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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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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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3
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Dong Y, Wei X, Qiang T, Liu J, Che P, Qi Y, Zhang B, Liu H. RAD-Seq and Ecological Niche Reveal Genetic Diversity, Phylogeny, and Geographic Distribution of Kadsura interior and Its Closely Related Species. FRONTIERS IN PLANT SCIENCE 2022; 13:857016. [PMID: 35557741 PMCID: PMC9087809 DOI: 10.3389/fpls.2022.857016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Most plants of Kadsura have economic value and medicinal application. Among them, K. interior and its closely related species have been demonstrated to have definite efficacy. However, the taxonomy and phylogenetic relationship of Kadsura in terms of morphology and commonly used gene regions remain controversial, which adversely affects its rational application. In this study, a total of 107 individuals of K. interior, K. heteroclita, K. longipedunculata, K. oblongifolia, and K. coccinea were studied from the perspectives of genetic diversity, phylogeny, and ecology via single nucleotide polymorphisms (SNPs) developed through restriction site-associated DNA sequencing (RAD-seq). Based on these SNPs, the genetic diversity, phylogenetic reconstruction, and population genetic structure were analyzed. Subsequently, divergence time estimation and differentiation scenario simulation were performed. Meanwhile, according to the species distribution records and bioclimatic variables, the Last Glacial Maximum and current potential distributions of five species were constructed, and the main ecological factors affecting the distribution of different species were extracted. The F ST calculated showed that there was a moderate degree of differentiation among K. heteroclita, K. longipedunculata, and K. oblongifolia, and there was a high degree of genetic differentiation between K. interior and the above species. The phylogenetic tree indicated that each of the species was monophyletic. The results of population genetic structure and divergence scenario simulation and D-statistics showed that there were admixture and gene flow among K. heteroclita, K. longipedunculata, and K. oblongifolia. The results of ecological niche modeling indicated that the distribution areas and the bioclimatic variables affecting the distribution of K. interior and its related species were different. This study explored the differences in the genetic divergence and geographical distribution patterns of K. interior and its related species, clarifying the uniqueness of K. interior compared to its relatives and providing a reference for their rational application in the future.
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Affiliation(s)
- Yuqing Dong
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xueping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Tingyan Qiang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jiushi Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Peng Che
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yaodong Qi
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Bengang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Haitao Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Sun QH, Morales-Briones DF, Wang HX, Landis JB, Wen J, Wang HF. Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization. ANNALS OF BOTANY 2022; 129:201-216. [PMID: 34950959 PMCID: PMC8796676 DOI: 10.1093/aob/mcab139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/15/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Abelia (Caprifoliaceae) is a small genus with five species, including one artificial hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, Taiwan Island and the Ryukyu Islands, providing a model system to explore the mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within Abelia remain uncertain. METHODS We reconstructed the phylogenetic relationships within Abelia using nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction and ecological niche modelling (ENM) were used to examine the diversification history of Abelia. KEY RESULTS We found extensive cytonuclear discordance across the genus. By integrating lines of evidence from molecular phylogenies, divergence times and morphology, we propose to merge Abelia macrotera var. zabelioides into A. uniflora. Network analyses suggested that there have been multiple widespread hybridization events among Abelia species. These hybridization events may have contributed to the speciation mechanism and resulted in the high observed morphological diversity. The diversification of Abelia began in the early Eocene, followed by A. chinensis var. ionandra colonizing Taiwan Island during the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region and Taiwan Island is probably the consequence of topographical isolation and postglacial contraction. CONCLUSIONS We used genomic data to reconstruct the phylogeny of Abelia and found a clear pattern of reticulate evolution in the group. In addition, our results suggest that shrinkage of postglacial range and the heterogeneity of the terrain have led to the disjunction between Mainland China and Taiwan Island. This study provides important new insights into the speciation process and taxonomy of Abelia.
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Affiliation(s)
- Qing-Hui Sun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
| | - Diego F Morales-Briones
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, 140 Gortner Laboratory, Saint Paul, MN, USA
- Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638, Munich, Germany
| | - Hong-Xin Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
- Zhai Mingguo Academician Work Station, Sanya University, Sanya, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, USA
| | - Hua-Feng Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
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5
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Fan R, Ma W, Liu S, Huang Q. Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis. Ecol Evol 2021; 11:4550-4563. [PMID: 33976830 PMCID: PMC8093657 DOI: 10.1002/ece3.7350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Some ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution. MATERIALS AND METHODS The complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes. RESULTS The whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75-108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C-to-U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single-copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships. CONCLUSION The results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.
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Affiliation(s)
- Ruifeng Fan
- School of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Wei Ma
- School of PharmacyHeilongjiang University of Chinese MedicineHarbinChina
| | - Shilei Liu
- Experimental Teaching & Practical Training CenterHeilongjiang University of Chinese MedicineHarbinChina
| | - Qingyang Huang
- Department of EcologyInstitute of Natural Resources and EcologyHeilongjiang Academy of ScienceHarbinChina
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6
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Shah SN, Ahmad M, Zafar M, Hadi F, Khan MN, Noor A, Malik K, Rashid N, Kamal A, Iqbal M, Hussain M. Application of spore morphology to solve identification problems in certain species of family Dryopteridaceae from Malakand Division, Pakistan. Microsc Res Tech 2021; 84:1897-1910. [PMID: 33656223 DOI: 10.1002/jemt.23746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/27/2021] [Accepted: 02/20/2021] [Indexed: 11/09/2022]
Abstract
Here we investigate the morphology of the spores of 12 native taxa of Dryopteridaceae that grow in Malakand division, Pakistan; most of these species not fully described before. This study intends to survey the taxonomic significance of spore morphological features and their variation useful for species identification in 7 species of Polystichum and 5 taxa of Dryopteris. The spores examinations were accomplished utilizing a light microscope (LM), and scanning electron microscope (SEM). The spores are monolete, medium-sized, with variable shapes in both equatorial and polar views. The mean estimation of equatorial diameter ranging from 28.3 to 58.3 μm and the polar diameter varied from 27.6 to 45.8 μm. The exospore thickness ranges between 1.6 to 3.8 μm, and the thickness of perispore is 0.8-6.7 μm. The perispore is perforated, ornamentation elements occur in different ways in the studied taxa of Polystichum. In investigated Dryopteris taxa, rugate perispore type is found. Results of multivariate statistical analysis (UPGMA, and PCA) established on quantitative and qualitative morphological traits of spores demonstrate that the species form distinct groups, not reflecting any phylogenetic relationships. A key to the spores types is provided for species identification, which dependent on the diagnostic characters of spores. The results of this study indicate that variation of spore morphological traits; in particular, the ornamentation and perispore characteristics, which is surface texture, have diagnostic value at the species level. Our data will help in the identification of spores of the family Dryopteridaceae in palynological and taxonomic studies.
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Affiliation(s)
- Syed N Shah
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Science Laboratory, Government High School, Shangla, Pakistan
| | - Mushtaq Ahmad
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Zafar
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Hadi
- Department of Botany, University of Peshawar, Peshawar, Pakistan
| | - Muhammad N Khan
- Department of Botany, Bacha Khan University Charsadda, KP, Pakistan
| | - Adil Noor
- Department of Botany, Kohat University of Science & Technology, KP, Pakistan
| | - Khafsa Malik
- Department of Botany, Pir Mehr Ali Shah, Arid Agriculture University, Rawalpindi, Pakistan
| | - Neelam Rashid
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asif Kamal
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Majid Iqbal
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Murtaza Hussain
- Plant Eco-Physiology and Evolution Group, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio-resources, College of Forestry, Guangxi University Daxuedonglu 100, Nanning, Guangxi, China
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7
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Gorrer DA, Ramos Giacosa JP, Giudice GE. Palynological analysis of the genus Dryopteris Adans. (Dryopteridaceae) in Argentina. AN ACAD BRAS CIENC 2020; 92 Suppl 2:e20181052. [PMID: 32813768 DOI: 10.1590/0001-3765202020181052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/02/2019] [Indexed: 11/21/2022] Open
Abstract
The spore morphology and wall ultrastructure of Dryopteris filix-mas, D. patula and D. wallichiana from Argentina were studied using light microscope, scanning and transmission electron microscope. The study was carried out with herbarium material from Argentine institutions. Equatorial diameters, polar diameters and laesura length were measured. The spores are monoletes with a rugate ornamentation. The folds are short to long, inflate, irregular in shape and size, and varying from subglobose to elongate. The perispore surface is rugulate. The exospore of all the species analyzed is two-layered in section. Simple and branched channels are also present. The perispore is composed of two layers, the inner one forms the ornamentation and the outer covers all the outer and inner surfaces. Some abnormalities, such as globose, triangular or twisted spores were observed. The morphology and ultrastructure of the species are very similar. The differences observed are related to the length and thickness of the perispore folds. The characteristics of these spores would not provide relevant information to differentiate species or sections within the genus, but can provide information for phylogenetic studies as well as for alterations in the biological cycles.
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Affiliation(s)
- Daniel A Gorrer
- Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, CABA, Argentina
| | - Juan P Ramos Giacosa
- Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, CABA, Argentina
| | - Gabriela E Giudice
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
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8
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Kuo LY, Chang YH, Huang YH, Testo W, Ebihara A, Rouhan G, Quintanilla LG, Watkins JE, Huang YM, Li FW. A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision, historical biogeography and evolution of leaf architecture. Cladistics 2020; 36:164-183. [PMID: 34618958 DOI: 10.1111/cla.12399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
The thelypteroid fern genus Stegnogramma s.l. contains around 18-35 species and has a global, cross-continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a global phylogeny of Stegnogramma s.l. with the most comprehensive sampling to date and aim to pinpoint the phylogenetic positions of biogeographically and taxonomically important taxa. Based on the reconstructed historical biogeography and character evolution, we propose a new (infra)generic classification and discuss the diversification of Stegnogramma s.l. in a biogeographical context. New names or combinations are made for 12 (infra)species, including transferring the monotypic species of Craspedosorus to Leptogramma. Finally, we discuss a possible link between leaf architecture and ecological adaptation, and hypothesize that the increase in leaf dissection and free-vein proportion is an adaptive feature to cool climates in Stegnogramma s.l.
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Affiliation(s)
- Li-Yaung Kuo
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Yi-Hang Chang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Yu-Hsuan Huang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Weston Testo
- Biology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki, 305-0005, Japan
| | - Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, 16 rue Buffon CP39, F-75005, Paris, France
| | - Luis G Quintanilla
- School of Environmental Sciences and Technology, Rey Juan Carlos University, Móstoles, Spain
| | - James E Watkins
- Department of Biology, Colgate University, Hamilton, NY, 13346, USA
| | - Yao-Moan Huang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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9
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Lu NT, Ebihara A, He H, Zhang L, Zhou XM, Knapp R, Kamau P, Lorence D, Gao XF, Zhang LB. A plastid phylogeny of the fern genus Arachniodes (Dryopteridaceae). Mol Phylogenet Evol 2018; 133:214-235. [PMID: 30550964 DOI: 10.1016/j.ympev.2018.12.013] [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: 07/06/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
Arachniodes (Dryopteridaceae) is one of the most confusing and controversial fern genera in terms of its circumscription, nomenclature, and taxonomy. Estimates of species number range from 40 to 200. Previous molecular works included only 2-17 accessions representing 2-12 species of Arachniodes and allied genera, leaving most of the Asian species remain unsampled and the infragneric relationships unclear. In this study DNA sequences of seven plastid markers of 343 accessions representing ca. 68 species of Arachniodes (275 accessions), and 64 outgroup accessions from subfam. Dryopteridoideae and subfam. Polybotryoideae were used to infer a phylogeny with maximum likelihood, Bayesian inference, and maximum parsimony approaches. Our major results include: (1) Two species currently assigned in Arachniodes (A. macrostegia and A. ochropteroides are resolved outside of the core Arachniodes making the currently defined Arachniodes polyphyletic, confirming earlier findings; (2) Lithostegia, Leptorumohra, and Phanerophlebiopsis are indeed synonyms of Arachniodes; (3) Leptorumohra is confirmed to be monophyletic, but Phanerophlebiopsis is polyphyletic; (4) The New World species of Arachniodes are confirmed to be not monophyletic with A. denticulata being nested within the Old World species, suggesting that this species is dispersed from the Old World; (5) Arachniodes s.s is resolved into 12 major clades, some of which are further divisable into recognizable subclades and groups, with A. mutica from Japan being resolved as the sister to the rest of the genus; (6) A number of systematic implications of the phylogeny have been suggested; and (7) the genus is estimated to contain ca. 83 species.
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Affiliation(s)
- Ngan Thi Lu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biology, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18th Hoang Quoc Viet Road, Ha Noi, Viet Nam
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba-shi, Ibaraki 305-0005, Japan
| | - Hai He
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, China
| | - Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xin-Mao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, Yunnan, China
| | - Ralf Knapp
- Correspondent of the Muséum national d'Histoire naturelle (MNHN, Paris, France), Steigestrasse 78, 69412 Eberbach, Germany
| | - Peris Kamau
- Botany Department, National Museums of Kenya, P.O. Box 40658-00100, Nairobi, Kenya
| | - David Lorence
- National Tropical Botanical Garden, 3530 Papalina Road, Kalaheo, HI 96741-9599, USA
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China.
| | - Li-Bing Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China; Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA.
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Shah SN, Ahmad M, Zafar M, Malik K, Rashid N, Ullah F, Zaman W, Ali M. A light and scanning electron microscopic diagnosis of leaf epidermal morphology and its systematic implications in Dryopteridaceae: Investigating 12 Pakistani taxa. Micron 2018; 111:36-49. [PMID: 29857176 DOI: 10.1016/j.micron.2018.05.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/03/2018] [Accepted: 05/10/2018] [Indexed: 11/30/2022]
Abstract
Dryopteris and Polystichum are the 2 complex taxonomic genera of Dryopteridaceae. The comparative foliar epidermal anatomy of 12 species of both genera from Pakistan were studied using standard protocols of light microscopy (LM) and scanning electron microscopy (SEM). The objective of which was systematic comparison and investigation to elucidate the taxonomic importance of foliar micromorphology, which may be useful to taxonomists for identifying complex Dryopteridaceae taxa. Principal component analysis and UPGMA clustering analysis were performed to test the validity of leaf anatomical features as method of separating species and genera. The foliar epidermal anatomy described here is a good source of taxonomic characters in both groups that can help genera and species delimitation. This is the first report on leaf micromorphology in most of these species. Observation of foliar anatomy showed that stomata are only present on the abaxial surface; i.e., leaves of all species are hypostomatic. The shapes of epidermal cells in all studied species are irregular. The anticlinal walls are strongly lobed, irregular wavy and elongated wavy. However, substantial variation in epidermal cell size and other stomatal features were observed on both upper and lower surfaces in all investigated species. Two types of stomata were observed in all studied species. The presence of polocytic stomata in Dryopteris and staurocytic stomata in Polystichum are the important characters for the segregation of these genera. Elongate elliptic stomatal shape, narrow kidney shaped guard cells and broad elliptic shaped stomatal pores are diagnostic for all five species of Dryopteris selected. On the other hand, size and number of epidermal cells, lobes per cell, stomatal size, subsidiary cell size, stomatal pore size and stomatal index are the key features for species differentiation in Polystichum. An identification key was developed in order to apply the foliar anatomical characters in the discrimination of the species studied.
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Affiliation(s)
- Syed Nasar Shah
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan.
| | - Mushtaq Ahmad
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan.
| | - Muhammad Zafar
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan.
| | - Khafsa Malik
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan.
| | - Neelam Rashid
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan.
| | - Fazal Ullah
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan.
| | - Wajid Zaman
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Maroof Ali
- Department of Plant Sciences, Quaid- i- Azam University, Islamabad, 45320, Pakistan.
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Sessa EB, Chambers SM, Li D, Trotta L, Endara L, Burleigh JG, Baiser B. Community assembly of the ferns of Florida. AMERICAN JOURNAL OF BOTANY 2018; 105:549-564. [PMID: 29730880 DOI: 10.1002/ajb2.1073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. METHODS We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional trait data for both spatial scales and compared the results to null models to assess significance. KEY RESULTS Our results for over vs. underdispersion in functional and phylogenetic diversity differed depending on spatial scale and metric considered. At the county scale, MPD revealed evidence for phylogenetic overdispersion, while MNTD revealed phylogenetic and functional underdispersion, and at the conservation area scale, MPD revealed phylogenetic and functional underdispersion while MNTD revealed evidence only of functional underdispersion. CONCLUSIONS Our results are consistent with environmental filtering playing a larger role at the smaller, conservation area scale. The smaller spatial units are likely composed of fewer local habitat types that are selecting for closely related species, with the larger-scale units more likely to be composed of multiple habitat types that bring together a larger pool of species from across the phylogeny. Several aspects of fern biology, including their unique physiology and water relations and the importance of the independent gametophyte stage of the life cycle, make ferns highly sensitive to local, microhabitat conditions.
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Affiliation(s)
- Emily B Sessa
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Sally M Chambers
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
- Marie Selby Botanical Gardens, 900 S. Palm Avenue, Sarasota, FL, 34236, USA
| | - Daijiang Li
- Department of Wildlife Ecology & Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
| | - Lauren Trotta
- Department of Wildlife Ecology & Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
| | - Lorena Endara
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Benjamin Baiser
- Department of Wildlife Ecology & Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
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Krinitsina AA, Belenikin MS, Churikova OA, Kuptsov3 SV, Antipin MI, Logacheva MD, Speranskaya AS. The systematic position of Dryopteris blanfordii subsp. nigrosquamosa (Ching) Fraser-Jenkins within the genus Dryopteris Adans. PHYTOKEYS 2017; 90:89-112. [PMID: 29391852 PMCID: PMC5784233 DOI: 10.3897/phytokeys.90.14745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Dryopteris blanfordii (C.Hope) C.Chr. is a member of the Dryopteridaceae, growing in high altitude Picea or Abies forests (2900-3500 m) in China and India. Phylogenetic relationships between D. blanfordii subsp. nigrosquamosa and closely related species of Dryopteris were investigated using a combined analysis of multiple molecular data sets (the protein-coding region of rbcL and matK genes and intergenic spacers psbA-trnH, trnP-petG, rps4-trnS, trnL-trnF and rbcL-accD). An assumption about the position of D. blanfordii subsp. nigrosquamosa within Dryopteris was made by using the Maximum Likelihood and Bayesian Inference approach and chloroplast marker sequences of Dryopteris species from GenBank. The results demonstrated that Asian taxa D. blanfordii subsp. nigrosquamosa and D. laeta as well as two American species D. arguta and D. marginalis belong to the same clade, all four of them being part of Dryopteris section Dryopteris.
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Affiliation(s)
- Anastasiya A. Krinitsina
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Maxim S. Belenikin
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141700
| | - Olga A. Churikova
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Sergey V. Kuptsov3
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Maxim I. Antipin
- Botanical Garden, Lomonosov Moscow State University, Leninskie gory, Moscow, Russia, 119899
| | - Maria D. Logacheva
- Department of Evolutional Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, 1, 40, Moscow, Russia, 119992
| | - Anna S. Speranskaya
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
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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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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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Biogeography and diversification of Brassicales: A 103million year tale. Mol Phylogenet Evol 2016; 99:204-224. [PMID: 26993763 DOI: 10.1016/j.ympev.2016.02.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/23/2022]
Abstract
Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.
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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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Liu ZW, Jolles DD, Zhou J, Peng H, Milne RI. Multiple origins of circumboreal taxa in Pyrola (Ericaceae), a group with a Tertiary relict distribution. ANNALS OF BOTANY 2014; 114:1701-9. [PMID: 25326138 PMCID: PMC4649697 DOI: 10.1093/aob/mcu198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/26/2014] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS In the Northern Hemisphere, Tertiary relict disjunctions involve older groups of warm affinity and wide disjunctions, whereas circumboreal distributions in Arctic-Alpine taxa tend to be younger. Arctic-Alpine species are occasionally derived from Tertiary relict groups, but Pyrola species, in particular, are exceptional and they might have occurred multiple times. The aim of this study was to reconstruct the biogeographic history of Pyrola based on a clear phylogenetic analysis and to explore how the genus attained its circumboreal distribution. METHODS Estimates of divergence times and ancestral geographical distributions based on neutrally evolving DNA sequence variation were used to develop a spatio-temporal model of colonization patterns for Pyrola. KEY RESULTS Pyrola originated and most diversification occurred in Asia; North America was reached first by series Scotophyllae in the late Miocene, then by sub-clades of series Pyrola and Ellipticae around the Pliocene. The three circumboreal taxa, P. minor, P. chlorantha and the P. rotundifolia complex, originated independently of one another, with the last two originating in Asia. CONCLUSIONS Three circumboreal Pyrola lineages have arisen independently and at least two of these appear to have originated in Asia. The cool, high-altitude habitats of many Pyrola species and the fact that diversification in the genus coincided with global cooling from the late Miocene onwards fits a hypothesis of pre-adaptation to become circumboreal within this group.
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Affiliation(s)
- Zhen-Wen Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kuming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Diana D Jolles
- Rancho Santa Ana Botanic Garden, Claremont Graduate University, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Jing Zhou
- School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming 650500, China
| | - Hua Peng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kuming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
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Chen C, Qi ZC, Xu XH, Comes HP, Koch MA, Jin XJ, Fu CX, Qiu YX. Understanding the formation of Mediterranean-African-Asian disjunctions: evidence for Miocene climate-driven vicariance and recent long-distance dispersal in the Tertiary relict Smilax aspera (Smilacaceae). THE NEW PHYTOLOGIST 2014; 204:243-255. [PMID: 24975406 DOI: 10.1111/nph.12910] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/27/2014] [Indexed: 05/23/2023]
Abstract
Tethyan plant disjunctions, including Mediterranean-African-Asian disjunctions, are thought to be vicariant, but their temporal origin and underlying causes remain largely unknown. To address this issue, we reconstructed the evolutionary history of Smilax aspera, a hypothesized component of the European Tertiary laurel forest flora. Thirty-eight populations and herbarium specimens representing 57 locations across the species range were sequenced at seven plastid regions and the nuclear ribosomal internal transcribed spacer region. Time-calibrated phylogenetic and phylogeographic inferences were used to trace ancestral areas and biogeographical events. The deep intraspecific split between Mediterranean and African-Asian lineages is attributable to range fragmentation of a southern Tethyan ancestor, as colder and more arid climates developed shortly after the mid-Miocene. In the Mediterranean, climate-induced vicariance has shaped regional population structure since the Late Miocene/Early Pliocene. At around the same time, East African and South Asian lineages split by vicariance, with one shared haplotype reflecting long-distance dispersal. Our results support the idea that geographic range formation and divergence of Tertiary relict species are more or less gradual (mostly vicariant) processes over long time spans, rather than point events in history. They also highlight the importance of the Mediterranean Basin as a centre of intraspecific divergence for Tertiary relict plants.
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Affiliation(s)
- Chen Chen
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Plant Sciences, and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
| | - Zhe-Chen Qi
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Plant Sciences, and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
| | - Xi-Hui Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Plant Sciences, and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
| | - Hans Peter Comes
- Department of Organismic Biology, Salzburg University, A-5020, Salzburg, Austria
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics and Botanical Garden and Herbarium Heidelberg (HEID), Center for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Xin-Jie Jin
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Cheng-Xin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Plant Sciences, and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Plant Sciences, and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
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Relationships and origins of the Dryopteris varia (L.) Kuntze species complex (Dryopteridaceae) in Korea inferred from nuclear and chloroplast DNA sequences. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Sulman JD, Drew BT, Drummond C, Hayasaka E, Sytsma KJ. Systematics, biogeography, and character evolution of Sparganium (Typhaceae): diversification of a widespread, aquatic lineage. AMERICAN JOURNAL OF BOTANY 2013; 100:2023-2039. [PMID: 24091784 DOI: 10.3732/ajb.1300048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Sparganium (Typhaceae) is a genus of aquatic monocots containing ±14 species, with flowers aggregated in unisexual, spherical heads, and habit ranging from floating to emergent. Sparganium presents an opportunity to investigate diversification, character evolution, and biogeographical relationships in a widespread temperate genus of aquatic monocots. We present a fossil-calibrated, molecular phylogeny of Sparganium based on analysis of two chloroplast and two nuclear markers. Within this framework, we examine character evolution in both habit and stigma number and infer the ancestral area and biogeographic history of the genus. • METHODS Sequence data from two cpDNA and two nDNA markers were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We used the program BEAST to simultaneously estimate phylogeny and divergence times, S-DIVA and Lagrange for biogeographical reconstruction, and BayesTraits to examine locule number and habit evolution. • KEY RESULTS Two major clades were recovered with strong support: one composed of S. erectum and S. eurycarpum; and the other containing all remaining Sparganium. We realigned the subgenera to conform to these clades. Divergence time analysis suggests a Miocene crown origin but Pliocene diversification. Importantly, the floating-leaved habit has arisen multiple times in the genus, from emergent ancestors-contrary to past hypotheses. • CONCLUSIONS Cooling trends during the Tertiary are correlated with the isolation of temperate Eurasian and North American taxa. Vicariance, long-distance dispersal, and habitat specialization are proposed as mechanisms for Sparganium diversification.
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Affiliation(s)
- Joshua D Sulman
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706 USA
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Kershaw F, Leslie MS, Collins T, Mansur RM, Smith BD, Minton G, Baldwin R, LeDuc RG, Anderson RC, Brownell RL, Rosenbaum HC. Population Differentiation of 2 Forms of Bryde’s Whales in the Indian and Pacific Oceans. J Hered 2013; 104:755-64. [DOI: 10.1093/jhered/est057] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Sessa EB, Givnish TJ. Leaf form and photosynthetic physiology ofDryopterisspecies distributed along light gradients in eastern North America. Funct Ecol 2013. [DOI: 10.1111/1365-2435.12150] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emily B. Sessa
- Department of Botany; University of Wisconsin-Madison; 430 Lincoln Drive Madison WI 53706 USA
| | - Thomas J. Givnish
- Department of Botany; University of Wisconsin-Madison; 430 Lincoln Drive Madison WI 53706 USA
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Comparative phylogeography of the Smilax hispida group (Smilacaceae) in eastern Asia and North America – Implications for allopatric speciation, causes of diversity disparity, and origins of temperate elements in Mexico. Mol Phylogenet Evol 2013; 68:300-11. [DOI: 10.1016/j.ympev.2013.03.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 03/23/2013] [Accepted: 03/25/2013] [Indexed: 11/21/2022]
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Zhang LB, Zhang L, Dong SY, Sessa EB, Gao XF, Ebihara A. Molecular circumscription and major evolutionary lineages of the fern genus Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:180. [PMID: 22971160 PMCID: PMC3483261 DOI: 10.1186/1471-2148-12-180] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 09/04/2012] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The fern genus Dryopteris (Dryopteridaceae) is among the most common and species rich fern genera in temperate forests in the northern hemisphere containing 225-300 species worldwide. The circumscription of Dryopteris has been controversial and various related genera have, over the time, been included in and excluded from Dryopteris. The infrageneric phylogeny has largely remained unclear, and the placement of the majority of the supraspecific taxa of Dryopteris has never been tested using molecular data. RESULTS In this study, DNA sequences of four plastid loci (rbcL gene, rps4-trnS spacer, trnL intron, trnL-F spacer) were used to reconstruct the phylogeny of Dryopteris. A total of 122 accessions are sampled in our analysis and they represent 100 species of the expanded Dryopteris including Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema. All four subgenera and 19 sections currently recognized in Dryopteris s.s. are included. One species each of Arachniodes, Leptorumohra, and Lithostegia of Dryopteridaceae are used as outgroups. Our study confirms the paraphyly of Dryopteris and provides the first strong molecular evidence on the monophyly of Acrophorus, Diacalpe, Dryopsis, Nothoperanema, and Peranema. However, all these monophyletic groups together with the paraphyletic Acrorumohra are suggested to be merged into Dryopteris based on both molecular and morphological evidence. Our analysis identified 13 well-supported monophyletic groups. Each of the 13 clades is additionally supported by morphological synapomophies and is inferred to represent a major evolutionary lineage in Dryopteris. In contrast, monophyly of the four subgenera and 15 out of 19 sections currently recognized in Dryopteris s.s is not supported by plastid data. CONCLUSIONS The genera, Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema, should all be merged into Dryopteris. Most species of these genera share a short rhizome and catadromic arrangement of frond segments, unlike the sister genus of Dryopteris s.l., Arachniodes, which has anadromic arrangement of frond segments. The non-monophyly of the 19 out of the 21 supraspecific taxa (sections, subgenera) in Dryopteris strongly suggests that the current taxonomy of this genus is in need of revision. The disagreement between the previous taxonomy and molecular results in Dryopteris may be due partly to interspecific hybridization and polyplodization. More morphological studies and molecular data, especially from the nuclear genome, are needed to thoroughly elucidate the evolutionary history of Dryopteris. The 13 well-supported clades identified based on our data represent 13 major evolutionary lineages in Dryopteris that are also supported by morphological synapomophies.
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Affiliation(s)
- Li-Bing Zhang
- The ECORES Lab, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, P. R China
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Liang Zhang
- The ECORES Lab, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, P. R China
| | - Shi-Yong Dong
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Emily B Sessa
- Botany Department, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, 53706-1313, USA
| | - Xin-Fen Gao
- The ECORES Lab, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, P. R China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba-shi, Ibaraki, 305-0005, Japan
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McKeown M, Sundue M, Barrington DS. Phylogenetic analyses place the Australian monotypic Revwattsia in Dryopteris (Dryopteridaceae). PHYTOKEYS 2012; 14:43-56. [PMID: 23170072 PMCID: PMC3492925 DOI: 10.3897/phytokeys.14.3446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/18/2012] [Indexed: 05/23/2023]
Abstract
Revwattsia fragilis (Watts) D.L. Jones (Dryopteridaceae), originally described as a Polystichum Roth by the pioneer Australian botanist Reverend W.W. Watts in 1914, is a rare epiphytic fern endemic to northeastern Queensland, Australia. Known from only a few populations, it is restricted to tropical rainforests in the Atherton Tablelands. We used the cpDNA markers psbA-trnH, rbcL, rbcL-accD, rps4-trnS, trnG-trnR, trnL-trnF, and trnP-petG to infer the relationships of Revwattsia fragilis within Dryopteridaceae. Based on our molecular analysis, we were able to reject Watts's 1914 hypothesis of a close relationship to Polystichum. Its closest allies are a suite of Asian Dryopteris Adans. species including Dryopteris labordei, Dryopteris gymnosora, Dryopteris erythrosora and Dryopteris cystolepidota; maintaining Revwattsia renders Dryopteris paraphyletic. The epiphytic habit and distinctive long-creeping rhizome of Revwattsia appear to be autapomorphies and do not warrant its generic status. In the course of our investigation we confirmed that polyphyly of Dryopteris is also sustained by the inclusion of Acrorumohra (H.Itô) H.Itô, Acrophorus C.Presl, Arachniodes Blume, Diacalpe Blume, Dryopsis Holttum & P.J.Edwards, and Peranema D.Don. The epithet fragilis is occupied in Dryopteris, therefore we provide the name Dryopteris wattsiinom. nov. to accommodate Revwattsia fragilis in Dryopteris.
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Affiliation(s)
- Meghan McKeown
- Pringle Herbarium, Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington Vermont, 05405 USA
| | - Michael Sundue
- Pringle Herbarium, Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington Vermont, 05405 USA
| | - David S. Barrington
- Pringle Herbarium, Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington Vermont, 05405 USA
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Sessa EB, Zimmer EA, Givnish TJ. Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:104. [PMID: 22748145 PMCID: PMC3509404 DOI: 10.1186/1471-2148-12-104] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called "semicristata" hypothesis, contention over the group's history has continued in several recent, conflicting studies. RESULTS Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the "semicristata" hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. CONCLUSIONS This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis, including the existence of a missing diploid progenitor, and allow us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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Sessa EB, Zimmer EA, Givnish TJ. Reticulate evolution on a global scale: a nuclear phylogeny for New World Dryopteris (Dryopteridaceae). Mol Phylogenet Evol 2012; 64:563-81. [PMID: 22634937 DOI: 10.1016/j.ympev.2012.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/25/2012] [Accepted: 05/14/2012] [Indexed: 01/09/2023]
Abstract
Reticulate, or non-bifurcating, evolution is now recognized as an important phenomenon shaping the histories of many organisms. It appears to be particularly common in plants, especially in ferns, which have relatively few barriers to intra- and interspecific hybridization. Reticulate evolutionary patterns have been recognized in many fern groups, though very few have been studied rigorously using modern molecular phylogenetic techniques in order to determine the causes of the reticulate patterns. In the current study, we examine patterns of branching and reticulate evolution in the genus Dryopteris, the woodferns. The North American members of this group have long been recognized as a classic example of reticulate evolution in plants, and we extend analysis of the genus to all 30 species in the New World, as well as numerous taxa from other regions. We employ sequence data from the plastid and nuclear genomes and use maximum parsimony (MP), maximum likelihood (ML), Bayesian inference (BI), and divergence time analyses to explore the relationships of New World Dryopteris to other regions and to reconstruct the timing and events which may have led to taxa displaying reticulate rather than strictly branching histories. We find evidence for reticulation among both the North and Central/South American groups of species, and our data support a classic hypothesis for reticulate evolution via allopolyploid speciation in the North America taxa, including an extinct diploid progenitor in this group. In the Central and South American species, we find evidence of extensive reticulation involving unknown ancestors from Asia, and we reject deep coalescent processes such as incomplete lineage sorting in favor of more recent intercontinental hybridization and chloroplast capture as an explanation for the origin of the Latin American reticulate taxa.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin - Madison, 430 Lincoln Drive, Madison, WI 53706, USA.
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