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Albreht L, Bourland N, Klitgård B, Schley R, Janssens SB, Hardy OJ. Species delimitation and phylogenomics of economically important African Pterocarpus trees, with an implication for the development of DNA-based species identification tools. Mol Phylogenet Evol 2025; 204:108277. [PMID: 39701438 DOI: 10.1016/j.ympev.2024.108277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 12/07/2024] [Accepted: 12/15/2024] [Indexed: 12/21/2024]
Abstract
Reliable species delimitation is fundamental for establishing clear and equitable guidelines on the sustainable harvest of economically important organisms. Pterocarpus (Fabaceae) is a pantropical tree genus including several highly valuable timber-producing species, that face significant threats from intensive logging. However, a lack of taxonomic clarity has hindered the advance of logging regulations and has led to the inclusion of all African Pterocarpus populations under CITES regulations (CoP19). In our study, we addressed this issue by reassessing species delimitation of all twelve accepted African Pterocarpus species, including neotropical samples of the two trans-Atlantic species. Based on DNA sequences obtained by the Angiosperms353 probe set, we reconstructed a comprehensive phylogeny applying maximum likelihood and multispecies coalescent approaches. Additionally, we explored the potential of high-copy DNA for identifying African Pterocarpus species. This involved reconstructing chloroplast and ribosomal DNA phylogenies, using genome skimming and maximum likelihood approaches. Our results confirmed the monophyly of eleven Pterocarpus species and a paraphyletic P. rotundifolius, which presented geographically coherent subclades, suggesting the possibility of cryptic diversity within the complex. A similar situation arose in P. lucens, exhibiting two sister clades with disjunct distributions. Species delimitation based on high-copy DNA was congruent with the Angiosperms353 data for most species, indicating the reliability of chloroplast and ribosomal DNA markers for Pterocarpus species identification. Our findings give valuable insights into African Pterocarpus species delimitation, highlighting the need for further investigation of potential cryptic diversity within a clade including P. rotundifolius, P. brenanii and P. lucens. Finally, our study lays the groundwork for developing DNA-based tools aimed at improving logging regulations for African Pterocarpus species.
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Affiliation(s)
- Laura Albreht
- Université Libre de Bruxelles, Unit of Evolutionary Biology and Ecology CP160/12, Avenue Franklin Roosevelt 50, Brussels, B-1050, Belgium.
| | - Nils Bourland
- Royal Museum for Central Africa, Service of Wood Biology, Leuvensesteenweg 13, Tervuren, B-3080, Belgium
| | - Bente Klitgård
- Royal Botanic Gardens, Accelerated Taxonomy Department, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Rowan Schley
- University of Exeter, Department of Geography, Laver Building, North Park Road, Exeter, Devon, EX4 4QE, UK
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, Meise, 1860, Belgium; Leuven Plant Institute, Department of Biology, KU Leuven, Leuven, 3001, Belgium
| | - Olivier J Hardy
- Université Libre de Bruxelles, Unit of Evolutionary Biology and Ecology CP160/12, Avenue Franklin Roosevelt 50, Brussels, B-1050, Belgium
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2
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Nicholls JA, Ringelberg JJ, Dexter KG, Loiseau O, Stone GN, Coley PD, Hughes CE, Kursar TA, Koenen EJM, Garcia F, Lemes MR, Neves DRM, Endara MJ, de Lima HC, Kidner CA, Pennington RT. Continuous colonization of the Atlantic coastal rain forests of South America from Amazônia. Proc Biol Sci 2025; 292:20241559. [PMID: 39837505 PMCID: PMC11750371 DOI: 10.1098/rspb.2024.1559] [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: 06/29/2024] [Revised: 11/14/2024] [Accepted: 12/06/2024] [Indexed: 01/23/2025] Open
Abstract
The two main extensions of rain forest in South America are the Amazon (Amazônia) and the Atlantic rain forest (Mata Atlântica), which are separated by a wide 'dry diagonal' of seasonal vegetation. We used the species-rich tree genus Inga to test if Amazônia-Mata Atlântica dispersals have been clustered during specific time periods corresponding to past, humid climates. We performed hybrid capture DNA sequencing of 810 nuclear loci for 453 accessions representing 164 species that included 62% of Mata Atlântica species and estimated a dated phylogeny for all accessions using maximum likelihood, and a species-level tree using coalescent methods. There have been 16-20 dispersal events to the Mata Atlântica from Amazônia with only one or two dispersals in the reverse direction. These events have occurred over the evolutionary history of Inga, with no evidence for temporal clustering, and model comparisons of alternative biogeographic histories and null simulations showing the timing of dispersal events matches a random expectation. Time-specific biogeographic corridors are not required to explain dispersal between Amazônia and the Mata Atlântica for rain forest trees such as Inga, which are likely to have used a dendritic net of gallery forests to cross the dry diagonal.
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Affiliation(s)
- James A. Nicholls
- Institute of Evolutionary Biology, University of Edinburgh, EdinburghEH9 3FL, UK
- Royal Botanic Garden Edinburgh, EdinburghEH3 5LR, UK
- Australian National Insect Collection, CSIRO, CanberraACT 2601, Australia
| | - Jens J. Ringelberg
- School of Geosciences, University of Edinburgh, EdinburghEH9 3FF, UK
- Department of Systematic and Evolutionary Botany, University of Zurich, ZurichCH-8008, Switzerland
| | - Kyle G. Dexter
- Royal Botanic Garden Edinburgh, EdinburghEH3 5LR, UK
- School of Geosciences, University of Edinburgh, EdinburghEH9 3FF, UK
- Department of Life Sciences and Systems Biology, University of Turin, Torino10124, Italy
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, EdinburghEH9 3FF, UK
| | - Graham N. Stone
- Institute of Evolutionary Biology, University of Edinburgh, EdinburghEH9 3FL, UK
| | - Phyllis D. Coley
- Department of Biology, University of Utah, Salt Lake City,UT 84112-0840, USA
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, ZurichCH-8008, Switzerland
| | - Thomas A. Kursar
- Department of Biology, University of Utah, Salt Lake City,UT 84112-0840, USA
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, ZurichCH-8008, Switzerland
| | - Flávia Garcia
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG36570-900, Brazil
| | - Maristerra R. Lemes
- Laboratório de Genética e Biologia Reprodutiva de Plantas,Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazonia, Manaus, AM69067-375, Brazil
| | - Danilo R. M. Neves
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte31270-901, Brazil
| | - María José Endara
- Grupo de Investigación en Ecología y Evolución en los Trópicos- EETROP, Universidad de las Américas, Quito170513, Ecuador
| | | | - Catherine A. Kidner
- Royal Botanic Garden Edinburgh, EdinburghEH3 5LR, UK
- Institute of Molecular Plant Sciences, University of Edinburgh, EdinburghEH9 3BF, UK
| | - R. Toby Pennington
- Royal Botanic Garden Edinburgh, EdinburghEH3 5LR, UK
- Department of Geography, University of Exeter, ExeterEX4 4QE, UK
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3
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São-Mateus WMB, Fernandes MF, Queiroz LPD, Meireles JE, Jardim JG, Delgado-Salinas A, Dorado Ó, Lima HCD, Rodríguez RR, González Gutiérrez PA, Lewis GP, Wojciechowski MF, Cardoso D. Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas. Mol Phylogenet Evol 2024; 194:108031. [PMID: 38360081 DOI: 10.1016/j.ympev.2024.108031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood. Comprising 35 species, Harpalyce is one of these poorly studied genera. In this study, we present a comprehensive, multi-locus molecular phylogeny of the Brongniartieae, with an increased sampling of Harpalyce, to investigate morphological and biogeographical evolution within the group. Our results confirm the monophyly of Harpalyce and indicate that peltate glandular trichomes and a strongly bilabiate calyx with a carinal lip and three fused lobes are synapomorphies for the genus, which is internally divided into three distinct ecologically and geographically divergent lineages, corresponding to the previously recognized sections. Our biogeographical reconstructions demonstrate that Brongniartieae originated in South America during the Eocene, with subsequent pulses of diversification in South America, Mesoamerica, and Australia. Harpalyce also originated in South America during the Miocene at around 20 Ma, with almost synchronous later diversification in South America and Mexico/Mesoamerica beginning 10 Ma, but mostly during the Pliocene. Migration of Harpalyce from South to North America was accompanied by a biome and ecological shift from savanna to seasonally dry forest.
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Affiliation(s)
- Wallace M B São-Mateus
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59072-970, Natal, Rio Grande do Norte, Brazil.
| | - Moabe Ferreira Fernandes
- Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil; Department of Geography, University of Exeter, Exeter, UK; Royal Botanic Gardens, Kew, Richmond TW93AE, UK
| | - Luciano Paganucci de Queiroz
- Universidade Estadual de Feira de Santana (HUEFS), Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
| | - José Eduardo Meireles
- School of Biology and Ecology, University of Maine, 5735 Hitchner Hall, 04469 Orono, ME, USA
| | - Jomar Gomes Jardim
- Universidade Federal do Sul da Bahia, Centro de Formação em Ciências Agroflorestais, Campus Jorge Amado, 45613-204 Itabuna, Bahia, Brazil; Herbário Centro de Pesquisas do Cacau - CEPEC, Km 29, Rod. Ilhéus-Itabuna, 45603-811 Itabuna, Bahia, Brazil
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-233, 04510 Coyoacán, Cd. México, Mexico
| | - Óscar Dorado
- Centro de Educación Ambiental e Investigación Sierra de Huautla, Universidad Autónoma del Estado de Morelos, Mexico
| | - Haroldo Cavalcante de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915 22460-030 Rio de Janeiro, Brazil
| | - Rosa Rankin Rodríguez
- Jardín Botánico Nacional, Universidad de la Habana, Carretera "El Rocío", km 3.5, Calabazar C.P. 19230, Boyeros, La Habana, Cuba
| | - Pedro Alejandro González Gutiérrez
- Centro de Investigaciones y Servicios Ambientales de Holguín (CISAT), CITMA, Calle 18 sn, entre 1ª y Maceo, Reparto "El Llano", Holguín 80 100, Cuba
| | | | | | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil; Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915 22460-030 Rio de Janeiro, Brazil.
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4
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Tian Q, Stull GW, Kellermann J, Medan D, Nge FJ, Liu SY, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Folk RA, Onstein RE, Yi TS. Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales. THE NEW PHYTOLOGIST 2024; 241:1851-1865. [PMID: 38229185 DOI: 10.1111/nph.19504] [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: 08/27/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.
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Affiliation(s)
- Qin Tian
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jürgen Kellermann
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Diego Medan
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Ave San Martín 4453, C1417DSE, Buenos Aires, Argentina
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Hackney Road, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
- IRD - Institut de Recherche pour le Développement, Ave Agropolis BP 64501, Montpellier, 34394, France
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
| | - Heather R Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi, MS, 39762, USA
| | - Renske E Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands
- Evolution and Adaptation, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
- Leipzig University, Leipzig, 04013, Germany
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Plant Diversity and Specialty Crops, Chinese Academy of Sciences, Beijing, 100093, China
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5
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Dagallier LPMJ, Mbago FM, Couderc M, Gaudeul M, Grall A, Loup C, Wieringa JJ, Sonké B, Couvreur TLP. Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis. PHYTOKEYS 2023; 233:1-200. [PMID: 37811332 PMCID: PMC10552675 DOI: 10.3897/phytokeys.233.103096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
Monodoreae (Annonaceae) is a tribe composed of 11 genera and 90 species restricted to the tropical African rain forests. All the genera are taxonomically well circumscribed except the species rich genera Uvariodendron and Uvariopsis which lack a recent taxonomic revision. Here, we used a robust phylogenomic approach, including all the 90 currently accepted species, with several specimens per species, and based on more than 300 Annonaceae-specific nuclear genes, to infer the phylogenetic tree of the Monodoreae and test the limits between the genera and species. We recover all the genera as monophyletic, except the genus Uvariopsis for which the species Uvariopsistripetala falls outside this clade. We thus reinstate the monotypic genus Dennettia for its single species Dennettiatripetala. We also erect a new tribe, Ophrypetaleae trib. nov., to accommodate the genera Ophrypetalum and Sanrafaelia, as we recover them excluded from the Monodoreae tribe with good support. Below the genus level, the genera Isolona, Monodora, Uvariastrum, Uvariodendron and Uvariopsis show weakly supported nodes and phylogenetic conflicts, suggesting that population level processes of evolution might occur in these clades. Our results also support, at the molecular level, the description of several new species of Uvariodendron and Uvariopsis, as well as several new synonymies. Finally, we present a taxonomic revision of the genera Dennettia, Uvariodendron and Uvariopsis, which contain one, 18 and 17 species respectively. We provide a key to the 11 genera of the Monodoraeae and describe four new species to science: Uvariodendronkimbozaense Dagallier & Couvreur, sp. nov., Uvariodendronmossambicense Robson ex Dagallier & Couvreur, sp. nov., Uvariodendronpilosicarpum Dagallier & Couvreur, sp. nov. and Uvariopsisoligocarpa Dagallier & Couvreur, sp. nov., and provide provisional descriptions of three putatively new species. We also present lectotypifications and nomenclatural changes implying synonymies and new combinations (Uvariodendroncitriodorum (Le Thomas) Dagallier & Couvreur, comb. et stat. nov., Uvariodendronfuscumvar.magnificum (Verdc.) Dagallier & Couvreur, comb. et stat. nov., Uvariopsiscongensisvar.angustifolia Dagallier & Couvreur, var. nov., Uvariopsisguineensisvar.globiflora (Keay) Dagallier & Couvreur, comb. et stat. nov., and Uvariopsissolheidiivar.letestui (Pellegr.) Dagallier & Couvreur, comb. et stat. nov.).
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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, New York 10458, USA
| | - Frank M. Mbago
- The Herbarium, Botany Department, Box 35060, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Marie Couderc
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Aurélie Grall
- Herbaria Basel, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Caroline Loup
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jan J. Wieringa
- Herbier MPU, DCSPH – CC 99010, Université de Montpellier, 163 rue A. Broussonnet, F-34090 Montpellier, France
| | - Bonaventure Sonké
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, Netherlands
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6
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Lopes A, Demarchi LO, Piedade MTF, Schöngart J, Wittmann F, Munhoz CBR, Ferreira CS, Franco AC. Predicting the range expansion of invasive alien grasses under climate change in the Neotropics. Perspect Ecol Conserv 2023. [DOI: 10.1016/j.pecon.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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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: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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Yan M, Mao F, Du H, Li X, Chen Q, Ni C, Huang Z, Xu Y, Gong Y, Guo K, Sun J, Xu C. Spatiotemporal dynamic of subtropical forest carbon storage and its resistance and resilience to drought in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1067552. [PMID: 36733716 PMCID: PMC9886887 DOI: 10.3389/fpls.2023.1067552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Subtropical forests are rich in vegetation and have high photosynthetic capacity. China is an important area for the distribution of subtropical forests, evergreen broadleaf forests (EBFs) and evergreen needleleaf forests (ENFs) are two typical vegetation types in subtropical China. Forest carbon storage is an important indicator for measuring the basic characteristics of forest ecosystems and is of great significance for maintaining the global carbon balance. Drought can affect forest activity and may even lead to forest death and the stability characteristics of different forest ecosystems varied after drought events. Therefore, this study used meteorological data to simulate the standardized precipitation evapotranspiration index (SPEI) and the Biome-BGC model to simulate two types of forest carbon storage to quantify the resistance and resilience of EBF and ENF to drought in the subtropical region of China. The results show that: 1) from 1952 to 2019, the interannual drought in subtropical China showed an increasing trend, with five extreme droughts recorded, of which 2011 was the most severe one; 2) the simulated average carbon storage of the EBF and ENF during 1985-2019 were 130.58 t·hm-2 and 78.49 t·hm-2, respectively. The regions with higher carbon storage of EBF were mainly concentrated in central and southeastern subtropics, where those of ENF mainly distributed in the western subtropic; 3) The median of resistance of EBF was three times higher than that of ENF, indicating the EBF have stronger resistance to extreme drought than ENF. Moreover, the resilience of two typical forest to 2011 extreme drought and the continuous drought events during 2009 - 2011 were similar. The results provided a scientific basis for the response of subtropical forests to drought, and indicating that improve stand quality or expand the plantation of EBF may enhance the resistance to drought in subtropical China, which provided certain reference for forest protection and management under the increasing frequency of drought events in the future.
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Affiliation(s)
- Mengjie Yan
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Fangjie Mao
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Huaqiang Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Xuejian Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Qi Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Chi Ni
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Zihao Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Yanxin Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Yulin Gong
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Keruo Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Jiaqian Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
| | - Cenheng Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural & Forestry (A & F) University, Hangzhou, China
- Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration of Zhejiang Province, Zhejiang A & F University, Hangzhou, China
- School of Environmental and Resources Science, Zhejiang A & F University, Hangzhou, China
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9
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Dunning LT, Olofsson JK, Papadopulos AST, Hibdige SGS, Hidalgo O, Leitch IJ, Baleeiro PC, Ntshangase S, Barker N, Jobson RW. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Mol Ecol 2022; 31:5846-5860. [PMID: 36089907 PMCID: PMC9828686 DOI: 10.1111/mec.16691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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Affiliation(s)
- Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Jill K. Olofsson
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Samuel G. S. Hibdige
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Oriane Hidalgo
- Royal Botanic GardensSurreyUK,Institut Botànic de Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelonaSpain
| | | | - Paulo C. Baleeiro
- Department of Biological ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | | | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaHatfieldSouth Africa
| | - Richard W. Jobson
- National Herbarium of New South Wales, Australian Institute of Botanical ScienceSydneyNew South WalesAustralia
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10
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Finch KN, Jones FA, Cronn RC. Cryptic species diversity in a widespread neotropical tree genus: The case of Cedrela odorata. AMERICAN JOURNAL OF BOTANY 2022; 109:1622-1640. [PMID: 36098061 PMCID: PMC9827871 DOI: 10.1002/ajb2.16064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Reconciling the use of taxonomy to partition morphological variation and describe genetic divergence within and among closely related species is a persistent challenge in phylogenetics. We reconstructed phylogenetic relationships among Cedrela odorata (Meliaceae) and five closely allied species to test the genetic basis for the current model of species delimitation in this economically valuable and threatened genus. METHODS We prepared a nuclear species tree with the program SNPhylo and 16,000 single-nucleotide polymorphisms from 168 Cedrela specimens. Based on clades present and ancestral patterns ADMIXTURE, we designed nine species delimitation models and compared each model to current taxonomy with Bayes factor delimitation. Timing of major lineage divergences was estimated with the program SNAPP. RESULTS The resulting analysis revealed that modern C. odorata evolved from two genetically distinct ancestral sources. All species delimitation models tested better fit the data than the model representing current taxonomic delimitation. Models with the greatest marginal likelihoods separated Mesoamerican C. odorata and South American C. odorata into two species and lumped C. angustifolia and C. montana as a single species. We estimated that Cedrela diversified in South America within the last 19 million years following one or more dispersal events from Mesoamerican lineages. CONCLUSIONS Our analyses show that the present taxonomic understanding within the genus obscures divergent lineages in C. odorata due in part to morphological differentiation and taxonomic distinctions that are not predictably associated with genetic divergence. A more accurate application of taxonomy to C. odorata and related species may aid in its conservation, management, and restoration efforts.
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Affiliation(s)
- Kristen N. Finch
- Department of Botany and Plant PathologyOregon State University2082 Cordley Hall, 2701 SW Campus WayCorvallisOR97331USA
| | - F. Andrew Jones
- Department of Botany and Plant PathologyOregon State University2082 Cordley Hall, 2701 SW Campus WayCorvallisOR97331USA
- Smithsonian Tropical Research InstituteBalboa, AnconRepublic of Panama
| | - Richard C. Cronn
- USFS PNW Research Station3200 SW Jefferson WayCorvallisOR97331USA
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11
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Caddah MK, Meirelles J, Nery EK, Lima DF, Nicolas AN, Michelangeli FA, Goldenberg R. Beneath a hairy problem: Phylogeny, morphology, and biogeography circumscribe the new Miconia supersection Discolores (Melastomataceae: Miconieae). Mol Phylogenet Evol 2022; 171:107461. [DOI: 10.1016/j.ympev.2022.107461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
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12
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Cardoso D, Moonlight PW, Ramos G, Oatley G, Dudley C, Gagnon E, Queiroz LPD, Pennington RT, Särkinen TE. Defining Biologically Meaningful Biomes Through Floristic, Functional, and Phylogenetic Data. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.723558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a novel approach to biome delimitation and mapping, based upon combining individual regionalizations derived from floristic, functional, and phylogenetic data linked to environmentally trained species distribution models. We define “core Biomes” as areas where independent regionalizations agree and “transition zones” as those whose biome identity is not corroborated by all analyses. We apply this approach to delimiting the neglected Caatinga seasonally dry tropical forest biome in northeast Brazil. We delimit the “core Caatinga” as a smaller and more climatically limited area than previous definitions, and argue it represents a floristically, functionally, and phylogenetically coherent unit within the driest parts of northeast Brazil. “Caatinga transition zones” represent a large and biologically important area, highlighting that ecological and evolutionary processes work across environmental gradients and that biomes are not categorical variables. We discuss the differences among individual regionalizations in an ecological and evolutionary context and the potential limitations and utility of individual and combined biome delimitations. Our integrated ecological and evolutionary definition of the Caatinga and associated transition zones are argued to best describe and map biologically meaningful biomes.
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13
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Bacon CD, Gutiérrez‐Pinto N, Flantua S, Castellanos Suárez D, Jaramillo C, Pennington RT, Antonelli A. The seasonally dry tropical forest species
Cavanillesia chicamochae
has a middle Quaternary origin. Biotropica 2021. [DOI: 10.1111/btp.13031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christine D. Bacon
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
- Laboratório de Biología Molecular (CINBIN) Department of Biology Universidad Industrial de Santander Bucaramanga Colombia
| | - Natalia Gutiérrez‐Pinto
- Laboratório de Biología Molecular (CINBIN) Department of Biology Universidad Industrial de Santander Bucaramanga Colombia
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln Nebraska USA
| | - Suzette Flantua
- Department of Biological Sciences University of Bergen Bergen Norway
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam the Netherlands
| | - Diego Castellanos Suárez
- Laboratório de Biología Molecular (CINBIN) Department of Biology Universidad Industrial de Santander Bucaramanga Colombia
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute Balboa, Ancon Republic of Panama
- Institut des Sciences de l’Evolution Montpellier University of MontpellierCNRSEPHE Montpellier IRD France
- Department of Geology University of Salamanca Salamanca Spain
| | - R. Toby Pennington
- Royal Botanic Garden Edinburgh Edinburgh UK
- Geography University of Exeter Exeter UK
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
- Royal Botanic Gardens Kew Richmond Surrey UK
- Department of Plant Sciences University of Oxford Oxford UK
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14
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Guevara Andino JE, Pitman NCA, Ter Steege H, Peralvo M, Cerón C, Fine PVA. The contribution of environmental and dispersal filters on phylogenetic and taxonomic beta diversity patterns in Amazonian tree communities. Oecologia 2021; 196:1119-1137. [PMID: 34324078 PMCID: PMC8367926 DOI: 10.1007/s00442-021-04981-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 06/28/2021] [Indexed: 10/28/2022]
Abstract
Environmental and dispersal filters are key determinants of species distributions of Amazonian tree communities. However, a comprehensive analysis of the role of environmental and dispersal filters is needed to understand the ecological and evolutionary processes that drive phylogenetic and taxonomic turnover of Amazonian tree communities. We compare measures of taxonomic and phylogenetic beta diversity in 41 one-hectare plots to test the relative importance of climate, soils, geology, geomorphology, pure spatial variables and the spatial variation of environmental drivers of phylogenetic and taxonomic turnover in Ecuadorian Amazon tree communities. We found low phylogenetic and high taxonomic turnover with respect to environmental and dispersal filters. In addition, our results suggest that climate is a significantly better predictor of phylogenetic turnover and taxonomic turnover than geomorphology and soils at all spatial scales. The influence of climate as a predictor of phylogenetic turnover was stronger at broader spatial scales (50 km2) whereas geomorphology and soils appear to be better predictors of taxonomic turnover at mid (5 km2) and fine spatial scales (0.5 km2) but a weak predictor of phylogenetic turnover at broad spatial scales. We also found that the combined effect of geomorphology and soils was significantly higher for taxonomic turnover at all spatial scales but not for phylogenetic turnover at large spatial scales. Geographic distances as proxy of dispersal limitation was a better predictor of phylogenetic turnover at distances of 50 < 500 km. Our findings suggest that climatic variation at regional scales can better predict phylogenetic and taxonomic turnover than geomorphology and soils.
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Affiliation(s)
- Juan Ernesto Guevara Andino
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud-BIOMAS-Universidad de las Américas, Campus Queri, Quito, Ecuador.
- Keller Science Action Center, The Field Museum, 1400 South Lake Shore Dr., Chicago, IL, 60605-2496, USA.
| | - Nigel C A Pitman
- Keller Science Action Center, The Field Museum, 1400 South Lake Shore Dr., Chicago, IL, 60605-2496, USA
| | - Hans Ter Steege
- Naturalis Biodiversity Center, Vondellaan 55, Postbus 9517, 2300 RA, Leiden, The Netherlands
| | - Manuel Peralvo
- Consortium for the Sustainable Development of the Andean Ecoregion (CONDESAN), Andean Forest Program, German Aleman E12-123 and Carlos Arroyo del Río, Quito, 170504, Ecuador
| | - Carlos Cerón
- Escuela de Biología Herbario Alfredo Paredes, Universidad Central, Quito, Ecuador
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
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15
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Abstract
Drought can weaken forest activity and even lead to forest mortality, and the response of different forest types to drought can be diverse. Deciduous broadleaf forest (DBF) and deciduous needleleaf forest (DNF) are two of the majority forest types in northern China. In this region, a severe drought event happened in 2002. However, due to the lack of data, the spatio-temporal characteristics of the ecosystem stability of different forest types here remain unclear. In this study, we used a machine learning approach (model tree ensemble, MTE) to drive fluxsite gross primary productivity (GPP), combined with remote sensing-based GPP and a vegetation index data (EVI), to analyze the spatial and temporal characteristics of resistance and resilience of DNF and DBF in northern China during and after the 2002 drought. The results showed that the DBFs were more acclimatized to the drought, while the resistance and resilience of DNF and DBF were diverse under different consecutive drought events. These results could be suggestive for forest conservation and vegetation modeling.
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16
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Damasco G, Baraloto C, Vicentini A, Daly DC, Baldwin BG, Fine PVA. Revisiting the hyperdominance of Neotropical tree species under a taxonomic, functional and evolutionary perspective. Sci Rep 2021; 11:9585. [PMID: 33953271 PMCID: PMC8099866 DOI: 10.1038/s41598-021-88417-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/30/2021] [Indexed: 11/29/2022] Open
Abstract
Recent studies have leveraged large datasets from plot-inventory networks to report a phenomenon of hyperdominance in Amazonian tree communities, concluding that few species are common and many are rare. However, taxonomic hypotheses may not be consistent across these large plot networks, potentially masking cryptic diversity and threatened rare taxa. In the current study, we have reviewed one of the most abundant putatively hyperdominant taxa, Protium heptaphyllum (Aubl.) Marchand (Burseraceae), long considered to be a taxonomically difficult species complex. Using morphological, genomic, and functional data, we present evidence that P. heptaphyllum sensu lato may represent eight separately evolving lineages, each warranting species status. Most of these lineages are geographically restricted, and few if any of them could be considered hyperdominant on their own. In addition, functional trait data are consistent with the hypothesis that trees from each lineage are adapted to distinct soil and climate conditions. Moreover, some of the newly discovered species are rare, with habitats currently experiencing rapid deforestation. We highlight an urgent need to improve sampling and methods for species discovery in order to avoid oversimplified assumptions regarding diversity and rarity in the tropics and the implications for ecosystem functioning and conservation.
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Affiliation(s)
- Gabriel Damasco
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA. .,Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil.
| | - Christopher Baraloto
- Institute of Environment, Florida International University, Miami, FL, 33133, USA
| | - Alberto Vicentini
- Programa de Pós-Graduação em Botânica, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, 69080-971, Brazil
| | - Douglas C Daly
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458, USA
| | - Bruce G Baldwin
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
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17
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Schley RJ, Pennington RT, Pérez-Escobar OA, Helmstetter AJ, de la Estrella M, Larridon I, Sabino Kikuchi IAB, Barraclough TG, Forest F, Klitgård B. Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity. Mol Ecol 2020; 29:4170-4185. [PMID: 32881172 DOI: 10.1111/mec.15616] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.
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Affiliation(s)
- Rowan J Schley
- Royal Botanic Gardens, Kew, Richmond, UK.,Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK
| | - R Toby Pennington
- Geography, University of Exeter, Exeter, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Andrew J Helmstetter
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, Montpellier, France
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, UK.,Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L, Gent, Belgium
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK.,Department of Zoology, University of Oxford, Oxford, UK
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18
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Donkpegan ASL, Doucet JL, Hardy OJ, Heuertz M, Piñeiro R. Miocene Diversification in the Savannahs Precedes Tetraploid Rainforest Radiation in the African Tree Genus Afzelia (Detarioideae, Fabaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:798. [PMID: 32625223 PMCID: PMC7313659 DOI: 10.3389/fpls.2020.00798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis, A. pachyloba, and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09-14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 - 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome.
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Affiliation(s)
- Armel S. L. Donkpegan
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- INRAE, BFP, University of Bordeaux, Villenave d’Ornon, France
| | - Jean-Louis Doucet
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Olivier J. Hardy
- Evolutionary Biology and Ecology Unit, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Rosalía Piñeiro
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Evolutionary Genomics, Centre for Geogenetics – Natural History Museum of Denmark, Copenhagen, Denmark
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19
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Predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01282-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Murphy B, Forest F, Barraclough T, Rosindell J, Bellot S, Cowan R, Golos M, Jebb M, Cheek M. A phylogenomic analysis of Nepenthes (Nepenthaceae). Mol Phylogenet Evol 2020; 144:106668. [DOI: 10.1016/j.ympev.2019.106668] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
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21
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Choo LM, Forest F, Wieringa JJ, Bruneau A, de la Estrella M. Phylogeny and biogeography of the Daniellia clade (Leguminosae: Detarioideae), a tropical tree lineage largely threatened in Africa and Madagascar. Mol Phylogenet Evol 2020; 146:106752. [PMID: 32028029 DOI: 10.1016/j.ympev.2020.106752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 11/28/2022]
Abstract
The legume subfamily Detarioideae is exceptionally diverse in tropical Africa and Madagascar, compared to South America or Asia, a trend contrary to that shown by most other pantropical plant groups. We aim to elucidate the process of diversification giving rise to these high diversity levels by focussing our investigations on the Daniellia clade, which is present in both Africa and Madagascar. The Daniellia clade is an early-diverging lineage of subfamily Detarioideae (Leguminosae; pea family) and consists of three genera: Daniellia, Brandzeia and Neoapaloxylon. The species belonging to this group exhibit a wide range of habitat types. The Madagascar endemics Brandzeia (1 species) and Neoapaloxylon (3 species) occupy dry woodlands and arid succulent habitats respectively. Daniellia alsteeniana and D. oliveri are found in savannahs while the remaining eight species within Daniellia all occupy rainforest habitats. Phylogenetic analyses were generated from a dense, multi-individual species level sampling of the clade. Divergence time estimates were carried out using a molecular clock method to investigate biogeographical patterns and shifts in habitat types within the Daniellia clade, and conservation assessments were conducted to determine the levels of extinction risks these species are facing. We estimate that the Daniellia clade first emerged during the Early Eocene from an ancestor present in the rainforests of North Africa at that time, reflecting an ancestral habitat preference. There was a first major split over the course of the Eocene, giving rise to both African rainforest and Madagascan savannah lineages. With the emergence of a drier climate and vegetation type in Africa during the Eocene, it is likely that a dry-climate adapted lineage from the Daniellia clade ancestor could have dispersed through suitable savannah or woodland regions to reach Madagascar, subsequently giving rise to the savannah-adapted ancestor of Brandzeia and Neoapaloxylon in the Early Miocene. The African rainforest lineage gave rise to the genus Daniellia, which is postulated to have first diversified in the Middle Miocene, while savannah species of Daniellia emerged independently during the Pliocene, coinciding with the global rise of C4-dominated grasslands. More than half of the species in the Daniellia clade are near threatened or threatened, which highlights the need to understand the threats of anthropogenic pressures and climate change these species are facing to prioritise their conservation.
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Affiliation(s)
- Le Min Choo
- Herbarium, Research & Conservation Branch, Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569 Singapore; Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of the Netherlands, Darwinweg 2, 2333 CR Leiden, the Netherlands
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Manuel de la Estrella
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
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22
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Rossetti DF, Moulatlet GM, Tuomisto H, Gribel R, Toledo PM, Valeriano MM, Ruokolainen K, Cohen MCL, Cordeiro CLO, Rennó CD, Coelho LS, Ferreira CAC. White sand vegetation in an Amazonian lowland under the perspective of a young geological history. AN ACAD BRAS CIENC 2019; 91:e20181337. [PMID: 31800703 DOI: 10.1590/0001-3765201920181337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/22/2019] [Indexed: 11/21/2022] Open
Abstract
What controls the formation of patchy substrates of white sand vegetation in the Amazonian lowlands is still unclear. This research integrated the geological history and plant inventories of a white sand vegetation patch confined to one large fan-shaped sandy substrate of northern Amazonia, which is related to a megafan environment. We examined floristic patterns to determine whether abundant species are more often generalists than the rarer one, by comparing the megafan environments and older basement rocks. We also investigated the pattern of species accumulation as a function of increasing sampling effort. All plant groups recorded a high proportion of generalist species on the megafan sediments compared to older basement rocks. The vegetation structure is controlled by topographic gradients resulting from the smooth slope of the megafan morphology and microreliefs imposed by various megafan subenvironments. Late Pleistocene-Holocene environmental disturbances caused by megafan sedimentary processes controlled the distribution of white sand vegetation over a large area of the Amazonian lowlands, and may have also been an important factor in species diversification during this period. The integration of geological and biological data may shed new light on the existence of many patches of white sand vegetation from the plains of northern Amazonia.
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Affiliation(s)
- Dilce F Rossetti
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Gabriel M Moulatlet
- Universidad Regional Amazónica/IKIAM, Km 7, Vía Muyuna, Parroquia Muyuna, Tena, Napo, Ecuador
| | - Hanna Tuomisto
- University of Turku /UTU, Department of Biology, 20014, Turku, Finland
| | - Rogério Gribel
- Instituto Nacional de Pesquisas da Amazônia/ INPA, Coordenação de Biodiversidade, Av. André Araújo, 2936, 69067-375 Manaus, AM, Brazil
| | - Peter M Toledo
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Márcio M Valeriano
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Kalle Ruokolainen
- University of Turku/UTU, Department of Geography and Geology, 20014, Turku, Finland
| | - Marcelo C L Cohen
- Programa de Pós-Graduação em Geologia e Geoquímica, Universidade Federal do Pará/UFPA, Rua Augusto Correa 01, Guamá, 66075-110 Belém, PA, Brazil
| | - Carlos L O Cordeiro
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Camilo D Rennó
- Instituto Brasileiro de Pesquisas Espaciais/INPE, Coordenação Geral de Observação da Terra/CGOBT, Rua dos Astronautas, 1758, Jardim da Granja, 12245-970 São José dos Campos, SP, Brazil
| | - Luiz S Coelho
- Instituto Nacional de Pesquisas da Amazônia/ INPA, Coordenação de Biodiversidade, Av. André Araújo, 2936, 69067-375 Manaus, AM, Brazil
| | - Carlos A C Ferreira
- Instituto Nacional de Pesquisas da Amazônia/ INPA, Coordenação de Biodiversidade, Av. André Araújo, 2936, 69067-375 Manaus, AM, Brazil
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23
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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: 3.8] [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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24
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Prieto-Torres DA, Rojas-Soto OR, Bonaccorso E, Santiago-Alarcon D, Navarro-Sigüenza AG. Distributional patterns of Neotropical seasonally dry forest birds: a biogeographical regionalization. Cladistics 2019; 35:446-460. [PMID: 34633722 DOI: 10.1111/cla.12366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2018] [Indexed: 12/21/2022] Open
Abstract
Neotropical seasonally dry forests (NSDFs) are widely distributed and possess high levels of species richness and endemism; however, their biogeography remains only partially understood. Using species distribution modelling and parsimony analysis of endemicity, we analysed the distributional patterns of the NSDF avifauna in order to identify their areas of endemism and provide a better understanding of the historical relationships among those areas. The strict consensus trees revealed 17 areas of endemism for NSDFs, which involve four large regions: Baja California, Caribbean-Antilles islands, Mesoamerica and South America. These well-resolved clades are circumscribed by geographical and ecological barriers associated with the Gulf of California, the leading edge of the Caribbean plate, the Tehuantepec Isthmus, the Polochic-Motagua fault, the Nicaragua Depression, the Chocó forest, the Amazon basin and the Andean Cordillera. Relationships among groups of NSDFs found here suggest that evolution of their avifauna involved a mixture of vicariance and dispersal events. Our results support the idea of independent diversification patterns and biogeographical processes in each region, including those previously associated with the Pleistocene Arc Hypothesis for NSDFs of south-eastern South America. This study provides a biogeographical framework to open new lines of research related to the biotic diversification of NSDFs.
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Affiliation(s)
- David A Prieto-Torres
- Red de Biología Evolutiva, Laboratorio de Bioclimatología, Instituto de Ecología, A.C., carretera antigua a Coatepec No. 351, El Haya, 91070, Xalapa, Veracruz, México.,Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City, 04510, México
| | - Octavio R Rojas-Soto
- Red de Biología Evolutiva, Laboratorio de Bioclimatología, Instituto de Ecología, A.C., carretera antigua a Coatepec No. 351, El Haya, 91070, Xalapa, Veracruz, México
| | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA and Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, 17-1200-841, Quito, Ecuador.,Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Diego Santiago-Alarcon
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C., El Haya, Xalapa, Veracruz, México
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City, 04510, México
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25
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Loiseau O, Olivares I, Paris M, de La Harpe M, Weigand A, Koubínová D, Rolland J, Bacon CD, Balslev H, Borchsenius F, Cano A, Couvreur TLP, Delnatte C, Fardin F, Gayot M, Mejía F, Mota-Machado T, Perret M, Roncal J, Sanin MJ, Stauffer F, Lexer C, Kessler M, Salamin N. Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae. FRONTIERS IN PLANT SCIENCE 2019; 10:864. [PMID: 31396244 PMCID: PMC6640726 DOI: 10.3389/fpls.2019.00864] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/17/2019] [Indexed: 05/11/2023]
Abstract
The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genomic regions for 85% of the species of the tribe, including 84% of the species of the largest genus, Geonoma. Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.
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Affiliation(s)
- Oriane Loiseau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ingrid Olivares
- Department for Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Centre for Biodiversity and Environment Research, University College London, London, United Kingdom
| | - Margot Paris
- Department of Biology, Unit Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Anna Weigand
- Department for Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Darina Koubínová
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Natural History Museum of Geneva, Geneva, Switzerland
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Henrik Balslev
- Department of Bioscience, Biodiversity and Ecoinformatics, Aarhus University, Aarhus, Denmark
| | | | - Angela Cano
- Cambridge University Botanic Garden, Cambridge, United Kingdom
| | | | | | | | - Marc Gayot
- National Forestry Office, Guadeloupe, France
| | - Fabian Mejía
- Facultad de Ciencias y Biotecnología, Universidad CES, Medellin, Colombia
| | - Talita Mota-Machado
- Programa de Pós-Graduação em Biologia Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mathieu Perret
- Department of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, Geneva, Switzerland
| | - Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Maria José Sanin
- Facultad de Ciencias y Biotecnología, Universidad CES, Medellin, Colombia
| | - Fred Stauffer
- Department of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, Geneva, Switzerland
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael Kessler
- Department for Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
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26
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Toby Pennington R, Lavin M. Dispersal, isolation and diversification with continued gene flow in an Andean tropical dry forest. Mol Ecol 2019. [PMID: 28632343 DOI: 10.1111/mec.14182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Andes are the world's longest mountain chain, and the tropical Andes are the world's richest biodiversity hot spot. The origin of the tropical Andean cordillera is relatively recent because the elevation of the mountains was relatively low (400-2500 m palaeoelevations) only 10 MYA with final uplift being rapid. These final phases of the Andean orogeny are thought to have had a fundamental role in shaping processes of biotic diversification and biogeography, with these effects reaching far from the mountains themselves by changing the course of rivers and deposition of mineral-rich Andean sediments across the massive Amazon basin. In a recent issue of Molecular Ecology, Oswald, Overcast, Mauck, Andersen, and Smith (2017) investigate the biogeography and diversification of bird species in the Andes of Peru and Ecuador. Their study is novel in its focus on tropical dry forests (Figure 1) rather than more mesic biomes such as rain forests, cloud forests and paramos, which tend to be the focus of science and conservation in the Andean hot spot. It is also able to draw powerful conclusions via the first deployment of genomic approaches to a biogeographic question in the threatened dry forests of the New World.
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Affiliation(s)
| | - Matt Lavin
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA
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27
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Lima NED, Carvalho AA, Lima-Ribeiro MS, Manfrin MH. Caracterização e história biogeográfica dos ecossistemas secos neotropicais. RODRIGUÉSIA 2018. [DOI: 10.1590/2175-7860201869445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Resumo A região Neotropical, detentora da maior riqueza de espécies no globo, ocorre do México Central ao sul do Brasil. Neste trabalho, buscamos sumarizar as principais informações disponíveis na literatura que caracterizam os biomas neotropicais de Florestas Sazonalmente Seca (FTSS), Chaco e Savanas. Revisamos hipóteses biogeográficas concernentes a esses ambientes que buscam explicar sua dinâmica histórica. Nosso objetivo é oferecer uma caracterização desses biomas como etapa principal para o entendimento das principais hipóteses biogeográficas a eles associadas. Ainda que comporte como um cenário atraente para pesquisa, as espécies neotropicais são pouco estudas, sendo questões referentes a seus aspectos ecológicos, origem, história evolutiva e manutenção da elevada biodiversidade desconhecidas ou, ainda, pouco compreendidas. Embora, nossa revisão apresente pesquisas com diferentes pontos de vista quanto à dinâmica biogeográfica das formações vegetais, há consenso de que é produto de complexa interação entre os processos históricos, ecológicos e biológicos. Os estudos em biodiversidade de regiões ameaçadas, como os Neotrópicos, são norteadores para simulações e previsões de impactos, planos e estratégias de pesquisa.
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28
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Pirie MD, Chatrou LW, Maas PJM. A taxonomic revision of the Neotropical genus Cremastosperma (Annonaceae), including five new species. PHYTOKEYS 2018; 112:1-141. [PMID: 30524186 PMCID: PMC6277488 DOI: 10.3897/phytokeys.112.24897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
We present a taxonomic revision of Cremastosperma, a genus of Neotropical Annonaceae occurring in lowland to premontane wet forest, mostly in areas surrounding the Andean mountain chain. We recognise 34 species, describing five as new here: from east of the Andes, C.brachypodum Pirie & Chatrou, sp. nov. and C.dolichopodum Pirie & Maas, sp. nov., endemic to Peru; C.confusum Pirie, sp. nov., from southern Peru and adjacent Bolivia and Brazil; and C.alticola Pirie & Chatrou, sp. nov., at higher elevations in northern Peru and Ecuador; and from west of the Andes, C.osicola Pirie & Chatrou, sp. nov. endemic to Costa Rica, the most northerly distributed species of the genus. We provide an identification key, document diagnostic characters and distributions and provide illustrations and extensive lists of specimens, also presenting the latter in the form of mapping data with embedded links to images available online. Of the 34 species, 22 are regional endemics. On the basis of the extent of occurrence and area of occupancy of species estimated from the distribution data, we designate IUCN threat categries for all species. Fourteen species proved to be endangered (EN) and a further one critically endangered (CR), reflecting their rarity and narrow known distributions.
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Affiliation(s)
- Michael D. Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, GermanyJohannes Gutenberg-UniversitätMainzGermany
| | - Lars W. Chatrou
- Wageningen University and Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB Wageningen, The NetherlandsWageningen UniversityWageningenNetherlands
- Ghent University, Systematic and Evolutionary Botany lab, K.L. Ledeganckstraat 35, 9000 Ghent, BelgiumGhent UniversityGhentBelgium
| | - Paul J. M. Maas
- Naturalis Biodiversity Center, section Botany, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterWageningenNetherlands
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29
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Ramírez-Barrera SM, Hernández-Baños BE, Jaramillo-Correa JP, Klicka J. Deep divergence of Red-crowned Ant Tanager ( Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica. PeerJ 2018; 6:e5496. [PMID: 30225165 PMCID: PMC6139011 DOI: 10.7717/peerj.5496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/31/2018] [Indexed: 11/20/2022] Open
Abstract
Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species’ distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation “diagonal” (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species.
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Affiliation(s)
- Sandra M Ramírez-Barrera
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Blanca E Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seatle, WA, United States of America
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30
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Is Amazonia a ‘museum’ for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae). Mol Phylogenet Evol 2018; 126:279-292. [DOI: 10.1016/j.ympev.2018.04.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/28/2018] [Accepted: 04/19/2018] [Indexed: 01/10/2023]
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31
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Brancalion PHS, Oliveira GCX, Zucchi MI, Novello M, van Melis J, Zocchi SS, Chazdon RL, Rodrigues RR. Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm. Ecol Evol 2018; 8:7462-7475. [PMID: 30151163 PMCID: PMC6106193 DOI: 10.1002/ece3.4248] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/23/2018] [Accepted: 05/06/2018] [Indexed: 01/15/2023] Open
Abstract
One of the most intriguing questions in plant ecology is which evolutionary strategy allows widely distributed species to increase their ecological range and grow in changing environmental conditions. Phenotypic plasticity and local adaptations are major processes governing species range margins, but little is known about their relative contribution for tree species distribution in tropical forest regions. We investigated the relative role of phenotypic plasticity and local adaptation in the ecological distribution of the widespread palm Euterpe edulis in the Brazilian Atlantic Forest. Genetic sampling and experiments were performed in old-growth remnants of two forest types with higher (Seasonal Semideciduous Forests vs. Submontane Rainforest) and lower biogeographic association and environmental similarities (Submontane Rainforest vs. Restinga Forest). We first assessed the molecular genetic differentiation among populations, focusing on the group of loci potentially under selection in each forest, using single-nucleotide polymorphism (SNPs) outliers. Further, we looked for potential adaptive divergence among populations in a common garden experiment and in reciprocal transplants for two plant development phases: seedling establishment and sapling growth. Analysis with outlier loci indicated that all individuals from the Semideciduous Forest formed a single group, while another group was formed by overlapping individuals from Submontane Rainforest and Restinga Forest. Molecular differentiation was corroborated by reciprocal transplants, which yielded strong evidence of local adaptations for seedling establishment in the biogeographically divergent Rainforest and Semideciduous Forest, but not for Restinga Forest and Submontane Rainforest. Phenotypic plasticity for palm seedling establishment favors range expansion to biogeographically related or recently colonized forest types, while persistence in the newly colonized ecosystem may be favored by local adaptations if climatic conditions diverge over time, reducing gene flow between populations. SNPs obtained by next-generation sequencing can help exploring adaptive genetic variation in tropical trees, which impose several challenges to the use of reciprocal transplants.
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Affiliation(s)
- Pedro H S Brancalion
- Department of Forest Sciences "Luiz de Queiroz" College of Agriculture University of São Paulo Piracicaba SP Brazil
| | - Giancarlo C X Oliveira
- Department of Genetics, "Luiz de Queiroz" College of Agriculture University of São Paulo Piracicaba SP Brazil
| | - Maria I Zucchi
- Agribusiness Technological Development of São Paulo (APTA) Piracicaba SP Brazil
| | - Mariana Novello
- Agribusiness Technological Development of São Paulo (APTA) Piracicaba SP Brazil.,Departament of Genetics and Molecular Biology Institute of Biology University of Campinas Campinas SP Brazil
| | - Juliano van Melis
- Department of Forest Sciences "Luiz de Queiroz" College of Agriculture University of São Paulo Piracicaba SP Brazil
| | - Silvio S Zocchi
- Department of Math, Chemistry and Statistics "Luiz de Queiroz" College of Agriculture University of São Paulo Piracicaba SP Brazil
| | - Robin L Chazdon
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA.,International Institute for Sustainability Rio de Janeiro RJ Brazil
| | - Ricardo R Rodrigues
- Department of Biology, "Luiz de Queiroz" College of Agriculture University of São Paulo Piracicaba SP Brazil
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Alcantara S, Ree RH, Mello-Silva R. Accelerated diversification and functional trait evolution in Velloziaceae reveal new insights into the origins of the campos rupestres' exceptional floristic richness. ANNALS OF BOTANY 2018; 122:165-180. [PMID: 29800276 PMCID: PMC6025242 DOI: 10.1093/aob/mcy063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/12/2018] [Indexed: 05/06/2023]
Abstract
Background and Aims The greater diversity of plant clades in the Neotropics compared to their relatives in Africa is a pervasive pattern in biogeography. To better understand the causes of this imbalance, we studied the diversification dynamics of the monocot family Velloziaceae. In addition to being conspicuously richer in the Neotropics compared to the Palaeotropics, many species of Velloziaceae exhibit extreme desiccation tolerance (i.e. 'resurrection' behaviour), and other ecological specializations to life on rocky outcrops, poor sandy soils, open vegetation and seasonally dry climates. Velloziaceae is also ecologically dominant in the campos rupestres, a habitat having exceptionally high plant diversity and endemism in Brazil. Methods We reconstructed a densely sampled time-calibrated molecular phylogeny and used state-dependent and state-independent models to estimate rates of lineage diversification in relation to continent-scale geographical occurrence and functional traits associated with desiccation tolerance and water storage capacity. Key Results Independent shifts to faster diversification occurred within two Neotropical lineages, Vellozia and Barbacenia. The Vellozia radiation was associated with the presence of conspicuous aerial stems, and was followed by decreasing diversification rates during the Oligocene, a time of rising global temperatures and expanding open areas around the world. The Barbacenia radiation was faster and more recent, occurring during the cooling conditions of the Miocene, and associated with the acquisition of aquiferous parenchyma on the leaves. Conclusions High species richness of Velloziaceae in South America has been driven by faster diversification in lineages predominantly occurring in the campos rupestres, putatively by the evolution of adaptive strategies in response to independent climatic events. The radiation of Vellozia in particular might have played a key role in the assembly of the campos rupestres vegetation.
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Affiliation(s)
- Suzana Alcantara
- Departamento de Botânica, Universidade Federal de Santa Catarina, Centro de Ciências Biológicas, Campus Universitário, Trindade, Florianópolis, SC, Brazil
- Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Richard H Ree
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Renato Mello-Silva
- Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil
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Endara MJ, Coley PD, Wiggins NL, Forrister DL, Younkin GC, Nicholls JA, Pennington RT, Dexter KG, Kidner CA, Stone GN, Kursar TA. Chemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study. THE NEW PHYTOLOGIST 2018; 218:847-858. [PMID: 29436716 DOI: 10.1111/nph.15020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/04/2018] [Indexed: 05/12/2023]
Abstract
The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next-generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental-scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short.
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Affiliation(s)
- María-José Endara
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, EC170103, Ecuador
| | - Phyllis D Coley
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Republic of Panamá
| | - Natasha L Wiggins
- School of Biological Sciences, University of Tasmania, Sandy Bay, TAS, 7001, Australia
| | - Dale L Forrister
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - Gordon C Younkin
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
| | - James A Nicholls
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
| | | | - Kyle G Dexter
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Catherine A Kidner
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
| | - Graham N Stone
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JY, UK
| | - Thomas A Kursar
- Department of Biology, University of Utah, Salt Lake City, UT, 84112-0840, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Republic of Panamá
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Sprent JI, Ardley J, James EK. Biogeography of nodulated legumes and their nitrogen-fixing symbionts. THE NEW PHYTOLOGIST 2017; 215:40-56. [PMID: 28211601 DOI: 10.1111/nph.14474] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/22/2016] [Indexed: 05/21/2023]
Abstract
Contents 40 I. 40 II. 41 III. 44 IV. 48 V. 49 VI. 49 VII. 52 VIII. 53 53 References 53 SUMMARY: In the last decade, analyses of both molecular and morphological characters, including nodulation, have led to major changes in our understanding of legume taxonomy. In parallel there has been an explosion in the number of genera and species of rhizobia known to nodulate legumes. No attempt has been made to link these two sets of data or to consider them in a biogeographical context. This review aims to do this by relating the data to the evolution of the two partners: it highlights both longitudinal and latitudinal trends and considers these in relation to the location of major land masses over geological time. Australia is identified as being a special case and latitudes north of the equator as being pivotal in the evolution of highly specialized systems in which the differentiated rhizobia effectively become ammonia factories. However, there are still many gaps to be filled before legume nodulation is sufficiently understood to be managed for the benefit of a world in which climate change is rife.
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Affiliation(s)
- Janet I Sprent
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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Janet I. Sprent. THE NEW PHYTOLOGIST 2017; 215:38-39. [PMID: 28560789 DOI: 10.1111/nph.14618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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Eiserhardt WL, Couvreur TLP, Baker WJ. Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome. THE NEW PHYTOLOGIST 2017; 214:1408-1422. [PMID: 28277624 DOI: 10.1111/nph.14516] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/29/2017] [Indexed: 06/06/2023]
Abstract
I. II. III. IV. V. VI. VII. VIII. IX. References SUMMARY: Tropical rainforest (TRF) is the most species-rich terrestrial biome on Earth, harbouring just under half of the world's plant species in c. 7% of the land surface. Phylogenetic trees provide important insights into mechanisms underpinning TRF hyperdiversity that are complementary to those obtained from the fossil record. Phylogenetic studies of TRF plant diversity have mainly focused on whether this biome is an evolutionary 'cradle' or 'museum', emphasizing speciation and extinction rates. However, other explanations, such as biome age, immigration and ecological limits, must also be considered. We present a conceptual framework for addressing the drivers of TRF diversity, and review plant studies that have tested them with phylogenetic data. Although surprisingly few in number, these studies point to old age of TRF, low extinction and high speciation rates as credible drivers of TRF hyperdiversity. There is less evidence for immigration and ecological limits, but these cannot be dismissed owing to the limited number of studies. Rapid methodological developments in DNA sequencing, macroevolutionary analysis and the integration of phylogenetics with other disciplines may improve our grasp of TRF hyperdiversity in the future. However, such advances are critically dependent on fundamental systematic research, yielding numerous, additional, well-sampled phylogenies of TRF lineages.
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Affiliation(s)
| | - Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR DIADE, F-34394, Montpellier, France
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de la Estrella M, Forest F, Wieringa JJ, Fougère-Danezan M, Bruneau A. Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees. THE NEW PHYTOLOGIST 2017; 214:1722-1735. [PMID: 28323330 DOI: 10.1111/nph.14523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity.
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Affiliation(s)
- Manuel de la Estrella
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
| | - Félix Forest
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of the Netherlands, Darwinweg 2, 2333, CR Leiden, the Netherlands
| | - Marie Fougère-Danezan
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
- Université de Toulouse, EDB (Laboratoire Evolution et Diversité Biologique), UMR5174, F-31062, Toulouse, France
- CNRS, UPS, EDB (Laboratoire Evolution et Diversité Biologique), UMR5174, 118 route de Narbonne, F-31062, Toulouse, France
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
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Borges LM, Simon MF, Pirani JR. Less is more. Adjusting the taxonomy of the polytypic Mimosa setosa (Leguminosae, Mimosoid). RODRIGUÉSIA 2017. [DOI: 10.1590/2175-7860201768215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Resumo Mimosa setosa, em sua circunscrição atual, é uma espécie politípica que inclui quatro subespécies e oito variedades. Estudos filogenéticos recentes indicam que esses táxons infraespecíficos não formam um grupo monofilético. A análise morfológica de um conjunto de espécimes obtidos em diversos herbários, incluindo tipos e coletas recentes, associada à aplicação do Conceito Filogenético de espécie permite desmembrar M. setosa em seis diferentes espécies sem táxons infraespecíficos. Congruência entre dados filogenéticos, geografia e adoção do nível de espécie como a unidade mínima para descrição de táxons permite uma melhor comparação da diversidade biológica e uma circunscrição mais adequada dos táxons envolvidos no complexo M. setosa.
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40
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Jana C. Vamosi. THE NEW PHYTOLOGIST 2017; 214:19-20. [PMID: 28239891 DOI: 10.1111/nph.14444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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Dexter KG, Lavin M, Torke BM, Twyford AD, Kursar TA, Coley PD, Drake C, Hollands R, Pennington RT. Dispersal assembly of rain forest tree communities across the Amazon basin. Proc Natl Acad Sci U S A 2017; 114:2645-2650. [PMID: 28213498 PMCID: PMC5347625 DOI: 10.1073/pnas.1613655114] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin.
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Affiliation(s)
- Kyle G Dexter
- School of GeoSciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom;
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - Mathew Lavin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717
| | - Benjamin M Torke
- Institute of Systematic Botany, New York Botanical Garden, Bronx, NY 10458
| | - Alex D Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Thomas A Kursar
- Biology Department, University of Utah, Salt Lake City, UT 84112
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Phyllis D Coley
- Biology Department, University of Utah, Salt Lake City, UT 84112
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Camila Drake
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - Ruth Hollands
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
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Cardoso D, Harris DJ, Wieringa JJ, São-Mateus WMB, Batalha-Filho H, Torke BM, Prenner G, Queiroz LPD. A molecular-dated phylogeny and biogeography of the monotypic legume genus Haplormosia, a missing African branch of the otherwise American-Australian Brongniartieae clade. Mol Phylogenet Evol 2016; 107:431-442. [PMID: 27965083 DOI: 10.1016/j.ympev.2016.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 11/17/2022]
Abstract
A comprehensively sampled reassessment of the molecular phylogeny of the genistoid legumes questions the traditional placement of Haplormosia, an African monotypic genus traditionally classified within tribe Sophoreae close to the Asian-American geographically disjunct genus Ormosia. Plastid matK sequences placed Haplormosia as sister to the American-Australian tribe Brongniartieae. Despite a superficial resemblance between Haplormosia and Ormosia, a re-examination of the morphology of Haplormosia corroborates the new phylogenetic result. The reciprocally monophyletic deep divergence of the Haplormosia stem lineage from the remaining Brongniartieae is dated to ca. 52Mya, thus supporting a signature of an old single long-distance dispersal during the early Eocene. Conversely, we estimated a relatively recent long-distance dispersal rooted in the Early Miocene for the Australian Brongniartieae clade emerging from within a grade of American Brongniartieae. The Bayesian ancestral area reconstruction revealed the coming and going of neotropical ancestors during the diversification history of the Brongniartieae legumes in Africa and all over the Americas and Australia.
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Affiliation(s)
- Domingos Cardoso
- 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, 40170-115 Salvador, Bahia, Brazil; Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil.
| | - David J Harris
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, Botany Section, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Wallace M B São-Mateus
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59072-970 Natal, Rio Grande do Norte, Brazil
| | - Henrique Batalha-Filho
- 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, 40170-115 Salvador, Bahia, Brazil
| | - Benjamin M Torke
- Institute of Systematic Botany, The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458-5126, USA
| | - Gerhard Prenner
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
| | - Luciano Paganucci de Queiroz
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
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Donkpegan ASL, Doucet JL, Migliore J, Duminil J, Dainou K, Piñeiro R, Wieringa JJ, Champluvier D, Hardy OJ. Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae). Mol Phylogenet Evol 2016; 107:270-281. [PMID: 27825871 DOI: 10.1016/j.ympev.2016.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 10/26/2016] [Accepted: 11/04/2016] [Indexed: 11/30/2022]
Abstract
Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20Ma while extant tetraploid species started diverging c. 7.0 or 9.4Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics.
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Affiliation(s)
- Armel S L Donkpegan
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030 Gembloux, Belgium; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium.
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030 Gembloux, Belgium; BIOSE, Management of Forest Resources, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030, Belgium.
| | - Jérémy Migliore
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium.
| | - Jérôme Duminil
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium; Bioversity International, c/o CIFOR Central Africa Regional Office P.O. Box 2008 Messa, Yaoundé, Cameroon; Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, 34394 Montpellier, France.
| | - Kasso Dainou
- BIOSE, Management of Forest Resources, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030, Belgium; Nature+ asbl, Winstar Park, Rue Provinciale 62, 1301, Wavre, Belgium; Université d'Agriculture de Kétou, BP: 43, Kétou, Benin.
| | - Rosalía Piñeiro
- Conservation, Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, Richmond, Surrey, UK.
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of The Netherlands, Darwinweg 2, 2333 CR Leiden, The Netherlands.
| | | | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium.
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Gagnon E, Bruneau A, Hughes CE, de Queiroz LP, Lewis GP. A new generic system for the pantropical Caesalpinia group (Leguminosae). PHYTOKEYS 2016; 71:1-160. [PMID: 28814915 PMCID: PMC5558824 DOI: 10.3897/phytokeys.71.9203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/14/2016] [Indexed: 05/02/2023]
Abstract
The Caesalpinia group is a large pantropical clade of ca. 205 species in subfamily Caesalpinioideae (Leguminosae) in which generic delimitation has been in a state of considerable flux. Here we present new phylogenetic analyses based on five plastid and one nuclear ribosomal marker, with dense taxon sampling including 172 (84%) of the species and representatives of all previously described genera in the Caesalpinia group. These analyses show that the current classification of the Caesalpinia group into 21 genera needs to be revised. Several genera (Poincianella, Erythrostemon, Cenostigma and Caesalpinia sensu Lewis, 2005) are non-monophyletic and several previously unclassified Asian species segregate into clades that merit recognition at generic rank. In addition, the near-completeness of our taxon sampling identifies three species that do not belong in any of the main clades and these are recognised as new monospecific genera. A new generic classification of the Caesalpinia group is presented including a key for the identification of genera, full generic descriptions, illustrations (drawings and photo plates of all genera), and (for most genera) the nomenclatural transfer of species to their correct genus. We recognise 26 genera, with reinstatement of two previously described genera (Biancaea Tod., Denisophytum R. Vig.), re-delimitation and expansion of several others (Moullava, Cenostigma, Libidibia and Erythrostemon), contraction of Caesalpinia s.s. and description of four new ones (Gelrebia, Paubrasilia, Hererolandia and Hultholia), and make 75 new nomenclatural combinations in this new generic system.
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Affiliation(s)
- Edeline Gagnon
- Institut de recherche en biologie végétale and Département de sciences
biologiques, Université de Montréal, H1X 2B2, Montréal, Québec, Canada
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de sciences
biologiques, Université de Montréal, H1X 2B2, Montréal, Québec, Canada
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zürich, 8008,
Zürich, Switzerland
| | - Luciano Paganucci de Queiroz
- Universidade Estadual de Feira de Santana, BR 116, Km 03, Campus Universitário,
Feira de Santana 44031-460, Bahia, Brasil
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew,
Richmond, Surrey, TW9 3AB, United Kingdom
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Ramos G, de Lima HC, Prenner G, de Queiroz LP, Zartman CE, Cardoso D. Molecular systematics of the Amazonian genus Aldina, a phylogenetically enigmatic ectomycorrhizal lineage of papilionoid legumes. Mol Phylogenet Evol 2016; 97:11-18. [DOI: 10.1016/j.ympev.2015.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/23/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
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