, such as changes in rainfall, which may be important for the palm diversity in the protected area. However, we know little about the population dynamics of these palms, how persistent their populations are or if they behave similarly over long time frames. In 1998, populations of five co-occurring species of Pinanga at several locations in the Ulu Temburong National Park were documented. This project aimed to undertake a comprehensive resurvey of the original five Pinanga palm species populations in order to assess if they showed similar population changes across sites and species after two decades. Overall, most species maintained their population size in the surveyed region but not consistently among sites, and one species significantly declined in abundance. There was considerable variation in population growth rate (R) within and among species and sites that was significantly correlated with density and the percentage of multi-stemmed plants. There was evidence of pulsed recruitment in some species and or sites rather than steady or exponential patterns of population growth.
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14
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Gorel AP, Hardy OJ, Dauby G, Dexter KG, Segovia RA, Steppe K, Fayolle A. Climatic niche lability but growth form conservatism in the African woody flora. Ecol Lett 2022; 25:1164-1176. [PMID: 35229970 DOI: 10.1111/ele.13985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/16/2021] [Accepted: 02/03/2022] [Indexed: 11/30/2022]
Abstract
Climatic niche evolution during the diversification of tropical plants has received little attention in Africa. To address this, we characterised the climatic niche of >4000 tropical African woody species, distinguishing two broad bioclimatic groups (forest vs. savanna) and six subgroups. We quantified niche conservatism versus lability at the genus level and for higher clades, using a molecular phylogeny of >800 genera. Although niche stasis at speciation is prevalent, numerous clades individually cover vast climatic spaces suggesting a general ease in transcending ecological limits, especially across bioclimatic subgroups. The forest biome was the main source of diversity, providing many lineages to savanna, but reverse shifts also occurred. We identified clades that diversified in savanna after shifts from forest. The forest-savanna transition was not consistently associated with a growth form change, though we found evolutionarily labile clades whose presence in forest or savanna is associated respectively with climbing or shrubby species diversification.
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Affiliation(s)
- Anaïs-Pasiphaé Gorel
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology, Faculté Des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Gilles Dauby
- AMAP, Univ. Montpellier, IRD, CNRS, CIRAD, INRAE, Montpellier University, Montpellier, France
| | - Kyle G Dexter
- Tropical School of GeoSciences, University of Edinburgh, Edinburgh, UK.,Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Ricardo A Segovia
- Instituto de Ecologia y Biodiversidad (IEB), Santiago, Chile.,Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Kat, Valdivia, Chile
| | - Kathy Steppe
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Adeline Fayolle
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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15
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Vasconcelos T, O’Meara BC, Beaulieu JM. Retiring “Cradles” and “Museums” of Biodiversity. Am Nat 2021; 199:194-205. [DOI: 10.1086/717412] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Brian C. O’Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Jeremy M. Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
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16
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Earth history events shaped the evolution of uneven biodiversity across tropical moist forests. Proc Natl Acad Sci U S A 2021; 118:2026347118. [PMID: 34599095 PMCID: PMC8501849 DOI: 10.1073/pnas.2026347118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 02/07/2023] Open
Abstract
Tropical moist forests harbor much of the world’s biodiversity, but this diversity is not evenly distributed globally, with tropical moist forests in the Neotropics and Indomalaya generally exhibiting much greater diversity than in the Afrotropics. Here, we assess the ubiquity of this “pantropical diversity disparity” (PDD) using the present-day distributions of over 150,000 species of plants and animals, and we compare these distributions with a spatial model of diversification combined with reconstructions of plate tectonics, temperature, and aridity. Our study demonstrates that differences in paleoenvironmental dynamics between continents, including mountain building, aridification, and global temperature fluxes, can explain the PDD by shaping spatial and temporal patterns of species origination and extinction, providing a close match to observed distributions of plants and animals. Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.
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17
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Dale EE, Larcombe MJ, Lee WG. The effect of single biome occupancy on the estimation of biome shifts and the detection of biome conservatism. PLoS One 2021; 16:e0248839. [PMID: 33784318 PMCID: PMC8009365 DOI: 10.1371/journal.pone.0248839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Biome conservatism is often regarded as common in diversifying lineages, based on the detection of low biome shift rates or high phylogenetic signal. However, many studies testing biome conservatism utilise a single-biome-per-species approach, which may influence the detection of biome conservatism. Meta-analyses show that biome shift rates are significantly lower (less than a tenth), when single biome occupancy approaches are adopted. Using New Zealand plant lineages, estimated biome shifts were also significantly lower (14-67% fewer biome shifts) when analysed under the assumption of a single biome per species. Although a single biome approach consistently resulted in lower biome shifts, it detected fewer instances of biome conservatism. A third of clades (3 out of 9) changed status in biome conservatism tests between single and multiple biome occupancy approaches, with more instances of significant biome conservatism when using a multiple biome occupancy approach. A single biome approach may change the likelihood of finding biome conservatism because it assumes biome specialisation within species, falsely recognises some biome shift types and fails to include other biome shift types. Our results indicate that the degree of biome fidelity assumed has a strong influence on analyses assessing biome shift rates, and biome conservatism testing. We advocate analyses that allow species to occupy multiple biomes.
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Affiliation(s)
- Esther E. Dale
- Manaaki Whenua—Landcare Research, Dunedin, New Zealand
- Department of Botany, University of Otago, Dunedin, New Zealand
| | | | - William G. Lee
- Manaaki Whenua—Landcare Research, Dunedin, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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18
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Kuhnhäuser BG, Bellot S, Couvreur TLP, Dransfield J, Henderson A, Schley R, Chomicki G, Eiserhardt WL, Hiscock SJ, Baker WJ. A robust phylogenomic framework for the calamoid palms. Mol Phylogenet Evol 2021; 157:107067. [PMID: 33412273 DOI: 10.1016/j.ympev.2020.107067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 01/11/2023]
Abstract
Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550 species in 17 genera, 10 subtribes and three tribes, but their phylogenetic relationships remain insufficiently understood. Here, we sequenced almost one thousand nuclear genomic regions for 75 systematically selected Calamoideae, representing the taxonomic diversity within all calamoid genera. Our phylogenomic analyses resolved a maximally supported phylogenetic backbone for the Calamoideae, including several higher-level relationships not previously inferred. In-depth analysis revealed low gene tree conflict for the backbone but complex deep evolutionary histories within several subtribes. Overall, our phylogenomic framework sheds new light on the evolution of palms and provides a robust foundation for future comparative studies, such as taxonomy, systematics, biogeography, and macroevolutionary research.
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Affiliation(s)
- Benedikt G Kuhnhäuser
- Department of Plant Sciences, University of Oxford, United Kingdom; Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | | | | | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, United Kingdom; Department of Biology, Aarhus University, Denmark
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, United Kingdom
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19
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Rapini A, Bitencourt C, Luebert F, Cardoso D. An escape-to-radiate model for explaining the high plant diversity and endemism in campos rupestres†. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
With extraordinary levels of plant diversity and endemism, the Brazilian campos rupestres across the Espinhaço Range have a species/area ratio 40 times higher than the lowland Amazon. Although diversification drivers in campos rupestres remain a matter of debate, the Pleistocene refugium hypothesis (PRH) is often adopted as the most plausible explanation for their high diversity. The PRH has two main postulates: highland interglacial refugia and a species pump mechanism catalysed by climatic changes. We critically assessed studies on campos rupestres diversification at different evolutionary levels and conclude that most of them are affected by sampling biases, unrealistic assumptions or inaccurate results that do not support the PRH. By modelling the palaeo-range of campos rupestres based on the distribution of 1123 species of vascular plants endemic to the Espinhaço Range and using climate and edaphic variables, we projected a virtually constant suitable area for campos rupestres across the last glacial cycle. We challenge the great importance placed on Pleistocene climatic oscillations in campos rupestres plant diversification and offer an alternative explanation named escape-to-radiate model, which emphasizes niche shifts. Under this biogeographic model of diversification, the long-term fragmentation of campos rupestres combined with recurrent extinctions after genetic drift and sporadic events of adaptive radiation may provide an explanation for the current diversity and endemism in the Espinhaço Range. We conclude that long-term diversification dynamics in campos rupestres are mainly driven by selection, while most endemic diversity is ephemeral, extremely fragile and mainly driven by drift.
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Affiliation(s)
- Alessandro Rapini
- Programa de Pós-graduação em Botânica, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana, Bahia, Brazil
| | - Cássia Bitencourt
- Programa de Pós-graduação em Botânica, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana, Bahia, Brazil
| | - Federico Luebert
- Departmento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile
| | - Domingos Cardoso
- Programa de Pós-graduação em Botânica, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana, Bahia, Brazil
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, Salvador, Bahia, Brazil
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20
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Individualistic evolutionary responses of Central African rain forest plants to Pleistocene climatic fluctuations. Proc Natl Acad Sci U S A 2020; 117:32509-32518. [PMID: 33277432 DOI: 10.1073/pnas.2001018117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Understanding the evolutionary dynamics of genetic diversity is fundamental for species conservation in the face of climate change, particularly in hyper-diverse biomes. Species in a region may respond similarly to climate change, leading to comparable evolutionary dynamics, or individualistically, resulting in dissimilar patterns. The second-largest expanse of continuous tropical rain forest (TRF) in the world is found in Central Africa. Here, present-day patterns of genetic structure are thought to be dictated by repeated expansion and contraction of TRFs into and out of refugia during Pleistocene climatic fluctuations. This refugia model implies a common response to past climate change. However, given the unrivalled diversity of TRFs, species could respond differently because of distinct environmental requirements or ecological characteristics. To test this, we generated genome-wide sequence data for >700 individuals of seven codistributed plants from Lower Guinea in Central Africa. We inferred species' evolutionary and demographic histories within a comparative phylogeographic framework. Levels of genetic structure varied among species and emerged primarily during the Pleistocene, but divergence events were rarely concordant. Demographic trends ranged from repeated contraction and expansion to continuous growth. Furthermore, patterns in genetic variation were linked to disparate environmental factors, including climate, soil, and habitat stability. Using a strict refugia model to explain past TRF dynamics is too simplistic. Instead, individualistic evolutionary responses to Pleistocene climatic fluctuations have shaped patterns in genetic diversity. Predicting the future dynamics of TRFs under climate change will be challenging, and more emphasis is needed on species ecology to better conserve TRFs worldwide.
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Phylogenomic Study of Monechma Reveals Two Divergent Plant Lineages of Ecological Importance in the African Savanna and Succulent Biomes. DIVERSITY 2020. [DOI: 10.3390/d12060237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Monechma Hochst. s.l. (Acanthaceae) is a diverse and ecologically important plant group in sub-Saharan Africa, well represented in the fire-prone savanna biome and with a striking radiation into the non-fire-prone succulent biome in the Namib Desert. We used RADseq to reconstruct evolutionary relationships within Monechma s.l. and found it to be non-monophyletic and composed of two distinct clades: Group I comprises eight species resolved within the Harnieria clade, whilst Group II comprises 35 species related to the Diclipterinae clade. Our analyses suggest the common ancestors of both clades of Monechma occupied savannas, but both of these radiations (~13 mya crown ages) pre-date the currently accepted origin of the savanna biome in Africa, 5–10 mya. Diversification in the succulent biome of the Namib Desert is dated as beginning only ~1.9 mya. Inflorescence and seed morphology are found to distinguish Groups I and II and related taxa in the Justicioid lineage. Monechma Group II is morphologically diverse, with variation in some traits related to ecological diversification including plant habit. The present work enables future research on these important lineages and provides evidence towards understanding the biogeographical history of continental Africa.
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Loiseau O, Weigand A, Noben S, Rolland J, Silvestro D, Kessler M, Lehnert M, Salamin N. Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae. ANNALS OF BOTANY 2020; 125:93-103. [PMID: 31562744 PMCID: PMC6948215 DOI: 10.1093/aob/mcz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 09/26/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogeneity in their dynamics of diversification. Testing and characterizing the processes driving the evolution of clades with steady rates of diversification over long periods of time are of importance in order to have a full understanding of the build-up of biodiversity through time. METHODS We studied the macroevolutionary history of the species-rich tree fern family Cyatheaceae and inferred a time-calibrated phylogeny of the family including extinct and extant species using the recently developed fossilized birth-death method. We tested whether the high diversity of Cyatheaceae is the result of episodes of rapid diversification associated with phenotypic and ecological differentiation or driven by stable but low rates of diversification. We compared the rates of diversification across clades, modelled the evolution of body size and climatic preferences and tested for trait-dependent diversification. KEY RESULTS This ancient group diversified at a low and constant rate during its long evolutionary history. Morphological and climatic niche evolution were found to be overall highly conserved, although we detected several shifts in the rates of evolution of climatic preferences, linked to changes in elevation. The diversification of the family occurred gradually, within limited phenotypic and ecological boundaries, and yet resulted in a remarkable species richness. CONCLUSIONS Our study indicates that Cyatheaceae is a diverse clade which slowly accumulated morphological, ecological and taxonomic diversity over a long evolutionary period and provides a compelling example of the tropics as a museum of biodiversity.
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Affiliation(s)
- Oriane Loiseau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Weigand
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Sarah Noben
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Zoology, University of British Columbia, #4200-6270 University Blvd, Vancouver, B.C., Canada
| | - Daniele Silvestro
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Global Gothenburg Biodiversity Center, Gothenburg, Sweden
| | - Michael Kessler
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
| | - Marcus Lehnert
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
- Department of Geobotany and Botanical Garden, Herbarium, Martin-Luther-University Halle-Wittenberg, Neuwerk 21, 06108 Halle, Germany
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
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Pérez-Escobar OA, Lucas E, Jaramillo C, Monro A, Morris SK, Bogarín D, Greer D, Dodsworth S, Aguilar-Cano J, Sanchez Meseguer A, Antonelli A. The Origin and Diversification of the Hyperdiverse Flora in the Chocó Biogeographic Region. FRONTIERS IN PLANT SCIENCE 2019; 10:1328. [PMID: 31867022 PMCID: PMC6910151 DOI: 10.3389/fpls.2019.01328] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Extremely high levels of plant diversity in the American tropics are derived from multiple interactions between biotic and abiotic factors. Previous studies have focused on macro-evolutionary dynamics of the Tropical Andes, Amazonia, and Brazil's Cerrado and Atlantic forests during the last decade. Yet, other equally important Neotropical biodiversity hotspots have been severely neglected. This is particularly true for the Chocó region on the north-western coast of South and Central America. This geologically complex region is Earth's ninth most biodiverse hotspot, hosting approximately 3% of all known plant species. Here, we test Gentry's [1982a,b] hypothesis of a northern Andean-Central American Pleistocene origin of the Chocoan flora using phylogenetic reconstructions of representative plant lineages in the American tropics. We show that plant diversity in the Chocó is derived mostly from Andean immigrants. Contributions from more distant biogeographical areas also exist but are fewer. We also identify a strong floristic connection between the Chocó and Central America, revealed by multiple migrations into the Chocó during the last 5 Ma. The dated phylogenetic reconstructions suggest a Plio-Pleistocene onset of the extant Chocó flora. Taken together, these results support to a limited extend Gentry's hypothesis of a Pleistocene origin and of a compound assembly of the Chocoan biodiversity hotspot. Strong Central American-Chocoan floristic affinity may be partly explained by the accretion of a land mass derived from the Caribbean plate to north-western South America. Additional densely sampled phylogenies of Chocoan lineages also well represented across the Neotropics could enlighten the role of land mass movements through time in the assembly of floras in Neotropical biodiversity hotspots.
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Affiliation(s)
- Oscar Alejandro Pérez-Escobar
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Eve Lucas
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Panama, Panama
- ISEM, U. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Alexandre Monro
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Sarah K. Morris
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Diego Bogarín
- Universidad de Costa Rica, Jardín Botánico Lankester, Cartago, Costa Rica
| | - Deborah Greer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Department of Environment, Food and Rural Affairs, London, United Kingdom
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
| | | | | | - Alexandre Antonelli
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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Dick CW, Pennington RT. History and Geography of Neotropical Tree Diversity. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110617-062314] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.
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Affiliation(s)
- Christopher W. Dick
- Department of Ecology and Evolutionary Biology and Herbarium, University of Michigan, Ann Arbor, Michigan 48109, USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Exeter EX4 4QE, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
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Gamisch A, Comes HP. Clade-age-dependent diversification under high species turnover shapes species richness disparities among tropical rainforest lineages of Bulbophyllum (Orchidaceae). BMC Evol Biol 2019; 19:93. [PMID: 31014234 PMCID: PMC6480529 DOI: 10.1186/s12862-019-1416-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/31/2019] [Indexed: 01/05/2023] Open
Abstract
Background Tropical rainforests (TRFs) harbour almost half of the world’s vascular plant species diversity while covering only about 6–7% of land. However, why species richness varies amongst the Earth’s major TRF regions remains poorly understood. Here we investigate the evolutionary processes shaping continental species richness disparities of the pantropical, epiphytic and mostly TRF-dwelling orchid mega-genus Bulbophyllum (c. 1948 spp. in total) using diversification analyses based on a time-calibrated molecular phylogeny (including c. 45–50% spp. each from Madagascar, Africa, Neotropics, and 8.4% from the Asia-Pacific region), coupled with ecological niche modelling (ENM) of geographic distributions under present and past (Last Glacial Maximum; LGM) conditions. Results Our results suggest an early-to-late Miocene scenario of ‘out-of-Asia-Pacific’ origin and progressive, dispersal-mediated diversification in Madagascar, Africa and the Neotropics, respectively. Species richness disparities amongst these four TRF lineages are best explained by a time-for-speciation (i.e. clade age) effect rather than differences in net diversification or diversity-dependent diversification due to present or past spatial-bioclimatic limits. For each well-sampled lineage (Madagascar, Africa, Neotropics), we inferred high rates of speciation and extinction over time (i.e. high species turnover), yet with the origin of most extant species falling into the Quaternary. In contrast to predictions of classical ‘glacial refuge’ theories, all four lineages experienced dramatic range expansions during the LGM. Conclusions As the Madagascan, African and Neotropical lineages display constant-rate evolution since their origin (early-to-mid-Miocene), Quaternary environmental change might be a less important cause of their high species turnover than intrinsic features generally conferring rapid population turnover in tropical orchids (e.g., epiphytism, specialization on pollinators and mycorrhizal fungi, wind dispersal). Nonetheless, climate-induced range fluctuations during the Quaternary could still have played an influential role in the origination and extinction of Bulbophyllum species in those three, if not in all four TRF regions. Electronic supplementary material The online version of this article (10.1186/s12862-019-1416-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Gamisch
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
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Mucina L. Biome: evolution of a crucial ecological and biogeographical concept. THE NEW PHYTOLOGIST 2019; 222:97-114. [PMID: 30481367 PMCID: PMC6590505 DOI: 10.1111/nph.15609] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/09/2018] [Indexed: 05/03/2023]
Abstract
A biome is a key community ecological and biogeographical concept and, as such, has profited from the overall progress of community ecology, punctuated by two major innovations: shifting the focus from pure pattern description to understanding functionality, and changing the approach from observational to explanatory and, most importantly, from descriptive to predictive. The functional focus enabled development of mechanistic and function-focused predictive and retrodictive modelling; it also shaped the current understanding of the concept of a biome as a dynamic biological entity having many aspects, with deep roots in the evolutionary past, and which is undergoing change. The evolution of the biome concept was punctuated by three synthetic steps: the first synthesis formulated a solid body of theory explaining the ecological and biogeographical meaning of zonality and collated our knowledge on drivers of vegetation patterns at large spatial scales; the second translated this knowledge into effective mechanistic modelling tools, developing further the link between ecosystem functionality and biogeography; and the third (still in progress) is seeking common ground between large-scale ecological and biogeographic phenomena, using macroecology and macroevolutionary research tools.
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Affiliation(s)
- Ladislav Mucina
- Iluka Chair in Vegetation Science and BiogeographySchool of Biological SciencesThe University of Western Australia35 Stirling Hwy, CrawleyPerthWA6009Australia
- Department of Geography & Environmental StudiesStellenbosch UniversityPrivate Bag X1, MatielandStellenbosch7602South Africa
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Different degrees of water-related stress affect evolutionary diversity in a seasonally dry biome. Oecologia 2019; 189:795-802. [PMID: 30798355 DOI: 10.1007/s00442-019-04358-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/13/2019] [Indexed: 10/27/2022]
Abstract
Environmental gradients play a key role in shaping diversity in tropical forests. However, we have a little understanding of how evolutionary diversity is affected by gradients and the role of niche persistence in flooded forests in dry biomes. Here, we assessed the evolutionary diversity across a flooding gradient in the Caatinga Domain of South America. We established 120 plots across four tributaries of the São Francisco River, eastern Brazil, consisting of 72 plots in flooded, 24 in occasionally flooded, and 24 in unflooded forests. We computed richness, phylogenetic diversity (PD), mean nearest taxon distance (MNTD), and mean pairwise phylogenetic distance (MPD) and their standardized effect sizes (ses.PD, ses.MNTD, and ses.MPD). We found low richness, low PD, and high MNTD values in flooded forests relative to unflooded and occasionally flooded forests. MPD did not differ across the flooding gradient. The standardized effect size metrics were higher in flooded forests. Despite the unflooded and occasionally flooded forests being rich in terms of species and correlated phylogenetic structure, flooded forests showed more lineage diversity than expected by chance. We assessed whether this pattern could be driven by resprouting ability testing its phylogenetic signal. Resprouting is randomly distributed across phylogeny, but plant communities are likely assembled from random draws of the resprouters' lineage pool. Quantifying evolutionary diversity across flooding gradients in dry environments brought new insights to how the same environmental filters may lead to disparate patterns of evolutionary diversity and the role of response traits in allowing certain clades to persist in flooded habitats.
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Pichardo-Marcano FJ, Nieto-Blázquez ME, MacDonald AN, Galeano G, Roncal J. Phylogeny, historical biogeography and diversification rates in an economically important group of Neotropical palms: Tribe Euterpeae. Mol Phylogenet Evol 2018; 133:67-81. [PMID: 30594734 DOI: 10.1016/j.ympev.2018.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 01/23/2023]
Abstract
Tribe Euterpeae is an economically and ecologically important group of Neotropical palms (Arecaceae). Some species are hyperdominant in the Neotropics, and many constitute a good source of revenue. To reconstruct the biogeographical history and diversification of the Euterpeae, we inferred a robust dated molecular phylogenetic hypothesis including 82% of the species sequenced for five DNA regions (trnD-trnT, CISP4, WRKY6, RPB2, and PHYB). Ancestral range was estimated using all models available in BioGeoBEARS and Binary State Speciation and Extinction analysis was used to evaluate the association of biome and inflorescence type with diversification rates. All intergeneric relationships were resolved providing insight on the taxonomic controversy of Jessenia, Euterpe and Prestoea. Three widely distributed Neotropical species were non-monophyletic, inviting a revision of species circumscriptions. The Euterpeae started its diversification in the mid Eocene (40 Mya), with most species-level divergence events occurring in the last 10 million years. Four colonization events from Central to South America were inferred. Different diversification rates were associated with biomes. Lowland rainforest was inferred as the ancestral biome of Euterpeae, attesting to the importance of lowland adapted lineages on the assembly of the montane flora. The two-fold higher speciation rate for montane taxa (compared with lowland rainforest taxa) was contemporaneous to the Andean orogenic uplift. The specialized beetle pollination of Oenocarpus with its hippuriform (horsetail shape) inflorescence was not associated with diversification rates in Euterpeae.
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Affiliation(s)
- Fritz José Pichardo-Marcano
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
| | - María Esther Nieto-Blázquez
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
| | - Ashley Nicolle MacDonald
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
| | - Gloria Galeano
- Universidad Nacional de Colombia, Instituto de Ciencias Naturales, Apartado 7495, Bogotá, Colombia
| | - Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada.
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Wu SD, Zhang LJ, Lin L, Yu SX, Chen ZD, Wang W. Insights into the historical assembly of global dryland floras: the diversification of Zygophyllaceae. BMC Evol Biol 2018; 18:166. [PMID: 30413147 PMCID: PMC6234786 DOI: 10.1186/s12862-018-1277-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 10/18/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Drylands cover nearly 41% of Earth's land surface and face a high risk of degradation worldwide. However, the actual timeframe during which dryland floras rose on a global scale remains unknown. Zygophyllaceae, an important characteristic component of dryland floras worldwide, offers an ideal model group to investigate the diversification of dryland floras. Here, we used an integration of the phylogenetic, molecular dating, biogeographic, and diversification methods to investigate the timing and patterns of lineage accumulation for Zygophyllaceae overall and regionally. We then incorporated the data from other dominant components of dryland floras in different continents to investigate the historical construction of dryland floras on a global scale. RESULTS We provide the most comprehensive phylogenetic tree for Zygophyllaceae so far based on four plastid and nuclear markers. Detailed analyses indicate that Zygophyllaceae colonized Africa, Asia, Australia, and the New World at different periods, sometimes multiple times, but Zygophyllaceae lineages in the four regions all experienced a rapid accumulation beginning at the mid-late Miocene (~ 15-10 Ma). Other eleven essential elements of dryland floras become differentiated at the same time. CONCLUSIONS Our results suggest that the rise of global dryland floras is near-synchronous and began at the mid-late Miocene, possibly resulting from the mid-Miocene global cooling and regional orogenetic and climate changes. The mid-late Miocene is an essential period for the assembly and evolution of global dryland floras.
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Affiliation(s)
- Sheng-Dan Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
- College of Life Sciences, Shanxi Normal University, 1 Gongyuan, Yaodu, Linfen, 041000 China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049 China
| | - Lin-Jing Zhang
- College of Life Sciences, Shanxi Normal University, 1 Gongyuan, Yaodu, Linfen, 041000 China
| | - Li Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Sheng-Xiang Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049 China
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Gerhold P, Carlucci MB, Procheş Ş, Prinzing A. The Deep Past Controls the Phylogenetic Structure of Present, Local Communities. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062348] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coexisting species may be evolutionarily proximate or distant, resulting in phylogenetically poor or rich communities. This variation is often considered to result from present assembly processes. We argue that, under certain conditions, deep-past processes might control the phylogenetic diversity of communities. First, deep-past effects involve macroevolutionary processes, such as diversification rate, niche conservatism, or dispersal, in the lineages that constitute communities. Second, deep-past processes in the respective region or in the habitat type play a role, for instance, through age, area, stability, or connectivity. Third, the deep past may affect communities via trophic interactions (i.e., communities of enemies or mutualists or communities of hosts). We suggest that deep-past effects can be identified in local communities by measuring phylogenetic diversity in different species pools. We also show how community phylogenetic diversity results in positive or negative eco-evolutionary feedback, and we identify present-day conservation challenges that may profit from a deep-time perspective.
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Affiliation(s)
- Pille Gerhold
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 51014, Estonia
| | - Marcos B. Carlucci
- Department of Botany, Federal University of Paraná, Curitiba, PR 81531–980, Brazil
| | - Şerban Procheş
- Discipline of Geography, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Andreas Prinzing
- Research Unit “Ecosystèmes Biodiversité, Evolution,” University of Rennes 1, CNRS UMR 6553 “Ecobio,” Rennes 35042, France
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Abstract
Amazonia is not only the world’s most diverse rainforest but is also the region in tropical America that has contributed most to its total biodiversity. We show this by estimating and comparing the evolutionary history of a large number of animal and plant species. We find that there has been extensive interchange of evolutionary lineages among different regions and biomes, over the course of tens of millions of years. Amazonia stands out as the primary source of diversity, which can be mainly explained by the total amount of time Amazonian lineages have occupied the region. The exceedingly rich and heterogeneous diversity of the American tropics could only be achieved by high rates of dispersal events across the continent. The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing >2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (∼1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for >60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas.
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A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica. Mol Phylogenet Evol 2018; 122:80-94. [PMID: 29407482 DOI: 10.1016/j.ympev.2018.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/27/2018] [Accepted: 01/27/2018] [Indexed: 01/20/2023]
Abstract
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.
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Hipp AL, Manos PS, González-Rodríguez A, Hahn M, Kaproth M, McVay JD, Avalos SV, Cavender-Bares J. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. THE NEW PHYTOLOGIST 2018; 217:439-452. [PMID: 28921530 DOI: 10.1111/nph.14773] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/29/2017] [Indexed: 05/21/2023]
Abstract
Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.
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Affiliation(s)
- Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
| | | | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Col. Ex Hacienda de Sán José de la Huerta, Morelia, Michoacán, 58190, México
| | - Marlene Hahn
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
| | - Matthew Kaproth
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Biological Sciences, Minnesota State University, Mankato, MN 56001, USA
| | | | - Susana Valencia Avalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán, CP, 04510, México City, México
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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Pérez‐Escobar OA, Chomicki G, Condamine FL, Karremans AP, Bogarín D, Matzke NJ, Silvestro D, Antonelli A. Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot. THE NEW PHYTOLOGIST 2017; 215:891-905. [PMID: 28631324 PMCID: PMC5575461 DOI: 10.1111/nph.14629] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/07/2017] [Indexed: 05/07/2023]
Abstract
The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with c. 15% of the world's plant species, in only 1% of the world's land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification. We address this knowledge gap by inferring the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely sampled orchid phylogenies (including more than 400 newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets. We find that the majority of Andean orchid lineages only originated in the last 20-15 million yr. Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales. Our study sheds new light on the timing and geography of a major Neotropical diversification, and suggests that mountain uplift promotes species diversification across all elevational zones.
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Affiliation(s)
| | - Guillaume Chomicki
- Systematic Botany and MycologyUniversity of Munich (LMU)67 Menzinger Str.Munich80638Germany
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier)Place Eugène Bataillon34095MontpellierFrance
| | - Adam P. Karremans
- Lankester Botanical GardenUniversity of Costa RicaPO Box 302‐7050CartagoCosta Rica
- Naturalis Biodiversity CenterLeiden2333 CRthe Netherlands
| | - Diego Bogarín
- Lankester Botanical GardenUniversity of Costa RicaPO Box 302‐7050CartagoCosta Rica
- Naturalis Biodiversity CenterLeiden2333 CRthe Netherlands
| | - Nicholas J. Matzke
- Division of Ecology, Evolution, and GeneticsResearch School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Daniele Silvestro
- Department of Biological and Environmental SciencesUniversity of Gothenburg413 19GothenburgSweden
- Department of Computational Biology, BiophoreUniversity of Lausanne1015LausanneSwitzerland
- Gothenburg Global Biodiversity CentreBox 461SE‐405 30GöteborgSweden
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of Gothenburg413 19GothenburgSweden
- Gothenburg Global Biodiversity CentreBox 461SE‐405 30GöteborgSweden
- Gothenburg Botanical GardenCarl Skottsbergs gata 22A41319GothenburgSweden
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