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Ogutcen E, de Lima Ferreira P, Wagner ND, Marinček P, Vir Leong J, Aubona G, Cavender-Bares J, Michálek J, Schroeder L, Sedio BE, Vašut RJ, Volf M. Phylogenetic insights into the Salicaceae: The evolution of willows and beyond. Mol Phylogenet Evol 2024; 199:108161. [PMID: 39079595 DOI: 10.1016/j.ympev.2024.108161] [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: 03/01/2024] [Revised: 07/05/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Abstract
The Salicaceae includes approximately 54 genera and over 1,400 species with a cosmopolitan distribution. Members of the family are well-known for their diverse secondary plant metabolites, and they play crucial roles in tropical and temperate forest ecosystems. Phylogenetic reconstruction of the Salicaceae has been historically challenging due to the limitations of molecular markers and the extensive history of hybridization and polyploidy within the family. Our study employs whole-genome sequencing of 74 species to generate an extensive phylogeny of the Salicaceae. We generated two RAD-Seq enriched whole-genome sequence datasets and extracted two additional gene sets corresponding to the universal Angiosperms353 and Salicaceae-specific targeted-capture arrays. We reconstructed maximum likelihood-based molecular phylogenies using supermatrix and coalescent-based supertree approaches. Our fossil-calibrated phylogeny estimates that the Salicaceae originated around 128 million years ago and unravels the complex taxonomic relationships within the family. Our findings confirm the non-monophyly of the subgenus Salix s.l. and further support the merging of subgenera Chamaetia and Vetrix, both of which exhibit intricate patterns within and among different sections. Overall, our study not only enhances our understanding of the evolution of the Salicaceae, but also provides valuable insights into the complex relationships within the family.
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Affiliation(s)
- Ezgi Ogutcen
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Salzburg, Austria.
| | - Paola de Lima Ferreira
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Department of Biology, Aarhus University, Aarhus, Denmark
| | - Natascha D Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Pia Marinček
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Jing Vir Leong
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Gibson Aubona
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | | | - Jan Michálek
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Trebon, Czech Republic
| | - Lucy Schroeder
- College of Biological Sciences, University of Minnesota, St. Paul, MN, United States
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States; Smithsonian Tropical Research Institute, Apartado, 0843-03092 Balboa, Ancón, Republic of Panama
| | - Radim J Vašut
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic; Department of Biology, Faculty of Education, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Volf
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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2
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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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Hu H, Wang Q, Hao G, Zhou R, Luo D, Cao K, Yan Z, Wang X. Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome. PeerJ 2023; 11:e16642. [PMID: 38099308 PMCID: PMC10720482 DOI: 10.7717/peerj.16642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Abstract
Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.
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Affiliation(s)
- Huan Hu
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Qian Wang
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Guoqian Hao
- School of Life Science and Food Engineering, Yibin University, Yibin, China
| | - Ruitao Zhou
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Dousheng Luo
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Kejun Cao
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Zhimeng Yan
- School of Medical Information Engineering, Zunyi Medical University, Zunyi, China
| | - Xinyu Wang
- Key Laboratory of Medical Electrophysiology, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Francisco-Gutiérrez A, Cházaro-Basáñez M, Carral-Domínguez R, Narave-Flores H, Islas-Tello L. Eugeniasarahchazaroi (Myrtaceae, Myrteae), a new species from the cloud forest of Mexico. PHYTOKEYS 2023; 236:53-64. [PMID: 38076004 PMCID: PMC10701900 DOI: 10.3897/phytokeys.236.111421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/12/2023] [Indexed: 01/24/2024]
Abstract
Following the description of Eugenianaraveana in 2016 from the cloud forest of the Cofre de Perote volcano, Mexico, the doubt about the existence of another unlocalized and sympatric species of Eugenia remained. After years of searching, the second endemic species of the Cofre de Perote volcano, Eugeniasarahchazaroi, is presented here. It belongs to the section Umbellatae, and is described, illustrated, and compared with E.naraveana and E.coetzalensis, recently described from Veracruz, the second state with the highest diversity of Eugenia in Mexico. The species is only known from the type locality and is classified in the Critically Endangered CR B1+B2(a,biii) category of the IUCN Red List conservation assessments.
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Affiliation(s)
- Antonio Francisco-Gutiérrez
- Facultad de Biología, Universidad Veracruzana, Circuito Universitario Gonzalo Aguirre Beltrán s.n., Zona Universitaria 91000, Xalapa, Veracruz, MexicoUniversidad VeracruzanaXalapaMexico
| | - Miguel Cházaro-Basáñez
- Facultad de Biología, Universidad Veracruzana, Circuito Universitario Gonzalo Aguirre Beltrán s.n., Zona Universitaria 91000, Xalapa, Veracruz, MexicoUniversidad VeracruzanaXalapaMexico
| | - Rodrigo Carral-Domínguez
- Dirección de Recursos Naturales, Secretaría de Medio Ambiente del Estado de Veracruz, Anastacio Bustamante esq. Manlio Fabio Altamirano s/n, Centro, 91000, Xalapa, Veracruz, MexicoDirección de Recursos Naturales, Secretaría de Medio Ambiente del Estado de VeracruzXalapaMexico
| | - Héctor Narave-Flores
- Facultad de Biología, Universidad Veracruzana, Circuito Universitario Gonzalo Aguirre Beltrán s.n., Zona Universitaria 91000, Xalapa, Veracruz, MexicoUniversidad VeracruzanaXalapaMexico
| | - Luis Islas-Tello
- Dirección de Recursos Naturales, Secretaría de Medio Ambiente del Estado de Veracruz, Anastacio Bustamante esq. Manlio Fabio Altamirano s/n, Centro, 91000, Xalapa, Veracruz, MexicoDirección de Recursos Naturales, Secretaría de Medio Ambiente del Estado de VeracruzXalapaMexico
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Chen JT, Lidén M, Huang XH, Zhang L, Zhang XJ, Kuang TH, Landis JB, Wang D, Deng T, Sun H. An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2138-2156. [PMID: 37119474 DOI: 10.1111/jipb.13499] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/25/2023] [Indexed: 06/19/2023]
Abstract
The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent "series". Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (ii) among all 42 sections and five "series", 25 sections and one "series" are resolved as monophyletic in both data sets; (iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (iv) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.
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Affiliation(s)
- Jun-Tong Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Magnus Lidén
- Evolutionary Biology Centre, Systematic Biology, Uppsala University, Uppsala, 75236, Sweden
| | - Xian-Han Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Liang Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xin-Jian Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tian-Hui Kuang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Dong Wang
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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