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McLaughlin JF, Aguilar C, Bernstein JM, Navia-Gine WG, Cueto-Aparicio LE, Alarcon AC, Alarcon BD, Collier R, Takyar A, Vong SJ, López-Chong OG, Driver R, Loaiza JR, De León LF, Saltonstall K, Lipshutz SE, Arcila D, Brock KM, Miller MJ. Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.530646. [PMID: 36993716 PMCID: PMC10055050 DOI: 10.1101/2023.03.15.530646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.
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Affiliation(s)
- J. F. McLaughlin
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Celestino Aguilar
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Justin M. Bernstein
- Department of Biology, Villanova University, Villanova, PA, USA
- Center for Genomics, University of Kansas, Lawrence, KS, USA
| | - Wayra G. Navia-Gine
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA, USA
| | | | | | | | - Rugger Collier
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Anshule Takyar
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Sidney J. Vong
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | | | - Robert Driver
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Jose R. Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Luis F. De León
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | | | | | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
| | - Kinsey M. Brock
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Matthew J. Miller
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Reneco International Wildlife Consultants, Abu Dhabi, UAE
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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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Chung SW, Huang WJ, Chen ZH, Liu SH. Blumea chishangensis sp. nov. (Asteraceae: Inuleae) from Taiwan and new insights into the phylogeny of Blumea. BOTANICAL STUDIES 2022; 63:21. [PMID: 35821129 PMCID: PMC9276887 DOI: 10.1186/s40529-022-00350-z] [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: 01/28/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Blumea plants are widely distributed in the tropical areas of Asia, Africa, and Australia, especially tropical Asia. Limited studies left the taxonomy and infrageneric phylogeny of Blumea insubstantial. Here, a new species, Blumea chishangensis S. W. Chung, Z. H. Chen, S. H. Liu & W. J. Huang, from Taiwan is described, and an extended phylogeny is reconstructed to provide new perceptions of Blumea evolution. RESULTS The new species is distinguished from B. hieraciifolia by the following features: leaf blade sparsely pilose or glabrescent (vs. silky villous), the leaves margins regularly remote mucronulate (vs. double serrate or dentate), capitula pedicelled (vs. capitula sessile or subsessile), and leaves basal rosette or sub-basal rosette and a few cauline (vs. mostly cauline). Phylogenetic analysis based on the ITS, trnL-trnF, and trnH-psbA regions places the new species in the subclade II in B. lacera clade and shows a close relationship with B. axillaris and B. oxyodonta. A key to Blumea species in Taiwan and the studied species in the subclade II is provided. Moreover, the evolutionary inferences of B. conspicua, B. linearis, and B. sinuata are first reported here. The paraphyly of B. formosana and B. sinuata are also revealed for the first time. CONCLUSIONS Both morphological and molecular data support that B. chishangensis is a new species. Our phylogeny highlights the need for further taxonomic and evolutionary studies on Blumea.
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Affiliation(s)
- Shih-Wen Chung
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, 100, Taiwan
- Forestry Research Institute Herbarium (TAIF), Taiwan Forestry Research Institute, Taipei, 100, Taiwan
| | - Wei-Jie Huang
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, 100, Taiwan
| | - Zhi-Hao Chen
- Observer Ecological Consultant Co., Ltd., Taipei, 103, Taiwan
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
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Ross AC, Bryer MA, Chapman CA, Rothman JM, Nevo O, Valenta K. Why eat flowers? Symphonia globulifera flowers provide a fatty resource for red-tailed monkeys. Folia Primatol (Basel) 2022. [DOI: 10.1163/14219980-20211003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Flowers are ubiquitous in primate environments, yet their nutritional advantages are underexamined. Symphonia globulifera is a widely distributed tree exploited by a variety of animals in Africa and the Americas. We collected S. globulifera flower samples consumed by red-tailed monkeys (Cercopithecus ascanius) and compared them nutritionally to flower samples from other plant species in Kibale National Park, Uganda. Flowers were assayed for three fiber fractions (NDF, ADF, lignin), fat, crude protein, acid detergent insoluble nitrogen (ADIN), ash, and soluble sugars. We estimated available protein, total nonstructural carbohydrates (TNC), and metabolizable energy (ME). We calculated the mean and standard deviation for all nutrient categories and applied nutritional geometry to illustrate the balance among the energetic gains from available protein, fat, fiber, and TNC across flower species. Our results suggest that S. globulifera flowers provide an unusually high fat resource (14.82% ± 1.41%) relative to other flowers (1.38% ± 5.79%) and other foods exploited in the same habitat.
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Affiliation(s)
- Abigail C. Ross
- Department of Anthropology, Rock Valley College, 3301 N. Mulford Road, Rockford, IL 61114, USA
| | - Margaret A.H. Bryer
- Department of Psychology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Psychology, University of California- Berkeley, Berkeley, CA 94720, USA
| | - Colin A. Chapman
- Department of Anthropology, George Washington University, Washington, DC 20052, USA
- Wilson Center, Environmental Change and Security Program, Washington, DC 20004, USA
| | - Jessica M. Rothman
- Department of Anthropology, Hunter College of the City University of New York, New York, NY 10065, USA
| | - Omer Nevo
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biodiversity, Friedrich-Schiller University Jena, 07743 Jena, Germany
| | - Kim Valenta
- Department of Anthropology, University of Florida, Gainesville, FL 32611, USA
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Diel KAP, Marinho LC, von Poser GL. The ethnobotanical relevance of the tribe Symphonieae (Clusiaceae) around the world. JOURNAL OF ETHNOPHARMACOLOGY 2022; 284:114745. [PMID: 34656665 DOI: 10.1016/j.jep.2021.114745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The tribe Symphonieae (Clusiaceae) encompasses 48 species accommodated in seven genera (Lorostemon, Montrouziera, Moronobea, Pentadesma, Platonia, Symphonia and Thysanostemon). Parts of these plants, mainly the exudates and the seeds oil are useful for different purposes, especially for treating dermatological conditions. In addition to the role in the folk medicine, some species are of great economic and cultural importance for native people from different continents. AIM OF THE REVIEW The goal of this review is to critically summarize the current knowledge on systematics, ethnobotanical, chemical and pharmacological aspects of species from the tribe Symphonieae, as well as to provide support for future taxonomic and phylogenetic studies on the Clusiaceae family. MATERIALS AND METHODS The available information was gathered from many different databases (Web of Science, ScienceDirect, Scopus, Pubmed, ChemSpider, SciFinder, ACS Publications, Wiley Online Library, Useful Tropical Plants Database, Google Scholar). Additional data from books, theses and dissertations were also included in this review. RESULTS Chemical studies of Symphonieae have demonstrated that the genera are a source of benzophenones, xanthones and biflavonoids. Components as sesquiterpenoids, triterpenoids, flavonoids, free fatty acids, among others, have also been reported. Extracts and compounds isolated from a variety of species have been exhibiting antimicrobial, cytotoxic and antiprotozoal activities, corroborating part of their medicinal uses. In addition, certain species produce edible fruits and a kind of "butter" with economic importance. All species produce exudate, which often has great relevance in the daily lives of local people. CONCLUSION Several species of Symphonieae have potential therapeutic applications and some of them have been investigated to scientifically validate their popular uses. In addition, a number of species have proved to be a rich source of promising pharmacologically active compounds. Finally, the value of fruits, exudate and butter, for instance, should serve as a stimulus for the sustainable development of products that aim to take advantage of these natural resources.
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Affiliation(s)
- Kriptsan Abdon Poletto Diel
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Farmacêuticas, Avenida Ipiranga 2752, Santana, 90610-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lucas Cardoso Marinho
- Universidade Federal do Maranhão, Departamento de Biologia, Avenida dos Portugueses 1966, Bacanga, 65080-805, São Luís, Maranhão, Brazil
| | - Gilsane Lino von Poser
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Farmacêuticas, Avenida Ipiranga 2752, Santana, 90610-000, Porto Alegre, Rio Grande do Sul, Brazil.
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Baraloto C, Vleminckx J, Engel J, Petronelli P, Dávila N, RÍos M, Valderrama Sandoval EH, Mesones I, Guevara Andino JE, Fortunel C, Allie E, Paine CET, Dourdain A, Goret J, Valverde‐Barrantes OJ, Draper F, Fine PVA. Biogeographic history and habitat specialization shape floristic and phylogenetic composition across Amazonian forests. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christopher Baraloto
- Institute of Environment Department of Biological Sciences Florida International University 11200 Southwest 8th Street Miami Florida 33199 USA
- INRAE UMR Ecologie des Forêts de Guyane Université de Guyane Université des Antilles Campus agronomique, BP 316 Kourou Cedex 97379 France
| | - Jason Vleminckx
- Institute of Environment Department of Biological Sciences Florida International University 11200 Southwest 8th Street Miami Florida 33199 USA
| | - Julien Engel
- AMAP (botAnique et Modélisation de l’Architecture des Plantes et des végétations) Université de Montpellier, CIRAD, CNRS, INRAE, IRD Boulevard de la Lironde Montpellier Cedex 5 TA A‐51/PS234398 France
| | - Pascal Petronelli
- CIRAD, UMR Ecologie des Forêts de Guyane Université de Guyane Université des Antilles Campus agronomique, BP 316 Kourou Cedex 97379 France
| | - Nállarett Dávila
- Instituto de Investigaciones de la Amazonia Peruana Iquitos, Peru, Avenida José A. Quiñones km 2.5 Iquitos Loreto Perú
| | - Marcos RÍos
- Instituto de Investigaciones de la Amazonia Peruana Iquitos, Peru, Avenida José A. Quiñones km 2.5 Iquitos Loreto Perú
| | | | - Italo Mesones
- Department of Integrative Biology and Jepson Herbaria University of California, Berkeley 3040 Valley Life Sciences Building 3140 Berkeley California 94720‐3140 USA
| | | | - Claire Fortunel
- AMAP (botAnique et Modélisation de l’Architecture des Plantes et des végétations) Université de Montpellier, CIRAD, CNRS, INRAE, IRD Boulevard de la Lironde Montpellier Cedex 5 TA A‐51/PS234398 France
| | - Elodie Allie
- INRAE UMR Ecologie des Forêts de Guyane Université de Guyane Université des Antilles Campus agronomique, BP 316 Kourou Cedex 97379 France
| | - C. E. Timothy Paine
- Environmental and Rural Sciences University of New England Armidale New South Wales 2351 Australia
| | - Aurélie Dourdain
- CIRAD, UMR Ecologie des Forêts de Guyane Université de Guyane Université des Antilles Campus agronomique, BP 316 Kourou Cedex 97379 France
| | - Jean‐Yves Goret
- INRAE UMR Ecologie des Forêts de Guyane Université de Guyane Université des Antilles Campus agronomique, BP 316 Kourou Cedex 97379 France
| | - Oscar J. Valverde‐Barrantes
- Institute of Environment Department of Biological Sciences Florida International University 11200 Southwest 8th Street Miami Florida 33199 USA
| | - Freddie Draper
- Institute of Environment Department of Biological Sciences Florida International University 11200 Southwest 8th Street Miami Florida 33199 USA
- Center for Global Discovery and Conservation Science Arizona State University 1001 South McAllister Avenue Tempe Tempe Arizona 85287 USA
- School of Geography University of Leeds Woodhouse Leeds LS2 9JT UK
| | - Paul V. A. Fine
- Department of Integrative Biology and Jepson Herbaria University of California, Berkeley 3040 Valley Life Sciences Building 3140 Berkeley California 94720‐3140 USA
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Silva LM, Batalha-Filho H, Japyassú HF, El-Hani CN. Population history of a social spider reveals connection between South American tropical forests. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Hamdan B, Guedes TB, Carrasco PA, Melville J. A complex biogeographic history of diversification in Neotropical lancehead pitvipers (Serpentes, Viperidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12398] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Breno Hamdan
- Departamento de Genética Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Laboratório de Coleções Biológicas e Biodiversidade Instituto Vital Brazil Niterói Brazil
| | - Thaís B. Guedes
- Programa de Pós‐Graduação em Biodiversidade, Ambiente e Saúde Centro de Estudos Superiores de Caxias Universidade Estadual do Maranhão Caxias Brazil
- Department of Biological and Environmental Sciences and Gothenburg Global Biodiversity Center University of Gothenburg Göteborg Sweden
| | - Paola A. Carrasco
- Facultad de Ciencias Exactas Físicas y Naturales Centro de Zoología Aplicada Universidad Nacional de Córdoba Córdoba Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Instituto de Diversidad y Ecología Animal (IDEA) Córdoba Argentina
| | - Jane Melville
- Sciences Department Museum Victoria Melbourne Vic. Australia
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Reis CA, Dias C, Araripe J, Aleixo A, Anciães M, Sampaio I, Schneider H, Rêgo PS. Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance. ZOOL SCR 2019. [DOI: 10.1111/zsc.12395] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Camila Alves Reis
- Curso de Pós‐Graduação em Zoologia Universidade Federal do ParáMuseu Paraense Emílio Goeldi Belém Brazil
| | - Cleyssian Dias
- Curso de Pós‐Graduação em Zoologia Universidade Federal do ParáMuseu Paraense Emílio Goeldi Belém Brazil
| | - Juliana Araripe
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Alexandre Aleixo
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Marina Anciães
- Laboratório de Evolução e Comportamento Animal COBIO Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Horacio Schneider
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
| | - Péricles Sena Rêgo
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Brazil
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10
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Dick CW, Pennington RT. History and Geography of Neotropical Tree Diversity. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110617-062314] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.
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Affiliation(s)
- Christopher W. Dick
- Department of Ecology and Evolutionary Biology and Herbarium, University of Michigan, Ann Arbor, Michigan 48109, USA
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Exeter EX4 4QE, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
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11
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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: 17] [Impact Index Per Article: 3.4] [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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Honorio Coronado EN, Dexter KG, Hart ML, Phillips OL, Pennington RT. Comparative phylogeography of five widespread tree species: Insights into the history of western Amazonia. Ecol Evol 2019; 9:7333-7345. [PMID: 31380054 PMCID: PMC6662334 DOI: 10.1002/ece3.5306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/20/2019] [Accepted: 05/04/2019] [Indexed: 11/26/2022] Open
Abstract
Various historical processes have been put forth as drivers of patterns in the spatial distribution of Amazonian trees and their population genetic variation. We tested whether five widespread tree species show congruent phylogeographic breaks and similar patterns of demographic expansion, which could be related to proposed Pleistocene refugia or the presence of geological arches in western Amazonia. We sampled Otoba parvifolia/glycycarpa (Myristicaceae), Clarisia biflora, Poulsenia armata, Ficus insipida (all Moraceae), and Jacaratia digitata (Caricaceae) across the western Amazon Basin. Plastid DNA (trnH-psbA; 674 individuals from 34 populations) and nuclear ribosomal internal transcribed spacers (ITS; 214 individuals from 30 populations) were sequenced to assess genetic diversity, genetic differentiation, population genetic structure, and demographic patterns. Overall genetic diversity for both markers varied among species, with higher values in populations of shade-tolerant species than in pioneer species. Spatial analysis of molecular variance (SAMOVA) identified three genetically differentiated groups for the plastid marker for each species, but the areas of genetic differentiation were not concordant among species. Fewer SAMOVA groups were found for ITS, with no detectable genetic differentiation among populations in pioneers. The lack of spatially congruent phylogeographic breaks across species suggests no common biogeographic history of these Amazonian tree species. The idiosyncratic phylogeographic patterns of species could be due instead to species-specific responses to geological and climatic changes. Population genetic patterns were similar among species with similar biological features, indicating that the ecological characteristics of species impact large-scale phylogeography.
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Affiliation(s)
| | - Kyle G. Dexter
- School of GeoSciencesUniversity of EdinburghEdinburghUK
- Royal Botanic Garden EdinburghEdinburghUK
| | | | | | - R. Toby Pennington
- Royal Botanic Garden EdinburghEdinburghUK
- Department of GeographyUniversity of ExeterExeterUK
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Escobar S, Pintaud J, Balslev H, Bernal R, Moraes Ramírez M, Millán B, Montúfar R. Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis-scenario. Ecol Evol 2018; 8:8030-8042. [PMID: 30250682 PMCID: PMC6144996 DOI: 10.1002/ece3.4216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/22/2018] [Accepted: 04/30/2018] [Indexed: 12/27/2022] Open
Abstract
Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape-Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.
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Affiliation(s)
- Sebastián Escobar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
- Department of Bioscience, Ecoinformatics and Biodiversity GroupAarhus UniversityAarhusDenmark
| | | | - Henrik Balslev
- Department of Bioscience, Ecoinformatics and Biodiversity GroupAarhus UniversityAarhusDenmark
| | - Rodrigo Bernal
- Instituto de Ciencias NaturalesUniversidad Nacional de ColombiaBogotáColombia
| | | | - Betty Millán
- Museo de Historia NaturalUniversidad Nacional Mayor de San Marcos (UNMSM)LimaPerú
| | - Rommel Montúfar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
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Vicentini A. The Evolutionary History of
Pagamea
(Rubiaceae), a White‐sand Specialist Lineage in Tropical South America. Biotropica 2018. [DOI: 10.1111/btp.12295] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alberto Vicentini
- Bolsista do CNPq‐Brasil Department of Biology University of Missouri‐St. Louis and Missouri Botanical Garden St. Louis Missouri U.S.A
- Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus Brazil
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15
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Kim SH, Cho MS, Li P, Kim SC. Phylogeography and Ecological Niche Modeling Reveal Reduced Genetic Diversity and Colonization Patterns of Skunk Cabbage ( Symplocarpus foetidus; Araceae) From Glacial Refugia in Eastern North America. FRONTIERS IN PLANT SCIENCE 2018; 9:648. [PMID: 29872442 PMCID: PMC5972301 DOI: 10.3389/fpls.2018.00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Alternating glacial and interglacial periods during the Quaternary have dramatically affected the distribution and population genetic structure of plant and animal species throughout the northern hemisphere. Surprisingly, little is known about the post-glacial recolonization history of wetland herbaceous perennials that are widely distributed in the understory of deciduous or mixed deciduous-evergreen forests in eastern North America. In this study, we investigated infraspecific variation among 32 populations of skunk cabbage, Symplocarpus foetidus, to test the hypothesis that the extant species diversity of skunk cabbage is the result of a post-glacial range expansion from southern refugia during the Quaternary Ice Age. A total of 4041 base pairs (bp) of the chloroplast intergenic spacer region (cpDNA) was sequenced from 485 individuals sampled from glaciated (18 populations, 275 individuals) and unglaciated (14 populations, 210 individuals) regions east and west of the Appalachian Mountains. Haplotype number, haplotype diversity, and nucleotide diversity were calculated, and genetic variation within and among populations was assessed by analysis of molecular variance (AMOVA). The geographic pattern of genetic differentiation was further investigated with a spatial analysis of molecular variance (SAMOVA). A total of eight haplotypes and three genetic groups (SAMOVA) were recovered and a much higher haplotype number (eight haplotypes) and haplotype diversity (0.7425) was observed in unglaciated compared to glaciated populations (five haplotypes, haplotype diversity = 0.6099). All haplotypes found in glaciated regions represented a subset of haplotypes found in unglaciated regions. Haplotypes of S. foetidus likely diverged during the Tertiary (mid-Miocene and late Pliocene), predating the last glacial maximum (LGM). Predictions based on ecological niche modeling (ENM) suggested that there was considerably less suitable habitat for skunk cabbage during the LGM, and the habitat range was further south compared to the current distribution. Reduced variation and a subset of haplotypes in glaciated regions suggest a founder effect associated with range expansion via long-distance seed dispersal. Our results do not support the "Driftless Area" scenario for the northern refugium, rather the data suggest a "Northeastern" refugium near the southernmost extent of the LGM.
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Affiliation(s)
- Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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16
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A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica. Mol Phylogenet Evol 2018; 122:80-94. [PMID: 29407482 DOI: 10.1016/j.ympev.2018.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/27/2018] [Accepted: 01/27/2018] [Indexed: 01/20/2023]
Abstract
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.
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Pirie MD, Maas PJM, Wilschut RA, Melchers-Sharrott H, Chatrou LW. Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171561. [PMID: 29410860 PMCID: PMC5792937 DOI: 10.1098/rsos.171561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/21/2017] [Indexed: 05/15/2023]
Abstract
Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of Lake Pebas and closure of the Panama isthmus on two clades of tropical trees (Cremastosperma, ca 31 spp.; and Mosannona, ca 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma. Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrast with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma, suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees.
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Affiliation(s)
- Michael D. Pirie
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099 Mainz, Germany
| | - Paul J. M. Maas
- Naturalis Biodiversity Center, Section Botany, PO Box 9517, 2300 RA Leiden, The Netherlands
| | - Rutger A. Wilschut
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | | | - Lars W. Chatrou
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Tosso F, Hardy OJ, Doucet JL, Daïnou K, Kaymak E, Migliore J. Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology. Mol Phylogenet Evol 2017; 120:83-93. [PMID: 29222064 DOI: 10.1016/j.ympev.2017.11.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022]
Abstract
Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction. All species except G. demeusei and G. copallifera appear monophyletic. Dispersal from Africa to America across the Atlantic Ocean is the most plausible hypothesis to explain the occurrence of Neotropical Guibourtia species, which diverged ca. 11.8 Ma from their closest African relatives. The diversification of the three main clades of African Guibourtia is concomitant to Miocene global climate changes, highlighting pre-Quaternary speciation events. These clades differ by their reproductive characters, which validates the three subgenera previously described: Pseudocopaiva, Guibourtia and Gorskia. Within most monophyletic species, plastid lineages start diverging from each other during the Pliocene or early Pleistocene, suggesting that these species already arose during this period. The multiple transitions between rain forests and dry forests/savannahs inferred here through the plastid phylogeny in each Guibourtia subgenus address thus new questions about the role of phylogenetic relationships in shaping ecological niche and morphological similarity among taxa.
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Affiliation(s)
- Félicien Tosso
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium.
| | - Kasso Daïnou
- Nature + asbl / TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030 Gembloux, Belgium; BIOSE Department, Management of Forest Resources, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium; Université Nationale d'Agriculture, BP 43 Kétou, Benin.
| | - Esra Kaymak
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Jérémy Migliore
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
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Torroba-Balmori P, Budde KB, Heer K, González-Martínez SC, Olsson S, Scotti-Saintagne C, Casalis M, Sonké B, Dick CW, Heuertz M. Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species. PLoS One 2017; 12:e0182515. [PMID: 28771629 PMCID: PMC5542443 DOI: 10.1371/journal.pone.0182515] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/08/2017] [Indexed: 01/08/2023] Open
Abstract
The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
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Affiliation(s)
- Paloma Torroba-Balmori
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
| | | | - Katrin Heer
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Conservation Biology and Ecology, University of Marburg, Marburg, Germany
| | - Santiago C. González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
| | | | | | - Bonaventure Sonké
- Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Smithsonian Tropical Research Institute, Republic of Panama
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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20
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Song J, Cui BK. Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales). BMC Evol Biol 2017; 17:102. [PMID: 28424048 PMCID: PMC5397748 DOI: 10.1186/s12862-017-0948-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU). RESULTS Results of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area. CONCLUSIONS Four intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.
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Affiliation(s)
- Jie Song
- Institute of Microbiology, Beijing Forestry University, P.O. Box 61, 35#, Qinghua East Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Bao-Kai Cui
- Institute of Microbiology, Beijing Forestry University, P.O. Box 61, 35#, Qinghua East Road, Haidian District, Beijing, 100083, People's Republic of China.
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21
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Chávez-Pesqueira M, Núñez-Farfán J. Genetic diversity and structure of wild populations of Carica papaya in Northern Mesoamerica inferred by nuclear microsatellites and chloroplast markers. ANNALS OF BOTANY 2016; 118:1293-1306. [PMID: 27974326 PMCID: PMC5155600 DOI: 10.1093/aob/mcw183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/31/2016] [Accepted: 07/04/2016] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Few studies have evaluated the genetic structure and evolutionary history of wild varieties of important crop species. The wild papaya (Carica papaya) is a key element of early successional tropical and sub-tropical forests in Mexico, and constitutes the genetic reservoir for evolutionary potential of the species. In this study we aimed to determine how diverse and structured is the genetic variability of wild populations of C. papaya in Northern Mesoamerica. Moreover, we assessed if genetic structure and evolutionary history coincide with hypothetized (1) pre-Pleistocene events (Isthmus of Tehuantepec sinking), (2) Pleistocene refugia or (3) recent patterns. METHODS We used six nuclear and two chloroplast (cp) DNA markers to assess the genetic diversity and phylogeographical structure of 19 wild populations of C. papaya in its natural distribution in Northern Mesoamerica. KEY RESULTS We found high genetic diversity (Ho = 0·681 for nuclear markers, and h = 0·701 for cpDNA markers) and gene flow between populations of C. papaya (migration r up to 420 km). A lack of phylogeographical structure was found with the cpDNA markers (NST < GST), whereas a recent population structure was inferred with the nuclear markers. Evidence indicates that pre-Pleistocene events or refugia did not play an important role in the genetic structuring of wild papaya. CONCLUSIONS Because of its life history characteristics and lack of an ancient phylogeographical structure found with the cpDNA markers, we suggest that C. papaya was dispersed throughout the lowland rain forests of Mexico (along the coastal plains and foothills of Sierras). This scenario supports the hypothesis that tropical forests in Northern Mesoamerica did not experience important climate fluctuations during the Pleistocene, and that the life history of C. papaya could have promoted long-distance dispersal and rapid colonization of lowland rainforests. Moreover, the results obtained with the nuclear markers suggest recent human disturbances. The fragmentation of tropical habitats in Northern Mesoamerica appears to be the main driver of genetic structuring, and the major threat to the dispersion and survival of the species in the wild.
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Affiliation(s)
- Mariana Chávez-Pesqueira
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, México 04510 Distrito Federal, México
| | - Juan Núñez-Farfán
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, México 04510 Distrito Federal, México
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22
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Olsson S, Seoane-Zonjic P, Bautista R, Claros MG, González-Martínez SC, Scotti I, Scotti-Saintagne C, Hardy OJ, Heuertz M. Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers. Mol Ecol Resour 2016; 17:614-630. [PMID: 27718316 DOI: 10.1111/1755-0998.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain
| | - Pedro Seoane-Zonjic
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Rocío Bautista
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France
| | - Ivan Scotti
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Caroline Scotti-Saintagne
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Olivier J Hardy
- Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France.,Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
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Phylogeny and biogeography of the remarkable genus Bondarzewia (Basidiomycota, Russulales). Sci Rep 2016; 6:34568. [PMID: 27680391 PMCID: PMC5041112 DOI: 10.1038/srep34568] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/15/2016] [Indexed: 11/08/2022] Open
Abstract
Bondarzewia is a conspicuous and widely distributed mushroom genus, but little is known about its origin and biogeography. Here, we investigated the systematics and biogeography of Bondarzewia species using multi-locus phylogenetic analysis. Four genetic markers, including the internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (nLSU), elongation factor 1-α (tef1) and mitochondrial small subunit rDNA (mtSSU), were used to infer the phylogenetic relationships of Bondarzewia. We performed Bayesian evolutionary analysis on the gene datasets of the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). From the results, we inferred that the maximum crown age of Bondarzewia is approximately 25.5 million-years-ago (Mya) and that tropical East Asia is likely to be its ancestral area, with three possible expansions leading to its distribution in North America, Europe and Oceania.
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Ruhfel BR, Bove CP, Philbrick CT, Davis CC. Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade. AMERICAN JOURNAL OF BOTANY 2016; 103:1117-1128. [PMID: 27335391 DOI: 10.3732/ajb.1500537] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation. METHODS Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny. KEY RESULTS Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia. In contrast, dispersal occurred on > 25% of the branches, indicating the current distribution of the clade likely reflects extensive recent dispersal during the Cenozoic (< 65 Ma), most of which occurred after the beginning of the Eocene (∼56 Ma). CONCLUSIONS These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been influenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.
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Affiliation(s)
- Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, 521 Lancaster Avenue, Richmond, Kentucky 40475 USA Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138 USA
| | - Claudia P Bove
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro 20940-040, Brazil
| | - C Thomas Philbrick
- Biological & Environmental Sciences, Western Connecticut State University, 181 White Street, Danbury, Connecticut 06810 USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138 USA
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New ambrosia beetles (Coleoptera: Curculionidae: Platypodinae) from Miocene Mexican and Dominican ambers and their paleobiogeographical implications. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0213-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Willis CG, Franzone BF, Xi Z, Davis CC. The establishment of Central American migratory corridors and the biogeographic origins of seasonally dry tropical forests in Mexico. Front Genet 2014; 5:433. [PMID: 25566320 PMCID: PMC4271706 DOI: 10.3389/fgene.2014.00433] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/22/2014] [Indexed: 11/13/2022] Open
Abstract
Biogeography and community ecology can mutually illuminate the formation of a regional species pool or biome. Here, we apply phylogenetic methods to a large and diverse plant clade, Malpighiaceae, to characterize the formation of its species pool in Mexico, and its occupancy of the seasonally dry tropical forest (SDTF) biome that occurs there. We find that the ~162 species of Mexican Malpighiaceae represent ~33 dispersals from South America beginning in the Eocene and continuing until the Pliocene (~46.4-3.8 Myr). Furthermore, dispersal rates between South America and Mexico show a significant six-fold increase during the mid-Miocene (~23.9 Myr). We hypothesize that this increase marked the availability of Central America as an important corridor for Neotropical plant migration. We additionally demonstrate that this high rate of dispersal contributed substantially more to the phylogenetic diversity of Malpighiaceae in Mexico than in situ diversification. Finally, we show that most lineages arrived in Mexico pre-adapted with regard to one key SDTF trait, total annual precipitation. In contrast, these lineages adapted to a second key trait, precipitation seasonality, in situ as mountain building in the region gave rise to the abiotic parameters of extant SDTF. The timing of this in situ adaptation to seasonal precipitation suggests that SDTF likely originated its modern characteristics by the late Oligocene, but was geographically more restricted until its expansion in the mid-Miocene. These results highlight the complex interplay of dispersal, adaptation, and in situ diversification in the formation of tropical biomes. Our results additionally demonstrate that these processes are not static, and their relevance can change markedly over evolutionary time. This has important implications for understanding the origin of SDTF in Mexico, but also for understanding the temporal and spatial origin of biomes and regional species pools more broadly.
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Affiliation(s)
- Charles G Willis
- Center for the Environment, Harvard University Cambridge, MA, USA ; Department of Organismic and Evolutionary Biology, Harvard University Herbaria Cambridge, MA, USA
| | - Brian F Franzone
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria Cambridge, MA, USA
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria Cambridge, MA, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria Cambridge, MA, USA
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Cottet K, Genta-Jouve G, Fromentin Y, Odonne G, Duplais C, Laprévote O, Michel S, Lallemand MC. Comparative LC-MS-based metabolite profiling of the ancient tropical rainforest tree Symphonia globulifera. PHYTOCHEMISTRY 2014; 108:102-108. [PMID: 25301665 DOI: 10.1016/j.phytochem.2014.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 09/04/2014] [Accepted: 09/16/2014] [Indexed: 06/04/2023]
Abstract
In the last few years, several phytochemical studies have been undertaken on the tropical tree Symphonia globulifera leading to the isolation and characterisation of several compounds exhibiting antiparasitic activities against Plasmodium falciparum, Trypanosoma brucei and Leishmania donovani. The comparative LC-MS based metabolite profiling study conducted on the tree led to the identification of compounds originating from specific tissues. The results showed that renewable organs/tissues can be used as the starting material for the production of polycyclic poly-prenylated-acylphloroglucinols, therefore reducing impacts on biodiversity. This study also underlined the lack of knowledge on the secondary metabolites produced by S. globulifera since only a small number of the total detected features were putatively identified using the database of known compounds for the species.
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Affiliation(s)
- Kévin Cottet
- Laboratoire de Pharmacognosie, UMR 8638, Université Paris Descartes Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006 Paris, France
| | - Grégory Genta-Jouve
- Laboratoire de Pharmacognosie, UMR 8638, Université Paris Descartes Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006 Paris, France.
| | - Yann Fromentin
- Laboratoire de Pharmacognosie, UMR 8638, Université Paris Descartes Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006 Paris, France
| | - Guillaume Odonne
- CNRS Guyane, USR3456, 2 Avenue Gustave Charlery, 97300 Cayenne, France
| | - Christophe Duplais
- CNRS-UMR 8172 ECOFOG, Institut Pasteur de la Guyane, 23 Avenue Pasteur, 97306 Cayenne, France
| | - Olivier Laprévote
- Laboratoire de Chimie et Toxicologie Analytique et Cellulaire, UMR 8638, Université Paris Descartes Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006 Paris, France
| | - Sylvie Michel
- Laboratoire de Pharmacognosie, UMR 8638, Université Paris Descartes Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006 Paris, France
| | - Marie-Christine Lallemand
- Laboratoire de Pharmacognosie, UMR 8638, Université Paris Descartes Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006 Paris, France
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Conflict in outcomes for conservation based on population genetic diversity and genetic divergence approaches: a case study in the Japanese relictual conifer Sciadopitys verticillata (Sciadopityaceae). CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0615-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Brousseau L, Tinaut A, Duret C, Lang T, Garnier-Gere P, Scotti I. High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species. BMC Genomics 2014; 15:238. [PMID: 24673733 PMCID: PMC3986928 DOI: 10.1186/1471-2164-15-238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/13/2014] [Indexed: 12/30/2022] Open
Abstract
Background The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. Results In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs. Conclusion The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-238) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Ivan Scotti
- INRA, UMR 0745 EcoFoG, Campus agronomique BP 709, F-97387 Cedex, France.
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Bagley JC, Johnson JB. Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas. Biol Rev Camb Philos Soc 2014; 89:767-90. [PMID: 24495219 DOI: 10.1111/brv.12076] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 11/29/2013] [Accepted: 12/03/2013] [Indexed: 01/06/2023]
Abstract
Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene-Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.
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Affiliation(s)
- Justin C Bagley
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, 401 WIDB (Widtsoe Building), Provo, UT, 84602, U.S.A
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Ferreira WAS, Borges BDN, Rodrigues-Antunes S, de Andrade FAG, Aguiar GFDS, de Sousa e Silva-Junior J, Marques-Aguiar SA, Harada ML. Phylogeography of the dark fruit-eating bat Artibeus obscurus in the Brazilian Amazon. ACTA ACUST UNITED AC 2013; 105:48-59. [PMID: 24127548 DOI: 10.1093/jhered/est066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Artibeus obscurus (Mammalia: Chiroptera) is endemic to South America, being found in at least 18 Brazilian states. Recent studies revealed that different populations of this genus present distinct phylogeographic patterns; however, very little is known on the population genetics structure of A. obscurus in the Amazon rainforest. Here, using a fragment (1010bp) of the mitochondrial gene cytochrome b from 87 samples, we investigated patterns of genetic divergence among populations of A. obscurus from different locations in the Brazilian Amazon rainforest and compared them with other Brazilian and South American regions. Analysis of molecular variance (AMOVA), fixation index (Fst) analysis, and phylogeographic patterns showed divergence between two major monophyletic groups, each one corresponding to a geographic region associated with the Atlantic and Amazon forest biomes. The Atlantic forest clusters formed a monophyletic group with a high bootstrap support and a fragmented distribution that follows the pattern predicted by the Refuge Theory. On the other hand, a different scenario was observed for the Amazon forest, where no fragmentation was identified. The AMOVA results revealed a significant geographic heterogeneity in the distribution of genetic variation, with 70% found within populations across the studied populations (Fst values ranging from 0.05864 to 0.09673; φST = 0.55). The intrapopulational analysis revealed that one population (Bragança) showed significant evidence of population expansion, with the formation of 2 distinct phylogroups, suggesting the occurrence of a subspecies or at least a different population in this region. These results also suggest considerable heterogeneity for A. obscurus in the Amazon region.
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Affiliation(s)
- Wallax Augusto Silva Ferreira
- the Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará 66075-110, Brasil
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Fresia P, Azeredo-Espin AML, Lyra ML. The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis. PLoS One 2013; 8:e76168. [PMID: 24098436 PMCID: PMC3788763 DOI: 10.1371/journal.pone.0076168] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 08/21/2013] [Indexed: 11/20/2022] Open
Abstract
Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.
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Affiliation(s)
- Pablo Fresia
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, São Paulo, Brasil
- * E-mail:
| | - Ana Maria L. Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brasil
| | - Mariana L. Lyra
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, São Paulo, Brasil
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Surget-Groba Y, Kay KM. Restricted gene flow within and between rapidly diverging Neotropical plant species. Mol Ecol 2013; 22:4931-42. [PMID: 23952304 DOI: 10.1111/mec.12442] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 11/30/2022]
Abstract
Speciation involves the evolution of traits and genetic differences that contribute to reproductive isolation and the cessation of gene flow, and studying closely related species and divergent populations gives insight into how these phenomena proceed. Here, we document patterns of gene flow within and between two members of a rapid Neotropical species radiation, Costus pulverulentus and Costus scaber (Costaceae). These species co-occur in the tropical rainforest and share pollinators, but are reproductively isolated by a series of prezygotic barriers, some of which show evidence of reinforcement at sympatric sites. Here, we genotype microsatellite markers in plants from eight sites that span the geographical range of both species, including four sympatric sites. We also genotype putative hybrids found at two sympatric sites. We find high levels of genetic isolation among populations within each species and low but detectable levels of introgression between species at sympatric sites. Putative hybrids identified by morphology are consistent with F1 or more advanced hybrids. Our results highlight the effectiveness of prezygotic isolating mechanisms at maintaining species boundaries in young radiations and provide empirical data on levels of gene flow consistent with reinforcement.
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Affiliation(s)
- Yann Surget-Groba
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Menglun, Yunnan, 666303, China
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Bittrich V, Nascimento-Junior JED, Amaral MDCE, de Lima Nogueira PC. The anther oil of Symphonia globulifera L.f. (Clusiaceae). BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Leigh EG, O'Dea A, Vermeij GJ. Historical biogeography of the Isthmus of Panama. Biol Rev Camb Philos Soc 2013; 89:148-72. [DOI: 10.1111/brv.12048] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 05/24/2013] [Accepted: 06/06/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Egbert G. Leigh
- Smithsonian Tropical Research Institute; Panamá 0843-03092 Republic of Panamá
| | - Aaron O'Dea
- Smithsonian Tropical Research Institute; Panamá 0843-03092 Republic of Panamá
| | - Geerat J. Vermeij
- Department of Geology; University of California at Davis; Davis California 95616 U.S.A
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37
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Henss JM, Moeller JR, Theim TJ, Givnish TJ. Spatial scales of genetic structure and gene flow in Calochortus albus (Liliaceae). Ecol Evol 2013; 3:1461-70. [PMID: 23789059 PMCID: PMC3686183 DOI: 10.1002/ece3.566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 03/11/2013] [Accepted: 03/14/2013] [Indexed: 12/27/2022] Open
Abstract
Calochortus (Liliaceae) displays high species richness, restriction of many individual taxa to narrow ranges, geographic coherence of individual clades, and parallel adaptive radiations in different regions. Here we test the first part of a hypothesis that all of these patterns may reflect gene flow at small geographic scales. We use amplified fragment length polymorphism variation to quantify the geographic scales of spatial genetic structure and apparent gene flow in Calochortus albus, a widespread member of the genus, at Henry Coe State Park in the Coast Ranges south of San Francisco Bay. Analyses of 254 mapped individuals spaced 0.001–14.4 km apart show a highly significant decline in genetic identity with ln distance, implying a root-mean-square distance of gene flow σ of 5–43 m. STRUCTURE analysis implies the existence of 2–4 clusters over the study area, with frequent reversals among clusters over short distances (<200 m) and a relatively high frequency of admixture within individuals at most sampling sites. While the intensity of spatial genetic structure in C. albus is weak, as measured by the Sp statistic, that appears to reflect low genetic identity of adjacent plants, which might reflect repeated colonizations at small spatial scales or density-dependent mortality of individual genotypes by natural enemies. Small spatial scales of gene flow and spatial genetic structure should permit, under a variety of conditions, genetic differentiation within species at such scales, setting the stage ultimately for speciation and adaptive radiation as such scales as well.
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Affiliation(s)
- Jillian M Henss
- Department of Entomology, University of Wisconsin-Madison Madison, Wisconsin, 53706
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Budde KB, González-Martínez SC, Hardy OJ, Heuertz M. The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa. Heredity (Edinb) 2013; 111:66-76. [PMID: 23572126 DOI: 10.1038/hdy.2013.21] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation-coastal or swamp vs terra firme-in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.
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Affiliation(s)
- K B Budde
- INIA, Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7.5, Madrid, Spain.
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Turchetto-Zolet AC, Pinheiro F, Salgueiro F, Palma-Silva C. Phylogeographical patterns shed light on evolutionary process in South America. Mol Ecol 2012; 22:1193-213. [PMID: 23279129 DOI: 10.1111/mec.12164] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 11/28/2022]
Abstract
The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.
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Affiliation(s)
- A C Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, IB/UFRGS, Porto Alegre, RS, Brazil
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Dick CW, Lewis SL, Maslin M, Bermingham E. Neogene origins and implied warmth tolerance of Amazon tree species. Ecol Evol 2012; 3:162-9. [PMID: 23404439 PMCID: PMC3568851 DOI: 10.1002/ece3.441] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 10/27/2012] [Accepted: 11/01/2012] [Indexed: 11/05/2022] Open
Abstract
Tropical rain forest has been a persistent feature in South America for at least 55 million years. The future of the contemporary Amazon forest is uncertain, however, as the region is entering conditions with no past analogue, combining rapidly increasing air temperatures, high atmospheric carbon dioxide concentrations, possible extreme droughts, and extensive removal and modification by humans. Given the long-term Cenozoic cooling trend, it is unknown whether Amazon forests can tolerate air temperature increases, with suggestions that lowland forests lack warm-adapted taxa, leading to inevitable species losses. In response to this uncertainty, we posit a simple hypothesis: the older the age of a species prior to the Pleistocene, the warmer the climate it has previously survived, with Pliocene (2.6–5 Ma) and late-Miocene (8–10 Ma) air temperature across Amazonia being similar to 2100 temperature projections under low and high carbon emission scenarios, respectively. Using comparative phylogeographic analyses, we show that 9 of 12 widespread Amazon tree species have Pliocene or earlier lineages (>2.6 Ma), with seven dating from the Miocene (>5.6 Ma) and three >8 Ma. The remarkably old age of these species suggest that Amazon forests passed through warmth similar to 2100 levels and that, in the absence of other major environmental changes, near-term high temperature-induced mass species extinction is unlikely.
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Affiliation(s)
- Christopher W Dick
- Department of Ecology and Evolutionary Biology, University of Michigan 830 North University Avenue, Ann Arbor, MI, 48109-1048 ; Smithsonian Tropical Research Institute P.O. Box 0843-03092, Balboa Ancón, Republic of Panamá
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Cerón-Souza I, Bermingham E, McMillan WO, Jones FA. Comparative genetic structure of two mangrove species in Caribbean and Pacific estuaries of Panama. BMC Evol Biol 2012; 12:205. [PMID: 23078287 PMCID: PMC3543234 DOI: 10.1186/1471-2148-12-205] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/11/2012] [Indexed: 11/22/2022] Open
Abstract
Background Mangroves are ecologically important and highly threatened forest communities. Observational and genetic evidence has confirmed the long distance dispersal capacity of water-dispersed mangrove seeds, but less is known about the relative importance of pollen vs. seed gene flow in connecting populations. We analyzed 980 Avicennia germinans for 11 microsatellite loci and 940 Rhizophora mangle for six microsatellite loci and subsampled two non-coding cpDNA regions in order to understand population structure, and gene flow within and among four major estuaries on the Caribbean and Pacific coasts of Panama. Results Both species showed similar rates of outcrossing (t= 0.7 in A. germinans and 0.8 in R. mangle) and strong patterns of spatial genetic structure within estuaries, although A. germinans had greater genetic structure in nuclear and cpDNA markers (7 demes > 4 demes and Sp= 0.02 > 0.002), and much greater cpDNA diversity (Hd= 0.8 > 0.2) than R. mangle. The Central American Isthmus serves as an exceptionally strong barrier to gene flow, with high levels nuclear (FST= 0.3-0.5) and plastid (FST= 0.5-0.8) genetic differentiation observed within each species between coasts and no shared cpDNA haplotypes between species on each coast. Finally, evidence of low ratios of pollen to seed dispersal (r = −0.6 in A. germinans and 7.7 in R. mangle), coupled with the strong observed structure in nuclear and plastid DNA among most estuaries, suggests low levels of gene flow in these mangrove species. Conclusions We conclude that gene dispersal in mangroves is usually limited within estuaries and that coastal geomorphology and rare long distance dispersal events could also influence levels of structure.
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Poelchau MF, Hamrick JL. Differential effects of landscape-level environmental features on genetic structure in three codistributed tree species in Central America. Mol Ecol 2012; 21:4970-82. [PMID: 22988889 DOI: 10.1111/j.1365-294x.2012.05755.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 07/13/2012] [Accepted: 07/23/2012] [Indexed: 11/29/2022]
Abstract
Landscape genetic studies use spatially explicit population genetic information to determine the physical and environmental causes of population genetic structure on regional scales. Comparative studies that identify common barriers to gene flow across multiple species within a community are important to both understand the evolutionary trajectories of populations and prioritize habitat conservation. Here, we use a comparative landscape genetic approach to ask whether gradients in temperature or precipitation seasonality structure genetic variation across three codistributed tree species in Central America, or whether a simpler (geographic distance) or more complex, species-specific environmental niche model is necessary to individually explain population genetic structure. Using descriptive statistics and causal modelling, we find that different factors best explain genetic distance in each of the three species: environmental niche distance in Bursera simaruba, geographic distance in Ficus insipida and historical barriers to gene flow or cryptic reproductive barriers for Brosimum alicastrum. This study confirms suggestions from previous studies of Central American tree species that imply that population genetic structure of trees in this region is determined by complex interactions of both historical and current barriers to gene flow.
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Affiliation(s)
- Monica F Poelchau
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Collevatti RG, de Castro TG, de Souza Lima J, de Campos Telles MP. Phylogeography of Tibouchina papyrus (Pohl) Toledo (Melastomataceae), an endangered tree species from rocky savannas, suggests bidirectional expansion due to climate cooling in the Pleistocene. Ecol Evol 2012; 2:1024-35. [PMID: 22837846 PMCID: PMC3399167 DOI: 10.1002/ece3.236] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 02/05/2012] [Accepted: 02/08/2012] [Indexed: 11/05/2022] Open
Abstract
Many endemic species present disjunct geographical distribution; therefore, they are suitable models to test hypotheses about the ecological and evolutionary mechanisms involved in the origin of disjunct distributions in these habitats. We studied the genetic structure and phylogeography of Tibouchina papyrus (Melastomataceae), endemic to rocky savannas in Central Brazil, to test hypothesis of vicariance and dispersal in the origin of the disjunct geographical distribution. We sampled 474 individuals from the three localities where the species is reported: Serra dos Pirineus, Serra Dourada, and Serra de Natividade. Analyses were based on the polymorphisms at cpDNA and on nuclear microsatellite loci. To test for vicariance and dispersal we constructed a median-joining network and performed an analysis of molecular variance (AMOVA). We also tested population bottleneck and estimated demographic parameters and time to most recent common ancestor (TMRCA) using coalescent analyses. A remarkable differentiation among populations was found. No significant effect of population expansion was detected and coalescent analyses showed a negligible gene flow among populations and an ancient coalescence time for chloroplast genome. Our results support that the disjunct distribution of T. papyrus may represent a climatic relict. With an estimated TMRCA dated from ∼836.491 ± 107.515 kyr BP (before present), we hypothesized that the disjunct distribution may be the outcome of bidirectional expansion of the geographical distribution favored by the drier and colder conditions that prevailed in much of Brazil during the Pre-Illinoian glaciation, followed by the retraction as the climate became warmer and moister.
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Affiliation(s)
- Rosane Garcia Collevatti
- Laboratório de Genética e Biodiversidade, Departamento de Biologia Geral, ICB, Universidade Federal de Goiás CxP. 131, 74001-970 Goiânia, GO, Brazil
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Turchetto-Zolet AC, Cruz F, Vendramin GG, Simon MF, Salgueiro F, Margis-Pinheiro M, Margis R. Large-scale phylogeography of the disjunct Neotropical tree species Schizolobium parahyba (Fabaceae-Caesalpinioideae). Mol Phylogenet Evol 2012; 65:174-82. [PMID: 22750114 DOI: 10.1016/j.ympev.2012.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 05/28/2012] [Accepted: 06/01/2012] [Indexed: 10/28/2022]
Abstract
Neotropical rainforests exhibit high levels of endemism and diversity. Although the evolutionary genetics of plant diversification has garnered increased interest, phylogeographic studies of widely distributed species remain scarce. Here we describe chloroplast and nuclear variation patterns in Schizolobium parahyba (Fabaceae), a widespread tree in Neotropical rainforests that harbor two varieties with a disjunct distribution. Chloroplast and nuclear sequence analyses yielded 21 and 4 haplotypes, respectively. Two genetic diversity centers that correlate with the two known varieties were identified: the Southeastern Atlantic forest and the Amazonian basin. In contrast, the populations from southern and northeastern Atlantic forests and Andean-Central American forests exhibited low levels of genetic diversity and divergent haplotypes, likely related to historical processes that impact the flora and fauna in these regions, such as a founder's effect after dispersion and demographic expansion. Phylogeographic and demographic patterns suggest that episodes of genetic isolation and dispersal events have shaped the evolutionary history for this species, and different patterns have guided the evolution of S. parahyba. Moreover, the results of this study suggest that the dry corridor formed by Cerrado and Caatinga ecoregions and the Andean uplift acted as barriers to this species' gene flow, a picture that may be generalized to most of the plant biodiversity tropical woodlands and forests. These results also reinforce the importance of evaluating multiple genetic markers for a more comprehensive understanding of population structure and history. Our results provide insight into the conservation efforts and ongoing work on the genetics of population divergence and speciation in these Neotropical rainforests.
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Affiliation(s)
- Andreia C Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Dexter KG, Terborgh JW, Cunningham CW. Historical effects on beta diversity and community assembly in Amazonian trees. Proc Natl Acad Sci U S A 2012; 109:7787-92. [PMID: 22547831 PMCID: PMC3356654 DOI: 10.1073/pnas.1203523109] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a unique perspective on the role of historical processes in community assembly by synthesizing analyses of species turnover among communities with environmental data and independent, population genetic-derived estimates of among-community dispersal. We sampled floodplain and terra firme communities of the diverse tree genus Inga (Fabaceae) across a 250-km transect in Amazonian Peru and found patterns of distance-decay in compositional similarity in both habitat types. However, conventional analyses of distance-decay masked a zone of increased species turnover present in the middle of the transect. We estimated past seed dispersal among the same communities by examining geographic plastid DNA variation for eight widespread Inga species and uncovered a population genetic break in the majority of species that is geographically coincident with the zone of increased species turnover. Analyses of these and 12 additional Inga species shared between two communities located on opposite sides of the zone showed that the populations experienced divergence 42,000-612,000 y ago. Our results suggest that the observed distance decay is the result not of environmental gradients or dispersal limitation coupled with ecological drift--as conventionally interpreted under neutral ecological theory--but rather of secondary contact between historically separated communities. Thus, even at this small spatial scale, historical processes seem to significantly impact species' distributions and community assembly. Other documented zones of increased species turnover found in the western Amazon basin or elsewhere may be related to similar historical processes.
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Affiliation(s)
- Kyle G. Dexter
- Biology Department, University Program in Genetics and Genomics and
| | - John W. Terborgh
- Center for Tropical Conservation, Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC 27708
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Dick CW, Toby Pennington R. Molecular systematic perspectives on biome origins and dynamics. THE NEW PHYTOLOGIST 2012; 193:9-11. [PMID: 22136499 DOI: 10.1111/j.1469-8137.2011.03991.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Christopher W Dick
- Departments of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
- Smithsonian Tropical Research Institute, Gamboa, Republic of Panamá
- (Author for correspondence: tel +1 734 764 9408; email )
| | - R Toby Pennington
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
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Govindarajulu R, Hughes CE, Bailey CD. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation. AMERICAN JOURNAL OF BOTANY 2011; 98:2049-2063. [PMID: 22123714 DOI: 10.3732/ajb.1100259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. METHODS Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. RESULTS Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. CONCLUSIONS Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.
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Fresia P, Lyra ML, Coronado A, De Azeredo-Espin AML. Genetic structure and demographic history of new world screwworm across its current geographic range. JOURNAL OF MEDICAL ENTOMOLOGY 2011; 48:280-290. [PMID: 21485363 DOI: 10.1603/me10153] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The phylogeographical history of the pest fly screwworm, Cochliomyia hominivorax (Coquerel), was studied using partial mitochondrial DNA sequences of the control region, Cytochrome c oxidase (CO) subunit I and CO subunit II from 361 individuals collected across its current geographic range. Analyses showed marked genetic differentiation on a macrogeographic scale. The genetic diversity in the species is structured into four main "regional groups," corresponding to Cuba, the Dominican Republic, and the North and South Amazon region. Results indicated that the distribution of screwworm genetic diversity was mainly shaped by historical events, i.e., colonization of Caribbean islands, vicariance in the Amazon region and population expansion. Demographic history analyses revealed that the population expansion started approximately 20-25,000 yr ago and recently increased exponentially. We hypothesized that the initial period of expansion was probably associated with environmental amelioration in the late Pleistocene and the exponential increase with resource availability in recent times. The population expansion is probably responsible for the low divergence and the lack of genetic and geographic correlation in the South Amazon region but did not erase the genetic structure pattern on a continental scale. The screwworm is one of the most damaging livestock pests in South and Central America, and the pattern of genetic variability distribution reported here suggests that the Caribbean area and the North and South Amazon regions could be considered as independent units for future pest control programs.
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Affiliation(s)
- Pablo Fresia
- Laboratório de Genética e Evolução Animal-Centro de Biologia Molecular e Engenharia Genética and Instituto de Biologia, Universidade Estadual de Campinas, CEP 13083-875, Campinas, São Paulo, Brazil.
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Ruhfel BR, Bittrich V, Bove CP, Gustafsson MHG, Philbrick CT, Rutishauser R, Xi Z, Davis CC. Phylogeny of the clusioid clade (Malpighiales): evidence from the plastid and mitochondrial genomes. AMERICAN JOURNAL OF BOTANY 2011; 98:306-325. [PMID: 21613119 DOI: 10.3732/ajb.1000354] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY The clusioid clade includes five families (i.e., Bonnetiaceae, Calophyllaceae, Clusiaceae s.s., Hypericaceae, and Podostemaceae) represented by 94 genera and ≈1900 species. Species in this clade form a conspicuous element of tropical forests worldwide and are important in horticulture, timber production, and pharmacology. We conducted a taxon-rich multigene phylogenetic analysis of the clusioids to clarify phylogenetic relationships in this clade. METHODS We analyzed plastid (matK, ndhF, and rbcL) and mitochondrial (matR) nucleotide sequence data using parsimony, maximum likelihood, and Bayesian inference. Our combined data set included 194 species representing all major clusioid subclades, plus numerous species spanning the taxonomic, morphological, and biogeographic breadth of the clusioid clade. KEY RESULTS Our results indicate that Tovomita (Clusiaceae s.s.), Harungana and Hypericum (Hypericaceae), and Ledermanniella s.s. and Zeylanidium (Podostemaceae) are not monophyletic. In addition, we place four genera that have not been included in any previous molecular study: Ceratolacis, Diamantina, and Griffithella (Podostemaceae), and Santomasia (Hypericaceae). Finally, our results indicate that Lianthus, Santomasia, Thornea, and Triadenum can be safely merged into Hypericum (Hypericaceae). CONCLUSIONS We present the first well-resolved, taxon-rich phylogeny of the clusioid clade. Taxon sampling and resolution within the clade are greatly improved compared to previous studies and provide a strong basis for improving the classification of the group. In addition, our phylogeny will form the foundation for our future work investigating the biogeography of tropical angiosperms that exhibit Gondwanan distributions.
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Affiliation(s)
- Brad R Ruhfel
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138, USA.
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GOODALL-COPESTAKE WILLIAMP, PÉREZ-ESPONA SÍLVIA, HARRIS DAVIDJ, HOLLINGSWORTH PETERM. The early evolution of the mega-diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01489.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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