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Staggemeier VG, Amorim B, Bünger M, Costa IR, de Faria JEQ, Flickinger J, Giaretta A, Kubo MT, Lima DF, Dos Santos LL, Lourenço AR, Lucas E, Mazine FF, Murillo-A J, de Oliveira MIU, Parra-O C, Proença CEB, Reginato M, Rosa PO, Santos MF, Stadnik A, Tuler AC, Valdemarin KS, Vasconcelos T. Towards a species-level phylogeny for Neotropical Myrtaceae: Notes on topology and resources for future studies. AMERICAN JOURNAL OF BOTANY 2024; 111:e16330. [PMID: 38725388 DOI: 10.1002/ajb2.16330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
PREMISE Increasingly complete phylogenies underpin studies in systematics, ecology, and evolution. Myrteae (Myrtaceae), with ~2700 species, is a key component of the exceptionally diverse Neotropical flora, but given its complicated taxonomy, automated assembling of molecular supermatrices from public databases often lead to unreliable topologies due to poor species identification. METHODS Here, we build a taxonomically verified molecular supermatrix of Neotropical Myrteae by assembling 3909 published and 1004 unpublished sequences from two nuclear and seven plastid molecular markers. We infer a time-calibrated phylogenetic tree that covers 712 species of Myrteae (~28% of the total diversity in the clade) and evaluate geographic and taxonomic gaps in sampling. RESULTS The tree inferred from the fully concatenated matrix mostly reflects the topology of the plastid data set and there is a moderate to strong incongruence between trees inferred from nuclear and plastid partitions. Large, species-rich genera are still the poorest sampled within the group. Eastern South America is the best-represented area in proportion to its species diversity, while Western Amazon, Mesoamerica, and the Caribbean are the least represented. CONCLUSIONS We provide a time-calibrated tree that can be more reliably used to address finer-scale eco-evolutionary questions that involve this group in the Neotropics. Gaps to be filled by future studies include improving representation of taxa and areas that remain poorly sampled, investigating causes of conflict between nuclear and plastid partitions, and the role of hybridization and incomplete lineage sorting in relationships that are poorly supported.
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Affiliation(s)
- Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, 59092-970, RN, Brazil
| | - Bruno Amorim
- Programa de Pós-Graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Mariana Bünger
- Programa de Pós-Graduação em Sistemática, Uso e Conservação da Biodiversidade, Department de Biologia, Universidade Federal do Ceará, Fortaleza, 60355-636, CE, Brazil
| | - Itayguara R Costa
- Programa de Pós-Graduação em Sistemática, Uso e Conservação da Biodiversidade, Department de Biologia, Universidade Federal do Ceará, Fortaleza, 60355-636, CE, Brazil
| | - Jair Eustáquio Quintino de Faria
- Instituto Interamericano de Cooperação para a Agricultura - IICA - SHIS QI 5, Chácara 16, Lago Sul, Brasília, 71600-530, DF, Brazil
| | - Jonathan Flickinger
- Lady Bird Johnson Wildflower Center, The University of Texas at Austin, 4801 La Crosse Ave., Austin, 78739, TX, USA
| | - Augusto Giaretta
- Universidade Federal da Grande Dourados, Faculdade de Ciências Biológicas e Ambientais, Unidade II, Dourados, 79804-970, MS, Brazil
| | - Marcelo T Kubo
- Departamento de Botânica, Laboratório de Sistemática Vegetal, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-900, São Paulo, Brazil
| | - Duane Fernandes Lima
- Programa de Pós-Graduação em Biologia de Fungos, Algas e Plantas, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | | | | | - Eve Lucas
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Fiorella Fernanda Mazine
- Universidade Federal de São Carlos, Campus Sorocaba, Rodovia João Leme dos Santos (SP-264), km 110, Sorocaba, 18052-780, SP, Brazil
| | - José Murillo-A
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Marla Ibrahim Uehbe de Oliveira
- Departamento de Biologia, Universidade Federal de Sergipe, Av. Marcelo Déda Chagas, s/n, Bairro Jardim Rosa Elze, São Cristóvão, 49107-230, SE, Brazil
| | - Carlos Parra-O
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Carolyn E B Proença
- Departamento de Botânica, Universidade de Brasília, Brasília, 70910-900, DF, Brazil
| | - Marcelo Reginato
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90650-001, RS, Brazil
| | - Priscila Oliveira Rosa
- Jardim Botânico de Brasília, Diretoria de Vegetação e Flora, Área Especial SMDB Estação Ecológica Jardim Botânico de Brasília, Brasília, 71.680-001, DF, Brazil
| | - Matheus Fortes Santos
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Alameda da Universidade s/n, Anchieta, São Bernardo do Campo, 09606-045, SP, Brazil
| | - Aline Stadnik
- Instituto Interamericano de Cooperação para a Agricultura - IICA - SHIS QI 5, Chácara 16, Lago Sul, Brasília, 71600-530, DF, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Feira de Santana, 44036-900, BA, Brazil
| | - Amélia Carlos Tuler
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Campus Paricarana, Av. Cap. Ene Garcez, 2413, Boa Vista, 69304-000, RR, Brazil
| | - Karinne Sampaio Valdemarin
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, 13418-260, SP, Brazil
| | - Thais Vasconcelos
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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Velasco JA, Pinto-Ledezma JN. Mapping species diversification metrics in macroecology: Prospects and challenges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.951271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.
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Wei X, Li L, Xu L, Zhang X, Zeng L, Xu J. Complete chloroplast genome sequence of Syzygium samarangense (Myrtaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:977-979. [PMID: 35712540 PMCID: PMC9196770 DOI: 10.1080/23802359.2022.2080022] [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] [Indexed: 11/08/2022] Open
Abstract
Syzygium samarangense (Blume) Merr. et Perry, 1938, commonly known as wax apple, is a Myrtaceae species that is known for its unique fruit shape, flavorful and colorful fruits, medicinal value and increasing economic relevance. In this study, we reported the complete chloroplast genome sequence of S. samarangense. The complete genome is 159,109 bp in length with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,155 bp) and a Small Single Copy region (SSC, 18,796 bp) separated by Inverted Repeat regions (IRs, 26,079 bp). The GC content was 37.0%. It encoded 126 genes, including 81 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The phylogenetic relationships of 20 species inferred that all Syzygium species formed a single cluster belonging to Syzygieae tribe. Our results offer insights into the evolutionary relationship of S. samarangense within Myrtaceae, indicating a closer relationship between S. samarangense and S. forrestii.
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Affiliation(s)
- Xiuqing Wei
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Liang Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Ling Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xijuan Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lihui Zeng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiahui Xu
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
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Identification of Potential Host Plants of Sap-Sucking Insects (Hemiptera: Cicadellidae) Using Anchored Hybrid By-Catch Data. INSECTS 2021; 12:insects12110964. [PMID: 34821765 PMCID: PMC8617646 DOI: 10.3390/insects12110964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022]
Abstract
Reliable host plant records are available for only a small fraction of herbivorous insect species, despite their potential agricultural importance. Most available data on insect-plant associations have been obtained through field observations of occurrences of insects on particular plants. Molecular methods have more recently been used to identify potential host plants using DNA extracted from insects, but most prior studies using these methods have focused on chewing insects that ingest tissues expected to contain large quantities of plant DNA. Screening of Illumina data obtained from sap feeders of the hemipteran family Cicadellidae (leafhoppers) using anchored hybrid enrichment indicates that, despite feeding on plant fluids, these insects often contain detectable quantities of plant DNA. Although inclusion of probes for bacterial 16S in the original anchored hybrid probe kit yielded relatively high detection rates for chloroplast 16S, the Illumina short reads also, in some cases, included DNA for various plant barcode genes as "by-catch". Detection rates were generally only slightly higher for Typhlocybinae, which feed preferentially on parenchyma cell contents, compared to other groups of leafhoppers that feed preferentially on phloem or xylem. These results indicate that next-generation sequencing provides a powerful tool to investigate the specific association between individual insect and plant species.
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Lima DF, Goldenberg R, Forest F, Cowan RS, Lucas EJ. Phylogeny and biogeography of Myrcia sect. Aguava (Myrtaceae, Myrteae) based on phylogenomic and Sanger data provide evidence for a Cerrado origin and geographically structured clades. Mol Phylogenet Evol 2020; 157:107043. [PMID: 33346112 DOI: 10.1016/j.ympev.2020.107043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/18/2022]
Abstract
Myrcia is one of the largest exclusively Neotropical angiosperm genera, including ca. 800 species divided into nine sections. Myrcia sect. Aguava is one of most complex sections of Myrcia due to high morphological variation and wide distribution range of some species, including M. guianensis, with distribution throughout South America and a complex taxonomic history. We used complete plastid DNA sequences data generated using next-generation sequencing of 45 terminals, mostly from Myrcia sect. Aguava. These data were combined with five target DNA regions (ITS, psbA-trnH, trnL-trnF, trnQ-rps16, ndhF) of additional terminals to increase taxonomic coverage. Phylogenetic analyses were conducted using a maximum likelihood approach, and divergence times and ancestral range distributions were estimated. Myrcia sect. Aguava is monophyletic and exclusively comprises species with trilocular ovaries but has no relationship with other groups within Myrcia that possess trilocular ovaries. Three main lineages that correspond to geographical distribution are recognized within Myrcia sect. Aguava. Multiple accessions reveal a non-monophyletic Myrcia guianensis and stress the biogeographical structure inside the group. Myrcia sect. Aguava had a probable mid-Miocene origin in the Cerrado, but lineages that persisted there diversified only more recently, when the present-day vegetation started to stabilize. Posterior migrations to Atlantic Forest, Amazon and Caribbean occurred at the end of Miocene, evidencing transitions from open and dry to forested and more humid areas that are less frequent in the Neotropics. Overall, it is observed that related lineages remained in ecologically similar environments. Future perspectives on Myrcia and Myrteae in the phylogenomic era are also discussed.
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Affiliation(s)
- Duane F Lima
- Programa de Pós-Graduação em Biologia Vegetal, IB, Universidade Estadual de Campinas, 13083-970 Campinas, SP, Brazil.
| | - Renato Goldenberg
- Departamento de Botânica, SCB, Universidade Federal do Paraná, 81531-970 Curitiba, PR, Brazil
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Robyn S Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Eve J Lucas
- Herbarium, Royal Botanic Gardens, Kew, TW9 3AB Richmond, Surrey, United Kingdom
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Giaretta A, Vasconcelos TN, Mazine FF, Faria JEQ, Flores R, Holst B, Sano PT, Lucas E. Calyx (con)fusion in a hyper-diverse genus: Parallel evolution of unusual flower patterns in Eugenia (Myrtaceae). Mol Phylogenet Evol 2019; 139:106553. [DOI: 10.1016/j.ympev.2019.106553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 11/29/2022]
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7
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Amorim BS, Vasconcelos TN, Souza G, Alves M, Antonelli A, Lucas E. Advanced understanding of phylogenetic relationships, morphological evolution and biogeographic history of the mega-diverse plant genus Myrcia and its relatives (Myrtaceae: Myrteae). Mol Phylogenet Evol 2019; 138:65-88. [DOI: 10.1016/j.ympev.2019.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 02/18/2019] [Accepted: 05/17/2019] [Indexed: 01/10/2023]
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Nic Lughadha EM, Graziele Staggemeier V, Vasconcelos TNC, Walker BE, Canteiro C, Lucas EJ. Harnessing the potential of integrated systematics for conservation of taxonomically complex, megadiverse plant groups. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:511-522. [PMID: 30779869 PMCID: PMC6850456 DOI: 10.1111/cobi.13289] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 05/30/2023]
Abstract
The value of natural history collections for conservation science research is increasingly recognized, despite their well-documented limitations in terms of taxonomic, geographic, and temporal coverage. Specimen-based analyses are particularly important for tropical plant groups for which field observations are scarce and potentially unreliable due to high levels of diversity-amplifying identification challenges. Specimen databases curated by specialists are rich sources of authoritatively identified, georeferenced occurrence data, and such data are urgently needed for large genera. We compared entries in a monographic database for the large Neotropical genus Myrcia in 2007 and 2017. We classified and quantified differences in specimen records over this decade and determined the potential impact of these changes on conservation assessments. We distinguished misidentifications from changes due to taxonomic remodeling and considered the effects of adding specimens and georeferences. We calculated the potential impact of each change on estimates of extent of occurrence (EOO), the most frequently used metric in extinction-risk assessments of tropical plants. We examined whether particular specimen changes were associated with species for which changes in EOO over the decade were large enough to change their conservation category. Corrections to specimens previously misidentified or lacking georeferences were overrepresented in such species, whereas changes associated with taxonomic remodeling (lumping and splitting) were underrepresented. Among species present in both years, transitions to less threatened status outnumbered those to more threatened (8% vs 3%, respectively). Species previously deemed data deficient transitioned to threatened status more often than to not threatened (10% vs 7%, respectively). Conservation scientists risk reaching unreliable conclusions if they use specimen databases that are not actively curated to reflect changing knowledge.
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Affiliation(s)
| | - Vanessa Graziele Staggemeier
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de BotânicaLaboratório de FenologiaAvenida 24A 1515, CEP 13506–900Rio ClaroSão PauloBrazil
- Departamento de Ecologia, Centro de BiociênciasUniversidade Federal do Rio Grande do NorteCEP 59072–970NatalRio Grande do NorteBrazil
| | - Thais N. C. Vasconcelos
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
- Laboratório de Sistemática VegetalDepartamento de Botânica, Universidade de São Paulo, São PauloSP 05508–090Brazil
| | | | | | - Eve J. Lucas
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
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Vasconcelos TNC, Chartier M, Prenner G, Martins AC, Schönenberger J, Wingler A, Lucas E. Floral uniformity through evolutionary time in a species-rich tree lineage. THE NEW PHYTOLOGIST 2019; 221:1597-1608. [PMID: 30284282 DOI: 10.1111/nph.15453] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
Changes in floral morphology are expected across evolutionary time and are often promoted as important drivers in angiosperm diversification. Such a statement, however, is in contrast to empirical observations of species-rich lineages that show apparent conservative floral morphologies even under strong selective pressure to change from their environments. Here, we provide quantitative evidence for prolific speciation despite uniform floral morphology in a tropical species-rich tree lineage. We analyse floral disparity in the environmental and phylogenetic context of Myrcia (Myrtaceae), one of the most diverse and abundant tree genera in Neotropical biomes. Variation in floral morphology among Myrcia clades is exceptionally low, even among distantly related species. Discrete floral specialisations do occur, but these are few, present low phylogenetic signal, have no strong correlation with abiotic factors, and do not affect overall macroevolutionary dynamics in the lineage. Results show that floral form and function may be conserved over large evolutionary time scales even in environments full of opportunities for ecological interactions and niche specialisation. Species accumulation in diverse lineages with uniform flowers apparently does not result from shifts in pollination strategies, but from speciation mechanisms that involve other, nonfloral plant traits.
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Affiliation(s)
- Thais N C Vasconcelos
- Jodrell Laboratory, Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, Richmond, TW9 3DS, UK
- Laboratório de Sistemética Vegetal, Departamento de Botânica, Universidade de São Paulo, São Paulo, SP 05508- 090, Brazil
| | - Marion Chartier
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Gerhard Prenner
- Jodrell Laboratory, Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, Richmond, TW9 3DS, UK
| | - Aline C Martins
- Departamento de Botânica, Centro Politécnico, Universidade Federal do Paraná, Curitiba, PR 81531-980, Brazil
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Astrid Wingler
- School of Biological, Earth & Environmental Sciences and Environmental Research Institute, University College Cork, Distillery Fields, North Mall, Cork, T23 XA50, Ireland
| | - Eve Lucas
- Jodrell Laboratory, Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, Richmond, TW9 3DS, UK
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Atlantic forests to the all Americas: Biogeographical history and divergence times of Neotropical Ficus (Moraceae). Mol Phylogenet Evol 2018; 122:46-58. [PMID: 29371027 DOI: 10.1016/j.ympev.2018.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 01/20/2018] [Accepted: 01/20/2018] [Indexed: 11/22/2022]
Abstract
Ficus (Moraceae) is well diversified in the Neotropics with two lineages inhabiting the wet forests of this region. The hemiepiphytes of section Americanae are the most diversified with c. 120 species, whereas section Pharmacosycea includes about 20 species mostly with a terrestrial habit. To reconstruct the biogeographical history and diversification of Ficus in the Americas, we produced a dated Bayesian phylogenetic hypothesis of Neotropical Ficus including two thirds of the species sequenced for five nuclear regions (At103, ETS, G3pdh, ITS/5.8S and Tpi). Ancestral range was estimated using all models available in Biogeobears and Binary State Speciation and Extinction analysis was used to evaluate the role of the initial habit and propagule size in diversification. The phylogenetic analyses resolved both Neotropical sections as monophyletic but the internal relationships between species in section Americanae remain unclear. Ficus started their diversification in the Neotropics between the Oligocene and Miocene. The genus experienced two bursts of diversification: in the middle Miocene and the Pliocene. Colonization events from the Amazon to adjacent areas coincide with the end of the Pebas system (10 Mya) and the connection of landmasses. Divergence of endemic species in the Atlantic forest is inferred to have happened after its isolation and the opening and consolidation of the Cerrado. Our results suggest a complex diversification in the Atlantic forest differing between postulated refuges and more instable areas in the South distribution of the forest. Finally the selection for initial hemiepiphytic habit and small to medium propagule size influenced the diversification and current distribution of the species at Neotropical forests marked by the historical instability and long-distance dispersal.
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Alves DMCC, Diniz-Filho JAF, Villalobos F. Geographical diversification and the effect of model and data inadequacies: the bat diversity gradient as a case study. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Vasconcelos TN, Proença CE, Ahmad B, Aguilar DS, Aguilar R, Amorim BS, Campbell K, Costa IR, De-Carvalho PS, Faria JE, Giaretta A, Kooij PW, Lima DF, Mazine FF, Peguero B, Prenner G, Santos MF, Soewarto J, Wingler A, Lucas EJ. Myrteae phylogeny, calibration, biogeography and diversification patterns: Increased understanding in the most species rich tribe of Myrtaceae. Mol Phylogenet Evol 2017; 109:113-137. [DOI: 10.1016/j.ympev.2017.01.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/29/2016] [Accepted: 01/04/2017] [Indexed: 01/21/2023]
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Biogeographical patterns of Myrcia s.l. (Myrtaceae) and their correlation with geological and climatic history in the Neotropics. Mol Phylogenet Evol 2017; 108:34-48. [DOI: 10.1016/j.ympev.2017.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/24/2016] [Accepted: 01/19/2017] [Indexed: 11/21/2022]
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de Oliveira Bünger M, Fernanda Mazine F, Forest F, Leandro Bueno M, Renato Stehmann J, Lucas EJ. The evolutionary history of Eugenia sect. Phyllocalyx (Myrtaceae) corroborates historically stable areas in the southern Atlantic forests. ANNALS OF BOTANY 2016; 118:1209-1223. [PMID: 27974324 PMCID: PMC5155605 DOI: 10.1093/aob/mcw209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/28/2016] [Accepted: 08/26/2016] [Indexed: 06/02/2023]
Abstract
BACKGROUND AND AIMS Eugenia sect. Phyllocalyx Nied. includes 14 species endemic to the Neotropics, mostly distributed in the Atlantic coastal forests of Brazil. Here the first comprehensive phylogenetic study of this group is presented, and this phylogeny is used as the basis to evaluate the recent infrageneric classification in Eugenia sensu lato (s.l.) to test the history of the evolution of traits in the group and test hypotheses associated with the history of this clade. METHODS A total of 42 taxa were sampled, of which 14 were Eugenia sect. Phyllocalyx for one nuclear (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, rpl16, trnL-rpl32 and trnQ-rps16). The relationships were reconstructed based on Bayesian analysis and maximum likelihood. Additionally, ancestral area analysis and modelling methods were used to estimate species dispersal, comparing historically climatic stable (refuges) and unstable areas. KEY RESULTS Maximum likelihood and Bayesian inferences indicate that Eugenia sect. Phyllocalyx is paraphyletic and the two clades recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Cerrado and south-eastern species and a difference in the composition of species from north-eastern and south-eastern Atlantic forest. Refugia and stable areas identified within unstable areas suggest that these areas were important to maintain diversity in the Atlantic forest biodiversity hotspot. CONCLUSION This study provides a robust phylogenetic framework to address important historical questions for Eugenia s.l. within an evolutionary context, supporting the need for better taxonomic study of one of the largest genera in the Neotropics. Furthermore, valuable insight is offered into diversification and biome shifts of plant species in the highly environmentally impacted Atlantic forest of South America. Evidence is presented that climate stability in the south-eastern Atlantic forest during the Quaternary contributed to the highest levels of plant diversity in this region that acted as a refugium.
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Affiliation(s)
- Mariana de Oliveira Bünger
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - Fiorella Fernanda Mazine
- Departamento de Ciências Ambientais, Universidade Federal de São Carlos-campus Sorocaba, João Leme dos Santos, Km 110-SP-264, CEP 18052-780, Sorocaba, SP, Brazil
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Marcelo Leandro Bueno
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - João Renato Stehmann
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - Eve J Lucas
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
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15
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Freitas L, Salino A, Neto LM, Elias Almeida T, Mortara SR, Stehmann JR, Amorim AM, Guimarães EF, Coelho MN, Zanin A, Forzza RC. A comprehensive checklist of vascular epiphytes of the Atlantic Forest reveals outstanding endemic rates. PHYTOKEYS 2016; 58:65-79. [PMID: 26884706 PMCID: PMC4743015 DOI: 10.3897/phytokeys.58.5643] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/14/2015] [Indexed: 06/05/2023]
Abstract
Knowledge of the geographic distribution of plants is essential to underpin the understanding of global biodiversity patterns. Vascular epiphytes are important components of diversity and functionality of Neotropical forests but, unlike their terrestrial counterparts, they are under-represented in large-scale diversity and biogeographic analyses. This is the case for the Atlantic Forest - one of the most diverse and threatened biomes worldwide. We provide the first comprehensive species list of Atlantic Forest vascular epiphytes; their endemism patterns and threatened species occurrence have also been analyzed. A list with 2,256 species of (hemi-)epiphytes - distributed in 240 genera and 33 families - is presented based on the updated Brazilian Flora Checklist. This represents more than 15% of the total vascular plant richness in the Atlantic Forest. Moreover, 256 species are included on the Brazilian Red List. More than 93% of the overall richness is concentrated in ten families, with 73% represented by Orchidaceae and Bromeliaceae species alone. A total of 78% of epiphytic species are endemic to the Atlantic Forest, in contrast to overall vascular plant endemism in this biome estimated at 57%. Among the non-endemics, 13% of epiphytic species also occur either in the Amazon or in the Cerrado - the other two largest biomes of Brazil - and only 8% are found in two or more Brazilian biomes. This pattern of endemism, in addition to available dated phylogenies of some genera, indicate the dominance of recent radiations of epiphytic groups in the Atlantic Forest, showing that the majority of divergences dating from the Pliocene onwards are similar to those that were recently reported for other Neotropical plants.
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Affiliation(s)
| | | | | | | | | | | | - André Marcio Amorim
- Universidade Estadual de Santa Cruz e Herbário do Centro de Pesquisas do Cacau
| | | | | | - Ana Zanin
- Universidade Federal de Santa Catarina
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16
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Cascaes MM, Guilhon GMSP, de Aguiar Andrade EH, das Graças Bichara Zoghbi M, da Silva Santos L. Constituents and Pharmacological Activities of Myrcia (Myrtaceae): A Review of an Aromatic and Medicinal Group of Plants. Int J Mol Sci 2015; 16:23881-904. [PMID: 26473832 PMCID: PMC4632730 DOI: 10.3390/ijms161023881] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/24/2015] [Accepted: 09/25/2015] [Indexed: 11/16/2022] Open
Abstract
Myrcia is one of the largest genera of the economically important family Myrtaceae. Some of the species are used in folk medicine, such as a group known as “pedra-hume-caá” or “pedra-ume-caá” or “insulina vegetal” (insulin plant) that it is used for the treatment of diabetes. The species are an important source of essential oils, and most of the chemical studies on Myrcia describe the chemical composition of the essential oils, in which mono- and sesquiterpenes are predominant. The non-volatile compounds isolated from Myrcia are usually flavonoids, tannins, acetophenone derivatives and triterpenes. Anti-inflammatory, antinociceptive, antioxidant, antimicrobial activities have been described to Myrcia essential oils, while hypoglycemic, anti-hemorrhagic and antioxidant activities were attributed to the extracts. Flavonoid glucosides and acetophenone derivatives showed aldose reductase and α-glucosidase inhibition, and could explain the traditional use of Myrcia species to treat diabetes. Antimicrobial and anti-inflammatory are some of the activities observed for other isolated compounds from Myrcia.
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Affiliation(s)
- Márcia Moraes Cascaes
- Programa de Pós-graduação em Química, Universidade Federal do Pará, Belém 66075-110, PA, Brazil.
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17
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Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Mol Ecol Resour 2015; 16:138-49. [PMID: 26084789 DOI: 10.1111/1755-0998.12438] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 04/20/2015] [Accepted: 06/09/2015] [Indexed: 01/22/2023]
Abstract
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
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Affiliation(s)
- Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Lei
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Changhao Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yu Zhang
- Beijing Botanic Gardens, Beijing, 100093, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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