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Dalling JW, Garcia E, Espinosa C, Pizano C, Ferrer A, Lira Viana J. Zombie leaves: Novel repurposing of senescent fronds in the tree fern Cyathea rojasiana in a tropical montane forest. Ecology 2024; 105:e4248. [PMID: 38238992 DOI: 10.1002/ecy.4248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/01/2023] [Accepted: 12/06/2023] [Indexed: 03/02/2024]
Affiliation(s)
- James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Evidelio Garcia
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Carlos Espinosa
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Camila Pizano
- Department of Biology, Lake Forest College, Lake Forest, Illinois, USA
| | - Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jéssica Lira Viana
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
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2
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Peng Y, Wang Z, Li M, Wang T, Su Y. Characterization and analysis of multi-organ full-length transcriptomes in Sphaeropteris brunoniana and Alsophila latebrosa highlight secondary metabolism and chloroplast RNA editing pattern of tree ferns. BMC PLANT BIOLOGY 2024; 24:73. [PMID: 38273309 PMCID: PMC10811885 DOI: 10.1186/s12870-024-04746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events. RESULTS In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species. CONCLUSIONS Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research.
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Affiliation(s)
- Yang Peng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ting Wang
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
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3
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Wan X, Zhang L, Lehtonen S, Tuomisto H, Zhang DW, Gao XF, Zhang LB. Five long-distance dispersals shaped the major intercontinental disjunctions in Tectariaceae s.l. (Polypodiales, Polypodiopsida). Mol Phylogenet Evol 2023:107845. [PMID: 37301485 DOI: 10.1016/j.ympev.2023.107845] [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: 02/02/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Intercontinental disjunct distributions can arise either from vicariance, from long-distance dispersal, or through extinction of an ancestral population with a broader distribution. Tectariaceae s.l., a clade of ferns in Polypodiales with ca. 300 species mainly distributed in the tropics and subtropics, provide an excellent opportunity to investigate global distribution patterns. Here, we assembled a dataset of eight plastid markers and one nuclear marker of 636 (92% increase of the earlier largest sampling) accessions representing ca. 210 species of all eight genera in Tectariaceae s.l. (Arthropteridaceae, Pteridryaceae, and Tectariaceae s.s.) and 35 species of other families of eupolypods Ⅰ. A new phylogeny is reconstructed to study the biogeography and trait-associated diversification. Our major results include: (1) a distinct lineage of Tectaria sister to the rest of the American Tectaria is identified; (2) Tectariaceae s.l., and the three families: Arthropteridaceae (Arthropteris), Pteridryaceae (Draconopteris, Malaifilix, Polydictyum, Pteridrys), and Tectariaceae s.s. (Hypoderris, Tectaria, and Triplophyllum), might have all originated in late Cretaceous; (3) only five intercontinental dispersals occurred in Pteridryaceae and Tectariaceae s.s. giving rise to their current intercontinental disjunction; (4) we provide the second evidence in ferns that a long-distance dispersal between Malesia and Americas during the Paleocene to Eocene led to the establishment/origin of a new genus (Draconopteris); and (5) diversification rate of each state of leaf dissection is different, and the lowest is in the simple-leaved taxa.
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Affiliation(s)
- Xia Wan
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China; University of Chinese Academy of Sciences, Beijing 100049, China; Missouri Botanical Garden, St. Louis, Missouri 63110, USA
| | - Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Missouri Botanical Garden, St. Louis, Missouri 63110, USA
| | - Samuli Lehtonen
- Biodiversity Unit, University of Turku, FI-20014 Turku, Finland
| | - Hanna Tuomisto
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Da-Wei Zhang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xin-Fen Gao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Li-Bing Zhang
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Missouri Botanical Garden, St. Louis, Missouri 63110, USA.
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Yi H, Dong S, Yang L, Wang J, Kidner C, Kang M. Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns. Mol Phylogenet Evol 2023; 184:107801. [PMID: 37088242 DOI: 10.1016/j.ympev.2023.107801] [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: 12/06/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.
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Affiliation(s)
- Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Shiying Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Catherine Kidner
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK; Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China.
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5
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Chamberland L, Agnarsson I, Quayle IL, Ruddy T, Starrett J, Bond JE. Biogeography and eye size evolution of the ogre-faced spiders. Sci Rep 2022; 12:17769. [PMID: 36273015 PMCID: PMC9588044 DOI: 10.1038/s41598-022-22157-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 10/10/2022] [Indexed: 01/19/2023] Open
Abstract
Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group's historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.
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Affiliation(s)
- Lisa Chamberland
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Ingi Agnarsson
- grid.14013.370000 0004 0640 0021Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102 Reykjavik, Iceland
| | - Iris L. Quayle
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Tess Ruddy
- grid.267778.b0000 0001 2290 5183Vassar College, Poughkeepsie, NY 12604 USA
| | - James Starrett
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Jason E. Bond
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
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Testo WL, de Gasper AL, Molino S, Galán JMGY, Salino A, Dittrich VADO, Sessa EB. Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family. AMERICAN JOURNAL OF BOTANY 2022; 109:1579-1595. [PMID: 36063431 DOI: 10.1002/ajb2.16062] [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: 03/15/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. METHODS We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. RESULTS Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. CONCLUSIONS Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.
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Affiliation(s)
- Weston L Testo
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76102, USA
- Department of Science and Education, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - André L de Gasper
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, Rua Antônio da Veiga, 140, Victor Konder, CEP 89030-903, Blumenau, SC, Brazil
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | - Sonia Molino
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - José María Gabriel Y Galán
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - Alexandre Salino
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | | | - Emily B Sessa
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
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Zhu M, Feng P, Ping J, Li J, Su Y, Wang T. Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae. Ecol Evol 2021; 11:14327-14340. [PMID: 34707858 PMCID: PMC8525152 DOI: 10.1002/ece3.8151] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 11/07/2022] Open
Abstract
The simple sequence repeats (SSRs) of plant chloroplasts show considerable genetic variation and have been widely used in species identification and phylogenetic relationship determination. Whether chloroplast genome SSRs can be used to classify Cyatheaceae species has not yet been studied. Therefore, the chloroplast genomes of eight Cyatheaceae species were sequenced, and their SSR characteristics were compared and statistically analyzed. The results showed that the chloroplast genome structure was highly conserved (genome size: 154,046-166,151 bp), and the gene content (117 genes) and gene order were highly consistent. The distribution characteristics of SSRs (number, relative abundance, relative density, GC content) showed taxon specificity. The primary results were the total numbers of SSRs and mononucleotides: Gymnosphaera (61-67 and 40-47, respectively), Alsophila (121-122 and 95-96), and Sphaeropteris (102-103 and 77-80). Statistical and clustering analyses of SSR characteristics showed that their distribution was consistent with the recent classification of Cyatheaceae, which divided the eight Cyatheaceae species into three genera. This study indicates that the distribution characteristics of Cyatheaceae chloroplast SSRs can provide useful phylogenic information at the genus level.
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Affiliation(s)
- Ming Zhu
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Peipei Feng
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jingyao Ping
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jinye Li
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - YingJuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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8
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Donoghue S, Turner PAM. A review of Australian tree fern ecology in forest communities. AUSTRAL ECOL 2021. [DOI: 10.1111/aec.13103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shavawn Donoghue
- Forest Practices Authority 30 Patrick Street Hobart Tasmania 7000 Australia
- Institute of Marine and Antarctic Studies University of Tasmania Hobart Tasmania Australia
| | - Perpetua A. M. Turner
- Forest Practices Authority 30 Patrick Street Hobart Tasmania 7000 Australia
- School of Natural Sciences and ARC Training Centre for Forest Value University of Tasmania Hobart Tasmania Australia
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9
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Zhang J, Phookamsak R, Mapook A, Lu Y, Lv M. Monilochaetes pteridophytophila (Australiascaceae, Glomerellales), a new fungus from tree fern. Biodivers Data J 2021; 9:e67248. [PMID: 34393583 PMCID: PMC8346447 DOI: 10.3897/bdj.9.e67248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/17/2021] [Indexed: 11/12/2022] Open
Abstract
Background During taxonomic and phylogenetic studies of fungi on pteridophytes in Thailand, Monilochaetes pteridophytophila sp. nov. was collected from the frond stalks of a tree fern (Alsophila costularis, Cyatheaceae). The new species is introduced, based on evidence from morphology and phylogenetic analyses of a concatenated dataset of LSU, ITS, SSU and RPB2 sequences. New information Monilochaetes pteridophytophila differs from extant species of Monilochaetes in having darker conidiophores with fewer septae (1-4-septate). Monilochaetes pteridophytophila forms a distinct clade, basal from other species of Monilochaetes in Australiascaceae. A detailed description and illustrations of the new species are provided. We also provided a synopsis of accepted species of Monilochaetes.
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Affiliation(s)
- Jingyi Zhang
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology Guiyang China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai Thailand.,School of Science, Mae Fah Luang University, Chaing Rai, Thailand School of Science, Mae Fah Luang University Chaing Rai Thailand
| | - Rungtiwa Phookamsak
- East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming, China East and Central Asia Regional Office, World Agroforestry Centre (ICRAF) Kunming China.,Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming, China Centre for Mountain Futures (CMF), Kunming Institute of Botany Kunming China.,Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai, Thailand Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University Chiang Mai Thailand.,Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe, China Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences Honghe China
| | - Ausana Mapook
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand Center of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai Thailand
| | - Yongzhong Lu
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology Guiyang China
| | - Menglan Lv
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology Guiyang China
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10
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Wang J, Dong S, Yang L, Harris A, Schneider H, Kang M. Allopolyploid Speciation Accompanied by Gene Flow in a Tree Fern. Mol Biol Evol 2021; 37:2487-2502. [PMID: 32302390 DOI: 10.1093/molbev/msaa097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid speciation as an evolutionary process in fern lineages remains poorly understood. Here, we employ flow cytometry, phylogeny, genomewide single nucleotide polymorphism data sets, and admixture and coalescent modeling to show that the scaly tree fern, Gymnosphaera metteniana is a naturally occurring allotetraploid species derived from hybridization between the diploids, G. denticulata and G. gigantea. Moreover, we detected ongoing gene flow between the hybrid species and its progenitors, and we found that G. gigantea and G. metteniana inhabit distinct niches, whereas climatic niches of G. denticulata and G. metteniana largely overlap. Taken together, these results suggest that either some degree of intrinsic genetic isolation between the hybrid species and its parental progenitors or ecological isolation over short distances may be playing an important role in the evolution of reproductive barriers. Historical climate change may have facilitated the origin of G. metteniana, with the timing of hybridization coinciding with a period of intensification of the East Asian monsoon during the Pliocene and Pleistocene periods in southern China. Our study of allotetraploid G. metteniana represents the first genomic-level documentation of hybrid speciation in scaly tree ferns and, thus, provides a new perspective on evolution in the lineage.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Shiyong Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Aj Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Department of Biology, Oberlin College, Oberlin, OH
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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11
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de Almeida RF, van den Berg C. Biogeography of Stigmaphyllon (Malpighiaceae) and a Meta-Analysis of Vascular Plant Lineages Diversified in the Brazilian Atlantic Rainforests Point to the Late Eocene Origins of This Megadiverse Biome. PLANTS 2020; 9:plants9111569. [PMID: 33203045 PMCID: PMC7696469 DOI: 10.3390/plants9111569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/03/2022]
Abstract
We investigated the biogeography of Stigmaphyllon, the second-largest lianescent genus of Malpighiaceae, as a model genus to reconstruct the age and biogeographic history of the Brazilian Atlantic Rainforest (BAF). Few studies to date have focused on the tertiary diversification of plant lineages in the BAFs, especially on Stigmaphyllon. Phylogenetic relationships for 24 species of Stigmaphyllon (18 ssp. From the Atlantic forest (out of 31 spp.), three spp. from the Amazon Rainforest, two spp. from the Caatinga biome, and a single species from the Cerrado biome) were inferred based on one nuclear DNA (PHYC) and two ribosomal DNA (ETS, ITS) regions using parsimony and Bayesian methods. A time-calibrated phylogenetic tree for ancestral area reconstructions was additionally generated, coupled with a meta-analysis of vascular plant lineages diversified in the BAFs. Our results show that: (1) Stigmaphyllon is monophyletic, but its subgenera are paraphyletic; (2) the most recent common ancestor of Stigmaphyllon originated in the Brazilian Atlantic Rainforest/Caatinga region in Northeastern Brazil ca. 26.0 Mya; (3) the genus colonized the Amazon Rainforest at two different times (ca. 22.0 and 6.0 Mya), the Caatinga biome at least four other times (ca. 14.0, 9.0, 7.0, and 1.0 Mya), the Cerrado biome a single time (ca. 15.0 Mya), and the Southern Atlantic Rainforests five times (from 26.0 to 9.0 Mya); (4) a history of at least seven expansion events connecting the Brazilian Atlantic Rainforest to other biomes from 26.0 to 9.0 Mya, and (5) a single dispersion event from South America to Southeastern Asia and Oceania at 22.0 Mya via Antarctica was proposed. Compared to a meta-analysis of time-calibrated phylogenies for 64 lineages of vascular plants diversified in the Brazilian Atlantic Rainforests, our results point to a late Eocene origin for this megadiverse biome.
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Affiliation(s)
- Rafael Felipe de Almeida
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Molecular Biology of Plants and Fungi Lab (LAMOL), Av. Transnordestina s/n, Novo Horizonte, Feira de Santana 44036-900, Bahia, Brazil;
- Scientifik Consultoria, Petrópolis, Rio de Janeiro 25651-090, Brazil
- Correspondence:
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Molecular Biology of Plants and Fungi Lab (LAMOL), Av. Transnordestina s/n, Novo Horizonte, Feira de Santana 44036-900, Bahia, Brazil;
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12
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Griffiths AR, Silman MR, Farfán Rios W, Feeley KJ, García Cabrera K, Meir P, Salinas N, Dexter KG. Evolutionary heritage shapes tree distributions along an Amazon‐to‐Andes elevation gradient. Biotropica 2020. [DOI: 10.1111/btp.12843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Miles R. Silman
- Biology Department and Center for Energy, Environment and Sustainability Wake Forest University Winston‐Salem NC USA
| | - William Farfán Rios
- Living Earth Collaborative Washington University in Saint Louis St. Louis MO USA
- Center for Conservation and Sustainable Development Missouri Botanical Garden St. Louis MO USA
- Herbario Vargas (CUZ), Escuela Profesional de Biología Universidad Nacional de San Antonio Abad del Cusco Cusco Peru
| | - Kenneth J. Feeley
- Department of Biology University of Miami Coral Gables FL USA
- Fairchild Tropical Botanic Garden Coral Gables FL USA
| | - Karina García Cabrera
- Biology Department and Center for Energy, Environment and Sustainability Wake Forest University Winston‐Salem NC USA
| | - Patrick Meir
- School of Geosciences University of Edinburgh Edinburgh UK
- Research School of Biology Australian National University Canberra ACT Australia
| | - Norma Salinas
- Instituto de Ciencias de la Naturaleza, Territorio y Energías Renovables Pontificia Universidad Católica del Peru Lima Peru
| | - Kyle G. Dexter
- School of Geosciences University of Edinburgh Edinburgh UK
- Royal Botanic Garden Edinburgh Edinburgh UK
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13
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Loiseau O, Weigand A, Noben S, Rolland J, Silvestro D, Kessler M, Lehnert M, Salamin N. Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae. ANNALS OF BOTANY 2020; 125:93-103. [PMID: 31562744 PMCID: PMC6948215 DOI: 10.1093/aob/mcz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 09/26/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogeneity in their dynamics of diversification. Testing and characterizing the processes driving the evolution of clades with steady rates of diversification over long periods of time are of importance in order to have a full understanding of the build-up of biodiversity through time. METHODS We studied the macroevolutionary history of the species-rich tree fern family Cyatheaceae and inferred a time-calibrated phylogeny of the family including extinct and extant species using the recently developed fossilized birth-death method. We tested whether the high diversity of Cyatheaceae is the result of episodes of rapid diversification associated with phenotypic and ecological differentiation or driven by stable but low rates of diversification. We compared the rates of diversification across clades, modelled the evolution of body size and climatic preferences and tested for trait-dependent diversification. KEY RESULTS This ancient group diversified at a low and constant rate during its long evolutionary history. Morphological and climatic niche evolution were found to be overall highly conserved, although we detected several shifts in the rates of evolution of climatic preferences, linked to changes in elevation. The diversification of the family occurred gradually, within limited phenotypic and ecological boundaries, and yet resulted in a remarkable species richness. CONCLUSIONS Our study indicates that Cyatheaceae is a diverse clade which slowly accumulated morphological, ecological and taxonomic diversity over a long evolutionary period and provides a compelling example of the tropics as a museum of biodiversity.
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Affiliation(s)
- Oriane Loiseau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Weigand
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Sarah Noben
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Zoology, University of British Columbia, #4200-6270 University Blvd, Vancouver, B.C., Canada
| | - Daniele Silvestro
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Global Gothenburg Biodiversity Center, Gothenburg, Sweden
| | - Michael Kessler
- Institute for Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
| | - Marcus Lehnert
- Nees Institute for Biodiversity of Plants, Rheinische Friedrich-Wilhelms University Bonn, Bonn, Germany
- Department of Geobotany and Botanical Garden, Herbarium, Martin-Luther-University Halle-Wittenberg, Neuwerk 21, 06108 Halle, Germany
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
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Wolf PG, Rowe CA, Kinosian SP, Der JP, Lockhart PJ, Shepherd LD, McLenachan PA, Thomson JA. Worldwide relationships in the fern genus Pteridium (bracken) based on nuclear genome markers. AMERICAN JOURNAL OF BOTANY 2019; 106:1365-1376. [PMID: 31545874 PMCID: PMC6856829 DOI: 10.1002/ajb2.1365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Spore-bearing plants are capable of dispersing very long distances. However, it is not known if gene flow can prevent genetic divergence in widely distributed taxa. Here we address this issue, and examine systematic relationships at a global geographic scale for the fern genus Pteridium. METHODS We sampled plants from 100 localities worldwide, and generated nucleotide data from four nuclear genes and two plastid regions. We also examined 2801 single nucleotide polymorphisms detected by a restriction site-associated DNA approach. RESULTS We found evidence for two distinct diploid species and two allotetraploids between them. The "northern" species (Pteridium aquilinum) has distinct groups at the continental scale (Europe, Asia, Africa, and North America). The northern European subspecies pinetorum appears to involve admixture among all of these. A sample from the Hawaiian Islands contained elements of both North American and Asian P. aquilinum. The "southern" species, P. esculentum, shows little genetic differentiation between South American and Australian samples. Components of African genotypes are detected on all continents. CONCLUSIONS We find evidence of distinct continental-scale genetic differentiation in Pteridium. However, on top of this is a clear signal of recent hybridization. Thus, spore-bearing plants are clearly capable of extensive long-distance gene flow; yet appear to have differentiated genetically at the continental scale. Either gene flow in the past was at a reduced level, or vicariance is possible even in the face of long-distance gene flow.
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Affiliation(s)
- Paul G. Wolf
- Department of Biology and Ecology CenterUtah State UniversityLoganUtah84322USA
- Present address:
Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleAlabama35899USA
| | - Carol A. Rowe
- Department of Biology and Ecology CenterUtah State UniversityLoganUtah84322USA
| | - Sylvia P. Kinosian
- Department of Biology and Ecology CenterUtah State UniversityLoganUtah84322USA
| | - Joshua P. Der
- Department of Biological ScienceCalifornia State UniversityFullertonCalifornia92831USA
| | - Peter J. Lockhart
- Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa TongarewaPO Box 467Wellington6140New Zealand
| | | | - John A. Thomson
- National Herbarium of New South WalesRoyal Botanic Gardens and Domain TrustMrs. Macquaries RoadSydneyNew South Wales2000Australia
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15
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Dong S, Xiao Y, Kong H, Feng C, Harris A, Yan Y, Kang M. Nuclear loci developed from multiple transcriptomes yield high resolution in phylogeny of scaly tree ferns (Cyatheaceae) from China and Vietnam. Mol Phylogenet Evol 2019; 139:106567. [DOI: 10.1016/j.ympev.2019.106567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 11/27/2022]
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Morero RE, Deanna R, Barboza GE, Barrington DS. Historical biogeography of the fern genus Polystichum (Dryopteridaceae) in Austral South America. Mol Phylogenet Evol 2019; 137:168-189. [PMID: 31077789 DOI: 10.1016/j.ympev.2019.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
Abstract
A group of seven endemic Polystichum species inhabit Patagonia, the southern region of South America. To date, evolutionary relationships of these Austral South American Polystichum remain unknown. The biota of the Southern Andes appears to be more closely related to the temperate Australasian species than to northern South American ones. Differences in morphological characters suggested that Austral South American Polystichum follows that biogeographical pattern, not being closely related to their congeners in the Northern and Central Andes. We sought to reveal the evolutionary relationships, estimate the divergence times and reconstruct both ancestral areas and ancestral ploidy levels of Austral South America Polystichum. Phylogenetic relationships were estimated using maximum likelihood and Bayesian approaches. The seven Austral South American species plus 31 Polystichum species spanning all other major biogeographic regions were sampled for three DNA markers. Divergence times were estimated in BEAST and Bayesian binary Markov chain Monte Carlo reconstruction was applied in order to infer ancestral areas. The evolution of ploidy was reconstructed on the maximum clade credibility tree, using stochastic character mapping. Austral South American Polystichum was recovered as monophyletic. The earliest divergence reconstructed within the Austral South American Clade was that of Polystichum andinum; subsequently two other lineages diverged comprising the remaining Austral South American species. The Austral South American lineage is not closely allied to North and Central Andes congeners. Long-distance dispersal of an ancestral tetraploid from Australasia during the late Miocene is the most likely explanation for the origin of Patagonian Polystichum. Then, Pliocene and Pleistocene orogenic and climatic changes may have shaped its diversification in Patagonia.
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Affiliation(s)
- Rita E Morero
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), CC 495, Córdoba 5000, Argentina; Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Córdoba, Argentina.
| | - Rocío Deanna
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), CC 495, Córdoba 5000, Argentina; Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Córdoba, Argentina
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), CC 495, Córdoba 5000, Argentina; Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Córdoba, Argentina
| | - David S Barrington
- University of Vermont, Pringle Herbarium, Torrey Hall, 27 Colchester Avenue, Burlington, VT 05405, United States
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Cardinal-McTeague WM, Wurdack KJ, Sigel EM, Gillespie LJ. Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species. BMC Evol Biol 2019; 19:29. [PMID: 30670006 PMCID: PMC6341577 DOI: 10.1186/s12862-018-1308-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/23/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BIOGEOBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model. RESULTS Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas. CONCLUSIONS The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.
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Affiliation(s)
- Warren M. Cardinal-McTeague
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Kenneth J. Wurdack
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Billeaud Hall, Room 108, 410 E. St. Mary Blvd, Lafayette, LA 70503 USA
| | - Lynn J. Gillespie
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
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Bauret L, Field AR, Gaudeul M, Selosse MA, Rouhan G. First insights on the biogeographical history of Phlegmariurus (Lycopodiaceae), with a focus on Madagascar. Mol Phylogenet Evol 2018; 127:488-501. [DOI: 10.1016/j.ympev.2018.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 10/17/2022]
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Barrera-Redondo J, Ramírez-Barahona S, Eguiarte LE. Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity. Evolution 2018; 72:1050-1062. [PMID: 29604055 DOI: 10.1111/evo.13475] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/11/2018] [Indexed: 12/31/2022]
Abstract
Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level.
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Affiliation(s)
- Josué Barrera-Redondo
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad de México 04510, México
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad de México 04510, México
| | - Luis E Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad de México 04510, México
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20
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Neretina AN, Garibian PG, Sinev AY, Kotov AA. Diversity of the subgenus Disparalona (Mixopleuroxus) Hudec, 2010 (Crustacea: Cladocera) in the New and Old World. J NAT HIST 2018. [DOI: 10.1080/00222933.2017.1411987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anna N. Neretina
- Laboratory for ecology of aquatic communities and invasions, A.N. Severtsov Institute of Ecology and Evolution, Moscow, Russia
| | - Petr G. Garibian
- Laboratory for ecology of aquatic communities and invasions, A.N. Severtsov Institute of Ecology and Evolution, Moscow, Russia
| | - Artem Y. Sinev
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey A. Kotov
- Laboratory for ecology of aquatic communities and invasions, A.N. Severtsov Institute of Ecology and Evolution, Moscow, Russia
- Laboratory of Paleoclimatology, Paleoecology, Paleomagnetism, Kazan Federal University, Kazan, Russia
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Ramírez-Barahona S, Barrera-Redondo J, Eguiarte LE. Rates of ecological divergence and body size evolution are correlated with species diversification in scaly tree ferns. Proc Biol Sci 2017; 283:rspb.2016.1098. [PMID: 27412279 DOI: 10.1098/rspb.2016.1098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 06/16/2016] [Indexed: 12/21/2022] Open
Abstract
Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this 'ancient' fern lineage across the tropics.
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Affiliation(s)
- Santiago Ramírez-Barahona
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología. Circuito Exterior s/n. Universidad Nacional Autónoma de México, 04510, Distrito Federal, Mexico
| | - Josué Barrera-Redondo
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología. Circuito Exterior s/n. Universidad Nacional Autónoma de México, 04510, Distrito Federal, Mexico
| | - Luis E Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología. Circuito Exterior s/n. Universidad Nacional Autónoma de México, 04510, Distrito Federal, Mexico
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Blair DP, Blanchard W, Banks SC, Lindenmayer DB. Non-linear growth in tree ferns, Dicksonia antarctica and Cyathea australis. PLoS One 2017; 12:e0176908. [PMID: 28493884 PMCID: PMC5426625 DOI: 10.1371/journal.pone.0176908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 04/19/2017] [Indexed: 12/04/2022] Open
Abstract
Tree ferns are an important structural component of forests in many countries. However, because their regeneration is often unrelated to major disturbances, their age is often difficult to determine. In addition, rates of growth may not be uniform, which further complicates attempts to determine their age. In this study, we measured 5 years of growth of Cyathea australis and Dicksonia antarctica after a large wildfire in 2009 in south-eastern Australia. We found growth rates of these two species were unaffected by aspect and elevation but slope had a minor effect with D. antarctica growing 0.3mm faster for each additional degree of slope. Geographic location influenced growth in both species by up to 12 - 14mm/yr. The most consistent factor influencing growth rate, however, was initial height at the time of the 2009 fire; a finding consistent in both species and all geographic locations. For both tree fern species, individuals that were taller at the commencement of the study had greater overall growth for the duration of the study. This effect did not decrease even among the tallest tree ferns in our study (up to 6 metres tall). Overall, Cyathea australis averaged 73 (± 22)mm/year of growth (± 1SD), with the rate increasing 5mm/yr per metre of additional height. Dicksonia antarctica averaged 33 (± 13)mm/year, increasing by 6mm/yr/m. Growth rates dependent on initial height were unexpected and we discuss possible reasons for this finding. Variable growth rates also suggest that common age estimation methods of dividing height by average growth rate are likely to underestimate the age of short tree ferns, while overestimating the age of tall tree ferns, particularly if they have been subject to a fire.
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Affiliation(s)
- David P. Blair
- Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
- Long-term Ecological Research Network, Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Wade Blanchard
- Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
- Long-term Ecological Research Network, Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sam C. Banks
- Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
- Long-term Ecological Research Network, Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - David B. Lindenmayer
- Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
- Long-term Ecological Research Network, Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
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Sosa V, Ornelas JF, Ramírez-Barahona S, Gándara E. Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica. PeerJ 2016; 4:e2696. [PMID: 27896030 PMCID: PMC5119233 DOI: 10.7717/peerj.2696] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/18/2016] [Indexed: 12/27/2022] Open
Abstract
Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations. Conclusions Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors.
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Affiliation(s)
- Victoria Sosa
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Etelvina Gándara
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico.,Instituto de Ciencias/Herbario y Jardín Botánico, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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Kuo LY, Ebihara A, Shinohara W, Rouhan G, Wood KR, Wang CN, Chiou WL. Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy. Mol Phylogenet Evol 2016; 104:123-134. [DOI: 10.1016/j.ympev.2016.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 08/06/2016] [Accepted: 08/09/2016] [Indexed: 12/14/2022]
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Phylogeny and biogeography of the remarkable genus Bondarzewia (Basidiomycota, Russulales). Sci Rep 2016; 6:34568. [PMID: 27680391 PMCID: PMC5041112 DOI: 10.1038/srep34568] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/15/2016] [Indexed: 11/08/2022] Open
Abstract
Bondarzewia is a conspicuous and widely distributed mushroom genus, but little is known about its origin and biogeography. Here, we investigated the systematics and biogeography of Bondarzewia species using multi-locus phylogenetic analysis. Four genetic markers, including the internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (nLSU), elongation factor 1-α (tef1) and mitochondrial small subunit rDNA (mtSSU), were used to infer the phylogenetic relationships of Bondarzewia. We performed Bayesian evolutionary analysis on the gene datasets of the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). From the results, we inferred that the maximum crown age of Bondarzewia is approximately 25.5 million-years-ago (Mya) and that tropical East Asia is likely to be its ancestral area, with three possible expansions leading to its distribution in North America, Europe and Oceania.
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Range size heritability and diversification patterns in the liverwort genus Radula. Mol Phylogenet Evol 2016; 106:73-85. [PMID: 27664347 DOI: 10.1016/j.ympev.2016.09.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 11/20/2022]
Abstract
Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively. The congruence between the divergence time of these lineages and continental split suggests that plate tectonics could have played a major role in their present distribution, suggesting that a strong imprint of vicariance can still be found in extant distribution patterns in these highly mobile organisms. Amentuloradula, Volutoradula and Metaradula species did not appear to exhibit losses of dispersal capacities in terms of dispersal life-history traits, but evidence for significant phylogenetic signal in macroecological niche traits suggests that niche conservatism accounts for their restricted geographic ranges. Despite their greatly restricted distribution to Australasia and Neotropics respectively, Amentuloradula and Volutoradula did not exhibit significantly lower diversification rates than more widespread lineages, in contrast with the hypothesis that the probability of speciation increases with range size by promoting geographic isolation and increasing the rate at which novel habitats are encountered. We suggest that stochastic long-distance dispersal events may balance allele frequencies across large spatial scales, leading to low genetic structure among geographically distant areas or even continents, ultimately decreasing the diversification rates in highly mobile, widespread lineages.
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A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals. Mol Phylogenet Evol 2016; 98:324-36. [DOI: 10.1016/j.ympev.2016.02.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/15/2016] [Accepted: 02/20/2016] [Indexed: 11/18/2022]
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Arana MD, Larsen C, Ponce MM. Revisión y análisis panbiogeográfico de las Hymenophyllaceae de las Yungas meridionales de Argentina (Selva Tucumano-Boliviana). RODRIGUÉSIA 2016. [DOI: 10.1590/2175-7860201667105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hymenophyllaceae constituye uno de los linajes más tempranamente divergente dentro de los helechos, habitan lugares hiperhúmedos y su aparición se ha datado en el cretácico temprano, previa a la ruptura de Gondwana; estas características determinan que sean especialmente útiles para establecer patrones biogeográficos. En este trabajo se discuten la diversidad de la familia Hymenophyllaceae en las Yungas meridionales y sus vinculaciones biogeográficas, mediante un análisis panbiogeográfico. Se han encontrado nueve especies, comprendidas en cuatro géneros: Crepidomanes, Didymoglossum, Hymenophyllum y Polyphlebium; Crepidomanes pyxidiferum constituye una novedad florística a nivel genérico para Argentina. Se brindan una clave para todos los géneros de Hymenophyllaceae presentes en Argentina, así como claves entre todas las especies presentes en las Yungas, que además son descriptas e ilustradas.
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Affiliation(s)
| | - Cristian Larsen
- Academia Nacional de Ciencias Exactas, Físicas y Naturales, Argentina
| | - M. Mónica Ponce
- Academia Nacional de Ciencias Exactas, Físicas y Naturales, Argentina
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Berger BA, Kriebel R, Spalink D, Sytsma KJ. Divergence times, historical biogeography, and shifts in speciation rates of Myrtales. Mol Phylogenet Evol 2015; 95:116-36. [PMID: 26585030 DOI: 10.1016/j.ympev.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 10/04/2015] [Indexed: 01/22/2023]
Abstract
We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.
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Affiliation(s)
- Brent A Berger
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11432, USA; Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Daniel Spalink
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
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Sundue MA, Parris BS, Ranker TA, Smith AR, Fujimoto EL, Zamora-Crosby D, Morden CW, Chiou WL, Chen CW, Rouhan G, Hirai RY, Prado J. Global phylogeny and biogeography of grammitid ferns (Polypodiaceae). Mol Phylogenet Evol 2014; 81:195-206. [DOI: 10.1016/j.ympev.2014.08.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 10/24/2022]
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