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Vera-Paz SI, Granados Mendoza C, Díaz Contreras Díaz DD, Jost M, Salazar GA, Rossado AJ, Montes-Azcué CA, Hernández-Gutiérrez R, Magallón S, Sánchez-González LA, Gouda EJ, Cabrera LI, Ramírez-Morillo IM, Flores-Cruz M, Granados-Aguilar X, Martínez-García AL, Hornung-Leoni CT, Barfuss MH, Wanke S. Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage. FRONTIERS IN PLANT SCIENCE 2023; 14:1205511. [PMID: 37426962 PMCID: PMC10326849 DOI: 10.3389/fpls.2023.1205511] [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: 04/13/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]
Abstract
Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.
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Affiliation(s)
- Sandra I. Vera-Paz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Daniel D. Díaz Contreras Díaz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andrés J. Rossado
- Laboratorio de Sistemática de Plantas Vasculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia A. Montes-Azcué
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rebeca Hernández-Gutiérrez
- Departament of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis A. Sánchez-González
- Museo de Zoología “Alfonso L. Herrera”, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric J. Gouda
- Botanical Garden, Utrecht University, Utrecht, Netherlands
| | - Lidia I. Cabrera
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - María Flores-Cruz
- Departamento El Hombre y su Ambiente, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Xochimilco, Mexico City, Mexico
| | - Xochitl Granados-Aguilar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana L. Martínez-García
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Investigaciones Biológicas, Herbario HGOM, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Hidalgo, Mexico
| | - Claudia T. Hornung-Leoni
- Centro de Investigaciones Biológicas, Herbario HGOM, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Hidalgo, Mexico
| | - Michael H.J. Barfuss
- Departament of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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Leal BSS, Graciano VA, Chaves CJN, Huacre LAP, Heuertz M, Palma-Silva C. Dispersal and local persistence shape the genetic structure of a widespread Neotropical plant species with a patchy distribution. ANNALS OF BOTANY 2019; 124:499-512. [PMID: 31219156 PMCID: PMC6798837 DOI: 10.1093/aob/mcz105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND AIMS Isolated populations constitute an ideal laboratory to study the consequences of intraspecific divergence, because intrinsic incompatibilities are more likely to accumulate under reduced gene flow. Here, we use a widespread bromeliad with a patchy distribution, Pitcairnia lanuginosa, as a model to infer processes driving Neotropical diversification and, thus, to improve our understanding of the origin and evolutionary dynamics of biodiversity in this highly speciose region. METHODS We assessed the timing of lineage divergence, genetic structural patterns and historical demography of P. lanuginosa, based on microsatellites, and plastid and nuclear sequence data sets using coalescent analyses and an Approximate Bayesian Computation framework. Additionally, we used species distribution models (SDMs) to independently estimate potential changes in habitat suitability. KEY RESULTS Despite morphological uniformity, plastid and nuclear DNA data revealed two distinct P. lanuginosa lineages that probably diverged through dispersal from the Cerrado to the Central Andean Yungas, following the final uplift of the Andes, and passed through long-term isolation with no evidence of migration. Microsatellite data indicate low genetic diversity and high levels of inbreeding within populations, and restricted gene flow among populations, which are likely to be a consequence of bottlenecks (or founder events), and high selfing rates promoting population persistence in isolation. SDMs showed a slight expansion of the suitable range for P. lanuginosa lineages during the Last Glacial Maximum, although molecular data revealed a signature of older divergence. Pleistocene climatic oscillations thus seem to have played only a minor role in the diversification of P. lanuginosa, which probably persisted through adverse conditions in riparian forests. CONCLUSIONS Our results imply drift as a major force shaping the evolution of P. lanuginosa, and suggest that dispersal events have a prominent role in connecting Neotropical open and forest biomes.
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Affiliation(s)
- Bárbara Simões Santos Leal
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Vanessa Araujo Graciano
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Cleber Juliano Neves Chaves
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Luis Alberto Pillaca Huacre
- Departamento de Ecología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - Clarisse Palma-Silva
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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Leal BSS, Medeiros LR, Peres EA, Sobral-Souza T, Palma-Silva C, Romero GQ, Carareto CMA. Insights into the evolutionary dynamics of Neotropical biomes from the phylogeography and paleodistribution modeling of Bromelia balansae. AMERICAN JOURNAL OF BOTANY 2018; 105:1725-1734. [PMID: 30324691 DOI: 10.1002/ajb2.1167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/04/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Historical abiotic and biotic factors have strongly affected species diversification and speciation. Although pre-Pleistocene events have been linked to the divergence of several Neotropical organisms, studies have highlighted a more prominent role of Pleistocene climatic oscillations in shaping current patterns of genetic variation of plants. METHODS We performed phylogeographic analyses based on plastidial markers and modeled the current distribution and paleodistribution of Bromelia balansae (Bromeliaceae), an herbaceous species with a wide geographical distribution in South America, to infer the processes underlying its evolutionary history. KEY RESULTS Combined molecular and paleodistributional modeling analyses indicated retraction during the Last Glacial Maximum followed by interglacial expansion. Populations occurring in the semideciduous Atlantic Forest and the Cerrado formed two distinct genetic clusters, which have been historically or ecologically isolated since late Pliocene to early Pleistocene. Populations located in the transition zone had higher levels of genetic diversity, as expected by the long-term climatic stability in the region detected in our ecological niche models. CONCLUSIONS Our study adds important information on how herbaceous species have been affected by past climate in Central and Southeast Brazil, helping to disentangle the complex processes that have triggered the evolution of Neotropical biota.
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Affiliation(s)
- Bárbara S S Leal
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Câmpus de Rio Claro, SP, 13506-900, Brazil
| | - Lilian R Medeiros
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, 15054-000, Brazil
| | - Elen A Peres
- Universidade de São Paulo (USP), Instituto de Biociências, São Paulo, SP, 05508-090, Brazil
| | - Thadeu Sobral-Souza
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Câmpus de Rio Claro, SP, 13506-900, Brazil
| | - Clarisse Palma-Silva
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Câmpus de Rio Claro, SP, 13506-900, Brazil
- Universidade Estadual de Campinas (Unicamp), Instituto de Biologia, Campinas, SP, 13083-862, Brazil
| | - Gustavo Q Romero
- Universidade Estadual de Campinas (Unicamp), Instituto de Biologia, Campinas, SP, 13083-862, Brazil
| | - Claudia M A Carareto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, 15054-000, Brazil
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Winter K, Holtum JAM, Smith JAC. Crassulacean acid metabolism: a continuous or discrete trait? THE NEW PHYTOLOGIST 2015; 208:73-8. [PMID: 25975197 DOI: 10.1111/nph.13446] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/22/2015] [Indexed: 05/27/2023]
Abstract
The key components of crassulacean acid metabolism (CAM) - nocturnal fixation of atmospheric CO2 and its processing via Rubisco in the subsequent light period - are now reasonably well understood in terms of the biochemical reactions defining this water-saving mode of carbon assimilation. Phenotypically, however, the degree to which plants engage in the CAM cycle relative to regular C3 photosynthesis is highly variable. Depending upon species, ontogeny and environment, the contribution of nocturnal CO2 fixation to 24-h carbon gain can range continuously from close to 0% to 100%. Nevertheless, not all possible combinations of light and dark CO2 fixation appear equally common. Large-scale surveys of carbon-isotope ratios typically show a strongly bimodal frequency distribution, with relatively few intermediate values. Recent research has revealed that many species capable of low-level CAM activity are nested within the peak of C3 -type isotope signatures. While questions remain concerning the adaptive significance of dark CO2 fixation in such species, plants with low-level CAM should prove valuable models for investigating the discrete changes in genetic architecture and gene expression that have enabled the evolutionary transition from C3 to CAM.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - Joseph A M Holtum
- Centre for Tropical Biodiversity and Climate Change, James Cook University, Townsville, QLD, 4811, Australia
| | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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