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Ramírez-Barahona S. Incorporating fossils into the joint inference of phylogeny and biogeography of the tree fern order Cyatheales. Evolution 2024; 78:919-933. [PMID: 38437579 DOI: 10.1093/evolut/qpae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
Present-day geographic and phylogenetic patterns often reflect the geological and climatic history of the planet. Neontological distribution data are often sufficient to unravel a lineage's biogeographic history, yet ancestral range inferences can be at odds with fossil evidence. Here, I use the fossilized birth-death process and the dispersal-extinction cladogenesis model to jointly infer the dated phylogeny and range evolution of the tree fern order Cyatheales. I use data for 101 fossil and 442 extant tree ferns to reconstruct the biogeographic history of the group over the last 220 million years. Fossil-aware reconstructions evince a prolonged occupancy of Laurasia over the Triassic-Cretaceous by Cyathealean tree ferns, which is evident in the fossil record but hidden from analyses relying on neontological data alone. Nonetheless, fossil-aware reconstructions are affected by uncertainty in fossils' phylogenetic placement, taphonomic biases, and specimen sampling and are sensitive to interpretation of paleodistributions and how these are scored. The present results highlight the need and challenges of incorporating fossils into joint inferences of phylogeny and biogeography to improve the reliability of ancestral geographic range estimation.
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Affiliation(s)
- Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
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2
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Skema C, Jourdain-Fievet L, Dubuisson JY, Le Péchon T. Out of Madagascar, repeatedly: The phylogenetics and biogeography of Dombeyoideae (Malvaceae s.l.). Mol Phylogenet Evol 2023; 182:107687. [PMID: 36581141 DOI: 10.1016/j.ympev.2022.107687] [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: 05/11/2022] [Revised: 11/23/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Dispersals have been shown to be critical to the evolution of the long isolated but megadiverse flora of Madagascar and the surrounding islands of the western Indian Ocean, but we are just beginning to understand the directionality of these dispersals. With more than half of its species occurring in the western Indian Ocean region (WIOR), the paleotropical subfamily Dombeyoideae provides a particularly useful case study through which to better understand the biogeography of the WIOR, and yet its biogeography is poorly understood. Here we sampled six molecular markers from all 20 genera in the Dombeyoideae to reconstruct the most complete phylogeny to date for the subfamily. From this, divergence times, calibrated with three fossils (two dombeyoid, one malvoid), and ancestral range estimations were hypothesized. Biogeographic stochastic mapping (BSM) analyses on the maximum clade credibility tree were completed and compared to BSM analyses on 1,000 trees randomly sampled from the posterior distribution of trees resulting from the dating analysis. We found the Dombeyoideae crown node diverged ca. 53 million years ago out of a broad ancestral range involving all three major areas of its distribution: Madagascar, Africa, and Asia. The majority of diversification and dispersals in the subfamily occurred within the last ca. 10 million years, mostly from the Pliocene onwards. There were roughly five dispersals from Madagascar to Africa (and only one in reverse), at least six from Madagascar to surrounding islands of the WIOR (Mascarenes and Comoros), and one dispersal from Madagascar to Asia (and ca. 1 in reverse). Other long-distance dispersals included one from Africa to St. Helena and one from Africa to Australasia, both from within the most widespread clade, the Cheirolaena & allies clade, and one dispersal from Asia to Africa. Critically, the Dombeyoideae provide strong evidence for considering the island of Madagascar as a source for the colonization of continents, as well as the surrounding islands of the WIOR. Furthermore, narrow sympatry was a key process in the evolution of the subfamily, particularly in Madagascar and the Mascarenes.
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Affiliation(s)
- Cynthia Skema
- Morris Arboretum of the University of Pennsylvania, 100 E. Northwestern Avenue, Philadelphia, PA 19118, USA.
| | - Lucile Jourdain-Fievet
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Université des Antilles, CP 48, 57 rue Cuvier, 75005 Paris, France; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Jean-Yves Dubuisson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Université des Antilles, CP 48, 57 rue Cuvier, 75005 Paris, France
| | - Timothée Le Péchon
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium; Fédération Wallonie-Bruxelles, Service Général de l'Enseignement supérieur et de la Recherche scientifique, 1 rue A. Lavallée, 1080 Bruxelles, Belgium
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Shang H, Xue ZQ, Liang ZL, Kessler M, Pollawatn R, Lu NT, Gu YF, Fan XP, Tan YH, Zhang L, Zhou XM, Wan X, Zhang LB. Splitting one species into 22: an unusual tripling of molecular, morphological, and geographical differentiation in the fern family Didymochlaenaceae (Polypodiales). Cladistics 2023. [PMID: 37084123 DOI: 10.1111/cla.12539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
The pantropical fern genus Didymochlaena (Didymochlaenaceae) has long been considered to contain one species only. Recent studies have resolved this genus/family as either sister to the rest of eupolypods I or as the second branching lineage of eupolypods I, and have shown that this genus is not monospecific, but the exact species diversity is unknown. In this study, a new phylogeny is reconstructed based on an expanded taxon sampling and six molecular markers. Our major results include: (i) Didymochlaena is moderately or weakly supported as sister to the rest of eupolypods I, highlighting the difficulty in resolving the relationships of this important fern lineage in the polypods; (ii) species in Didymochlaena are resolved into a New World clade and an Old World clade, and the latter further into an African clade and an Asian-Pacific clade; (iii) an unusual tripling of molecular, morphological and geographical differentiation in Didymochlaena is detected, suggesting single vicariance or dispersal events in individual regions and no evidence for reversals at all, followed by allopatric speciation at more or less homogeneous rates; (iv) evolution of 18 morphological characters is inferred and two morphological synapomorphies defining the family are recognized-the elliptical sori and fewer than 10 sori per pinnule, the latter never having been suggested before; (v) based on morphological and molecular variation, 22 species in the genus are recognized contrasting with earlier estimates of between one and a few; and (vi) our biogeographical analysis suggests an origin for Didymochlaena in the latest Jurassic-earliest Cretaceous and the initial diversification of the extant lineages in the Miocene-all but one species diverged from their sisters within the last 27 Myr, in most cases associated with allopatric speciation owing to geologic and climatic events, or dispersal.
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Affiliation(s)
- Hui Shang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
| | - Zhi-Qing Xue
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Zhen-Long Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
| | - Michael Kessler
- Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Rossarin Pollawatn
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ngan Thi Lu
- Department of Biology, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18th Hoang Quoc Viet Road, Ha Noi, Vietnam
| | - Yu-Feng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation & Research Center of Shenzhen, Shenzhen, Guangdong, 518114, China
| | - Xue-Ping Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Yun-Hong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, 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, Yunnan, 650091, China
| | - Xia Wan
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Bing Zhang
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
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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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Hong Y, Wang Z, Li M, Su Y, Wang T. First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes. Front Genet 2022; 12:784546. [PMID: 35186007 PMCID: PMC8854977 DOI: 10.3389/fgene.2021.784546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alsophila spinulosa, a relict tree fern, is a valuable plant for investigating environmental adaptations. Its genetic resources, however, are scarce. We used the PacBio and Illumina platforms to sequence the polyadenylated RNA of A. spinulosa root, rachis, and pinna, yielding 125,758, 89,107, and 89,332 unigenes, respectively. Combining the unigenes from three organs yielded a non-redundant reference transcriptome with 278,357 unigenes and N50 of 4141 bp, which were further reconstructed into 38,470 UniTransModels. According to functional annotation, pentatricopeptide repeat genes and retrotransposon-encoded polyprotein genes are the most abundant unigenes. Clean reads mapping to the full-length transcriptome is used to assess the expression of unigenes. The stress-induced ASR genes are highly expressed in all three organs, which is validated by qRT-PCR. The organ-specific upregulated genes are enriched for pathways involved in stress response, secondary metabolites, and photosynthesis. Genes for five types of photoreceptors, CRY signaling pathway, ABA biosynthesis and transduction pathway, and stomatal movement-related ion channel/transporter are profiled using the high-quality unigenes. The gene expression pattern coincides with the previously identified stomatal characteristics of fern. This study is the first multi-organ full-length transcriptome report of a tree fern species, the abundant genetic resources and comprehensive analysis of A. spinulosa, which provides the groundwork for future tree fern research.
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Affiliation(s)
- Yongfeng Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
| | - Ting Wang
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
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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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Farminhão JNM, Verlynde S, Kaymak E, Droissart V, Simo-Droissart M, Collobert G, Martos F, Stévart T. Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability. Mol Phylogenet Evol 2021; 159:107105. [PMID: 33601026 DOI: 10.1016/j.ympev.2021.107105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/13/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Angraecoid orchids present a remarkable diversity of chromosome numbers, which makes them a highly suitable system for exploring the impact of karyotypic changes on cladogenesis, diversification and morphological differentiation. We compiled an annotated cytotaxonomic checklist for 126 species of Angraecinae, which was utilised to reconstruct chromosomal evolution using a newly-produced, near-comprehensive phylogenetic tree that includes 245 angraecoid taxa. In tandem with this improved phylogenetic framework, using combined Bayesian, maximum likelihood and parsimony approaches on ITS-1 and five plastid markers, we propose a new cladistic nomenclature for the angraecoids, and we estimate a new timeframe for angraecoid radiation based on a secondary calibration, and calculate diversification rates using a Bayesian approach. Coincident divergence dates between clades with identical geographical distributions in the angraecoids and the pantropical orchid genus Bulbophyllum suggest that the same events may have intervened in the dispersal of these two epiphytic groups between Asia, continental Africa, Madagascar and the Neotropics. The major angraecoid lineages probably began to differentiate in the Middle Miocene, and most genera and species emerged respectively around the Late Miocene-Pliocene boundary and the Pleistocene. Ancestral state reconstruction using maximum likelihood estimation revealed an eventful karyotypic history dominated by descending dysploidy. Karyotypic shifts seem to have paralleled cladogenesis in continental tropical Africa, where approximately 90% of the species have descended from at least one inferred transition from n = 17-18 to n = 25 during the Middle Miocene Climatic Transition, followed by some clade-specific descending and ascending dysploidy from the Late Miocene to the Pleistocene. Conversely, detected polyploidy is restricted to a few species lineages mostly originating during the Pleistocene. No increases in net diversification could be related to chromosome number changes, and the apparent net diversification was found to be highest in Madagascar, where karyotypic stasis predominates. Finally, shifts in chromosome number appear to have paralleled the evolution of rostellum structure, leaflessness, and conspicuous changes in floral colour.
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Affiliation(s)
- João N M Farminhão
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; Plant Ecology and Biogeochemistry, C.P. 244, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe, 1050, Brussels, Belgium.
| | - Simon Verlynde
- Cullman Program for Molecular Systematics, New York Botanical Garden, Bronx, NY 10458-5126, USA; PhD Program in Biology, Graduate Center, City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Esra Kaymak
- Evolutionary Biology and Ecology, Faculté des Sciences, C.P. 160/12, Université Libre de Bruxelles, 50 Avenue F. Roosevelt, BE-1050 Brussels, Belgium
| | - Vincent Droissart
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; AMAP Lab, Univ Montpellier, IRD, CNRS, INRAE, CIRAD, Montpellier, France; Missouri Botanical Garden, Africa and Madagascar Department, 4344 Shaw Blvd., St. Louis, MO 63110, USA; Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, P. O. Box 047, Yaoundé, Cameroon
| | - Murielle Simo-Droissart
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, P. O. Box 047, Yaoundé, Cameroon
| | - Géromine Collobert
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Florent Martos
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Tariq Stévart
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; Missouri Botanical Garden, Africa and Madagascar Department, 4344 Shaw Blvd., St. Louis, MO 63110, USA; Meise Botanic Garden, Domein van Bouchout, Nieuwelaan 38, B-1860 Meise, Belgium
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Rimlinger A, Raharimalala N, Letort V, Rakotomalala JJ, Crouzillat D, Guyot R, Hamon P, Sabatier S. Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar. ANNALS OF BOTANY 2020; 126:849-863. [PMID: 32303759 PMCID: PMC7539352 DOI: 10.1093/aob/mcaa073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Like other clades, the Coffea genus is highly diversified on the island of Madagascar. The 66 endemic species have colonized various environments and consequently exhibit a wide diversity of morphological, functional and phenological features and reproductive strategies. The trends of interspecific trait variation, which stems from interactions between genetically defined species and their environment, still needed to be addressed for Malagasy coffee trees. METHODS Data acquisition was done in the most comprehensive ex situ collection of Madagascan wild Coffea. The structure of endemic wild coffees maintained in an ex situ collection was explored in terms of morphological, phenological and functional traits. The environmental (natural habitat) effect was assessed on traits in species from distinct natural habitats. Phylogenetic signal (Pagel's λ, Blomberg's K) was used to quantify trait proximities among species according to their phylogenetic relatedness. KEY RESULTS Despite the lack of environmental difference in the ex situ collection, widely diverging phenotypes were observed. Phylogenetic signal was found to vary greatly across and even within trait categories. The highest values were exhibited by the ratio of internode mass to leaf mass, the length of the maturation phase and leaf dry matter content (ratio of dry leaf mass to fresh leaf mass). By contrast, traits weakly linked to phylogeny were either constrained by the original natural environment (leaf size) or under selective pressures (phenological traits). CONCLUSIONS This study gives insight into complex patterns of trait variability found in an ex situ collection, and underlines the opportunities offered by living ex situ collections for research characterizing phenotypic variation.
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Affiliation(s)
- Aurore Rimlinger
- AMAP Univ Montpellier CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | | | - Véronique Letort
- Laboratoire de Mathématiques et Informatique pour la Complexité et les Systèmes, CentraleSupélec, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | - Romain Guyot
- DIADE, Univ Montpellier IRD CIRAD, Montpellier, France
| | - Perla Hamon
- DIADE, Univ Montpellier IRD CIRAD, Montpellier, France
| | - Sylvie Sabatier
- AMAP Univ Montpellier CIRAD, CNRS, INRAE, IRD, Montpellier, France
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Lee GE, Condamine FL, Bechteler J, Pérez-Escobar OA, Scheben A, Schäfer-Verwimp A, Pócs T, Heinrichs J. An ancient tropical origin, dispersals via land bridges and Miocene diversification explain the subcosmopolitan disjunctions of the liverwort genus Lejeunea. Sci Rep 2020; 10:14123. [PMID: 32839508 PMCID: PMC7445168 DOI: 10.1038/s41598-020-71039-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the biogeographical and diversification processes explaining current diversity patterns of subcosmopolitan-distributed groups is challenging. We aimed at disentangling the historical biogeography of the subcosmopolitan liverwort genus Lejeunea with estimation of ancestral areas of origin and testing if sexual system and palaeotemperature variations can be factors of diversification. We assembled a dense taxon sampling for 120 species sampled throughout the geographical distribution of the genus. Lejeunea diverged from its sister group after the Paleocene-Eocene boundary (52.2 Ma, 95% credibility intervals 50.1-54.2 Ma), and the initial diversification of the crown group occurred in the early to middle Eocene (44.5 Ma, 95% credibility intervals 38.5-50.8 Ma). The DEC model indicated that (1) Lejeunea likely originated in an area composed of the Neotropics and the Nearctic, (2) dispersals through terrestrial land bridges in the late Oligocene and Miocene allowed Lejeunea to colonize the Old World, (3) the Boreotropical forest covering the northern regions until the late Eocene did not facilitate Lejeunea dispersals, and (4) a single long-distance dispersal event was inferred between the Neotropics and Africa. Biogeographical and diversification analyses show the Miocene was an important period when Lejeunea diversified globally. We found slight support for higher diversification rates of species with both male and female reproductive organs on the same individual (monoicy), and a moderate positive influence of palaeotemperatures on diversification. Our study shows that an ancient origin associated with a dispersal history facilitated by terrestrial land bridges and not long-distance dispersals are likely to explain the subcosmopolitan distribution of Lejeunea. By enhancing the diversification rates, monoicy likely favoured the colonisations of new areas, especially in the Miocene that was a key epoch shaping the worldwide distribution.
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Affiliation(s)
- Gaik Ee Lee
- Faculty of Science and Marine Environment, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Julia Bechteler
- Nees Institute for Biodiversity of Plants, University of Bonn, 53115, Bonn, Germany
| | | | - Armin Scheben
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Tamás Pócs
- Botany Department, Institute of Biology, Eszterházy University, Pf. 43, Eger, 3301, Hungary
| | - Jochen Heinrichs
- Department of Biology I, Systematic Botany and Mycology, Geobio-Center, University of Munich (LMU), Menzinger Str. 67, 80638, Munich, Germany
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10
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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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11
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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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12
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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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13
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Khodaei Z, Van Wyk BE, Wink M. Divergence Time Estimation of Aloes and Allies (Xanthorrhoeaceae) Based on Three Marker Genes. DIVERSITY 2018; 10:60. [DOI: 10.3390/d10030060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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14
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Federman S, Donoghue MJ, Daly DC, Eaton DAR. Reconciling species diversity in a tropical plant clade (Canarium, Burseraceae). PLoS One 2018; 13:e0198882. [PMID: 29906281 PMCID: PMC6003679 DOI: 10.1371/journal.pone.0198882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 04/11/2018] [Indexed: 11/18/2022] Open
Abstract
The challenges associated with sampling rare species or populations can limit our ability to make accurate and informed estimates of biodiversity for clades or ecosystems. This may be particularly true for tropical trees, which tend to be poorly sampled, and are thought to harbor extensive cryptic diversity. Here, we integrate genomics, morphology, and geography to estimate the number of species in a clade of dioecious tropical trees (Canarium L.; Burseraceae) endemic to Madagascar, for which previous taxonomic treatments have recognized between one and 33 species. By sampling genomic data from even a limited number of individuals per taxon, we were able to clearly reject both previous hypotheses, and support instead an intermediate number of taxa. We recognize at least six distinct clades based on genetic structure and species delimitation analyses that correspond clearly with geographic and discrete morphological differences. Two widespread clades co-occur broadly throughout eastern wet forests, one clade is endemic to western dry forests, and several slightly admixed clades are more narrowly distributed in mountainous regions in the north. Multiple previously described taxa were recovered as paraphyletic in our analyses, some of which were associated with admixed individuals, suggesting that hybridization contributes to taxonomic difficulties in Canarium. An improved understanding of Canarium species diversity has important implications for conservation efforts and understanding the origins of diversity in Madagascar. Our study shows that even limited genomic sampling, when combined with geography and morphology, can greatly improve estimates of species diversity for difficult tropical clades.
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Affiliation(s)
- Sarah Federman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
- * E-mail:
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Douglas C. Daly
- Institute of Systematic Botany, New York Botanical Garden, Bronx, NY, United States of America
| | - Deren A. R. Eaton
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States of America
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15
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Block PD, Rakotonasolo F, Ntore S, Sylvain G. Razafimandimbison, Janssens S. Four new endemic genera of Rubiaceae (Pavetteae) from Madagascar represent multiple radiations into drylands. PHYTOKEYS 2018; 99:1-66. [PMID: 29861651 PMCID: PMC5972148 DOI: 10.3897/phytokeys.99.23713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/24/2018] [Indexed: 10/29/2023]
Abstract
The taxonomic positions and phylogenetic relationships of six Pavetteae species endemic to Madagascar were tested with a phylogenetic study of the Afro-Madagascan representatives of the tribe Pavetteae based on sequence data from six markers rps16, trnT-F, petD, accD-psa1, PI and ITS. The six species were resolved into four well-supported and morphologically distinct clades which we here formally recognise at generic level. The new genera are the monospecific Exallosperma and Pseudocoptosperma, each with a single species, and Helictosperma and Tulearia, each with two species. Each genus is characterised by one or more autapomorphies or by a unique combination of plesiomorphic characters. Mostly, the distinguishing characters are found in fruit and seed; Exallosperma differs from all other Pavetteae genera by the fruit consisting of two stony pyrenes, each with a single laterally flattened seed with irregularly distributed ridges on the surface; Helictosperma is unique by its single spherical seed rolled-in on itself in the shape of a giant pill-millipede. Pseudocoptosperma is characterised by the combination of three ovules pendulous from a small placenta and triangular stipules with a strongly developed awn, whereas Tulearia is characterised by robust sericeous flowers, small leaves, uni- or pauciflorous inflorescences and fruits with two pyrenes, each with a single ruminate seed. The four new genera show marked adaptations to the dry habitats in which they grow. They represent multiple radiations into drylands and highlight the importance of the dry forest and scrub vegetation in western, southern and northern Madagascar for plant biodiversity. The description of the four new genera shows that the tribe Pavetteae exhibits the same pattern as many plant groups in Madagascar, which are characterised by a high proportion of endemic genera comprising a single or a few species. In the four new genera, five new species are described and one new combination is made: Exallosperma longiflora De Block; Helictosperma malacophylla (Drake) De Block, Helictosperma poissoniana De Block, Pseudocoptosperma menabense Capuron ex De Block; Tulearia capsaintemariensis De Block and Tulearia splendida De Block.
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Affiliation(s)
- Petra De Block
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Franck Rakotonasolo
- Kew Madagascar Conservation Centre, Lot II J 131 Ambodivoanjo, Ivandry, Antananarivo, Madagascar
- Parc Botanique et Zoologique de Tsimbazaza, Antananarivo-101, Madagascar
| | - Salvator Ntore
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
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16
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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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17
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Testo WL, Sundue MA. Are rates of species diversification and body size evolution coupled in the ferns? AMERICAN JOURNAL OF BOTANY 2018; 105:525-535. [PMID: 29637539 DOI: 10.1002/ajb2.1044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/09/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Understanding the relationship between phenotypic evolution and lineage diversification is a central goal of evolutionary biology. To extend our understanding of the role morphological evolution plays in the diversification of plants, we examined the relationship between leaf size evolution and lineage diversification across ferns. METHODS We tested for an association between body size evolution and lineage diversification using a comparative phylogenetic approach that combined a time-calibrated phylogeny and leaf size data set for 2654 fern species. Rates of leaf size change and lineage diversification were estimated using BAMM, and rate correlations were performed for rates obtained for all families and individual species. Rates and patterns of rate-rate correlation were also analyzed separately for terrestrial and epiphytic taxa. KEY RESULTS We find no significant correlation between rates of leaf area change and lineage diversification, nor was there a difference in this pattern when growth habit is considered. Our results are consistent with the findings of an earlier study that reported decoupled rates of body size evolution and diversification in the Polypodiaceae, but conflict with a recent study that reported a positive correlation between body size evolution and lineage diversification rates in the tree fern family Cyatheaceae. CONCLUSIONS Our findings indicate that lineage diversification in ferns is largely decoupled from shifts in body size, in contrast to several other groups of organisms. Speciation in ferns appears to be primarily driven by hybridization and isolation along elevational gradients, rather than adaptive radiations featuring prominent morphological restructuring. The exceptional diversity of leaf morphologies in ferns appears to reflect a combination of ecophysiological constraints and adaptations that are not key innovations.
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Affiliation(s)
- Weston L Testo
- The Pringle Herbarium, University of Vermont, 27 Colchester Drive, Burlington, VT, 05405, USA
| | - Michael A Sundue
- The Pringle Herbarium, University of Vermont, 27 Colchester Drive, Burlington, VT, 05405, USA
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18
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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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19
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Hennequin S, Rouhan G, Salino A, Duan YF, Lepeigneux MC, Guillou M, Ansell S, Almeida TE, Zhang LB, Schneider H. Global phylogeny and biogeography of the fern genus Ctenitis (Dryopteridaceae), with a focus on the Indian Ocean region. Mol Phylogenet Evol 2017; 112:277-289. [DOI: 10.1016/j.ympev.2017.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/10/2017] [Indexed: 12/24/2022]
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20
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Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events. Mol Phylogenet Evol 2017; 111:1-17. [DOI: 10.1016/j.ympev.2017.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022]
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21
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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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22
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Andriananjamanantsoa HN, Engberg S, Louis EE, Brouillet L. Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation. PLoS One 2016; 11:e0163194. [PMID: 27669569 PMCID: PMC5036805 DOI: 10.1371/journal.pone.0163194] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 09/06/2016] [Indexed: 11/19/2022] Open
Abstract
Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in Angraecum. The macroevolutionary model-based phylogeny failed to detect shifts in diversification that could be associated directly with morphological diversification. Diversification in Angraecum resulted from gradual species accumulation through time rather than from rapid radiation, a diversification pattern often encountered in tropical rain forests.
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Affiliation(s)
| | - Shannon Engberg
- Omaha’s Henry Doorly Zoo and Aquarium, Omaha, Nebraska, United States of America
| | - Edward E. Louis
- Omaha’s Henry Doorly Zoo and Aquarium, Omaha, Nebraska, United States of America
| | - Luc Brouillet
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
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23
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Gamisch A, Fischer GA, Comes HP. Frequent but asymmetric niche shifts in Bulbophyllum orchids support environmental and climatic instability in Madagascar over Quaternary time scales. BMC Evol Biol 2016; 16:14. [PMID: 26781289 PMCID: PMC4717530 DOI: 10.1186/s12862-016-0586-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/12/2016] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Species or clades may retain or shift their environmental niche space over evolutionary time. Understanding these processes offers insights into the environmental processes fuelling lineage diversification and might also provide information on past range dynamics of ecosystems. However, little is known about the relative contributions of niche conservatism versus niche divergence to species diversification in the tropics. Here, we examined broad-scale patterns of niche evolution within a Pliocene-Pleistocene clade of epiphytic Bulbophyllum orchids (30 spp.) whose collective distribution covers the northwest and eastern forest ecosystems of Madagascar. RESULTS Using species occurrence data, ecological niche models, and multivariate analyses of contributing variables, we identified a three-state niche distribution character for the entire clade, coinciding with three major forest biomes viz. phytogeographical provinces in Madagascar: A, Northwest 'Sambirano'; B, 'Eastern Lowlands'; and C, 'Central Highlands'. A time-calibrated phylogeny and Bayesian models of niche evolution were then used to detect general trends in the direction of niche change over the clade's history (≤5.3 Ma). We found highest transitions rates between lowlands (A and B) and (mostly from B) into the highland (C), with extremely low rates out of the latter. Lowland-to-highland transitions occurred frequently during the Quaternary, suggesting that climate-induced vegetational shifts promoted niche transitions and ecological speciation at this time. CONCLUSIONS Our results reveal that niche transitions occurred frequently and asymmetrically within this Madagascan orchid clade, and in particular over Quaternary time scales. Intrinsic features germane to Bulbophyllum (e.g., high dispersal ability, drought tolerance, multiple photosynthetic pathways) as well as extrinsic factors (ecological, historical) likely interacted to generate the niche transition patterns observed. In sum, our results support the emerging idea of dramatic environmental and climatic fluctuations in Madagascar during the recent geological past, which overturns the long-held paradigm of long-term stability in tropical forest settings. The generality of the patterns and timings reported here awaits the availability of additional comparative studies in other Madagascan endemics.
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Affiliation(s)
- Alexander Gamisch
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
| | | | - Hans Peter Comes
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
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Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar. Mol Phylogenet Evol 2015; 94:365-82. [PMID: 26432393 DOI: 10.1016/j.ympev.2015.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/11/2015] [Accepted: 09/15/2015] [Indexed: 01/05/2023]
Abstract
Of the 97 currently recognized genera of Celastraceae, 19 are native to Madagascar, including six endemics. In this study we conducted the most thorough phylogenetic analysis of Celastraceae yet completed with respect to both character and taxon sampling, and include representatives of five new endemic genera. Fifty-one new accessions, together with 328 previously used accessions of Celastrales, were sampled for morphological characters, two rDNA gene regions, and two plastid gene regions. The endemic Malagasy genera are resolved in two separate lineages-Xenodrys by itself and all other endemic genera in a clade that also includes four lineages inferred to have dispersed from Madagascar: Brexia madagascariensis (Mascarene Islands, coastal Africa), Elaeodendron (West Indies, Africa to New Caledonia), and Pleurostylia (Africa to New Caledonia). Of the 12 extant Malagasy Celastraceae lineages identified, eight are clearly of African origin. The origins of the remaining four lineages are less clear, but reasonable possibilities include America, Eurasia, Africa, southern India, Malesia, and Australia. Based on 95% credible age intervals from fossil-calibrated molecular dating, all 12 extant Malagasy Celastraceae lineages appear to have arisen following dispersal after the separation of Madagascar from other landmasses within the last 70 million years.
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Sundue MA, Testo WL, Ranker TA. Morphological innovation, ecological opportunity, and the radiation of a major vascular epiphyte lineage. Evolution 2015; 69:2482-95. [DOI: 10.1111/evo.12749] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 07/19/2015] [Accepted: 07/23/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Michael A. Sundue
- Department of Plant Biology; University of Vermont, Pringle Herbarium; 27 Colchester Avenue Burlington Vermont 05405
| | - Weston L. Testo
- Department of Plant Biology; University of Vermont, Pringle Herbarium; 27 Colchester Avenue Burlington Vermont 05405
| | - Tom A. Ranker
- Department of Botany; University of Hawai'i at Mānoa; 3190 Maile Way Honolulu Hawaii 96822
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Espeland M, Hall JPW, DeVries PJ, Lees DC, Cornwall M, Hsu YF, Wu LW, Campbell DL, Talavera G, Vila R, Salzman S, Ruehr S, Lohman DJ, Pierce NE. Ancient Neotropical origin and recent recolonisation: Phylogeny, biogeography and diversification of the Riodinidae (Lepidoptera: Papilionoidea). Mol Phylogenet Evol 2015; 93:296-306. [PMID: 26265256 DOI: 10.1016/j.ympev.2015.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/27/2015] [Accepted: 08/05/2015] [Indexed: 12/13/2022]
Abstract
We present the first dated higher-level phylogenetic and biogeographic analysis of the butterfly family Riodinidae. This family is distributed worldwide, but more than 90% of the c. 1500 species are found in the Neotropics, while the c. 120 Old World species are concentrated in the Southeast Asian tropics, with minor Afrotropical and Australasian tropical radiations, and few temperate species. Morphologically based higher classification is partly unresolved, with genera incompletely assigned to tribes. Using 3666bp from one mitochondrial and four nuclear markers for each of 23 outgroups and 178 riodinid taxa representing all subfamilies, tribes and subtribes, and 98 out of 145 described genera of riodinids, we estimate that Riodinidae split from Lycaenidae about 96Mya in the mid-Cretaceous and started to diversify about 81Mya. The Riodinidae are monophyletic and originated in the Neotropics, most likely in lowland proto-Amazonia. Neither the subfamily Euselasiinae nor the Nemeobiinae are monophyletic as currently constituted. The enigmatic, monotypic Neotropical genera Styx and Corrachia (most recently treated in Euselasiinae: Corrachiini) are highly supported as derived taxa in the Old World Nemeobiinae, with dispersal most likely occurring across the Beringia land bridge during the Oligocene. Styx and Corrachia, together with all other nemeobiines, are the only exclusively Primulaceae-feeding riodinids. The steadily increasing proliferation of the Neotropical Riodininae subfamily contrasts with the decrease in diversification in the Old World, and may provide insights into factors influencing the diversification rate of this relatively ancient clade of Neotropical insects.
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Affiliation(s)
- Marianne Espeland
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Powell Hall, 2315 Hull Road, Gainesville, FL 32611, USA.
| | - Jason P W Hall
- Department of Systematic Biology-Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-127, USA.
| | - Philip J DeVries
- Department of Biological Sciences, University of New Orleans, 2000 Lake Shore Drive, New Orleans, LA 70148, USA.
| | - David C Lees
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
| | - Mark Cornwall
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.
| | - Li-Wei Wu
- The Experimental Forest, College of Bio-Resources and Agriculture, National Taiwan University, Nantou, Taiwan.
| | - Dana L Campbell
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Division of Biological Sciences, School of Science, Technology, Engineering & Mathematics, University of Washington Bothell, Box 358500, 18115 Campus Way NE, Bothell, WA 98011-8246, USA.
| | - Gerard Talavera
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain; Faculty of Biology & Soil Science, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain.
| | - Shayla Salzman
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Sophie Ruehr
- Yale University, Yale College, PO Box 208241, New Haven, CT 06520, USA.
| | - David J Lohman
- Department of Biology, City College of New York, City University of New York, Convent Avenue at 138th Street, New York, NY 10031, USA.
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. AMERICAN JOURNAL OF BOTANY 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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Chao YS, Rouhan G, Amoroso VB, Chiou WL. Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae). ANNALS OF BOTANY 2014; 114:109-24. [PMID: 24908681 PMCID: PMC4071104 DOI: 10.1093/aob/mcu086] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/31/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. METHODS A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. KEY RESULTS The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. CONCLUSIONS This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.
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Affiliation(s)
- Yi-Shan Chao
- The Experimental Forest, National Taiwan University, Nantou, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Germinal Rouhan
- Muséum national d'Histoire naturelle, UMR CNRS 7205, Herbier National, 16 rue Buffon CP39, 75005 Paris, France
| | | | - Wen-Liang Chiou
- Division of Botanical Garden, Taiwan Forestry Research Institute, Taipei, Taiwan
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Korall P, Pryer KM. Global biogeography of scaly tree ferns (Cyatheaceae): evidence for Gondwanan vicariance and limited transoceanic dispersal. JOURNAL OF BIOGEOGRAPHY 2014; 41:402-413. [PMID: 25435648 PMCID: PMC4238398 DOI: 10.1111/jbi.12222] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
AIM Scaly tree ferns, Cyatheaceae, are a well-supported group of mostly tree-forming ferns found throughout the tropics, the subtropics and the south-temperate zone. Fossil evidence shows that the lineage originated in the Late Jurassic period. We reconstructed large-scale historical biogeographical patterns of Cyatheaceae and tested the hypothesis that some of the observed distribution patterns are in fact compatible, in time and space, with a vicariance scenario related to the break-up of Gondwana. LOCATION Tropics, subtropics and south-temperate areas of the world. METHODS The historical biogeography of Cyatheaceae was analysed in a maximum likelihood framework using Lagrange. The 78 ingroup taxa are representative of the geographical distribution of the entire family. The phylogenies that served as a basis for the analyses were obtained by Bayesian inference analyses of mainly previously published DNA sequence data using MrBayes. Lineage divergence dates were estimated in a Bayesian Markov chain Monte Carlo framework using beast. RESULTS Cyatheaceae originated in the Late Jurassic in either South America or Australasia. Following a range expansion, the ancestral distribution of the marginate-scaled clade included both these areas, whereas Sphaeropteris is reconstructed as having its origin only in Australasia. Within the marginate-scaled clade, reconstructions of early divergences are hampered by the unresolved relationships among the Alsophila, Cyathea and Gymnosphaera lineages. Nevertheless, it is clear that the occurrence of the Cyathea and Sphaeropteris lineages in South America may be related to vicariance, whereas transoceanic dispersal needs to be inferred for the range shifts seen in Alsophila and Gymnosphaera. MAIN CONCLUSIONS The evolutionary history of Cyatheaceae involves both Gondwanan vicariance scenarios as well as long-distance dispersal events. The number of transoceanic dispersals reconstructed for the family is rather few when compared with other fern lineages. We suggest that a causal relationship between reproductive mode (outcrossing) and dispersal limitations is the most plausible explanation for the pattern observed.
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Affiliation(s)
- Petra Korall
- Systematic Biology, Evolutionary Biology Centre, Uppsala UniversityNorbyvägen 18D, SE-752 36, Uppsala, Sweden
- *Correspondence: P. Korall, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden. E-mail:
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Patiño J, Carine M, Fernández-Palacios JM, Otto R, Schaefer H, Vanderpoorten A. The anagenetic world of spore-producing land plants. THE NEW PHYTOLOGIST 2014; 201:305-311. [PMID: 24010958 DOI: 10.1111/nph.12480] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
A fundamental challenge to our understanding of biodiversity is to explain why some groups of species diversify, whereas others do not. On islands, the gradual evolution of a new species from a founder event has been called 'anagenetic speciation'. This process does not lead to rapid and extensive speciation within lineages and has received little attention. Based on a survey of the endemic bryophyte, pteridophyte and spermatophyte floras of nine oceanic archipelagos, we show that anagenesis, as measured by the proportion of genera with single endemic species within a genus, is much higher in bryophytes (73%) and pteridophytes (65%) than in spermatophytes (55%). Anagenesis contributed 49% of bryophyte and 40% of endemic pteridophyte species, but only 17% of spermatophytes. The vast majority of endemic bryophytes and pteridophytes are restricted to subtropical evergreen laurel forests and failed to diversify in more open environments, in contrast with the pattern exhibited by spermatophytes. We propose that the dominance of anagenesis in island bryophytes and pteridophytes is a result of a mixture of intrinsic factors, notably their strong preference for (sub)tropical forest environments, and extrinsic factors, including the long-term macro-ecological stability of these habitats and the associated strong phylogenetic niche conservatism of their floras.
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Affiliation(s)
- Jairo Patiño
- Institute of Botany, University of Liège, 4000, Liège, Belgium
- Departmento de Ciências Agrárias, Azorean Biodiversity Group (CITA-A) and Platform for Enhancing Ecological Research & Sustainability (PEERS), Universidade dos Açores, 9700-042 Angra do Heroísmo, Terceira, Açores, Portugal
- Departmento de Biología Vegetal, Universidad de La Laguna, 38206, Tenerife, Spain
| | - Mark Carine
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | | | - Rüdiger Otto
- Departamento de Ecología, Facultad de Biología, Universidad de La Laguna, 38206, Tenerife, Spain
| | - Hanno Schaefer
- Technische Universitaet Muenchen, Plant Biodiversity Research, Maximus-von-Imhof Forum 2, 85354, Freising, Germany
| | - Alain Vanderpoorten
- Institute of Botany, University of Liège, 4000, Liège, Belgium
- Departmento de Ciências Agrárias, Azorean Biodiversity Group (CITA-A) and Platform for Enhancing Ecological Research & Sustainability (PEERS), Universidade dos Açores, 9700-042 Angra do Heroísmo, Terceira, Açores, Portugal
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Leong Pock Tsy JM, Lumaret R, Flaven-Noguier E, Sauve M, Dubois MP, Danthu P. Nuclear microsatellite variation in Malagasy baobabs (Adansonia, Bombacoideae, Malvaceae) reveals past hybridization and introgression. ANNALS OF BOTANY 2013; 112:1759-73. [PMID: 24187031 PMCID: PMC3838555 DOI: 10.1093/aob/mct230] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Adansonia comprises nine species, six of which are endemic to Madagascar. Genetic relationships between the Malagasy species remain unresolved due to conflicting results between nuclear and plastid DNA variation. Morphologically intermediate individuals between distinct species have been identified, indicative of interspecific hybridization. In this paper, microsatellite data are used to identify potential cases of hybridization and to provide insights into the evolutionary history of the genus on Madagascar. METHODS Eleven microsatellites amplified with new primers developed for Adansonia rubrostipa were used to analyse 672 individuals collected at 27 sites for the six Malagasy species and morphologically intermediate individuals. Rates of individual admixture were examined using three Bayesian clustering programs, STRUCTURE, BAPS and NewHybrids, with no a priori species assignment. KEY RESULTS Population differentiation was coherent, with recognized species boundaries. In the four Malagasy species of section Longitubae, 8·0, 9·0 and 9·5 % of individuals with mixed genotypes were identified by BAPS, NewHybrids and STRUCTURE, respectively. At sites with sympatric populations of A. rubrostipa and A. za, NewHybrids indicated these individuals to be F2 and, predominantly, backcrosses with both parental species. In northern Madagascar, two populations of trees combining A. za and A. perrieri morphology and microsatellite alleles were identified in the current absence of the parental species. CONCLUSIONS The clear genetic differentiation observed between the six species may reflect their adaptation to different assortments of climate regimes and habitats during the colonization of the island. Microsatellite variation reveals that hybridization probably occurred in secondary contact between species of section Longitubae. This type of hybridization may also have been involved in the differentiation of a local new stabilized entity showing specific microsatellite alleles and morphological characters, suggesting a potential role of hybridization in the recent history of diversification on Madagascar.
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Affiliation(s)
- Jean-Michel Leong Pock Tsy
- DP Forêts et Biodiversité Madagascar (CIRAD, Université d'Antananarivo, FOFIFA), BP 853, Antananarivo 101, Madagascar
- For correspondence: E-mail:
| | - Roselyne Lumaret
- CNRS-UMR 5175, Centre d'Ecologie Fonctionnelle et Evolutive, 1919 route de Mende, F-34293 Montpellier Cedex 5, France
| | - Elodie Flaven-Noguier
- CNRS-UMR 5175, Centre d'Ecologie Fonctionnelle et Evolutive, 1919 route de Mende, F-34293 Montpellier Cedex 5, France
| | - Mathieu Sauve
- CNRS-UMR 5175, Centre d'Ecologie Fonctionnelle et Evolutive, 1919 route de Mende, F-34293 Montpellier Cedex 5, France
| | - Marie-Pierre Dubois
- CNRS-UMR 5175, Centre d'Ecologie Fonctionnelle et Evolutive, 1919 route de Mende, F-34293 Montpellier Cedex 5, France
| | - Pascal Danthu
- DP Forêts et Biodiversité Madagascar (CIRAD, Université d'Antananarivo, FOFIFA), BP 853, Antananarivo 101, Madagascar
- CIRAD, UPR 105, Biens et Services des Ecosystèmes Forestiers Tropicaux, Campus de Baillarguet, F-34398 Montpellier Cedex 5, France
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Tosh J, Dessein S, Buerki S, Groeninckx I, Mouly A, Bremer B, Smets EF, De Block P. Evolutionary history of the Afro-Madagascan Ixora species (Rubiaceae): species diversification and distribution of key morphological traits inferred from dated molecular phylogenetic trees. ANNALS OF BOTANY 2013; 112:1723-42. [PMID: 24142919 PMCID: PMC3838549 DOI: 10.1093/aob/mct222] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/06/2013] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS Previous work on the pantropical genus Ixora has revealed an Afro-Madagascan clade, but as yet no study has focused in detail on the evolutionary history and morphological trends in this group. Here the evolutionary history of Afro-Madagascan Ixora spp. (a clade of approx. 80 taxa) is investigated and the phylogenetic trees compared with several key morphological traits in taxa occurring in Madagascar. METHODS Phylogenetic relationships of Afro-Madagascan Ixora are assessed using sequence data from four plastid regions (petD, rps16, rpoB-trnC and trnL-trnF) and nuclear ribosomal external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions. The phylogenetic distribution of key morphological characters is assessed. Bayesian inference (implemented in BEAST) is used to estimate the temporal origin of Ixora based on fossil evidence. KEY RESULTS Two separate lineages of Madagascan taxa are recovered, one of which is nested in a group of East African taxa. Divergence in Ixora is estimated to have commenced during the mid Miocene, with extensive cladogenesis occurring in the Afro-Madagascan clade during the Pliocene onwards. CONCLUSIONS Both lineages of Madagascan Ixora exhibit morphological innovations that are rare throughout the rest of the genus, including a trend towards pauciflorous inflorescences and a trend towards extreme corolla tube length, suggesting that the same ecological and selective pressures are acting upon taxa from both Madagascan lineages. Novel ecological opportunities resulting from climate-induced habitat fragmentation and corolla tube length diversification are likely to have facilitated species radiation on Madagascar.
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Affiliation(s)
- J. Tosh
- Laboratory of Plant Systematics, KU Leuven, Kasteelpark Arenberg 31, PO Box 2437, BE-3001 Leuven, Belgium
- Ashdown House School, Forest Row, East Sussex RH18 5JY, UK
| | - S. Dessein
- National Botanic Garden of Belgium, Domein van Bouchout, BE-1860 Meise, Belgium
| | - S. Buerki
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - I. Groeninckx
- Laboratory of Plant Systematics, KU Leuven, Kasteelpark Arenberg 31, PO Box 2437, BE-3001 Leuven, Belgium
| | - A. Mouly
- Laboratoire Chrono-environnement, UMR CNRS 6249, Université de Franche-Comté, 16 Route de Gray, F-25030 Besançon cedex, France
- Bergius Foundation, Royal Swedish Academy of Sciences and Botany Department, Stockholm University, SE-106 91, Stockholm, Sweden
| | - B. Bremer
- Bergius Foundation, Royal Swedish Academy of Sciences and Botany Department, Stockholm University, SE-106 91, Stockholm, Sweden
| | - E. F. Smets
- Laboratory of Plant Systematics, KU Leuven, Kasteelpark Arenberg 31, PO Box 2437, BE-3001 Leuven, Belgium
- National Herbarium of The Netherlands, Leiden University Branch, PO Box 9514, NL-2300 RA Leiden, The Netherlands
- Netherlands Centre for Biodiversity Naturalis, PO Box 9517, NL-2300 RA Leiden, The Netherlands
| | - P. De Block
- National Botanic Garden of Belgium, Domein van Bouchout, BE-1860 Meise, Belgium
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Dubuisson JY, Rouhan G, Grall A, Hennequin S, Senterre B, Pynee K, Ebihara A. New insights into the systematics and evolution of the filmy fern genusCrepidomanes(Hymenophyllaceae) in the Mascarene Archipelago with a focus on dwarf species. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/12538078.2013.819294] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lumbsch T, Kantvilas G, Parnmen S. Molecular data support placement of Cameronia in Ostropomycetidae (Lecanoromycetes, Ascomycota). MycoKeys 2012. [DOI: 10.3897/mycokeys.5.4140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Wang L, Schneider H, Zhang XC, Xiang QP. The rise of the Himalaya enforced the diversification of SE Asian ferns by altering the monsoon regimes. BMC PLANT BIOLOGY 2012; 12:210. [PMID: 23140168 PMCID: PMC3508991 DOI: 10.1186/1471-2229-12-210] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/06/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND The rise of high mountain chains is widely seen as one of the factors driving rapid diversification of land plants and the formation of biodiversity hotspots. Supporting evidence was reported for the impact of the rapid rise of the Andean mountains but this hypothesis has so far been less explored for the impact of the "roof of the world". The formation of the Himalaya, and especially the rise of the Qinghai-Tibetan Plateau in the recent 20 million years, altered the monsoon regimes that dominate the current climates of South East Asia. Here, we infer the hypothesis that the rise of Himalaya had a strong impact on the plant diversity in the biodiversity hotspot of the Southwest Chinese Mountains. RESULTS Our analyses of the diversification pattern of the derived fern genus Lepisorus recovered evidence for changes in plant diversity that correlated with the strengthening of South East Asian monsoon. Southwest China or Southwest China and Japan was recovered as the putative area of origin of Lepisorus and enhancing monsoon regime were found to shape the early diversification of the genus as well as subsequent radiations during the late Miocene and Pliocene. CONCLUSIONS We report new evidence for a coincidence of plant diversification and changes of the climate caused by the uplift of the Himalaya. These results are discussed in the context of the impact of incomplete taxon sampling, uncertainty of divergence time estimates, and limitations of current methods used to assess diversification rates.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Harald Schneider
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, The Natural History Museum London, London, SW7 5BD, UK
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
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Strijk JS, Noyes RD, Strasberg D, Cruaud C, Gavory F, Chase MW, Abbott RJ, Thébaud C. In and out of Madagascar: dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae). PLoS One 2012; 7:e42932. [PMID: 22900068 PMCID: PMC3416790 DOI: 10.1371/journal.pone.0042932] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 07/16/2012] [Indexed: 11/20/2022] Open
Abstract
Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.
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Affiliation(s)
- Joeri S Strijk
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, People's Republic of China.
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Simon MF, Grether R, de Queiroz LP, Särkinen TE, Dutra VF, Hughes CE. The evolutionary history of Mimosa (Leguminosae): toward a phylogeny of the sensitive plants. AMERICAN JOURNAL OF BOTANY 2011; 98:1201-21. [PMID: 21730340 DOI: 10.3732/ajb.1000520] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Large genera provide remarkable opportunities to investigate patterns of morphological evolution and historical biogeography in plants. A molecular phylogeny of the species-rich and morphologically and ecologically diverse genus Mimosa was generated to evaluate its infrageneric classification, reconstruct the evolution of a set of morphological characters, and establish the relationships of Old World species to the rest of the genus. METHODS We used trnD-trnT plastid sequences for 259 species of Mimosa (ca. 50% of the total) to reconstruct the phylogeny of the genus. Six morphological characters (petiolar nectary, inflorescence type, number of stamens, number of petals, pollen type, and seismonasty) were optimized onto the molecular tree. KEY RESULTS Mimosa was recovered as a monophyletic clade nested within the Piptadenia group and includes the former members of Schrankia, corroborating transfer of that genus to Mimosa. Although we found good support for several infrageneric groups, only one section (Mimadenia) was recovered as monophyletic. All but one of the morphological characters analyzed showed high levels of homoplasy. High levels of geographic structure were found, with species from the same area tending to group together in the phylogeny. Old World species of Mimosa form a monophyletic clade deeply nested within New World groups, indicating recent (6-10 Ma) long-distance dispersal. CONCLUSIONS Although based on a single plastid region, our results establish a preliminary phylogenetic framework for Mimosa that can be used to infer patterns of morphological evolution and relationships and which provides pointers toward a revised infrageneric classification.
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Affiliation(s)
- Marcelo F Simon
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK.
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Le Péchon T, Dubuisson JY, Haevermans T, Cruaud C, Couloux A, Gigord LDB. Multiple colonizations from Madagascar and converged acquisition of dioecy in the Mascarene Dombeyoideae (Malvaceae) as inferred from chloroplast and nuclear DNA sequence analyses. ANNALS OF BOTANY 2010; 106:343-57. [PMID: 20562131 PMCID: PMC2908169 DOI: 10.1093/aob/mcq116] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS In the Mascarenes, a young oceanic archipelago composed of three main islands, the Dombeyoideae (Malvaceae) have diversified extensively with a high endemism rate. With the exception of the genus Trochetia, Mascarene Dombeyoideae are described as dioecious whereas Malagasy and African species are considered to be monocline, species with individuals bearing hermaphrodite/perfect flowers. In this study, the phylogenetic relationships were reconstructed to clarify the taxonomy, understand the phylogeographic pattern of relationships and infer the evolution of the breeding systems for the Mascarenes Dombeyoideae. METHODS Parsimony and Bayesian analysis of four DNA markers (ITS, rpl16 intron and two intergenic spacers trnQ-rsp16 and psbM-trnD) was used. The molecular matrix comprised 2985 characters and 48 taxa. The Bayesian phylogeny was used to infer phylogeographical hypotheses and the evolution of breeding systems. KEY RESULTS Parsimony and Bayesian trees produced similar results. The Dombeyoideae from the Mascarenes are polyphyletic and distributed among four clades. Species of Dombeya, Trochetia and Ruizia are nested in the same clade, which implies the paraphyly of Dombeya. Additionally, it is shown that each of the four clades has an independent Malagasy origin. Two adaptive radiation events have occurred within two endemic lineages of the Mascarenes. The polyphyly of the Mascarene Dombeyoideae suggests at least three independent acquisitions of dioecy. CONCLUSIONS This molecular phylogeny highlights the taxonomic issues within the Dombeyoideae. Indeed, the limits and distinctions of the genera Dombeya, Trochetia and Ruizia should be reconsidered. The close phylogeographic relationships between the flora of the Mascarenes and Madagascar are confirmed. Despite their independent origins and a distinct evolutionary history, each endemic clade has developed a different breeding systems (dioecy) compared with the Malagasy Dombeyoideae. Sex separation appears as an evolutionary convergence and may be the consequence of selective pressures particular to insular environments.
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Affiliation(s)
- Timothée Le Péchon
- Université Pierre et Marie Curie, UMR CNRS-MNHN-UPMC "Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements", Paris, France.
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Bellstedt DU, Pirie MD, Visser JC, de Villiers MJ, Gehrke B. A rapid and inexpensive method for the direct PCR amplification of DNA from plants. AMERICAN JOURNAL OF BOTANY 2010; 97:e65-8. [PMID: 21616856 DOI: 10.3732/ajb.1000181] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
PREMISE OF THE STUDY We present a rapid and inexpensive alternative to DNA isolation for polymerase chain reaction (PCR) amplification from plants. • METHODS AND RESULTS The method involves direct PCR amplification from material macerated in one buffer, followed by dilution and incubation in a second buffer. We describe the procedure and demonstrate its application for nuclear and plastid DNA amplification across a broad range of vascular plants. • CONCLUSIONS The method is fast, easy to perform, cost-effective, and consequently ideal for large sample numbers. It represents a considerable simplification of present approaches requiring DNA isolation prior to PCR amplification and will be useful in plant systematics and biotechnology, including applications such as DNA barcoding.
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Affiliation(s)
- Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
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Bräuchler C, Meimberg H, Heubl G. Molecular phylogeny of Menthinae (Lamiaceae, Nepetoideae, Mentheae) – Taxonomy, biogeography and conflicts. Mol Phylogenet Evol 2010; 55:501-23. [DOI: 10.1016/j.ympev.2010.01.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
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Agnarsson I, Kuntner M, Coddington JA, Blackledge TA. Shifting continents, not behaviours: independent colonization of solitary and subsocialAnelosimusspider lineages on Madagascar (Araneae, Theridiidae). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00406.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vences M, Wollenberg KC, Vieites DR, Lees DC. Madagascar as a model region of species diversification. Trends Ecol Evol 2009; 24:456-65. [DOI: 10.1016/j.tree.2009.03.011] [Citation(s) in RCA: 244] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 03/09/2009] [Accepted: 03/11/2009] [Indexed: 12/18/2022]
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Gao L, Yi X, Yang YX, Su YJ, Wang T. Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol Biol 2009; 9:130. [PMID: 19519899 PMCID: PMC2706227 DOI: 10.1186/1471-2148-9-130] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 06/11/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ferns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp) genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae). RESULTS The Alsophila cp genome is 156,661 base pairs (bp) in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp) and small single copy (SSC, 21,623 bp) regions separated by two copies of an inverted repeat (IRs, 24,365 bp each). This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG) is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum). At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes. CONCLUSION By comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The Alsophila cp genome is very similar to that of the polypod fern Adiantum in terms of gene content, gene order and GC content. However, there exist some striking differences between them: the trnR-UCG gene represents a putative molecular apomorphy of tree ferns; and the repeats observed at one inversion endpoint may be a vestige of some unknown rearrangement(s). This work provided fresh insights into the fern cp genome evolution as well as useful data for future phylogenetic studies.
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Affiliation(s)
- Lei Gao
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, PR China.
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Meudt HM, Lockhart PJ, Bryant D. Species delimitation and phylogeny of a New Zealand plant species radiation. BMC Evol Biol 2009; 9:111. [PMID: 19457251 PMCID: PMC2700801 DOI: 10.1186/1471-2148-9-111] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 05/20/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation Ourisia species (Plantaginaceae) in the New Zealand archipelago. RESULTS New Zealand Ourisia are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4-1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of Ourisia produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties. CONCLUSION Ourisia radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in Ourisia. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data.
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Affiliation(s)
- Heidi M Meudt
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag, Palmerston North, New Zealand.
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