1
|
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.
Collapse
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
| |
Collapse
|
2
|
The complete chloroplast genome of critically endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and phylogenetic analysis. Sci Rep 2022; 12:9649. [PMID: 35688841 PMCID: PMC9187695 DOI: 10.1038/s41598-022-13204-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
Chimonobambusa hirtinoda, a threatened species, is only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used to obtain the complete chloroplast (cp) genome sequence of C. hirtinoda. The sequence was assembled and analyzed for phylogenetic and evolutionary studies. Additionally, we compared the cp genome of C. hirtinoda with previously published Chimonobambusa species. The cp genome of C. hirtinoda has a total length of 139, 561 bp and 38.90% GC content. This genome included a large single -copy (LSC) region of 83, 166 bp, a small single-copy (SSC) region of 20, 811 bp and a pair of inverted repeats of 21,792 bp each. We discovered 130 genes in the cp genome, including 85 protein-coding genes, 37 tRNA, and 8 rRNA genes. A total of 48 simple sequence repeats (SSRs) were detected. The A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained by measuring the codon usage frequency of amino acids. Furthermore, phylogenetic analysis using complete cp sequences and matK gene revealed a genetic relationship within the Chimonobambusa genus. This study reported the chloroplast genome of the C. hirtinoda.
Collapse
|
3
|
Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species. Heredity (Edinb) 2022; 128:141-153. [PMID: 35132209 PMCID: PMC8897506 DOI: 10.1038/s41437-021-00491-0] [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: 03/22/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022] Open
Abstract
The role of natural selection in shaping spatial patterns of genetic diversity in the Neotropics is still poorly understood. Here, we perform a genome scan with 24,751 probes targeting 11,026 loci in two Neotropical Bignoniaceae tree species: Handroanthus serratifolius from the seasonally dry tropical forest (SDTF) and Tabebuia aurea from savannas, and compared with the population genomics of H. impetiginosus from SDTF. OutFLANK detected 29 loci in 20 genes with selection signal in H. serratifolius and no loci in T. aurea. Using BayPass, we found evidence of selection in 335 loci in 312 genes in H. serratifolius, 101 loci in 92 genes in T. aurea, and 448 loci in 416 genes in H. impetiginosus. All approaches evidenced several genes affecting plant response to environmental stress and primary metabolic processes. The three species shared no SNPs with selection signal, but we found SNPs affecting the same gene in pair of species. Handroanthus serratifolius showed differences in allele frequencies at SNPs with selection signal among ecosystems, mainly between Caatinga/Cerrado and Atlantic Forest, while H. impetiginosus had one allele fixed across all populations, and T. aurea had similar allele frequency distribution among ecosystems and polymorphism across populations. Taken together, our results indicate that natural selection related to environmental stress shaped the spatial pattern of genetic diversity in the three species. However, the three species have different geographical distribution and niches, which may affect tolerances and adaption, and natural selection may lead to different signatures due to the differences in adaptive landscapes in different niches.
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Abreu‐Jardim TPF, Jardim L, Ballesteros‐Mejia L, Maciel NM, Collevatti RG. Predicting impacts of global climatic change on genetic and phylogeographical diversity of a Neotropical treefrog. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Tatianne P. F. Abreu‐Jardim
- Laboratório de Genética & Biodiversidade Instituto de Ciências Biológicas Universidade Federal de Goiás (UFG) Goiânia Brazil
- Laboratório de Herpetologia e Comportamento Animal Departamento de Ecologia Instituto de Ciências Biológicas Universidade Federal de Goiás Goiânia Brazil
| | - Lucas Jardim
- Instituto Nacional de Ciência e Tecnologia (INCT) em Evolução e Conservação da Biodiversidade Instituto de Ciências Biológicas Universidade Federal de Goiás (UFG) Goiânia Brazil
| | - Liliana Ballesteros‐Mejia
- Institut de Systématique, Evolution, Biodiversité (ISYEB) UMR 7205 – CNRS MNHN UMPC EPHE Muséum National d'Histoire NaturelleSorbonne Université Paris France
| | - Natan M. Maciel
- Laboratório de Herpetologia e Comportamento Animal Departamento de Ecologia Instituto de Ciências Biológicas Universidade Federal de Goiás Goiânia Brazil
| | - Rosane G. Collevatti
- Laboratório de Genética & Biodiversidade Instituto de Ciências Biológicas Universidade Federal de Goiás (UFG) Goiânia Brazil
| |
Collapse
|
6
|
Sobreiro MB, Vieira LD, Nunes R, Novaes E, Coissac E, Silva-Junior OB, Grattapaglia D, Collevatti RG. Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae. PLANTA 2020; 252:91. [PMID: 33098500 DOI: 10.1007/s00425-020-03498-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.
Collapse
Affiliation(s)
- Mariane B Sobreiro
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Lucas D Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Evandro Novaes
- Laboratório de Genética Molecular, Departamento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200-900, Brazil
| | - Eric Coissac
- Laboratoire d'Écologie Alpine (LECA), University Grenoble-Alpes, Grenoble, Switzerland
| | | | - Dario Grattapaglia
- EMBRAPA Recursos Genéticos e Biotecnologia, EPqB, Brasília, DF, 70770-910, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil.
| |
Collapse
|
7
|
Collevatti RG, Lima JS, Ballesteros-Mejia L. Megafauna Seed Dispersal in the Neotropics: A Meta-Analysis Shows No Genetic Signal of Loss of Long-Distance Seed Dispersal. Front Genet 2019; 10:788. [PMID: 31543903 PMCID: PMC6739635 DOI: 10.3389/fgene.2019.00788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/25/2019] [Indexed: 12/02/2022] Open
Abstract
Restricted gene flow may lead to the loss of genetic diversity and higher genetic differentiation among populations, but the genetic consequences of megafauna extinction for plant populations still remain to be assessed. We performed a phylogenetic-independent meta-analysis across 102 Neotropical plants to test the hypothesis that plant species with megafaunal seed dispersal syndrome have a lower genetic diversity and a higher genetic differentiation than those without it. We classified as megafauna-dependent plant species those that potentially relied only on megafauna to seed dispersal, and as megafauna-independent those that relied on megafauna and other seed dispersers. Our data comprised 98 studies using microsatellite markers. We found no statistical difference in genetic diversity and differentiation between plants with megafauna and non-megafauna seed dispersal syndrome, although the statistical power to detect differences in genetic differentiation was low. Moreover, we found no statistical difference between megafauna-dependent and megafauna-independent plant species. We then used generalized linear mixed models and phylogenetic generalized least square models to investigate the effects of megafaunal seed dispersal syndromes and reproductive traits on variation in genetic diversity and genetic differentiation. We found no effect of megafaunal syndrome, rather, reproductive traits, such as pollination mode, mating, and breeding systems, showed significant effects. Our findings show that the genetic studies of Neotropical plants performed so far show no difference in genetic diversity and differentiation in plants with megafaunal compared to those with non-megafaunal seed dispersal syndromes. Our results also provide evidence pointing out that plant species with megafaunal seed dispersal syndromes may have used different strategies to counterbalance the extinction of their mutualistic megafauna dispersers, such as the dispersal by extant mammals that may promote long-distance seed dispersal. Our results also reinforce the importance of pollination to long-distance gene flow in Neotropical plants.
Collapse
Affiliation(s)
- Rosane G Collevatti
- Laboratório de Genética and Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Jacqueline S Lima
- Laboratório de Genética and Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Liliana Ballesteros-Mejia
- Laboratório de Genética and Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| |
Collapse
|
8
|
Backes A, Mäder G, Turchetto C, Segatto AL, Fregonezi JN, Bonatto SL, Freitas LB. How diverse can rare species be on the margins of genera distribution? AOB PLANTS 2019; 11:plz037. [PMID: 31391895 PMCID: PMC6677564 DOI: 10.1093/aobpla/plz037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.
Collapse
Affiliation(s)
- Alice Backes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Geraldo Mäder
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Caroline Turchetto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Lúcia Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Jeferson N Fregonezi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandro L Bonatto
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| |
Collapse
|
9
|
Záveská E, Maylandt C, Paun O, Bertel C, Frajman B, The Steppe Consortium, Schönswetter P. Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae). Mol Phylogenet Evol 2019; 139:106572. [PMID: 31351183 DOI: 10.1016/j.ympev.2019.106572] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
The Eurasian steppes occupy a significant portion of the worldwide land surface and their biota have been affected by specific past range dynamics driven by ice ages-related climatic fluctuations. The dynamic alterations in conditions during the Pleistocene often triggered reticulate evolution and whole genome duplication events. Employing genomic, genetic and cytogenetic tools as well as morphometry we investigate the intricate evolution of Astragalus onobrychis, a widespread Eurasian steppe plant with diploid, tetraploid and octoploid cytotypes. To analyse the heteroploid RADseq dataset we employ both genotype-based and genotype-free methods that result in highly consistent results, and complement our inference with information from the plastid ycf1 region. We uncover a complex and reticulate evolutionary history, including at least one auto-tetraploidization event and two allo-octoploidization events; one of them involved also genetic contributions from other species, most likely A. goktschaicus. The present genetic structure points to the existence of four main clades within A. onobrychis, which only partly correspond to different ploidies. Time-calibrated diffusion models suggest that diversification within A. onobrychis was associated with ice age-related climatic fluctuations during the last million years. We finally argue for the usefulness of uniparentally inherited plastid markers, even in the genomic era, especially when investigating heteroploid systems.
Collapse
Affiliation(s)
- Eliška Záveská
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Clemens Maylandt
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Clara Bertel
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - The Steppe Consortium
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria; Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria; Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria; Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria; Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain; Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy; Institute for Alpine Environment, Eurac Research, Drususallee 1/Viale Druso 1, 39100 Bozen/Bolzano, Italy
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria.
| |
Collapse
|
10
|
Collevatti RG, Novaes E, Silva-Junior OB, Vieira LD, Lima-Ribeiro MS, Grattapaglia D. A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree. Heredity (Edinb) 2019; 123:117-137. [PMID: 30755734 PMCID: PMC6781148 DOI: 10.1038/s41437-019-0188-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 01/13/2023] Open
Abstract
The role of natural selection in shaping patterns of diversity is still poorly understood in the Neotropics. We carried out the first genome-wide population genomics study in a Neotropical tree, Handroanthus impetiginosus (Bignoniaceae), sampling 75,838 SNPs by sequence capture in 128 individuals across 13 populations. We found evidences for local adaptation using Bayesian correlations of allele frequency and environmental variables (32 loci in 27 genes) complemented by an analysis of selective sweeps and genetic hitchhiking events using SweepFinder2 (81 loci in 47 genes). Fifteen genes were identified by both approaches. By accounting for population genetic structure, we also found 14 loci with selection signal in a STRUCTURE-defined lineage comprising individuals from five populations, using Outflank. All approaches pinpointed highly diverse and structurally conserved genes affecting plant development and primary metabolic processes. Spatial interpolation forecasted differences in the expected allele frequencies at loci under selection over time, suggesting that H. impetiginosus may track its habitat during climate changes. However, local adaptation through natural selection may also take place, allowing species persistence due to niche evolution. A high genetic differentiation was seen among the H. impetiginosus populations, which, together with the limited power of the experiment, constrains the improved detection of other types of soft selective forces, such as background, balanced, and purifying selection. Small differences in allele frequency distribution among widespread populations and the low number of loci with detectable adaptive sweeps advocate for a polygenic model of adaptation involving a potentially large number of small genome-wide effects.
Collapse
Affiliation(s)
- Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil.
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200-000, Brazil
| | - Orzenil B Silva-Junior
- EMBRAPA Recursos Genéticos e Biotecnologia, EPqB, Brasília, DF, 70770-910, Brazil.,Programa de Ciências Genômicas e Biotecnologia-Universidade Católica de Brasília, SGAN 916 Modulo B, Brasilia, DF, 70790-160, Brazil
| | - Lucas D Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
| | - Matheus S Lima-Ribeiro
- Laboratório de Macroecologia, Universidade Federal de Goiás (UFG), Campus Jataí, Jataí, GO, 75801-615, Brazil
| | - Dario Grattapaglia
- EMBRAPA Recursos Genéticos e Biotecnologia, EPqB, Brasília, DF, 70770-910, Brazil.,Programa de Ciências Genômicas e Biotecnologia-Universidade Católica de Brasília, SGAN 916 Modulo B, Brasilia, DF, 70790-160, Brazil
| |
Collapse
|
11
|
Lima NED, Carvalho AA, Lima-Ribeiro MS, Manfrin MH. Caracterização e história biogeográfica dos ecossistemas secos neotropicais. RODRIGUÉSIA 2018. [DOI: 10.1590/2175-7860201869445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Resumo A região Neotropical, detentora da maior riqueza de espécies no globo, ocorre do México Central ao sul do Brasil. Neste trabalho, buscamos sumarizar as principais informações disponíveis na literatura que caracterizam os biomas neotropicais de Florestas Sazonalmente Seca (FTSS), Chaco e Savanas. Revisamos hipóteses biogeográficas concernentes a esses ambientes que buscam explicar sua dinâmica histórica. Nosso objetivo é oferecer uma caracterização desses biomas como etapa principal para o entendimento das principais hipóteses biogeográficas a eles associadas. Ainda que comporte como um cenário atraente para pesquisa, as espécies neotropicais são pouco estudas, sendo questões referentes a seus aspectos ecológicos, origem, história evolutiva e manutenção da elevada biodiversidade desconhecidas ou, ainda, pouco compreendidas. Embora, nossa revisão apresente pesquisas com diferentes pontos de vista quanto à dinâmica biogeográfica das formações vegetais, há consenso de que é produto de complexa interação entre os processos históricos, ecológicos e biológicos. Os estudos em biodiversidade de regiões ameaçadas, como os Neotrópicos, são norteadores para simulações e previsões de impactos, planos e estratégias de pesquisa.
Collapse
|
12
|
Collevatti RG, Rodrigues EE, Vitorino LC, Lima-Ribeiro MS, Chaves LJ, Telles MPC. Unravelling the genetic differentiation among varieties of the Neotropical savanna tree Hancornia speciosa Gomes. ANNALS OF BOTANY 2018; 122:973-984. [PMID: 29897397 PMCID: PMC6266125 DOI: 10.1093/aob/mcy060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Background and Aims Spatial distribution of species genetic diversity is often driven by geographical distance (isolation by distance) or environmental conditions (isolation by environment), especially under climate change scenarios such as Quaternary glaciations. Here, we used coalescent analyses coupled with ecological niche modelling (ENM), spatially explicit quantile regression analyses and the multiple matrix regression with randomization (MMRR) approach to unravel the patterns of genetic differentiation in the widely distributed Neotropical savanna tree, Hancornia speciosa (Apocynaceae). Due to its high morphological differentiation, the species was originally classified into six botanical varieties by Monachino, and has recently been recognized as only two varieties by Flora do Brasil 2020. Thus, H. speciosa is a good biological model for learning about evolution of phenotypic plasticity under genetic and ecological effects, and predicting their responses to changing environmental conditions. Methods We sampled 28 populations (777 individuals) of Monachino's four varieties of H. speciosa and used seven microsatellite loci to genotype them. Key Results Bayesian clustering showed five distinct genetic groups (K = 5) with high admixture among Monachino's varieties, mainly among populations in the central area of the species geographical range. Genetic differentiation among Monachino's varieties was lower than the genetic differentiation among populations within varieties, with higher within-population inbreeding. A high historical connectivity among populations of the central Cerrado shown by coalescent analyses may explain the high admixture among varieties. In addition, areas of higher climatic suitability also presented higher genetic diversity in such a way that the wide historical refugium across central Brazil might have promoted the long-term connectivity among populations. Yet, FST was significantly related to geographic distances, but not to environmental distances, and coalescent analyses and ENM predicted a demographical scenario of quasi-stability through time. Conclusions Our findings show that demographical history and isolation by distance, but not isolation by environment, drove genetic differentiation of populations. Finally, the genetic clusters do not support the two recently recognized botanical varieties of H. speciosa, but partially support Monachino's classification at least for the four sampled varieties, similar to morphological variation.
Collapse
Affiliation(s)
- Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Eduardo E Rodrigues
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | | | - Matheus S Lima-Ribeiro
- Laboratório de Macroecologia, Instituto de Biociências, Universidade Federal de Goiás (UFG), Regional Jataí, Jataí, GO, Brasil
| | - Lázaro J Chaves
- Escola de Agronomia, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Mariana P C Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil
- Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, Goiânia, GO, Brasil
| |
Collapse
|
13
|
Diversification of the widespread neotropical frog Physalaemus cuvieri in response to Neogene-Quaternary geological events and climate dynamics. Mol Phylogenet Evol 2018; 132:67-80. [PMID: 30508632 DOI: 10.1016/j.ympev.2018.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/06/2018] [Accepted: 11/10/2018] [Indexed: 11/24/2022]
Abstract
Here we reconstructed the demographical history and the dispersal dynamics of Physalemus cuvieri through the Neogene-Quaternary periods by coupling DNA regions with different mutation rates, ecological niche modelling, reconstruction of spatio-temporal lineage dispersal and coalescent simulations. Still, to test alternative diversification scenarios we used approximate Bayesian computation. Molecular phylogenetic analysis recovered four deep and strongly supported clades, which we interpret as population lineages. The ancestral location reconstruction placed the root in southcentral Amazonia, and the dispersal events indicate that spatial displacement was widespread early in the diversification of this species. The demographical scenario of "Multiple Refugia" with recent lineage admixture was the most likely hypothesis to predict the observed genetic parameters of P. cuvieri. Our results revealed that Neogene orogenic events might have played a prominent role in the early diversification of P. cuvieri. The species shows deep divergences with strong regional population structure, despite its widespread distribution. Final uplift of the central Brazilian Plateau and formation of the river basins in Central South America played an important role in the origin, diversification and the maintenance of P. cuvieri lineages.
Collapse
|
14
|
Oliveira HR, Staggemeier VG, Quintino Faria JE, de Oliveira G, Diniz-Filho JAF. Geographical ecology and conservation of Eugenia
L. (Myrtaceae) in the Brazilian Cerrado: Past, present and future. AUSTRAL ECOL 2018. [DOI: 10.1111/aec.12657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Hauanny Rodrigues Oliveira
- Programa de Pós-Graduação em Genética e Biologia Molecular; ICB; Universidade Federal de Goiás; CP 131 74001-970 Goiânia GO Brazil
| | - Vanessa G. Staggemeier
- Department of Botany; Phenology Lab; Institute of Biosciences; São Paulo State University (UNESP); Rio Claro São Paulo Brazil
| | | | - Guilherme de Oliveira
- Laboratório de Biogeografia da Conservação; Setor de Biologia; Centro de Ciências Agrárias, Ambientais e Biológicas; Universidade Federal do Recôncavo da Bahia; Cruz das Almas BA Brazil
| | | |
Collapse
|
15
|
Melo WA, Freitas CG, Bacon CD, Collevatti RG. The road to evolutionary success: insights from the demographic history of an Amazonian palm. Heredity (Edinb) 2018; 121:183-195. [PMID: 29588509 PMCID: PMC6039527 DOI: 10.1038/s41437-018-0074-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/23/2018] [Accepted: 03/15/2018] [Indexed: 12/22/2022] Open
Abstract
Evolutionary success, as demonstrated by high abundance and a wide geographical range, is related to genetic variation and historical demography. Here we assess how climatic change during the Quaternary influenced the demography and distribution of the Neotropical swamp palm Mauritia flexuosa. Using microsatellite loci and coalescent analyses we examined how demographical dynamics affected genetic diversity, effective population size and connectivity through time and space. Mauritia flexuosa presents significant genetic differentiation between the Amazonian and Cerrado biomes and among different river basins. Amazonian lineages are ancient compared to lineages from the Cerrado, a pattern corroborated using the fossil pollen record, where the species was absent from the Cerrado during the cold and dry periods of the last glacial cycles, then returned during the wet, interglacial phases. Coalescent simulations show that the pattern of observed genetic diversity for M. flexuosa is most likely due to a range retraction during the Last Glacial Maximum, leading to multiple refugia and resulting in high differentiation between Amazonian and Cerrado biomes. Isolation-by-distance and by-environment also shaped the distribution and evolutionary success of M. flexuosa. Our study provides new insights into the historical factors that affected geographical distribution and structure genetic diversity, contributing to long-term evolutionary success.
Collapse
Affiliation(s)
- Warita A Melo
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Cintia G Freitas
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil.
| |
Collapse
|
16
|
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: 18] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
17
|
Vitorino LC, Lima-Ribeiro MS, Terribile LC, Collevatti RG. Demographical expansion of Handroanthus ochraceus in the Cerrado during the Quaternary: implications for the genetic diversity of Neotropical trees. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Luciana Cristina Vitorino
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas (ICB), Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | - Matheus S Lima-Ribeiro
- Laboratório de Macroecologia, Instituto de Biociências, Universidade Federal de Goiás (UFG), Jataí, GO, Brazil
| | - Levi Carina Terribile
- Laboratório de Macroecologia, Instituto de Biociências, Universidade Federal de Goiás (UFG), Jataí, GO, Brazil
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas (ICB), Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| |
Collapse
|
18
|
Lima JS, Ballesteros-Mejia L, Lima-Ribeiro MS, Collevatti RG. Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species. GLOBAL CHANGE BIOLOGY 2017; 23:4639-4650. [PMID: 28295840 DOI: 10.1111/gcb.13685] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/09/2017] [Accepted: 03/01/2017] [Indexed: 05/07/2023]
Abstract
The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long-lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions.
Collapse
Affiliation(s)
- Jacqueline S Lima
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Liliana Ballesteros-Mejia
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | | | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Resende-Moreira LC, Vasconcelos PND, Souto AP, Menezes APA, Lemos-Filho JPD, Lovato MB. East-west divergence in central Brazilian Cerrado revealed by cpDNA sequences of a bird-dispersed tree species. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
22
|
Souza HAVE, Collevatti RG, Lima-Ribeiro MS, Lemos-Filho JPD, Lovato MB. A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species. ANNALS OF BOTANY 2017; 119:239-252. [PMID: 27311573 PMCID: PMC5321056 DOI: 10.1093/aob/mcw096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/02/2015] [Accepted: 03/29/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated. METHODS A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM). KEY RESULTS Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium. CONCLUSIONS The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary potential of the species under predicted future climatic changes.
Collapse
Affiliation(s)
- Helena Augusta Viana E Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás, Caixa Postal 131, 74001-970 Goiânia, GO, Brazil
| | - Matheus S Lima-Ribeiro
- Laboratório de Macroecologia, Universidade Federal de Goiás, Campus Jataí, 75801-615 Jataí, GO, Brazil
| | - José Pires de Lemos-Filho
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Maria Bernadete Lovato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
| |
Collapse
|
23
|
Vitorino LC, Lima-Ribeiro MS, Terribile LC, Collevatti RG. Demographical history and palaeodistribution modelling show range shift towards Amazon Basin for a Neotropical tree species in the LGM. BMC Evol Biol 2016; 16:213. [PMID: 27737632 PMCID: PMC5062830 DOI: 10.1186/s12862-016-0779-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We studied the phylogeography and demographical history of Tabebuia serratifolia (Bignoniaceae) to understand the disjunct geographical distribution of South American seasonally dry tropical forests (SDTFs). We specifically tested if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the last glacial maximum (LGM), the so called South American dry forest refugia hypothesis, using ecological niche modelling (ENM) and statistical phylogeography. We sampled 235 individuals of T. serratifolia in 17 populations in Brazil and analysed the polymorphisms at three intergenic chloroplast regions and ITS nuclear ribosomal DNA. RESULTS Coalescent analyses showed a demographical expansion at the last c. 130 ka (thousand years before present). Simulations and ENM also showed that the current spatial pattern of genetic diversity is most likely due to a scenario of range expansion and range shift towards the Amazon Basin during the colder and arid climatic conditions associated with the LGM, matching the expected for the South American dry forest refugia hypothesis, although contrasting to the Pleistocene Arc hypothesis. Populations in more stable areas or with higher suitability through time showed higher genetic diversity. Postglacial range shift towards the Southeast and Atlantic coast may have led to spatial genome assortment due to leading edge colonization as the species tracks suitable environments, leading to lower genetic diversity in populations at higher distance from the distribution centroid at 21 ka. CONCLUSION Haplotype sharing or common ancestry among populations from Caatinga in Northeast Brazil, Atlantic Forest in Southeast and Cerrado biome and ENM evince the past connection among these biomes.
Collapse
Affiliation(s)
- Luciana Cristina Vitorino
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Goiás (UFG), Cx.P. 131, Goiânia, GO, 74001-970, Brazil
| | - Matheus S Lima-Ribeiro
- Laboratório de Macroecologia, Universidade Federal de Goiás (UFG), Campus Jataí, Cx.P. 03, Jataí, GO, 75801-615, Brazil
| | - Levi Carina Terribile
- Laboratório de Macroecologia, Universidade Federal de Goiás (UFG), Campus Jataí, Cx.P. 03, Jataí, GO, 75801-615, Brazil
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Goiás (UFG), Cx.P. 131, Goiânia, GO, 74001-970, Brazil.
| |
Collapse
|
24
|
de Melo WA, Lima-Ribeiro MS, Terribile LC, Collevatti RG. Coalescent Simulation and Paleodistribution Modeling for Tabebuia rosealba Do Not Support South American Dry Forest Refugia Hypothesis. PLoS One 2016; 11:e0159314. [PMID: 27458982 PMCID: PMC4961443 DOI: 10.1371/journal.pone.0159314] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 06/30/2016] [Indexed: 11/18/2022] Open
Abstract
Studies based on contemporary plant occurrences and pollen fossil records have proposed that the current disjunct distribution of seasonally dry tropical forests (SDTFs) across South America is the result of fragmentation of a formerly widespread and continuously distributed dry forest during the arid climatic conditions associated with the Last Glacial Maximum (LGM), which is known as the modern-day dry forest refugia hypothesis. We studied the demographic history of Tabebuia rosealba (Bignoniaceae) to understand the disjunct geographic distribution of South American SDTFs based on statistical phylogeography and ecological niche modeling (ENM). We specifically tested the dry forest refugia hypothesis; i.e., if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the LGM. We sampled 235 individuals across 18 populations in Central Brazil and analyzed the polymorphisms at chloroplast (trnS-trnG, psbA-trnH and ycf6-trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. We performed coalescence simulations of alternative hypotheses under demographic expectations from two a priori biogeographic hypotheses (1. the Pleistocene Arc hypothesis and, 2. a range shift to Amazon Basin) and other two demographic expectances predicted by ENMs (3. expansion throughout the Neotropical South America, including Amazon Basin, and 4. retraction during the LGM). Phylogenetic analyses based on median-joining network showed haplotype sharing among populations with evidence of incomplete lineage sorting. Coalescent analyses showed smaller effective population sizes for T. roseoalba during the LGM compared to the present-day. Simulations and ENM also showed that its current spatial pattern of genetic diversity is most likely due to a scenario of range retraction during the LGM instead of the fragmentation from a once extensive and largely contiguous SDTF across South America, not supporting the South American dry forest refugia hypothesis.
Collapse
Affiliation(s)
- Warita Alves de Melo
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Cx.P. 131, Goiânia, GO, Brasil
| | - Matheus S. Lima-Ribeiro
- Laboratório de Macroecologia, Universidade Federal de Goiás (UFG), Campus Jataí, Jataí, GO, Brasil
| | - Levi Carina Terribile
- Laboratório de Macroecologia, Universidade Federal de Goiás (UFG), Campus Jataí, Jataí, GO, Brasil
| | - Rosane G. Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Cx.P. 131, Goiânia, GO, Brasil
- * E-mail:
| |
Collapse
|
25
|
Rešetnik I, Frajman B, Schönswetter P. Heteroploid Knautia drymeia includes K. gussonei and cannot be separated into diagnosable subspecies. AMERICAN JOURNAL OF BOTANY 2016; 103:1300-13. [PMID: 27425632 DOI: 10.3732/ajb.1500506] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/24/2016] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Knautia drymeia is a morphologically variable, diploid and tetraploid temperate forest understory species distributed in southeastern Europe and adjacent areas. The species is an excellent system to explore the influence of polypoidy on taxonomic delineations, the role of hybridization among genetically distant populations in polyploid evolution, and the impact of glacial refugia on the evolution of polyploids. METHODS Amplified fragment length polymorphism fingerprinting and multivariate analyses of morphological characters were performed on 57 populations spanning the distribution area of K. drymeia. K-means clustering, comparison of in-silico tetraploids and observed tetraploids, and a phylogeographic analysis using relaxed random walks were used to explore the genetic structure within the diploids, to infer the origin of the tetraploids and to reconstruct range expansion through time. Further, we contrasted the morphology and genetic groups with current taxonomy and evaluated the status of the tetraploid Apennine endemic K. gussonei and the intraspecific taxa of K. drymeia. KEY RESULTS The genetic structure was strongly geographically correlated and yielded four genetic groups; K. gussonei was inseparable from K. drymeia. Distributions of diploid lineages are suggestive of glacial refugia in the northwesternmost and southeastern Balkan Peninsula. Polyploids originated at least two times, as autopolyploids and probably additionally also as allopolyploids. Morphological divergence corresponded with neither genetic groups nor current taxonomy. CONCLUSIONS Genetic and morphometric data confirmed neither divergence of K. gussonei nor recognition of subspecies within K. drymeia. We therefore propose treating K. drymeia as a morphologically and genetically variable species without infraspecific taxa.
Collapse
Affiliation(s)
- Ivana Rešetnik
- Faculty of Science, University of Zagreb, Marulićev trg 20/II, HR-10000 Zagreb, Croatia
| | - Božo Frajman
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria
| |
Collapse
|