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Guillory WX, de Medeiros Magalhães F, Coelho FEA, Bonatelli IAS, Palma-Silva C, Moraes EM, Garda AA, Burbrink FT, Gehara M. Geoclimatic drivers of diversification in the largest arid and semi-arid environment of the Neotropics: Perspectives from phylogeography. Mol Ecol 2024; 33:e17431. [PMID: 38877815 DOI: 10.1111/mec.17431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.
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Affiliation(s)
- Wilson X Guillory
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey, USA
| | | | | | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York City, New York, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, Newark, New Jersey, USA
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Arenas S, Búrquez A, Bustamante E, Scheinvar E, Eguiarte LE. Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactus. PLoS One 2023; 18:e0282932. [PMID: 37384637 PMCID: PMC10309638 DOI: 10.1371/journal.pone.0282932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/26/2023] [Indexed: 07/01/2023] Open
Abstract
Genetic differentiations and phylogeographical patterns are controlled by the interplay between spatial isolation and gene flow. To assess the extent of gene flow across an oceanic barrier, we explored the effect of the separation of the peninsula of Baja California on the evolution of mainland and peninsular populations of the long-lived columnar cactus Stenocereus thurberi. We analyzed twelve populations throughout the OPC distribution range to assess genetic diversity and structure using chloroplast DNA sequences. Genetic diversity was higher (Hd = 0.81), and genetic structure was lower (GST = 0.143) in mainland populations vs peninsular populations (Hd = 0.71, GST = 0.358 respectively). Genetic diversity was negatively associated with elevation but positively with rainfall. Two mainland and one peninsular ancestral haplotypes were reconstructed. Peninsular populations were as isolated among them as with mainland populations. Peninsular haplotypes formed a group with one mainland coastal population, and populations across the gulf shared common haplotypes giving support to regular gene flow across the Gulf. Gene flow is likely mediated by bats, the main pollinators and seed dispersers. Niche modeling suggests that during the Last Glacial Maximum (c. 130 ka), OPC populations shrank to southern locations. Currently, Stenocereus thurberi populations are expanding, and the species is under population divergence despite ongoing gene flow. Ancestral populations are located on the mainland and although vicariant peninsular populations cannot be ruled out, they are likely the result of gene flow across the seemingly formidable barrier of the Gulf of California. Still, unique haplotypes occur in the peninsula and the mainland, and peninsular populations are more structured than those on the mainland.
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Affiliation(s)
- Sebastián Arenas
- DIADE, Université de Montpellier, IRD, Montpellier, France
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, México
| | - Alberto Búrquez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, México
| | - Enriquena Bustamante
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, México
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Chincoya DA, Arias S, Vaca-Paniagua F, Dávila P, Solórzano S. Phylogenomics and Biogeography of the Mammilloid Clade Revealed an Intricate Evolutionary History Arose in the Mexican Plateau. BIOLOGY 2023; 12:biology12040512. [PMID: 37106713 PMCID: PMC10135466 DOI: 10.3390/biology12040512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Mexico harbors ~45% of world’s cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera.
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Dantas-Queiroz MV, Hurbath F, de Russo Godoy FM, Lanna FM, Versieux LM, Palma-Silva C. Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species. Mol Ecol 2023. [PMID: 36934376 DOI: 10.1111/mec.16929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/20/2023]
Abstract
Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.
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Affiliation(s)
- Marcos Vinicius Dantas-Queiroz
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- Department of Evolutionary Plant Biology, Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, Czech Republic
| | - Fernanda Hurbath
- Universidade do Estado de Minas Gerais - Unidade Passos, Av. Juca Stockler, 1130, bairro Belo Horizonte, Passos, Brazil
| | - Fernanda Maria de Russo Godoy
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Flávia Mol Lanna
- Department of Evolution, Ecology and Organismal Biology. Museum of Biological Diversity, The Ohio State University, Columbus, Ohio, USA
| | - Leonardo M Versieux
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Clarisse Palma-Silva
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
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Romeiro-Brito M, Khan G, Perez MF, Zappi DC, Taylor NP, Olsthoorn G, Franco FF, Moraes EM. Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-17. [PMID: 36708517 DOI: 10.1002/ajb2.16134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts. METHODS We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts. RESULTS All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age. CONCLUSIONS We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky-University Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
| | - Manolo F Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), PO Box 04457, Brasília, DF, 70910-970, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, The Alameda, PO Box 843, GX11 1AA, Gibraltar
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
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Franco-Estrada D, Ortiz E, Villaseñor JL, Arias S. Species distribution modelling and predictor variables for species distribution and niche preferences of Pilosocereus leucocephalus group s.s. (Cactaceae). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2128928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Daniel Franco-Estrada
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Mexico City, 04510, Mexico
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Mexico City, 04510, Mexico
| | - Enrique Ortiz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Mexico City, 04510, Mexico
| | - José Luis Villaseñor
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Mexico City, 04510, Mexico
| | - Salvador Arias
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Mexico City, 04510, Mexico
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Bradbury D, Binks RM, van Leeuwen S, Coates DJ, McArthur SL, Macdonald BM, Hankinson M, Byrne M. The nuanced nature of mesic refugia in arid landscapes: a tale of two peas. ANNALS OF BOTANY 2022; 130:901-916. [PMID: 36219678 PMCID: PMC9758307 DOI: 10.1093/aob/mcac126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In temperate, glaciated environments, high genetic diversity in plant species is frequently found in refugial areas, which are often associated with southern non-glaciated landscapes. In arid, unglaciated environments, landscape features providing mesic conditions are likely to be refugia, although our understanding needs more refinement in these biomes. We test whether refugia and nuclear diversity hotspots occur in high-elevation, topographically complex areas for co-distributed shrubs (Petalostylis labicheoides and Indigofera monophylla; Fabaceae) in the ancient, arid Pilbara bioregion of north-western Australia. METHODS We conducted extensive sampling of the Pilbara (>1400 individuals from 62 widespread populations) to detect patterns in nuclear diversity and structure based on 13-16 microsatellite loci. Evidence of historical refugia was investigated based on patterns of diversity in three non-coding chloroplast (cp) sequence regions for approx. 240 individuals per species. Haplotype relationships were defined with median-joining networks and maximum likelihood phylogenetic trees. KEY RESULTS We found cpDNA evidence for a high-elevation refugium in P. labicheoides but not for I. monophylla that instead exhibited extraordinary haplotype diversity and evidence for persistence across a widespread area. Nuclear diversity hotspots occurred in, but were not exclusive to, high-elevation locations and extended to adjacent, low-elevation riparian areas in both species. CONCLUSIONS Phylogeographic refugia in arid environments may occur in high-elevation areas for some species but not all, and may be influenced by species-specific traits: a mesic montane refugium in P. labicheoides could be related to its preference for growth in water-gaining areas, while a lack of such evidence in I. monophylla could be related to maintenance of cpDNA diversity in a large soil seed bank and dynamic evolutionary history. Mesic environments created by the intersection of topographically complex landscapes with riparian zones can be contemporary reservoirs of genetic diversity in arid landscapes.
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Affiliation(s)
- Donna Bradbury
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Rachel M Binks
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Stephen van Leeuwen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - David J Coates
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Shelley L McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Bronwyn M Macdonald
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Margaret Hankinson
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, Perth, WA 6151, Australia
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Zhong H, Sun Y, Wu H, Li S, Shen Z, Yang C, Wen M, Chen P, Gu Q. Pleistocene climate and geomorphology drive the evolution and phylogeographic pattern of Triplophysa robusta (Kessler, 1876). Front Genet 2022; 13:955382. [PMID: 36171893 PMCID: PMC9510703 DOI: 10.3389/fgene.2022.955382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022] Open
Abstract
Montane systems provide excellent opportunities to study the rapid radiation influenced by geological and climatic processes. We assessed the role of Pleistocene climatic oscillations and mountain building on the evolution history of Triplophysa robusta, a cold-adapted species restricted to high elevations in China. We found seven differentiated sublineages of T. robusta, which were established during the Mid Pleistocene 0.87–0.61 Mya. The species distribution modeling (SDM) showed an expansion of T. robusta during the Last Glacial Maximum (LGM) and a considerable retraction during the Last Interglacial (LIG). The deep divergence between Clade I distributed in Qinling Mountains and Clade II in Northeastern Qinghai-Tibet Plateau (QTP) was mainly the result of a vicariance event caused by the rapid uplifting of Qinling Mountains during the Early Pleistocene. While the middling to high level of historical gene flow among different sublineages could be attributed to the dispersal events connected to the repetition of the glacial period during the Pleistocene. Our findings suggested that frequent range expansions and regressions due to Pleistocene glaciers likely have been crucial for driving the phylogeographic pattern of T. robusta. Finally, we urge a burning question in future conservation projection on the vulnerable cold-adapted species endemic to high elevations, as they would be negatively impacted by the recent rapid climate warming.
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Affiliation(s)
- Hui Zhong
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yaxian Sun
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Huihui Wu
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
| | - Shengnan Li
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zhongyuan Shen
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Conghui Yang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ming Wen
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Peng Chen
- Xinjiang Uygur Autonomous Region Fishery Research Institute, Urumchi, China
| | - Qianhong Gu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
- *Correspondence: Qianhong Gu,
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Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects. Genes (Basel) 2022; 13:genes13030452. [PMID: 35328006 PMCID: PMC8952820 DOI: 10.3390/genes13030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.
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Villalobos-Barrantes HM, Meriño BM, Walter HE, Guerrero PC. Independent Evolutionary Lineages in a Globular Cactus Species Complex Reveals Hidden Diversity in a Central Chile Biodiversity Hotspot. Genes (Basel) 2022; 13:genes13020240. [PMID: 35205285 PMCID: PMC8872226 DOI: 10.3390/genes13020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Unraveling the processes involved in the origin of a substantial fraction of biodiversity can be a particularly difficult task in groups of similar, and often convergent, morphologies. The genus Eriosyce (Cactaceae) might present a greater specific diversity since much of its species richness might be hidden in morphological species complexes. The aim of this study was to investigate species delimitation using the molecular data of the globose cacti “E. curvispina”, which harbor several populations of unclear evolutionary relationships. We ran phylogenetic inferences on 87 taxa of Eriosyce, including nine E. curvispina populations, and by analyzing three plastid noncoding introns, one plastid and one nuclear gene. Additionally, we developed 12 new pairs of nuclear microsatellites to evaluate the population-level genetic structure. We identified four groups that originated in independent cladogenetic events occurring at different temporal depths; these groups presented high genetic diversity, and their populations were genetically structured. These results suggest a complex evolutionary history in the origin of globular cacti, with independent speciation events occurring at different time spans. This cryptic richness is underestimated in the Mediterranean flora of central Chile, and thus unique evolutionary diversity could be overlooked in conservation and management actions.
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Affiliation(s)
- Heidy M. Villalobos-Barrantes
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4030000, Chile; (H.M.V.-B.); (B.M.M.)
- Escuela de Química, Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Beatriz M. Meriño
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4030000, Chile; (H.M.V.-B.); (B.M.M.)
- Institute of Ecology and Biodiversity (IEB), Concepción 4030000, Chile
| | - Helmut E. Walter
- The EXSIS Project: Cactaceae Ex-Situ & In-Situ Conservation, 31860 Emmerthal, Germany;
| | - Pablo C. Guerrero
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4030000, Chile; (H.M.V.-B.); (B.M.M.)
- Institute of Ecology and Biodiversity (IEB), Concepción 4030000, Chile
- Millennium Institute Biodiversity of Antarctic and Sub-Antarctic Ecosystems (BASE), Santiago 7800003, Chile
- Correspondence:
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Perez MF, Bonatelli IAS, Romeiro-Brito M, Franco FF, Taylor NP, Zappi DC, Moraes EM. Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system. Mol Ecol Resour 2021; 22:1016-1028. [PMID: 34669256 DOI: 10.1111/1755-0998.13534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 11/26/2022]
Abstract
Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P. aurisetus. Our results highlight the cryptic diversity within the P. aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.
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Affiliation(s)
- Manolo F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Isabel A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, Brazil
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
| | | | - Daniela C Zappi
- Programa de Pós Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
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12
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Bonatelli IAS, Gehara M, Carstens BC, Colli GR, Moraes EM. Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography. Mol Ecol 2021; 31:331-342. [PMID: 34614269 DOI: 10.1111/mec.16210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.
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Affiliation(s)
- Isabel A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, Brazil
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
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13
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Monteiro BL, Camargo MGG, Loiola PDP, Carstensen DW, Gustafsson S, Morellato LPC. Pollination in the campo rupestre: a test of hypothesis for an ancient tropical mountain vegetation. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The campo rupestre is a Neotropical OCBIL (old, climatically buffered infertile landscape), a grassy-shrub vegetation with high species richness and endemism, characterized by rocky outcrops surrounded by grasslands distributed in South American ancient mountaintops. We tested one OCBIL prediction: the prevalence of long-distance pollinators ensuring cross-pollination across the archipelago-like landscapes of the campo rupestre. We described the pollination systems and tested whether their frequency differed across vegetation types and elevation, focusing on long-distance systems. We performed non-systematic and systematic surveys of plants and plant-pollinator interactions across the elevation gradient and vegetation types. We also reviewed the literature on campo rupestre pollination and applied an accuracy criterion to infer 11 pollination systems. The bee system was split into large bee (long-distance) and small bee (shorter distances) to test the prevalence of long-distance pollination systems. We surveyed 413 pollinator species, mostly bees (220) and flies (69). Among the 636 plant species studied, the bee pollination system was dominant (56%), followed by wind and hummingbird. Wind, small-bee and fly pollination systems increased with elevation, and small-bee and wind pollination systems prevailed in grasslands. Large-bee and hummingbird long-distance pollination systems remained unchanged with elevation and were more frequent in the highly isolated rocky outcrops corroborating the OCBIL theory.
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Affiliation(s)
- Beatriz Lopes Monteiro
- Phenology Laboratory, Department of Biodiversity, Biosciences Institute, UNESP–São Paulo State University, Rio Claro, São Paulo, Brazil
| | - Maria Gabriela Gutierrez Camargo
- Phenology Laboratory, Department of Biodiversity, Biosciences Institute, UNESP–São Paulo State University, Rio Claro, São Paulo, Brazil
| | - Priscilla De Paula Loiola
- Phenology Laboratory, Department of Biodiversity, Biosciences Institute, UNESP–São Paulo State University, Rio Claro, São Paulo, Brazil
| | - Daniel Wisbech Carstensen
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Simone Gustafsson
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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14
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de Oliveira FFR, Gehara M, Solé M, Lyra M, Haddad CFB, Silva DP, de Magalhães RF, Leite FSF, Burbrink FT. Quaternary climatic fluctuations influence the demographic history of two species of sky-island endemic amphibians in the Neotropics. Mol Phylogenet Evol 2021; 160:107113. [PMID: 33610648 DOI: 10.1016/j.ympev.2021.107113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/13/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
We evaluated the role of Quaternary climatic fluctuations on the demographic history and population structure of amphibian species endemic to the 'campo rupestre' in the Neotropics, evaluating their distributional shifts, demographic changes, and lineage formation from the end of Pleistocene to present. We chose two anurans endemic to the high-elevation 'campo rupestre' in the Espinhaço Range (ER) in northeastern and southeastern Brazil (Bokermannohyla alvarengai and Bokermannohyla oxente), as models to test the role of Quaternary climatic fluctuations over their distribution range in this region. We collected tissue samples throughout their distribution range and used statistical phylogeography to examine processes of divergence and population demography. We generated spatial-temporal reconstructions using Bayesian inference in a coalescent framework in combination with hind-cast projections of species distribution models (SDMs). We also used the results and literature information to test alternative diversification scenarios via approximate Bayesian computation (ABC). Our results show that Quaternary climatic fluctuations influenced the geographic ranges of both species showing population expansion during the last glacial maximum (LGM) and range contraction during interglacial periods, as inferred from selected ABC models and from past projections of SDMs. We recovered Pleistocene diversification for both species occuring in distinctly unique periods for each taxon. An older and range-restricted lineage was recovered in a geographically isolated geological massif, deserving conservation and further taxonomic study. The diversification and distribution of these amphibian species endemic to the Neotropical 'campo rupestre' were influenced by Quaternary climatic fluctuations. The expansion of cold adapted species restricted to higher elevations during glacial periods and their concomitant retraction during interglacial periods may have been crucial for producing patterns of species richness and endemism along elevation gradients in tropical and subtropical domains. Such processes may influence the evolution of the biota distributed in heterogeneous landscapes with varied topography.
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Affiliation(s)
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University - Newark, USA
| | - Mirco Solé
- Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Bahia, Brazil; Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Mariana Lyra
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Célio Fernando Baptista Haddad
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Daniel Paiva Silva
- Instituto Federal Goiano - IF Goiano, Departamento de Biologia, Urutaí, Goiás, Brazil
| | - Rafael Félix de Magalhães
- Departamento de Ciências Naturais, Campus Dom Bosco, Universidade Federal de São João del-Rei, São João del Rei, MG 36301-160, Brazil
| | - Felipe Sá Fortes Leite
- Laboratório Sagarana, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa - UFV, Florestal, Minas Gerais, Brazil
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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15
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Carvalho TR, Seger KR, Magalhães FM, Lourenço LB, Haddad CFB. Systematics and cryptic diversification of
Leptodactylus
frogs in the Brazilian campo rupestre. ZOOL SCR 2020. [DOI: 10.1111/zsc.12470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thiago R. Carvalho
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
| | - Karin R. Seger
- Laboratório de Estudos Cromossômicos Departamento de Biologia Estrutural e Funcional Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Felipe M. Magalhães
- Programa de Pós‐Graduação em Ciências Biológicas Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa Brazil
| | - Luciana B. Lourenço
- Laboratório de Estudos Cromossômicos Departamento de Biologia Estrutural e Funcional Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Célio F. B. Haddad
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
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16
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Rapini A, Bitencourt C, Luebert F, Cardoso D. An escape-to-radiate model for explaining the high plant diversity and endemism in campos rupestres†. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
With extraordinary levels of plant diversity and endemism, the Brazilian campos rupestres across the Espinhaço Range have a species/area ratio 40 times higher than the lowland Amazon. Although diversification drivers in campos rupestres remain a matter of debate, the Pleistocene refugium hypothesis (PRH) is often adopted as the most plausible explanation for their high diversity. The PRH has two main postulates: highland interglacial refugia and a species pump mechanism catalysed by climatic changes. We critically assessed studies on campos rupestres diversification at different evolutionary levels and conclude that most of them are affected by sampling biases, unrealistic assumptions or inaccurate results that do not support the PRH. By modelling the palaeo-range of campos rupestres based on the distribution of 1123 species of vascular plants endemic to the Espinhaço Range and using climate and edaphic variables, we projected a virtually constant suitable area for campos rupestres across the last glacial cycle. We challenge the great importance placed on Pleistocene climatic oscillations in campos rupestres plant diversification and offer an alternative explanation named escape-to-radiate model, which emphasizes niche shifts. Under this biogeographic model of diversification, the long-term fragmentation of campos rupestres combined with recurrent extinctions after genetic drift and sporadic events of adaptive radiation may provide an explanation for the current diversity and endemism in the Espinhaço Range. We conclude that long-term diversification dynamics in campos rupestres are mainly driven by selection, while most endemic diversity is ephemeral, extremely fragile and mainly driven by drift.
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Affiliation(s)
- Alessandro Rapini
- Programa de Pós-graduação em Botânica, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana, Bahia, Brazil
| | - Cássia Bitencourt
- Programa de Pós-graduação em Botânica, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana, Bahia, Brazil
| | - Federico Luebert
- Departmento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile
| | - Domingos Cardoso
- Programa de Pós-graduação em Botânica, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana, Bahia, Brazil
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, Salvador, Bahia, Brazil
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17
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Andrino CO, Barbosa-Silva RG, Lovo J, Viana PL, Moro MF, Zappi DC. Iron islands in the Amazon: investigating plant beta diversity of canga outcrops. PHYTOKEYS 2020; 165:1-25. [PMID: 33192143 PMCID: PMC7642173 DOI: 10.3897/phytokeys.165.54819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/15/2020] [Indexed: 05/15/2023]
Abstract
The world's largest mineral iron province, Serra dos Carajás, is home to an open vegetation known as canga, found on top of isolated outcrops rising out of the Amazon rainforest. Over one thousand vascular plants species have been recorded in these canga sites, including 38 edaphic endemics. A new survey adds to our investigation of biogeographic relationships between sixteen canga outcrops and the effect of the distance between site pairs on the number of shared species, regional species turnover and species distribution patterns. Plant collecting expeditions to the westernmost site, the Serra de Campos of São Félix do Xingu (SFX), were carried out followed by the identification of all collected specimens and the creation of a species database, built to perform biogeographical analyses. Floristic relationships among the sites were investigated regarding their similarity, using multivariate analyses. The correlation between canga areas and species richness was tested, as well as the geographical distance between pairs of outcrops and their shared species. Vascular plants at SFX total 254 species including 17 edaphic endemics. All canga sites are grouped with 25% of minimum similarity, and the SFX falls within a large subgroup of outcrops. The total species number shared between site pairs does not change significantly with geographical distance but is positively correlated with the area of each outcrop. Meanwhile, shared endemic species numbers between site pairs decline when geographical distance increases, possibly imposed by the barrier of the rainforest. Our data suggest higher shared similarity between the largest and species-richest sites as opposed to geographically nearby sites, and provide useful insight for drafting conservation and compensation measures for canga locations. The size of the canga outcrops is associated to higher floristic diversity but connectivity among islands also plays a role in their similarity.
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Affiliation(s)
- Caroline Oliveira Andrino
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Rafael Gomes Barbosa-Silva
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Juliana Lovo
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Pedro Lage Viana
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
| | - Marcelo Freire Moro
- Instituto de Ciências do Mar (Labomar), Universidade Federal do Ceará, Fortaleza, Ceará, BrazilUniversidade Federal do CearáFortalezaBrazil
| | - Daniela Cristina Zappi
- Instituto Tecnológico Vale, Belém, Pará, BrazilInstituto Tecnológico ValeBelémBrazil
- Museu Paraense Emílio Goeldi, Coordenação Botânica, Belém, Pará, BrazilMuseu Paraense Emílio GoeldiBelémBrazil
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18
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From micro- to macroevolution: insights from a Neotropical bromeliad with high population genetic structure adapted to rock outcrops. Heredity (Edinb) 2020; 125:353-370. [PMID: 32681156 DOI: 10.1038/s41437-020-0342-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
Geographic isolation and reduced population sizes can lead to local extinction, low efficacy of selection and decreased speciation. However, population differentiation is an essential step of biological diversification. In allopatric speciation, geographically isolated populations differentiate and persist until the evolution of reproductive isolation and ecological divergence completes the speciation process. Pitcairnia flammea allows us to study the evolutionary consequences of habitat fragmentation on naturally disjoint rock-outcrop species from the Brazilian Atlantic Rainforest (BAF). Our main results showed low-to-moderate genetic diversity within populations, and deep population structuring caused by limited gene flow, low connectivity, genetic drift and inbreeding of long-term isolation and persistence of rock-outcrop populations throughout Quaternary climatic oscillations. Bayesian phylogenetic and model-based clustering analyses found no clear northern and southern phylogeographic structure commonly reported for many BAF organisms. Although we found two main lineages diverging by ~2 Mya during the early Pleistocene, species' delimitation analysis assigned most of the populations as independent evolving entities, suggesting an important role of disjoint rock outcrops in promoting high endemism in this rich biome. Lastly, we detected limited gene flow in sympatric populations although some hybridization and introgression were observed, suggesting a continuous speciation process in this species complex. Our data not only inform us about the extensive differentiation and limited gene flow found among Pitcairnia flammea species complex, but they also contain information about the mechanisms that shape the genetic architecture of small and fragmented populations of isolated rock outcrop of recently radiated plants.
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19
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Fraga DA, Carvalho AFD, Ribeiro CJB, Santana RS, Machado MC, Lacorte GA. Establishing population boundaries and conservation proposals for Coleocephalocereus purpureus, a critically endangered cactus species microendemic from Caatinga biome. J Nat Conserv 2020. [DOI: 10.1016/j.jnc.2020.125823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Guerrero PC, Majure LC, Cornejo-Romero A, Hernández-Hernández T. Phylogenetic Relationships and Evolutionary Trends in the Cactus Family. J Hered 2020; 110:4-21. [PMID: 30476167 DOI: 10.1093/jhered/esy064] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/21/2018] [Indexed: 12/29/2022] Open
Abstract
Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here, we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.
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Affiliation(s)
- Pablo C Guerrero
- Departamento de Botánica, Universidad de Concepción, Chile, Concepción, Chile
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Amelia Cornejo-Romero
- Departamento de Botánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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21
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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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22
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Khan G, Franco FF, Silva GAR, Bombonato JR, Machado M, Alonso DP, Ribolla PEM, Albach DC, Moraes EM. Maintaining genetic integrity with high promiscuity: Frequent hybridization with low introgression in multiple hybrid zones of Melocactus (Cactaceae). Mol Phylogenet Evol 2019; 142:106642. [PMID: 31605812 DOI: 10.1016/j.ympev.2019.106642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 09/27/2019] [Accepted: 10/06/2019] [Indexed: 10/25/2022]
Abstract
Hybridization and introgression between species in contact/hybrid zones provide important insight into the genetic and ecological mechanisms of speciation. Cactaceae represents the most important radiation of true succulent angiosperms in the New World. This diversification continues to date, with species experiencing few intrinsic barriers to gene flow and the frequent occurrence of natural hybridization. Here, we used RAD-Seq single-nucleotide polymorphism (SNP) data to investigate the genetic architecture of hybridization in four hybrid zones hosting Melocactus concinnus and four congeneric species (M. ernestii, M. glaucescens, M. paucispinus, and M. zehntneri). Our results revealed that M. concinnus is highly promiscuous in sympatric areas and hybridizes with various species distributed in Morro do Chapéu (Diamantina Plateau, Bahia), eastern Brazil. However, the contemporary genomic introgression among the investigated species is very low (c. 2-5%), confirming that even in the face of hybridization, Melocactus species maintain their genetic integrity. The genomic cline approach showed a large fraction of loci deviating from a model of neutral introgression, where most of the loci are consistent with selection favoring parental genotypes. Our results suggest the occurrence of weak premating but strong postmating reproductive isolation in the analyzed cactus species. Furthermore, as most of the Melocactus species are restricted in distribution, hybridization might negatively affect their integrity if hybrids replace the parental species.
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Affiliation(s)
- Gulzar Khan
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil
| | - Fernando F Franco
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil
| | - Gislaine A R Silva
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil
| | - Juliana R Bombonato
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil; Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Programa de Pós-graduação em Biologia Comparada, Brazil
| | - Marlon Machado
- Universidade Estadual de Feira de Santana, Bahia, Brazil
| | - Diego P Alonso
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), São Paulo State University (UNESP), Sao Paulo, Brazil
| | - Paulo E M Ribolla
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), São Paulo State University (UNESP), Sao Paulo, Brazil
| | - Dirk C Albach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Germany
| | - Evandro M Moraes
- Universidade Federal de São Carlos, Centro de Ciências Humanas e Biológicas, Departamento de Biologia, Brazil.
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Ossa CG, Montenegro P, Larridon I, Pérez F. Response of xerophytic plants to glacial cycles in southern South America. ANNALS OF BOTANY 2019; 124:15-26. [PMID: 30715148 PMCID: PMC6676391 DOI: 10.1093/aob/mcy235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND AIM Quaternary glaciations strongly affected the distribution of species from arid and semi-arid environments, as temperature drops were accompanied by strong fluctuations in rainfall. In this study, we examined the response of xerophytic species to glacial cycles, determining the genetic patterns and climatic niche of Echinopsis chiloensis var. chiloensis, an endemic columnar cactus of arid and semi-arid regions of Chile. METHODS We analysed 11 polymorphic microsatellites for 130 individuals from 13 populations distributed across the entire distribution of the species. We examined genetic diversity and structure, identified possible patterns of isolation by distance (IBD) and tested two competing population history scenarios using Approximate Bayesian Computation. The first scenario assumes a constant population size while the second includes a bottleneck in the southern population. The latter scenario assumed that the southernmost populations experienced a strong contraction during glaciation, followed by a postglacial expansion; by contrast, the area of the northernmost populations remained as a stable refugium. We also used ecological niche modelling (ENM) to evaluate the location and extension of suitable areas during the Last Glacial Maximum (LGM) and the mid-Holocene. KEY RESULTS We found a decline in genetic diversity towards high latitudes and a significant IBD pattern that together with ENM predictions suggest that E. chiloensis var. chiloensis experienced range contraction northwards during wet-cold conditions of the LGM, followed by expansion during aridification of the mid-Holocene. In addition to IBD, we detected the presence of a strong barrier to gene flow at 32°30'S, which according to coalescence analysis occurred 44 kyr BP. The resulting genetic clusters differed in realized climatic niche, particularly in the variables related to precipitation. CONCLUSIONS Our results suggest that the cactus E. chiloensis var. chiloensis experienced range contraction and fragmentation during the wet-cold conditions of the LGM, which may have facilitated ecological differentiation between northern and southern populations, promoting incipient speciation.
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Affiliation(s)
- Carmen G Ossa
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Escuela de Medicina Veterinaria, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Paz Montenegro
- Institute of Ecology and Biodiversity (IEB), Santiago, Chile
- Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Research Group Spermatophytes, Department of Biology, Ghent University, Ghent, Belgium
| | - Fernanda Pérez
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Santiago, Chile
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Dorsey BL, Gregory TJ, Sass C, Specht CD. Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae). AMERICAN JOURNAL OF BOTANY 2018; 105:1512-1530. [PMID: 30229556 DOI: 10.1002/ajb2.1149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation, thereby becoming separated by topography. METHODS We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences, we inferred dated species trees and lineage-specific diversification rates. KEY RESULTS Analyses of 84 newly sequenced nuclear orthologs and published plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa. CONCLUSIONS This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well-supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones.
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Affiliation(s)
- Brian L Dorsey
- The Huntington Library, Art Collections, and Botanical Gardens, San Marino, CA, 91108, USA
| | - Timothy J Gregory
- University of California Botanical Garden, 200 Centennial Drive, Berkeley, CA, 94720, USA
| | - Chodon Sass
- Department of Integrative Biology and the University and Jepson Herbaria, 431 Koshland Hall, University of California, Berkeley, CA, 94720, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, New York, 14853, USA
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Buzatti RSDO, Pfeilsticker TR, de Magalhães RF, Bueno ML, Lemos-Filho JP, Lovato MB. Genetic and Historical Colonization Analyses of an Endemic Savanna Tree, Qualea grandiflora, Reveal Ancient Connections Between Amazonian Savannas and Cerrado Core. FRONTIERS IN PLANT SCIENCE 2018; 9:981. [PMID: 30065733 PMCID: PMC6056688 DOI: 10.3389/fpls.2018.00981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/15/2018] [Indexed: 06/02/2023]
Abstract
The evolutionary processes underlying the high diversity and endemism in the Cerrado, the most extensive Neotropical savanna, remain unclear, including the factors promoting the presence and evolution of savanna enclaves in the Amazon forest. In this study, we investigated the effects of past climate changes on genetic diversity, dynamics of species range and the historical connections between the savanna enclaves and Cerrado core for Qualea grandiflora, a tree species widely distributed in the biome. Totally, 40 populations distributed in the Cerrado core and Amazon savannas were analyzed using chloroplast and nuclear DNA sequences. We used phylogeographic, coalescent and ecological niche modeling approaches. Genetic data revealed a phylogeographic structure shaped by Pleistocene climatic oscillations. An eastern-western split in the Cerrado core was observed. The central portion of the Cerrado core harbored most of the sampled diversity for cpDNA. Ecological niche models predicted the presence of a large historical refuge in this region and multiple small refuges in peripheral areas. Relaxed Random Walk (RRW) models indicated the ancestral population in the north-western border of the central portion of the Cerrado core and cyclical dynamics of colonization related to Pleistocene climatic oscillations. Central and western ancient connections between Cerrado core and Amazonian savannas were observed. No evidence of connections among the Amazonian savannas was detected. Our study highlights the importance of Pleistocene climatic oscillations for structuring the genetic diversity of Q. grandiflora and complex evolutionary history of ecotonal areas in the Cerrado. Our results do not support the recent replacement of a large area in the Amazon forest by savanna vegetation. The Amazonian savannas appear to be fragmented and isolated from each other, evolving independently a long ago.
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Affiliation(s)
| | - Thais R. Pfeilsticker
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rafael Félix de Magalhães
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcelo L. Bueno
- Departamento de Biologia Vegetal, Instituto de Ciências Biológicas, Universidade Federal de Viçosa, Viçosa, Brazil
| | - José P. Lemos-Filho
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria B. Lovato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Dequigiovanni G, Ramos SLF, Alves-Pereira A, Fabri EG, Picanço-Rodrigues D, Clement CR, Gepts P, Veasey EA. Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia. PLoS One 2018; 13:e0198593. [PMID: 29874280 PMCID: PMC5991381 DOI: 10.1371/journal.pone.0198593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/22/2018] [Indexed: 01/19/2023] Open
Abstract
Annatto (Bixa orellana L.) is a tropical American crop, commercially valuable due to its application in the food and cosmetics industries as a natural dye. The wild ancestor of cultivated annatto is B. orellana var. urucurana. Although never cultivated, this variety occurs in open forests and anthropogenic landscapes, and is always associated with riparian environments. In this study, we evaluated the genetic diversity and structure of B. orellana var. urucurana populations in Brazilian Amazonia using 16 microsatellite loci. We used Ecological Niche Modeling (ENM) to characterize the potential geographical range of this variety in northern South America. We analyzed 170 samples from 10 municipalities in the states of Rondônia, Pará and Roraima. A total of 194 alleles was observed, with an average of 12.1 alleles per locus. Higher levels of expected (HE) than observed (HO) heterozygosities were found for all populations. Bayesian analysis, Neighbor-Joining dendrograms and PCAs suggest the existence of three strongly structured groups of populations. A strong and positive correlation between genetic and geographic distances was found, suggesting that genetic differentiation might be caused by geographic isolation. From species distribution modelling, we detected that South Rondônia, Madre di Dios River basin, Llanos de Mojos, Llanos de Orinoco and eastern Ecuador are highly suitable areas for wild annatto to occur, providing additional targets for future exploration and conservation. Climatic adaptation analyses revealed strong differentiation among populations, suggesting that precipitation plays a key role in wild annatto’s current and potential distribution patterns.
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Affiliation(s)
- Gabriel Dequigiovanni
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
| | | | - Alessandro Alves-Pereira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
| | - Eliane Gomes Fabri
- Centro de Horticultura, Instituto Agronômico de Campinas, Campinas, São Paulo, Brasil
| | - Doriane Picanço-Rodrigues
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas (ICB-UFAM), Manaus, Amazonas, Brasil
| | | | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
- * E-mail:
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Weak population structure and no genetic erosion in Pilosocereus aureispinus: A microendemic and threatened cactus species from eastern Brazil. PLoS One 2018; 13:e0195475. [PMID: 29630653 PMCID: PMC5890996 DOI: 10.1371/journal.pone.0195475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/24/2018] [Indexed: 01/23/2023] Open
Abstract
Succulent cacti (Cactaceae) are among the most threatened taxonomic groups assessed to date. Here we evaluated the genetic diversity and population structure of a narrow endemic columnar cactus Pilosocereus aureispinus. This species is only found in a small area of c. 300 km2 of rocky savanna from eastern Brazil and it is currently classified as vulnerable (VU) on the International Union for Conservation of Nature (IUCN) red list. Eight microsatellite loci were genotyped for 91 individuals from four localities of the known P. aureispinus range. In contrast with expectations for narrow endemic species, we found relatively high levels of genetic diversity (e.g., HE = 0.390 to 0.525; HO = 0.394 to 0.572) and very low population structure based on the variation of six loci. All the analyzed individuals were clustered in one unique genetic group in assignment tests. We also generated the sequences of two plastid markers (trnT-trnL and psbD-trnT) and found no variation on a subsample of 39 individuals. We used Landsat 8 images and Normalized Difference Vegetation Index to estimate a potential extent of occurrence of c. 750 km2 for this species. Our results showed that P. aureispinus is not suffering from erosion of nuclear genetic variability due to its narrow distribution. However, we advocate that because of the extremely limited extent of occurrence, the ongoing anthropogenic disturbances in its habitat, and phylogenetic distinctiveness of P. aureispinus, this species should be classified as endangered (EN) on the IUCN Red List.
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Alvarado-Sizzo H, Casas A, Parra F, Arreola-Nava HJ, Terrazas T, Sánchez C. Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum. PLoS One 2018; 13:e0190385. [PMID: 29342184 PMCID: PMC5771577 DOI: 10.1371/journal.pone.0190385] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022] Open
Abstract
The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.
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Affiliation(s)
- Hernán Alvarado-Sizzo
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), Universidad Nacional Autónoma de México, Morelia, Michoacán, México
| | - Alejandro Casas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), Universidad Nacional Autónoma de México, Morelia, Michoacán, México
- * E-mail:
| | - Fabiola Parra
- Centro De Investigación De Zonas Áridas (CIZA), Universidad Nacional Agraria La Molina, La Molina, Lima, Perú
| | - Hilda Julieta Arreola-Nava
- Centro Universitario de Ciencias Biológicas y Agropecuarias (CUCBA), Universidad de Guadalajara, Zapopan, Jalisco, México
| | - Teresa Terrazas
- Instituto de Biología (IB), Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Cristian Sánchez
- Herbario de la Universidad de La Guajira, Riohacha, La Guajira, Colombia
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Barrios-Leal DY, Franco FF, Silva ECC, Santos CKB, Sene FM, Manfrin MH. Deep intraspecific divergence in Drosophila meridionalis, a cactophilic member of the New World Drosophila repleta group. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Franco FF, Jojima CL, Perez MF, Zappi DC, Taylor N, Moraes EM. The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti. Ecol Evol 2017; 7:9281-9293. [PMID: 29187968 PMCID: PMC5696397 DOI: 10.1002/ece3.3458] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/07/2017] [Accepted: 08/11/2017] [Indexed: 01/15/2023] Open
Abstract
In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS-trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.
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Affiliation(s)
- Fernando Faria Franco
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Cecília Leiko Jojima
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Manolo Fernandez Perez
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Daniela Cristina Zappi
- Museu Paraense Emilio GoeldiCoord. Botânica/Instituto Tecnológico ValeBelém do ParáBrazil
| | | | - Evandro Marsola Moraes
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
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de Magalhães RF, Lemes P, Camargo A, Oliveira U, Brandão RA, Thomassen H, Garcia PCDA, Leite FSF, Santos FR. Evolutionarily significant units of the critically endangered leaf frog Pithecopus ayeaye (Anura, Phyllomedusidae) are not effectively preserved by the Brazilian protected areas network. Ecol Evol 2017; 7:8812-8828. [PMID: 29177033 PMCID: PMC5689491 DOI: 10.1002/ece3.3261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/29/2017] [Accepted: 06/28/2017] [Indexed: 12/25/2022] Open
Abstract
Protected areas (PAs) are essential for biodiversity conservation, but their coverage is considered inefficient for the preservation of all species. Many species are subdivided into evolutionarily significant units (ESUs) and the effectiveness of PAs in protecting them needs to be investigated. We evaluated the usefulness of the Brazilian PAs network in protecting ESUs of the critically endangered Pithecopus ayeaye through ongoing climate change. This species occurs in a threatened mountaintop ecosystem known as campos rupestres. We used multilocus DNA sequences to delimit geographic clusters, which were further validated as ESUs with a coalescent approach. Ecological niche modeling was used to estimate spatial changes in ESUs' potential distributions, and a gap analysis was carried out to evaluate the effectiveness of the Brazilian PAs network to protect P. ayeaye in the face of climate changes. We tested the niche overlap between ESUs to gain insights for potential management alternatives for the species. Pithecopus ayeaye contains at least three ESUs isolated in distinct mountain regions, and one of them is not protected by any PA. There are no climatic niche differences between the units, and only 4% of the suitable potential area of the species is protected in present and future projections. The current PAs are not effective in preserving the intraspecific diversity of P. ayeaye in its present and future range distributions. The genetic structure of P. ayeaye could represent a typical pattern in campos rupestres endemics, which should be considered for evaluating its conservation status.
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Affiliation(s)
- Rafael Félix de Magalhães
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
- Programa de Desarrollo UniversitarioCentro Universitario de RiveraUniversidad de la República – UdelaRRiveraUruguay
| | - Priscila Lemes
- Laboratório de HerpetologiaDepartamento de ZoologiaInstituto de Biociências de Rio ClaroUniversidade Estadual “Júlio Mesquita Filho” – UNESPRio ClaroSão PauloBrasil
| | - Arley Camargo
- Programa de Desarrollo UniversitarioCentro Universitario de RiveraUniversidad de la República – UdelaRRiveraUruguay
| | - Ubirajara Oliveira
- Centro de Sensoriamento RemotoInstituto de GeociênciasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Reuber Albuquerque Brandão
- Laboratório de Fauna e Unidades de ConservaçãoDepartamento de Engenharia FlorestalFaculdade de TecnologiaUniversidade de Brasília – UnBBrasíliaDistrito FederalBrasil
| | - Hans Thomassen
- Graduação em Ciências BiológicasInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Paulo Christiano de Anchietta Garcia
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Felipe Sá Fortes Leite
- Laboratório SagaranaInstituto de Ciências Biológicas e da SaúdeUniversidade Federal de Viçosa – UFVFlorestalMinas GeraisBrasil
| | - Fabrício Rodrigues Santos
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
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Ramos EKS, de Magalhães RF, Sari EHR, Rosa AHB, Garcia PCA, Santos FR. Population genetics and distribution data reveal conservation concerns to the sky island endemic Pithecopus megacephalus (Anura, Phyllomedusidae). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1013-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Curto M, Puppo P, Kratschmer S, Meimberg H. Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons. BMC Evol Biol 2017; 17:198. [PMID: 28830342 PMCID: PMC5568322 DOI: 10.1186/s12862-017-1031-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 08/02/2017] [Indexed: 01/24/2023] Open
Abstract
Background Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572–575, 2005; Saunders and Gibson, J Ecol 93: 649–652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168–173, 2004; Silvertown et al., J Ecol 93: 653–657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. Results Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. Conclusions These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different effect: hybridization might always be related to colonization within the archipelago as well, making initial genetic diversity to be high to begin with. Thus the emergence of new islands promotes multiple colonization events, contributing to the establishment of hybrid swarms that may enhance adaptive ability and radiation events. With time, population sizes grow and niches start to fill. Consequently, gene-flow is not as effective at maintaining the species syngameon, which allows genetic differentiation and reproductive isolation to be established between species. This process contributes to an even further decrease in gene-flow between species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1031-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, A-1180, Vienna, Austria. .,CIBIO, Research Center in Biodiversity and Genetic Resources / InBio Associated Laboratory, University of Porto, Campus Vairão, 4485-661, Vairão, Portugal.
| | - P Puppo
- CIBIO, Research Center in Biodiversity and Genetic Resources / InBio Associated Laboratory, University of Porto, Campus Vairão, 4485-661, Vairão, Portugal
| | - S Kratschmer
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, A-1180, Vienna, Austria
| | - H Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, A-1180, Vienna, Austria
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Khan G, Godoy MO, Franco FF, Perez MF, Taylor NP, Zappi DC, Machado MC, Moraes EM. Extreme population subdivision or cryptic speciation in the cactus Pilosocereus jauruensis? A taxonomic challenge posed by a naturally fragmented system. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1359215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Gulzar Khan
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Mariana O. Godoy
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Fernando F. Franco
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Manolo F. Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Nigel P. Taylor
- Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Daniela C. Zappi
- Museu Paraense Emílio Goeldi, Av. Perimetral, 1901, Belém, Pará, Brazil
| | - Marlon C. Machado
- Universidade Estadual de Feira de Santana, Rodovia BR 116, km 03, 44031-460 Feira de Santana, Bahia, Brazil
| | - Evandro M. Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, 18052780 Sorocaba, São Paulo, Brazil
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Cornejo-Romero A, Vargas-Mendoza CF, Aguilar-Martínez GF, Medina-Sánchez J, Rendón-Aguilar B, Valverde PL, Zavala-Hurtado JA, Serrato A, Rivas-Arancibia S, Pérez-Hernández MA, López-Ortega G, Jiménez-Sierra C. Alternative glacial-interglacial refugia demographic hypotheses tested on Cephalocereus columna-trajani (Cactaceae) in the intertropical Mexican drylands. PLoS One 2017; 12:e0175905. [PMID: 28426818 PMCID: PMC5398652 DOI: 10.1371/journal.pone.0175905] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/02/2017] [Indexed: 12/27/2022] Open
Abstract
Historic demography changes of plant species adapted to New World arid environments could be consistent with either the Glacial Refugium Hypothesis (GRH), which posits that populations contracted to refuges during the cold-dry glacial and expanded in warm-humid interglacial periods, or with the Interglacial Refugium Hypothesis (IRH), which suggests that populations contracted during interglacials and expanded in glacial times. These contrasting hypotheses are developed in the present study for the giant columnar cactus Cephalocereus columna-trajani in the intertropical Mexican drylands where the effects of Late Quaternary climatic changes on phylogeography of cacti remain largely unknown. In order to determine if the historic demography and phylogeographic structure of the species are consistent with either hypothesis, sequences of the chloroplast regions psbA-trnH and trnT-trnL from 110 individuals from 10 populations comprising the full distribution range of this species were analysed. Standard estimators of genetic diversity and structure were calculated. The historic demography was analysed using a Bayesian approach and the palaeodistribution was derived from ecological niche modelling to determine if, in the arid environments of south-central Mexico, glacial-interglacial cycles drove the genetic divergence and diversification of this species. Results reveal low but statistically significant population differentiation (FST = 0.124, P < 0.001), although very clear geographic clusters are not formed. Genetic diversity, haplotype network and Approximate Bayesian Computation (ABC) demographic analyses suggest a population expansion estimated to have taken place in the Last Interglacial (123.04 kya, 95% CI 115.3–130.03). The species palaeodistribution is consistent with the ABC analyses and indicates that the potential area of palaedistribution and climatic suitability were larger during the Last Interglacial and Holocene than in the Last Glacial Maximum. Overall, these results suggest that C. columna-trajani experienced an expansion following the warm conditions of interglacials, in accordance with the GRH.
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Affiliation(s)
- Amelia Cornejo-Romero
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
| | - Carlos Fabián Vargas-Mendoza
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
- * E-mail:
| | - Gustavo F. Aguilar-Martínez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
| | | | - Beatriz Rendón-Aguilar
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | - Pedro Luis Valverde
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | | | - Alejandra Serrato
- Departamento de Hidrobiología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | | | | | - Gerardo López-Ortega
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | - Cecilia Jiménez-Sierra
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
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Lima JS, Telles MPC, Chaves LJ, Lima-Ribeiro MS, Collevatti RG. Demographic stability and high historical connectivity explain the diversity of a savanna tree species in the Quaternary. ANNALS OF BOTANY 2017; 119:645-657. [PMID: 28115317 PMCID: PMC5458718 DOI: 10.1093/aob/mcw257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/03/2016] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND AND AIMS Cyclic glaciations were frequent throughout the Quaternary and this affected species distribution and population differentiation worldwide. The present study reconstructed the demographic history and dispersal routes of Eugenia dysenterica lineages and investigated the effects of Quaternary climate change on its spatial pattern of genetic diversity. METHODS A total of 333 individuals were sampled from 23 populations and analysed by sequencing four regions of the chloroplast DNA and the internal transcribed spacer of the nuclear DNA. The analyses were performed using a multi-model inference approach based on ecological niche modelling and statistical phylogeography. KEY RESULTS Coalescent simulation showed that population stability through time is the most likely scenario. The palaeodistribution dynamics predicted by the ecological niche models revealed that the species was potentially distributed across a large area, extending over Central-Western Brazil through the last glaciation. The lineages of E. dysenterica dispersed from Central Brazil towards populations at the northern, western and south-eastern regions. A historical refugium through time may have favoured lineage dispersal and the maintenance of genetic diversity. CONCLUSIONS The results suggest that the central region of the Cerrado biome is probably the centre of distribution of E. dysenterica and that the spatial pattern of its genetic diversity may be the outcome of population stability throughout the Quaternary. The lower genetic diversity in populations in the south-eastern Cerrado biome is probably due to local climatic instability during the Quaternary.
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Affiliation(s)
- Jacqueline S. Lima
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, PO Box 131, 74001-970, Goiânia, Brazil
| | - Mariana P. C. Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, PO Box 131, 74001-970, Goiânia, Brazil
- Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, 74605-010, Goiânia, Brazil
| | - Lázaro J. Chaves
- Escola de Agronomia, Universidade Federal de Goiás, PO Box 131, 74001-970, Goiânia, Brazil
| | - Matheus S. Lima-Ribeiro
- Laboratório de Macroecologia, Universidade Federal de Goiás, PO Box 03, 75804-020, Jataí, Brazil
| | - Rosane G. Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, PO Box 131, 74001-970, Goiânia, Brazil
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Dayrell RLC, Garcia QS, Negreiros D, Baskin CC, Baskin JM, Silveira FAO. Phylogeny strongly drives seed dormancy and quality in a climatically buffered hotspot for plant endemism. ANNALS OF BOTANY 2017; 119:267-277. [PMID: 27568299 PMCID: PMC5321058 DOI: 10.1093/aob/mcw163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/24/2016] [Accepted: 06/22/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Models of costs and benefits of dormancy (D) predict that the evolutionarily stable strategy in long-term stable environments is for non-dormancy (ND), but this prediction remains to be tested empirically. We reviewed seed traits of species in the climatically buffered, geologically stable and nutrient-impoverished campo rupestre grasslands in Brazil to test the hypothesis that ND is favoured over D. We examined the relative importance of life-history traits and phylogeny in driving the evolution of D and assessed seed viability at the community level. METHODS Germination and viability data were retrieved from 67 publications and ND/D was determined for 168 species in 25 angiosperm families. We also obtained the percentage of embryoless, viable and dormant seeds for 74 species. Frequencies of species with dormant and non-dormant seeds were compared with global databases of dormancy distribution. KEY RESULTS The majority of campo rupestre taxa (62·5 %) had non-dormant seeds, and the ND/D ratio was the highest for any vegetation type on Earth. Dormancy was unrelated to other species life-history traits, suggesting that contemporary factors are poor predictors of D. We found a significant phylogenetic structure in the dormancy categorical trait. Dormancy diversity was highly skewed towards the root of the phylogenetic tree and there was a strong phylogenetic signal in the data, suggesting a major role of phylogeny in determining the evolution of D versus ND and seed viability. Quantitative analysis of the data revealed that at least half of the seeds produced by 46 % of the surveyed populations were embryoless and/or otherwise non-viable. CONCLUSIONS Our results support the view that long-term climatic and geological stability favour ND. Seed viability data show that campo rupestre species have a markedly low investment in regeneration from seeds, highlighting the need for specific in situ and ex situ conservation strategies to avoid loss of biodiversity.
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Affiliation(s)
- Roberta L C Dayrell
- Departamento de Botânica, ICB/UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais 31270-110, Brazil
| | - Queila S Garcia
- Departamento de Botânica, ICB/UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais 31270-110, Brazil
| | - Daniel Negreiros
- Instituto de Ciências Biológicas e Saúde, Centro Universitário UNA, Rua Guajajaras 175, 30180-100 Belo Horizonte, MG, Brazil
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Jerry M Baskin
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Fernando A O Silveira
- Departamento de Botânica, ICB/UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais 31270-110, Brazil
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Ribeiro PC, Souza ML, Muller LAC, Ellis VA, Heuertz M, Lemos-Filho JP, Lovato MB. Climatic drivers of leaf traits and genetic divergence in the tree Annona crassiflora: a broad spatial survey in the Brazilian savannas. GLOBAL CHANGE BIOLOGY 2016; 22:3789-3803. [PMID: 27062055 DOI: 10.1111/gcb.13312] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
The Cerrado is the largest South American savanna and encompasses substantial species diversity and environmental variation. Nevertheless, little is known regarding the influence of the environment on population divergence of Cerrado species. Here, we searched for climatic drivers of genetic (nuclear microsatellites) and leaf trait divergence in Annona crassiflora, a widespread tree in the Cerrado. The sampling encompassed all phytogeographic provinces of the continuous area of the Cerrado and included 397 individuals belonging to 21 populations. Populations showed substantial genetic and leaf trait divergence across the species' range. Our data revealed three spatially defined genetic groups (eastern, western and southern) and two morphologically distinct groups (eastern and western only). The east-west split in both the morphological and genetic data closely mirrors previously described phylogeographic patterns of Cerrado species. Generalized linear mixed effects models and multiple regression analyses revealed several climatic factors associated with both genetic and leaf trait divergence among populations of A. crassiflora. Isolation by environment (IBE) was mainly due to temperature seasonality and precipitation of the warmest quarter. Populations that experienced lower precipitation summers and hotter winters had heavier leaves and lower specific leaf area. The southwestern area of the Cerrado had the highest genetic diversity of A. crassiflora, suggesting that this region may have been climatically stable. Overall, we demonstrate that a combination of current climate and past climatic changes have shaped the population divergence and spatial structure of A. crassiflora. However, the genetic structure of A. crassiflora reflects the biogeographic history of the species more strongly than leaf traits, which are more related to current climate.
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Affiliation(s)
- Priciane C Ribeiro
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Matheus L Souza
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Larissa A C Muller
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Vincenzo A Ellis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Myriam Heuertz
- Forest Ecology and Genetics, Forest Research Centre, INIA, 28040, Madrid, Spain
- BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France
| | - José P Lemos-Filho
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Maria Bernadete Lovato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901, Belo Horizonte, Minas Gerais, Brazil.
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Puppo P, Curto M, Meimberg H. Genetic structure of Micromeria (Lamiaceae) in Tenerife, the imprint of geological history and hybridization on within-island diversification. Ecol Evol 2016; 6:3443-3460. [PMID: 28725348 PMCID: PMC5513284 DOI: 10.1002/ece3.2094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 02/26/2016] [Accepted: 03/03/2016] [Indexed: 01/17/2023] Open
Abstract
Geological history of oceanic islands can have a profound effect on the evolutionary history of insular flora, especially in complex islands such as Tenerife in the Canary Islands. Tenerife results from the secondary connection of three paleo‐islands by a central volcano, and other geological events that further shaped it. This geological history has been shown to influence the phylogenetic history of several taxa, including genus Micromeria (Lamiaceae). Screening 15 microsatellite markers in 289 individuals representing the eight species of Micromeria present in Tenerife, this study aims to assess the genetic diversity and structure of these species and its relation with the geological events on the island. In addition, we evaluate the extent of hybridization among species and discuss its influence on the speciation process. We found that the species restricted to the paleo‐islands present lower levels of genetic diversity but the highest levels of genetic differentiation suggesting that their ranges might have contracted over time. The two most widespread species in the island, M. hyssopifolia and M. varia, present the highest genetic diversity levels and a genetic structure that seems correlated with the geological composition of the island. Samples from M. hyssopifolia from the oldest paleo‐island, Adeje, appear as distinct while samples from M. varia segregate into two main clusters corresponding to the paleo‐islands of Anaga and Teno. Evidence of hybridization and intraspecific migration between species was found. We argue that species boundaries would be retained despite hybridization in response to the habitat's specific conditions causing postzygotic isolation and preserving morphological differentiation.
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Affiliation(s)
- Pamela Puppo
- CIBIO Research Center in Biodiversity and Genetic Resources/InBio Associated Laboratory University of Porto Campus Vairão Vairão 4485-661 Portugal.,Institute for Integrative Nature Conservation Research University of Natural Resources and Life Sciences A-1180 Vienna Austria
| | - Manuel Curto
- CIBIO Research Center in Biodiversity and Genetic Resources/InBio Associated Laboratory University of Porto Campus Vairão Vairão 4485-661 Portugal.,Institute for Integrative Nature Conservation Research University of Natural Resources and Life Sciences A-1180 Vienna Austria
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research University of Natural Resources and Life Sciences A-1180 Vienna Austria
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Perez MF, Bonatelli IAS, Moraes EM, Carstens BC. Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species. Heredity (Edinb) 2016; 116:550-7. [PMID: 27071846 DOI: 10.1038/hdy.2016.17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 02/06/2023] Open
Abstract
Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification.
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Affiliation(s)
- M F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - I A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - E M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - B C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Intra and interspecific sequence variation in closely related species of Cereus (CACTACEAE). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Perez MF, Carstens BC, Rodrigues GL, Moraes EM. Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America. Data Brief 2016; 6:456-60. [PMID: 26900589 PMCID: PMC4716445 DOI: 10.1016/j.dib.2015.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 11/26/2022] Open
Abstract
Supportive data related to the article “Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America” (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny.
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Affiliation(s)
- Manolo F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Gustavo L Rodrigues
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil
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Romeiro-Brito M, Moraes EM, Taylor NP, Zappi DC, Franco FF. Lineage-specific evolutionary rate in plants: Contributions of a screening for Cereus (Cactaceae). APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1500074. [PMID: 26819857 PMCID: PMC4716776 DOI: 10.3732/apps.1500074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Predictable chloroplast DNA (cpDNA) sequences have been listed for the shallowest taxonomic studies in plants. We investigated whether plastid regions that vary between closely allied species could be applied for intraspecific studies and compared the variation of these plastid segments with two nuclear regions. METHODS We screened 16 plastid and two nuclear intronic regions for species of the genus Cereus (Cactaceae) at three hierarchical levels (species from different clades, species of the same clade, and allopatric populations). RESULTS Ten plastid regions presented interspecific variation, and six of them showed variation at the intraspecific level. The two nuclear regions showed both inter- and intraspecific variation, and in general they showed higher levels of variability in almost all hierarchical levels than the plastid segments. DISCUSSION Our data suggest no correspondence between variation of plastid regions at the interspecific and intraspecific level, probably due to lineage-specific variation in cpDNA, which appears to have less effect in nuclear data. Despite the heterogeneity in evolutionary rates of cpDNA, we highlight three plastid segments that may be considered in initial screenings in plant phylogeographic studies.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos Km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Evandro M. Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos Km 110, 18052780 Sorocaba, São Paulo, Brazil
| | - Nigel P. Taylor
- National Parks Board, Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Daniela C. Zappi
- Conservation Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom
| | - Fernando F. Franco
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos Km 110, 18052780 Sorocaba, São Paulo, Brazil
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Perez MF, Carstens BC, Rodrigues GL, Moraes EM. Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America. Mol Phylogenet Evol 2015; 95:11-9. [PMID: 26582125 DOI: 10.1016/j.ympev.2015.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 11/30/2022]
Abstract
The Pilosocereus aurisetus complex consists of eight cactus species with a fragmented distribution associated to xeric enclaves within the Cerrado biome in eastern South America. The phylogeny of these species is incompletely resolved, and this instability complicates evolutionary analyses. Previous analyses based on both plastid and microsatellite markers suggested that this complex contained species with inherent phylogeographic structure, which was attributed to recent diversification and recurring range shifts. However, limitations of the molecular markers used in these analyses prevented some questions from being properly addressed. In order to better understand the relationship among these species and make a preliminary assessment of the genetic structure within them, we developed anonymous nuclear loci from pyrosequencing data of 40 individuals from four species in the P. aurisetus complex. The data obtained from these loci were used to identify genetic clusters within species, and to investigate the phylogenetic relationship among these inferred clusters using a species tree methodology. Coupled with a palaeodistributional modelling, our results reveal a deep phylogenetic and climatic disjunction between two geographic lineages. Our results highlight the importance of sampling more regions from the genome to gain better insights on the evolution of species with an intricate evolutionary history. The methodology used here provides a feasible approach to develop numerous genealogical molecular markers throughout the genome for non-model species. These data provide a more robust hypothesis for the relationship among the lineages of the P. aurisetus complex.
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Affiliation(s)
- Manolo F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Gustavo L Rodrigues
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil.
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Bonatelli IAS, Carstens BC, Moraes EM. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae). PLoS One 2015; 10:e0142602. [PMID: 26561396 PMCID: PMC4641700 DOI: 10.1371/journal.pone.0142602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.
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Affiliation(s)
| | - Bryan C. Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Evandro M. Moraes
- Department of Biology, Federal University of São Carlos, Sorocaba, São Paulo, Brazil
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Peterson AT, Anamza T. Ecological niches and present and historical geographic distributions of species: a 15-year review of frameworks, results, pitfalls, and promises. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a3.2015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- A. Townsend Peterson
- Biodiversity Institute, The University of Kansas, Lawrence, Kansas 66045, U.S.A.
| | - Tashitso Anamza
- Biodiversity Institute, The University of Kansas, Lawrence, Kansas 66045, U.S.A.
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Ingenloff K, Peterson AT. Trans-Amazon dispersal potential for Crotalus durissus during Pleistocene climate events. BIOTA NEOTROPICA 2015. [DOI: 10.1590/1676-06032015008113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two disjunct distributional areas of Crotalus durissus(Neotropical rattlesnake) are in open habitats north and south of the Amazon Basin and are presently separated by humid rainforest habitats. We used ecological niche modeling to identify and investigate potential dispersal pathways for this species between the two areas during the late Pleistocene. Niches estimated for the two populations did not differ significantly. Our analyses indicated two possible, but a single most likely, potential routes of dispersal during the last glacial cycle. These results are important to understanding the history of Amazon Basin humid forest biotas, as they suggest agents of isolation among putative humid forest refugia in the form of dry forest and scrub, and associated biotas.
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