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Chen S, Wang T, Shu J, Xiang Q, Yang T, Zhang X, Yan Y. Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes. Genes (Basel) 2022; 13:genes13071280. [PMID: 35886063 PMCID: PMC9316050 DOI: 10.3390/genes13071280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Although extant lycophytes represent the most ancient surviving lineage of early vascular plants, their plastomic diversity has long been neglected. The ancient evolutionary history and distinct genetic diversity patterns of the three lycophyte families, each with its own characteristics, provide an ideal opportunity to investigate the interfamilial relationships of lycophytes and their associated patterns of evolution. To compensate for the lack of data on Lycopodiaceae, we sequenced and assembled 14 new plastid genomes (plastomes). Combined with other lycophyte plastomes available online, we reconstructed the phylogenetic relationships of the extant lycophytes based on 93 plastomes. We analyzed, traced, and compared the plastomic diversity and divergence of the three lycophyte families (Isoëtaceae, Lycopodiaceae, and Selaginellaceae) in terms of plastomic diversity by comparing their plastome sizes, GC contents, substitution rates, structural rearrangements, divergence times, ancestral states, RNA editings, and gene losses. Comparative analysis of plastid phylogenomics and plastomic diversity of three lycophyte families will set a foundation for further studies in biology and evolution in lycophytes and therefore in vascular plants.
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Affiliation(s)
- Sisi Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jiangping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Qiaoping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
| | - Tuo Yang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- Correspondence: (X.Z.); (Y.Y.)
| | - Yuehong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- Correspondence: (X.Z.); (Y.Y.)
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Wei Z, Xia Z, Shu J, Shang H, Maxwell SJ, Chen L, Zhou X, Xi W, Adjie B, Yuan Q, Cao J, Yan Y. Phylogeny and Taxonomy on Cryptic Species of Forked Ferns of Asia. FRONTIERS IN PLANT SCIENCE 2021; 12:748562. [PMID: 34975938 PMCID: PMC8718997 DOI: 10.3389/fpls.2021.748562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Cryptic species comprise two or more taxa that are grounded under a single name because they are more-or-less indistinguishable morphologically. These species are potentially important for detailed assessments of biodiversity, but there now appear to be many more cryptic species than previously estimated. One taxonomic group likely to contain many cryptic species is Dicranopteris, a genus of forked ferns that occurs commonly along roadsides in Asia. The genus has a complex taxonomical history, and D. linearis has been particularly challenging with many intra-specific taxa dubiously erected to accommodate morphological variation that lacks clear discontinuities. To resolve species boundaries within Dicranopteris, we applied a molecular phylogenetic approach as complementary to morphology. Specifically, we used five chloroplast gene regions (rbcL, atpB, rps4, matK, and trnL-trnF) to generate a well-resolved phylogeny based on 37 samples representing 13 taxa of Dicranopteris, spanning the major distributional area in Asia. The results showed that Dicranopteris consists of ten highly supported clades, and D. linearis is polyphyletic, suggesting cryptic diversity within the species. Further through morphological comparison, we certainly erected Dicranopteris austrosinensis Y.H. Yan & Z.Y. Wei sp. nov. and Dicranopteris baliensis Y.H. Yan & Z.Y. Wei sp. nov. as distinct species and proposed five new combinations. We also inferred that the extant diversity of the genus Dicranopteris may result from relatively recent diversification in the Miocene based on divergence time dating. Overall, our study not only provided additional insights on the Gleicheniaceae tree of life, but also served as a case of integrating molecular and morphological approaches to elucidate cryptic diversity in taxonomically difficult groups.
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Affiliation(s)
- Zuoying Wei
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zengqiang Xia
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jiangping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Shang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Stephen J. Maxwell
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - Lijun Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Xile Zhou
- Xiangxi Tujia and Miao Autonomous Prefecture Forest Resources Monitoring Center, Jishou, China
| | - Wang Xi
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Bayu Adjie
- Research Center for Plants Conservation and Botanic Gardens, National Research and Innovation Agency of Indonesia, Bali, Indonesia
| | - Quan Yuan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jianguo Cao
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Lehtonen S, Muscarella R, Moulatlet G, Balslev H, Tuomisto H. Edaphic heterogeneity and the evolutionary trajectory of Amazonian plant communities. Ecol Evol 2021; 11:17672-17685. [PMID: 35003631 PMCID: PMC8717337 DOI: 10.1002/ece3.8477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
We investigated how the phylogenetic structure of Amazonian plant communities varies along an edaphic gradient within the non-inundated forests. Forty localities were sampled on three terrain types representing two kinds of soil: clayey soils of a high base cation concentration derived from the Solimões formation, and loamy soils with lower base cation concentration derived from the Içá formation and alluvial terraces. Phylogenetic community metrics were calculated for each locality for ferns and palms both with ferns as one group and for each of three fern clades with a crown group age comparable to that of palms. Palm and fern communities showed significant and contrasting phylogenetic signals along the soil gradient. Fern species richness increased but standard effect size of mean pairwise distance (SES.MPD) and variation of pairwise distances (VPD) decreased with increasing soil base cation concentration. In contrast, palm communities were more species rich on less cation-rich soils and their SES.MPD increased with soil base cation concentration. Species turnover between the communities reflected the soil gradient slightly better when based on species occurrences than when phylogenetic distances between the species were considered. Each of the three fern subclades behaved differently from each other and from the entire fern clade. The fern clade whose phylogenetic patterns were most similar to those of palms also resembled palms in being most species-rich on cation-poor soils. The phylogenetic structuring of local plant communities varies along a soil base cation concentration gradient within non-inundated Amazonian rain forests. Lineages can show either similar or different phylogenetic community structure patterns and evolutionary trajectories, and we suggest this to be linked to their environmental adaptations. Consequently, geological heterogeneity can be expected to translate into a potentially highly diverse set of evolutionarily distinct community assembly pathways in Amazonia and elsewhere.
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Affiliation(s)
| | - Robert Muscarella
- Plant Ecology and EvolutionEvolutionary Biology CenterUppsala UniversityUppsalaSweden
| | - Gabriel Moulatlet
- Facultad de Ciencias de la Tierra y AguaUniversidad Regional Amazónica IkiamTenaEcuador
| | - Henrik Balslev
- Section for Ecoinformatics & BiodiversityDepartment of BioscienceAarhus UniversityAarhusDenmark
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Zhang L, Fan XP, Petchsri S, Zhou L, Pollawatn R, Zhang X, Zhou XM, Thi Lu N, Knapp R, Chantanaorrapint S, Limpanasittichai P, Sun H, Gao XF, Zhang LB. Evolutionary relationships of the ancient fern lineage the adder's tongues (Ophioglossaceae) with description of Sahashia gen. nov. Cladistics 2020; 36:380-393. [PMID: 34618972 DOI: 10.1111/cla.12408] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2019] [Indexed: 02/04/2023] Open
Abstract
As an ancient lineage of ferns, Ophioglossaceae are evolutionarily among the most fascinating because they have the highest chromosome count of any known organism as well as the presence of sporophores, subterranean gametophytes, eusporangiate sporangia without annuli, and endophytic fungi. Previous studies have produced conflicting results, identifyingsome lineages with unresolved relationships, and have paid much attention to the subfamily Botrychioideae. But the other species-rich subfamily, Ophioglossoideae, has remained largely understudied and only up to 12 accessions of Ophioglossoideae have been sampled. In this study, DNA sequences of seven plastid markers of 149 accessions (75 in Ophioglossoideae) representing approximately 82 species (approximately 74% of estimated species diversity sensu J. Syst. Evol., 2016, 54, 563) in the family, and two Marattiaceae and two Psilotaceae, are used to infer a phylogeny. Our major results include: (1) Ophioglossaceae are resolved as monophyletic with strong support, and so are all four subfamilies and genera sensu PPG I except Botrypus and Ophioglossum; (2) a new genus Sahashia is segregated from Botrypus so that the monophyly of Botrypus can be retained; (3) the monophyly of Ophioglossum in its current circumscription is uncertain in spite of our large character sampling; (4) there is substantial cryptic speciation in Ophioderma detected by our molecular and morphological study; (5) the recognition of Holubiella is advocated based on its morphology and its sister relationship with Sceptridium; and (6) a novel sister relationship between Botrychium and the JHS clade (Japanobotrychium + (Holubiella + Sceptridium)) is discovered.
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Affiliation(s)
- Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Xue-Ping Fan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
| | - Sahanat Petchsri
- Department of Botany, Faculty of Liberal Arts and Science, Kasetsart University, Kampaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Lin Zhou
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Rossarin Pollawatn
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Xin Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Xin-Mao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, Yunnan, China
| | - Ngan Thi Lu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Department of Biology, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18th Hoang Quoc Viet Road, Ha Noi, Vietnam
| | - Ralf Knapp
- Muséum national d'Histoire naturelle (MNHN, Paris, France), Steigestrasse 78, Eberbach, 69412, Germany
| | - Sahut Chantanaorrapint
- Department of Biology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Ponpipat Limpanasittichai
- Department of Horticulture, Faculty of agriculture, Kasetsart University, 50 Ngam Wong Wan Rd., Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China
| | - Li-Bing Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China.,Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO, 63110, USA
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New insights into the evolution of the fern family Dennstaedtiaceae from an expanded molecular phylogeny and morphological analysis. Mol Phylogenet Evol 2020; 150:106881. [PMID: 32512193 DOI: 10.1016/j.ympev.2020.106881] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 11/21/2022]
Abstract
Dennstaedtiaceae has 270 species, a worldwide distribution, and an edge-colonizing habit that is unusual among ferns. Aneuploidy, polyploidy, and hybrids are common in the family. Combining morphology, anatomy, chromosome number, and geographical distributions with our newly generated molecular phylogeny, we provide new insights into the evolution of the family. We paid special attention to Hypolepis. Our molecular dataset of five cpDNA markers is the most comprehensive to date, comprising 72 species (and a total of 98 taxa), of which 33 are Hypolepis (45 taxa). We also generated divergence-time estimates through BEAST with four fossil calibrations. We recovered three sub-families in Dennstaedtiaceae: Monachosoroideae (monogeneric), Dennstaedtioideae, and Hypolepidoideae. Monachosoroideae has a chromosome base number of x = 28; Hypolepidoideae of x = 26; while in Dennstaedtioideae this is still obscure, with different numbers ranging from 30 to 47. Dennstaedtioideae genera require re-circumscriptions because Dennstaedtia is polyphyletic. In Hypolepidoideae, the six genera are monophyletic. Within Hypolepis, seven geographically distinct clades were recovered; but we found no strong morphological characters to define them. Within the family, the long-creeping rhizome evolved with a change in habit: from shade-tolerant to edge-colonizers, to thicket-formers. Short or extremely large leaves are derived conditions. Sorus shape and position, glandular hairs, and prickles are homoplastic. Hybridization/allotetraploidy in Hypolepis can be suggested by the combined data. In our phylogenetic hypothesis, Dennstaedtiaceae originated around 135 Ma, with the split of Monachosoroideae around 94 Ma, and the split between Dennstaedtioideae/Hypolepidoideae around 78 Ma. All extant genera are inferred to be relatively young. Hypolepis started to diversify around 10 Ma, and it probably originated in east Asia and/or Oceania. Hypolepis reached the Neotropics twice: through elements of the Hypolepis rugosula clade (which originated at 7 Ma), and through the ancestor of the Neotropical clade, which originated at 3.1 Ma and was prickly.
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Exploring phylogeny of the microsoroid ferns (Polypodiaceae) based on six plastid DNA markers. Mol Phylogenet Evol 2020; 143:106665. [DOI: 10.1016/j.ympev.2019.106665] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 01/11/2023]
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Genetic diversity and hybrid formation in Central European club-mosses (Diphasiastrum, Lycopodiaceae) - New insights from cp microsatellites, two nuclear markers and AFLP. Mol Phylogenet Evol 2018; 131:181-192. [PMID: 30415022 DOI: 10.1016/j.ympev.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023]
Abstract
In Europe, the genus Diphasiastrum (Lycopodiophyta) forms a reticulate network of six diploid taxa, including three parent species (D. alpinum, D. complanatum and D. tristachyum) and three hybrids (D. × issleri, D. × oellgaardii and D. × zeilleri). It was not clear if the hybrids arose once or repeatedly, if they have reproductive competence and if backcrossing occurs. We addressed these questions by analysing 209 accessions for chloroplast microsatellites (cp), two nuclear markers (introns of the RPB and LFY genes) and AFLP. For D. complanatum we show a sexual life cycle with alternation of generations: the gametophytic DNA amount is half of that of the sporophyte. With the exception of a single accession all hybrids display one of the two parental cp haplotypes; their frequencies do not differ significantly from a 1:1 ratio. Genotypes of nuclear markers are species-specific, displaying 2/4/1 (RPB) and 1/8/1 alleles (LFY) for the three parents mentioned above; all hybrids have one allele from each parent. All three hybrid taxa apparently represent independent F1 crosses. Hybridisation occurs bidirectional; no evidence for recent backcrossing was found. Asexual reproduction via agamospory is at least rare, since AFLP showed all hybrid plants to be different.
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Shang H, Sundue M, Wei R, Wei XP, Luo JJ, Liu L, Schwartsburd PB, Yan YH, Zhang XC. Hiya: A new genus segregated from Hypolepis in the fern family Dennstaedtiaceae, based on phylogenetic evidence and character evolution. Mol Phylogenet Evol 2018; 127:449-458. [PMID: 29723646 DOI: 10.1016/j.ympev.2018.04.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 01/10/2023]
Abstract
The relationship of Hypolepis brooksiae, H. nigrescens, and H. scabristipes to the remainder of Hypolepis (Dennstaedtiaceae) has been questioned by previous authors based on their unique combination of morphological characters and different base chromosome number. Using four chloroplast genes including rbcL, atpA, rpL6, and rps4-trnS intergenic spacer (IGS) from 32 samples, representing 24 species of Dennstaedtiaceae, we recovered a clade comprising H. brooksiae and H. nigrescens, distinct from the remaining species of Hypolepis. This clade is resolved as sister to the clade comprising Blotiella, Paesia and Histiopteris. We reconstructed ancestral states of 16 morphological characters and found that this clade is distinguished by indeterminate, scandent leaves exhibiting rhythmic growth, provided with recurved black-tipped prickles, and stipule-like pinnules that protect the emerging crosier and pinnae departures, rachis-costa architecture where the adaxial sulcus is confluent with the next lower order, and a base chromosome number of x = 29. In light of this molecular and morphological evidence, we describe a new genus, Hiya, and provide nomenclatural combinations to accommodate the three known species segregated from Hypolepis: Hiya brooksiae, Hiya nigrescens, and Hiya scabristipes.
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Affiliation(s)
- Hui Shang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Michael Sundue
- The Pringle Herbarium, Dept. of Plant Biology, University of Vermont, Burlington, VT 05405, USA
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xue-Ping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jun-Jie Luo
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Li Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Pedro B Schwartsburd
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. P.H. Rolfs s.n., Viçosa, MG 36570-900, Brazil
| | - Yue-Hong Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals. Mol Phylogenet Evol 2016; 98:324-36. [DOI: 10.1016/j.ympev.2016.02.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/15/2016] [Accepted: 02/20/2016] [Indexed: 11/18/2022]
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Le Péchon T, He H, Zhang L, Zhou XM, Gao XF, Zhang LB. Using a multilocus phylogeny to test morphology-based classifications of Polystichum (Dryopteridaceae), one of the largest fern genera. BMC Evol Biol 2016; 16:55. [PMID: 26928720 PMCID: PMC4772321 DOI: 10.1186/s12862-016-0626-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polystichum (Dryopteridaceae) is probably the third largest fern genus in the world and contains ca. 500 species. Species of Polystichum occur on all continents except Antarctica, but its highest diversity is found in East Asia, especially Southwest China and adjacent regions. Previous studies typically had sparse taxon sampling and used limited DNA sequence data. Consequently, the majority of morphological hypotheses/classifications have never been tested using molecular data. RESULTS In this study, DNA sequences of five plastid loci of 177 accessions representing ca. 140 species of Polystichum and 13 species of the closely related genera were used to infer a phylogeny using maximum likelihood, Bayesian inference, and maximum parsimony. Our analyses show that (1) Polystichum is monophyletic, this being supported by not only molecular data but also morphological features and distribution information; (2) Polystichum is resolved into two strongly supported monophyletic clades, corresponding to the two subgenera, P. subg. Polystichum and P. subg. Haplopolystichum; (3) Accessions of P. subg. Polystichum are resolved into three major clades: clade K (P. sect. Xiphophyllum), clade L (P. sect. Polystichum), and the HYMASO superclade dominated by accessions of P. sect. Hypopeltis, P. sect. Macropolystichum, and P. sect. Sorolepidium, while those of P. subg. Haplopolystichum are resolved into eight major clades; and (4) The monophyly of the Afra clade (weakly supported), the Australasian clade (weakly supported), and the North American clade (strongly supported) is confirmed. CONCLUSIONS Of the 23 sections of Polystichum recognized in a recent classification of the genus, four (P. sect. Hypopeltis, P. sect. Neopolystichum, P. sect. Sorolepidium, P. sect. Sphaenopolystichum) are resolved as non-monophyletic, 16 are recovered as monophyletic, and three are monospecific. Of the 16 monophyletic sections, two (P. sect. Adenolepia, P. sect. Cyrtogonellum) are weakly supported and 14 are strongly supported as monophyletic. The relationships of 11 sections (five in P. subg. Haplopolystichum; six in P. subg. Polystichum) are well resolved.
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Affiliation(s)
- Timothée Le Péchon
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China.
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X01 Scottsville, Pietermaritzburg, 3209, South Africa.
| | - Hai He
- School of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 400047, China.
| | - Liang Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China.
| | - Xin-Mao Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China.
- School of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
| | - Xin-Fen Gao
- Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, China.
| | - Li-Bing Zhang
- Missouri Botanical Garden, P.O. Box 299, St. Louis, MO, 63166-0299, USA.
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Wolf PG, Rowe CA, Der JP, Schilling MP, Visger CJ, Thomson JA. Origins and diversity of a cosmopolitan fern genus on an island archipelago. AOB PLANTS 2015; 7:plv118. [PMID: 26487677 PMCID: PMC4662730 DOI: 10.1093/aobpla/plv118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/09/2015] [Indexed: 05/12/2023]
Abstract
Isolated oceanic islands are characterized by patterns of biological diversity different from that on nearby continental mainlands. Isolation can provide the opportunity for evolutionary divergence, but also set the stage for hybridization between related taxa arriving from different sources. Ferns disperse by haploid spores, which are produced in large numbers and can travel long distances in air currents, enabling these plants to become established on most oceanic islands. Here, we examine the origins and patterns of diversity of the cosmopolitan fern genus Pteridium (Dennstaedtiaceae; bracken) on the Galapagos Islands. We use nucleotide sequences from two plastid genes, and two nuclear gene markers, to examine phylogeography of Pteridium on the Galapagos Islands. We incorporate data from a previous study to provide a worldwide context. We also sampled new specimens from South and Central America. We used flow cytometry to estimate genome size of some accessions. We found that both plastid and nuclear haplotypes fall into two distinct clades, consistent with a two-diploid-species taxonomy of P. aquilinum and P. esculentum. As predicted, the allotetraploid P. caudatum possesses nuclear haplotypes from both diploid species. Samples from the Galapagos include P. esculentum subsp. arachnoideum, P. caudatum and possible hybrids between them. Multiple Pteridium taxa were also observed growing together at some sites. We find evidence for multiple origins of Pteridium on the Galapagos Islands and multiple origins of tetraploid P. caudatum throughout its range in Central and South America. We also posit that P. caudatum may include recent diploid hybrids, backcrosses to P. esculentum, as well as allotetraploid plants. The Galapagos Islands are positioned close to the equator where they can receive dispersing propagules from both hemispheres. This may partly explain the high levels of diversity found for this cosmopolitan fern on these islands.
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Affiliation(s)
- Paul G Wolf
- Department of Biology, Utah State University, Logan, UT 84322, USA Ecology Center, Utah State University, Logan, UT 84322, USA
| | - Carol A Rowe
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | - Joshua P Der
- Department of Biological Science, California State University, Fullerton, CA 92834, USA
| | | | - Clayton J Visger
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - John A Thomson
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
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Chen T, Chen Q, Luo Y, Huang ZL, Zhang J, Tang HR, Pan DM, Wang XR. Phylogeography of Chinese cherry (Prunus pseudocerasus Lindl.) inferred from chloroplast and nuclear DNA: insights into evolutionary patterns and demographic history. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:787-97. [PMID: 25521479 DOI: 10.1111/plb.12294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 12/10/2014] [Indexed: 05/16/2023]
Abstract
Chinese cherry (Prunus pseudocerasus Lindl.) is a commercially valuable fruit crop in China. In order to obtain new insights into its evolutionary history and provide valuable recommendations for resource conservation, phylogeographic patterns of 26 natural populations (305 total individuals) from six geographic regions were analyzed using chloroplast and nuclear DNA fragments. Low levels of haplotype and nucleotide diversity were found in these populations, especially in landrace populations. It is likely that a combined effect of botanical characteristics impact the effective population size, such as inbreeding mating system, long life span, as well as vegetative reproduction. In addition, strong bottleneck effect caused by domestication, together with founder effect after dispersal and subsequent demographic expansion, might also accelerate the reduction of the genetic variation in landrace populations. Interestingly, populations from Longmen Mountain (LMM) and Daliangshan Mountain (DLSM) exhibited relatively higher levels of genetic diversity, inferring the two historical genetic diversity centers of the species. Moreover, moderate population subdivision was also detected by both chloroplast DNA (GST = 0.215; NST = 0.256) and nuclear DNA (GST = 0.146; NST = 0.342), respectively. We inferred that the episodes of efficient gene flow through seed dispersal, together with features of long generation cycle and inbreeding mating system, were likely the main contributors causing the observed phylogeographic patterns. Finally, factors that led to the present demographic patterns of populations from these regions and taxonomic varieties were also discussed.
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Affiliation(s)
- T Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Q Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Y Luo
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Z-L Huang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - J Zhang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - H-R Tang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - D-M Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - X-R Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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Diversification and reticulation in the circumboreal fern genus Cryptogramma. Mol Phylogenet Evol 2013; 67:589-99. [DOI: 10.1016/j.ympev.2013.02.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 02/03/2013] [Accepted: 02/15/2013] [Indexed: 01/04/2023]
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Sessa EB, Zimmer EA, Givnish TJ. Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:104. [PMID: 22748145 PMCID: PMC3509404 DOI: 10.1186/1471-2148-12-104] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called "semicristata" hypothesis, contention over the group's history has continued in several recent, conflicting studies. RESULTS Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the "semicristata" hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. CONCLUSIONS This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis, including the existence of a missing diploid progenitor, and allow us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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Sessa EB, Zimmer EA, Givnish TJ. Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:730-750. [PMID: 22434775 DOI: 10.3732/ajb.1100294] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Dryopteris is a large, cosmopolitan fern genus ideal for addressing questions about diversification, biogeography, hybridization, and polyploidy, which have historically been understudied in ferns. We constructed a highly resolved, well-supported phylogeny for New World Dryopteris and used it to investigate biogeographic patterns and divergence times. METHODS We analyzed relationships among 97 species of Dryopteris, including taxa from all major biogeographic regions, with analyses based on 5699 aligned nucleotides from seven plastid loci. Phylogenetic analyses used maximum parsimony, maximum likelihood, and Bayesian inference. We conducted divergence time analyses using BEAST and biogeographic analyses using maximum parsimony, maximum likelihood, Bayesian, and S-DIVA approaches. We explored the monophyly of subgenera and sections in the most recent generic classification and of geographic groups of taxa using Templeton tests. KEY RESULTS The genus Dryopteris arose ca. 42 million years ago (Ma). Most of the Central and South American species form a well-supported clade which arose 32 Ma, but the remaining New World species are the result of multiple, independent dispersal and vicariance events involving Asia, Europe, and Africa over the last 15 Myr. We identified six long-distance dispersal events and three vicariance events in the immediate ancestry of New World species; reconstructions for another four lineages were ambiguous. CONCLUSIONS New World Dryopteris are not monophyletic; vicariance has dominated the history of the North American species, while long-distance dispersal prevails in the Central and South American species, a pattern not previously seen in plants.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706, USA.
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Abstract
In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.
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CAPS markers using mitochondrial consensus primers for molecular identification of Panax species and Korean ginseng cultivars (Panax ginseng C. A. Meyer). Mol Biol Rep 2011; 39:729-36. [PMID: 21573801 DOI: 10.1007/s11033-011-0792-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 04/29/2011] [Indexed: 10/18/2022]
Abstract
Cleaved amplified polymorphic sequence (CAPS) marker system using mitochondrial consensus primers was applied for molecular identification of Korean ginseng cultivars (Panax ginseng). Initially, a total of 34 primers were tested to six Korean ginseng cultivars and two foreign Panax species, P. quinquefolius and P. notoginseng. In the polymerase chain reaction (PCR) amplification results, four primers (mt7, mt11, mt13, and mt18) generated co-dominant polymorphic banding patterns discriminating the Korean ginseng cultivars from P. quinquefolius and P. notoginseng. In the CAPS analysis results, the majority of the cleaved PCR products also yielded additional latent polymorphisms between the Korean ginseng cultivars and two foreign Panax species. Specific latent CAPS polymorphisms for cultivar Gopoong and Chunpoong were detected from internal region amplified with mt9 primer by treating HinfI and Tsp509I endonucleases, respectively. Sequencing analysis revealed that the length of amplified region of Korean ginseng cultivars was 2,179 bp, and those of P. quinquefolius and P. notoginseng were 2,178 and 2,185 bp, respectively. Blast search revealed that the amplified region was a mitochondrial cytochrome oxidase subunit 2 (cox2) gene intron II region. Nineteen single nucleotide polymorphisms (SNP) including each specific SNP for Gopoong and Chunpoong, and three insertion and deletion (InDel) polymorphisms were detected by sequence alignment. The CAPS markers developed in this study, which are specific to Gopoong and Chunpoong, and between the Korean ginseng cultivars and two foreign Panax species, will serve as a practical and reliable tool for their identification, purity maintenance, and selection of candidate lines and cultivars.
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19
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FITMAWATI, HARTANA ALEX. Phylogenetic Study of Mangifera laurina and its Related Species Using cpDNA trnL-F Spacer Markers. HAYATI JOURNAL OF BIOSCIENCES 2010. [DOI: 10.4308/hjb.17.1.9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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20
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Historical herbarium specimens in plant molecular systematics — an example from the fern genus Lindsaea (Lindsaeaceae). Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0008-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kress WJ, Erickson DL, Jones FA, Swenson NG, Perez R, Sanjur O, Bermingham E. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc Natl Acad Sci U S A 2009; 106:18621-6. [PMID: 19841276 PMCID: PMC2763884 DOI: 10.1073/pnas.0909820106] [Citation(s) in RCA: 379] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Indexed: 11/18/2022] Open
Abstract
The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.
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Affiliation(s)
- W John Kress
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA.
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22
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Grusz AL, Windham MD, Pryer KM. Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae). AMERICAN JOURNAL OF BOTANY 2009; 96:1636-1645. [PMID: 21622350 DOI: 10.3732/ajb.0900019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Deciphering species relationships and hybrid origins in polyploid agamic species complexes is notoriously difficult. In this study of cheilanthoid ferns, we demonstrate increased resolving power for clarifying the origins of polyploid lineages by integrating evidence from a diverse selection of biosystematic methods. The prevalence of polyploidy, hybridization, and apomixis in ferns suggests that these processes play a significant role in their evolution and diversification. Using a combination of systematic approaches, we investigated the origins of apomictic polyploids belonging to the Cheilanthes yavapensis complex. Spore studies allowed us to assess ploidy levels; plastid and nuclear DNA sequencing revealed evolutionary relationships and confirmed the putative progenitors (both maternal and paternal) of taxa of hybrid origin; enzyme electrophoretic evidence provided information on genome dosage in allopolyploids. We find here that the widespread apomictic triploid, Cheilanthes lindheimeri, is an autopolyploid derived from a rare, previously undetected sexual diploid. The apomictic triploid Cheilanthes wootonii is shown to be an interspecific hybrid between C. fendleri and C. lindheimeri, whereas the apomictic tetraploid C. yavapensis is comprised of two cryptic and geographically distinct lineages. We show that earlier morphology-based hypotheses of species relationships, while not altogether incorrect, only partially explain the complicated evolutionary history of these ferns.
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Affiliation(s)
- Amanda L Grusz
- Department of Biology, Duke University, Durham, North Carolina 27708-0338 USA
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Der JP, Thomson JA, Stratford JK, Wolf PG. Global chloroplast phylogeny and biogeography of bracken (Pteridium; Dennstaedtiaceae). AMERICAN JOURNAL OF BOTANY 2009; 96:1041-9. [PMID: 21628254 DOI: 10.3732/ajb.0800333] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Bracken ferns (genus Pteridium) represent an ancient species complex with a natural worldwide distribution. Pteridium has historically been treated as comprising a single species, but recent treatments have recognized several related species. Phenotypic plasticity, geographically structured morphological variation, and geographically biased sampling have all contributed to taxonomic confusion in the genus. We sampled bracken specimens worldwide and used variable regions of the chloroplast genome to investigate phylogeography and reticulate evolution within the genus. Our results distinguish two major clades within Pteridium, a primarily northern hemisphere Laurasian/African clade, which includes all taxa currently assigned to P. aquilinum, and a primarily southern hemisphere Austral/South American clade, which includes P. esculentum and P. arachnoideum. All European accessions of P. aquilinum subsp. aquilinum appear in a monophyletic group and are nested within a clade containing the African P. aquilinum taxa (P. aquilinum subsp. capense and P. aquilinum subsp. centrali-africanum). Our results allow us to hypothesize the maternal progenitors of two allotetraploid bracken species, P. caudatum and P. semihastatum. We also discuss the biogeography of bracken in the context of the chloroplast phylogeny. Our study is one of the first to take a worldwide perspective in addressing variation in a broadly distributed species complex.
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Affiliation(s)
- Joshua P Der
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, Utah 84322 USA
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Watts CD, Fisher AE, Shrum CD, Newbold WL, Hansen S, Liu C, Kelchner SA. The D4 set: primers that target highly variable intron loops in plant chloroplast genomes. Mol Ecol Resour 2008; 8:1344-7. [PMID: 21586041 DOI: 10.1111/j.1755-0998.2008.02229.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chloroplast group II introns offer high-quality, rapidly evolving single-copy loci for comparative sequence analysis. These introns feature diagnostic secondary structures with loops that are among the least evolutionarily constrained sequence in plastomes. We exploited these structures to develop universal primers that amplify and sequence the large Domain IV (D4) loop in several angiosperm introns. With a single sequence read, we recover 300-600 nucleotides of highly variable sequence across angiosperms, with rates of change that are equal to or higher than many of the best known intergenic spacers in plant chloroplast genomes.
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Affiliation(s)
- Chad D Watts
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209-8007, USA
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Bellusci F, Pellegrino G, Palermo A, Musacchio A. Phylogenetic relationships in the orchid genus Serapias L. based on noncoding regions of the chloroplast genome. Mol Phylogenet Evol 2008; 47:986-91. [DOI: 10.1016/j.ympev.2008.03.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 03/10/2008] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
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Murdock AG. Phylogeny of marattioid ferns (Marattiaceae): inferring a root in the absence of a closely related outgroup. AMERICAN JOURNAL OF BOTANY 2008; 95:626-641. [PMID: 21632388 DOI: 10.3732/ajb.2007308] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Closely related outgroups are optimal for rooting phylogenetic trees; however, such ideal outgroups are not always available. A phylogeny of the marattioid ferns (Marattiaceae), an ancient lineage with no close relatives, was reconstructed using nucleotide sequences of multiple chloroplast regions (rps4 + rps4-trnS spacer, trnS-trnG spacer + trnG intron, rbcL, atpB), from 88 collections, selected to cover the broadest possible range of morphologies and geographic distributions within the extant taxa. Because marattioid ferns are phylogenetically isolated from other lineages, and internal branches are relatively short, rooting was problematic. Root placement was strongly affected by long-branch attraction under maximum parsimony and by model choice under maximum likelihood. A multifaceted approach to rooting was employed to isolate the sources of bias and produce a consensus root position. In a statistical comparison of all possible root positions with three different outgroups, most root positions were not significantly less optimal than the maximum likelihood root position, including the consensus root position. This phylogeny has several important taxonomic implications for marattioid ferns: Marattia in the broad sense is paraphyletic; the Hawaiian endemic Marattia douglasii is most closely related to tropical American taxa; and Angiopteris is monophyletic only if Archangiopteris and Macroglossum are included.
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Affiliation(s)
- Andrew G Murdock
- Department of Integrative Biology, University of California, Berkeley, 1001 Valley Life Sciences Bldg., California 94720-2465 USA
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Li CX, Lu SG, Barrington DS. Phylogeny of Chinese Polystichum (Dryopteridaceae) based on chloroplast DNA sequence data (trnL-F and rps4-trnS). JOURNAL OF PLANT RESEARCH 2008; 121:19-26. [PMID: 18000642 DOI: 10.1007/s10265-007-0120-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 09/27/2007] [Indexed: 05/25/2023]
Abstract
Polystichum is one of the largest and most taxonomically complex fern genera in China. The evolutionary relationships of Chinese Polystichum and related genera, and the relationship between our Polystichum phylogeny and ecogeographic distribution, were tested by the use of DNA sequence data. Fifty-one species of Polystichum and 21 species in allied genera were sequenced for the plastid intergenic spacers rps4-trnS and trnL-F. Maximum parsimony and Bayesian phylogenetic analyses of both individual and combined data sets showed that Chinese Polystichum as commonly recognized was paraphyletic: one clade (the CCPC clade) included Cyrtomidictyum lepidocaulon, two Cyrtogonellum species, three Cyrtomium species, and a small number of Polystichum species usually occurring on limestone. A second clade, Polystichum sensu stricto, included the remainder of the Polystichum species; these often occur on non-limestone substrates. The remaining Cyrtomium species formed the third clade. Three subclades resolved within Polystichum sensu stricto (s.s.) clade do not correspond with recent sectional classifications, and we outline the issues relevant to a new classification for the genus.
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Affiliation(s)
- Chun-Xiang Li
- State Key Laboratory of Palaeobiology and Stratigraphy of the Nanjing Institute of Geology and Palaeontology, The Chinese Academy of Science, Nanjing, Jiangsu Province 210008, China.
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