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Wang L, Yang W, Zhang X, Zhang D, Zhang G. Insights into the evolutionary history and taxonomic status of Sinopteris (Pteridaceae). Mol Phylogenet Evol 2023; 180:107672. [PMID: 36539018 DOI: 10.1016/j.ympev.2022.107672] [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: 06/19/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
As an endemic Chinese genus, Sinopteris C. Chr. & Ching was once considered an early diverged taxon of cheilanthoid ferns, and its taxonomic status has long been controversial. In this study, eight datasets spanning the complete chloroplast genomes and three nuclear genes were used to reconstruct the phylogeny of Sinopteris and its relatives. In addition, combining morphological analyses, divergence time estimation, and ancestral trait reconstruction, the origin and evolutionary history of Sinopteris were comprehensively discussed. Based on the complete chloroplast genome dataset, our analyses yielded a phylogram with all clades strongly supported (ML-BS = 100, BI-PP = 1.0), and the topology was almost identical to that based on the concatenated sequences of nrDNA, CRY2, and IBR3. Two species of Sinopteris were united and sister to Aleuritopteris niphobola (C. Chr.) Ching. They constituted a stable monophyletic group embedded in Aleuritopteris Fée. This was also consistent with the results of morphological analyses. Divergence time estimation indicated that the clade of Aleuritopteris and Sinopteris originated in the early Miocene (ca. 16.80 Ma) and experienced two rapid diversifications, which could coincide with environmental heterogeneity caused by the progressive uplift of the Himalayas and the intense uplift of the Hengduan Mountains. Sinopteris originated in the late Miocene (ca. 6.96 Ma), accompanied by the sharp intensifications of Asian Monsoon, and began to diversify at 2.34 Ma, following the intense uplift of the Hengduan Mountains. Ancestral character reconstruction showed that monangial sori and subsessile sporangia were clearly late derived states rather than early diverged states. Both the molecular phylogenetic and morphological analyses support the inclusion of Sinopteris in Aleuritopteris.
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Affiliation(s)
- Lei Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, Henan 471023, China
| | - Wenli Yang
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Danke Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Gangmin Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.
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Fujiwara T, Egashira T, Gutiérrez-Ortega JS, Hori K, Ebihara A, Watano Y. Establishment of an allotetraploid fern species, Lepisorus yamaokae Seriz., between two highly niche-differentiated parental species. AMERICAN JOURNAL OF BOTANY 2022; 109:1456-1471. [PMID: 35938973 DOI: 10.1002/ajb2.16043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The successful establishment of polyploid species is hypothesized to be promoted by niche differentiation from the parental species or by range shifts during climate oscillations. However, few studies have considered both of these factors simultaneously. We resolved the origin of a tetraploid fern, Lepisorus yamaokae, and explored a pattern of niche differentiation among the allotetraploid and parental species in past and current climates. METHODS We reconstructed phylogenetic trees based on plastid marker and single-copy nuclear genes to resolve the allopolyploid origin of L. yamaokae. We also evaluated climatic niche differentiation among L. yamaokae and its two parental species using species distribution models in geographic space and principal component analysis. RESULTS We infer that L. yamaokae had a single allotetraploid origin from L. annuifrons and L. uchiyamae. Climatic niche analyses show that the parental species currently occupy different niche spaces. The predicted distribution of the parental species at the Last Glacial Maximum (LGM) suggests more opportunities for hybridization during the LGM or during other recent temporary range shifts. Lepisorus yamaokae has a narrower niche than the additive niche of the parental species. We also observed niche conservatism in L. yamaokae. CONCLUSIONS Range shifts of the parental species during climatic oscillations in the Quaternary likely facilitated the formation and establishment of L. yamaokae. Further, the genetic intermediacy of L. yamaokae may have enabled a niche shift in its microenvironment, resulting in its successful establishment without a macroclimatic niche shift in L. yamaokae.
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Affiliation(s)
- Tao Fujiwara
- Makino Herbarium, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo, 192-0397, Japan
| | - Tsubasa Egashira
- Department of Biology, Faculty of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | | | - Kiyotaka Hori
- The Kochi Prefectural Makino Botanical Garden, 4200-6 Godaisan, Kochi, 781-8125, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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Chao YS, Ebihara A, Chiou WL, Tsai JM, Huang YW, Ranker TA. Reticulate evolution in the Pteris fauriei group (Pteridaceae). Sci Rep 2022; 12:9145. [PMID: 35650209 PMCID: PMC9159987 DOI: 10.1038/s41598-022-11390-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
The Pteris fauriei group (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of the P. fauriei group and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a complicated reticulate evolution, consisting of seven parental taxa and 58 hybrids. The large number of hybrid taxa have added significant morphological complexity to the group leading to difficult taxonomic issues. The hybrids generally had broader ranges and more populations than their parental taxa. Genetic combination of different pairs of parental species created divergent phenotypes of hybrids, exhibited by both morphological characteristics and ecological fidelities. Niche novelty could facilitate hybrid speciation. Apogamy is common in this group and potentially contributes to the sustainability of the whole group. We propose that frequent hybridizations among members of the P. fauriei group generate and maintain genetic diversity, via novel genetic combinations, niche differentiation, and apogamy.
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Affiliation(s)
- Yi-Shan Chao
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan.
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba-shi, Ibaraki, 305-0005, Japan
| | - Wen-Liang Chiou
- Taiwan Forestry Research Institute, 53 Nan-Hai Rd., Taipei, 100051, Taiwan
| | - Jer-Min Tsai
- Department of Information and Communication, Kun Shan University, 195, Kunda Rd., Tainan, 710303, Taiwan
| | - Yu-Wen Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan
| | - Tom A Ranker
- University of Hawai'i at Mānoa, School of Life Sciences, Honolulu, HI, 96822, USA
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Wafula EK, Zhang H, Von Kuster G, Leebens-Mack JH, Honaas LA, dePamphilis CW. PlantTribes2: Tools for comparative gene family analysis in plant genomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1011199. [PMID: 36798801 PMCID: PMC9928214 DOI: 10.3389/fpls.2022.1011199] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/02/2022] [Indexed: 05/12/2023]
Abstract
Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range of genome assembly and annotation qualities across plant genomes due to their varying sizes, complexity, and the technology used for the assembly and annotation. To effectively work across genomes, researchers increasingly rely on comparative genomic approaches that integrate across plant community resources and data types. Such efforts have aided the genome annotation process and yielded novel insights into the evolutionary history of genomes and gene families, including complex non-model organisms. The essential tools to achieve these insights rely on gene family analysis at a genome-scale, but they are not well integrated for rapid analysis of new data, and the learning curve can be steep. Here we present PlantTribes2, a scalable, easily accessible, highly customizable, and broadly applicable gene family analysis framework with multiple entry points including user provided data. It uses objective classifications of annotated protein sequences from existing, high-quality plant genomes for comparative and evolutionary studies. PlantTribes2 can improve transcript models and then sort them, either genome-scale annotations or individual gene coding sequences, into pre-computed orthologous gene family clusters with rich functional annotation information. Then, for gene families of interest, PlantTribes2 performs downstream analyses and customizable visualizations including, (1) multiple sequence alignment, (2) gene family phylogeny, (3) estimation of synonymous and non-synonymous substitution rates among homologous sequences, and (4) inference of large-scale duplication events. We give examples of PlantTribes2 applications in functional genomic studies of economically important plant families, namely transcriptomics in the weedy Orobanchaceae and a core orthogroup analysis (CROG) in Rosaceae. PlantTribes2 is freely available for use within the main public Galaxy instance and can be downloaded from GitHub or Bioconda. Importantly, PlantTribes2 can be readily adapted for use with genomic and transcriptomic data from any kind of organism.
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Affiliation(s)
- Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Huiting Zhang
- Tree Fruit Research Laboratory, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Gregory Von Kuster
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | | | - Loren A Honaas
- Tree Fruit Research Laboratory, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Wenatchee, WA, United States
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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Nieves KG, van Ee BW. DNA Barcoding of Adiantum (Pteridaceae: Vittarioideae) in Puerto Rico. CARIBB J SCI 2021. [DOI: 10.18475/cjos.v51i2.a13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Benjamin W. van Ee
- Department of Biology, University of Puerto Rico, Mayagüez, Mayagüez, Puerto Rico
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Mossion V, Dauphin B, Grant J, Kessler M, Zemp N, Croll D. Transcriptome-wide SNPs for Botrychium lunaria ferns enable fine-grained analysis of ploidy and population structure. Mol Ecol Resour 2021; 22:254-271. [PMID: 34310066 PMCID: PMC9291227 DOI: 10.1111/1755-0998.13478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/02/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within‐species studies based on high‐resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0–23.7 Gb. We assembled 25,677 high‐quality transcripts with an average length of 1,333 bp based on deep RNA‐sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome‐wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High‐quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.
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Affiliation(s)
- Vinciane Mossion
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | - Benjamin Dauphin
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland.,Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Jason Grant
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zurich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
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8
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Modern Approaches for Transcriptome Analyses in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:11-50. [DOI: 10.1007/978-3-030-80352-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kao TT, Rothfels CJ, Melgoza-Castillo A, Pryer KM, Windham MD. Infraspecific diversification of the star cloak fern (Notholaena standleyi) in the deserts of the United States and Mexico. AMERICAN JOURNAL OF BOTANY 2020; 107:658-675. [PMID: 32253761 DOI: 10.1002/ajb2.1461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/04/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Not all ferns grow in moist and shaded habitats. One well-known example is Notholaena standleyi, a species that thrives in deserts of the southwestern United States and Mexico. This species exhibits several "chemotypes" that differ in farina (flavonoid exudates) color and chemistry. By integrating data from molecular phylogenetics, cytology, biochemistry, and biogeography, we circumscribed the major evolutionary lineages within N. standleyi and reconstructed their diversification histories. METHODS Forty-eight samples were selected from across the geographic distribution of N. standleyi. Phylogenetic relationships were inferred using four plastid and five nuclear markers. Ploidy levels were inferred using spore sizes calibrated by chromosome counts, and farina chemistry was compared using thin-layer chromatography. RESULTS Four clades are recognized, three of which roughly correspond to previously recognized chemotypes. The diploid clades G and Y are found in the Sonoran and Chihuahuan deserts, respectively; they are estimated to have diverged in the Pleistocene, congruent with the postulated timing of climatological events separating these two deserts. Clade P/YG is tetraploid and partially overlaps the distribution of clade Y in the eastern Chihuahuan Desert. It is apparently confined to limestone, a geologic substrate rarely occupied by members of the other clades. The cryptic (C) clade, a diploid group known only from southern Mexico and highly disjunct from the other three clades, is newly recognized here. CONCLUSIONS Our results reveal a complex intraspecific diversification history of N. standleyi, traceable to a variety of evolutionary drivers including classic allopatry, parapatry with or without changes in geologic substrate, and sympatric divergence through polyploidization.
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Affiliation(s)
- Tzu-Tong Kao
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Alicia Melgoza-Castillo
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua, Chihuahua CP, 31000, Mexico
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
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Granados Mendoza C, Jost M, Hágsater E, Magallón S, van den Berg C, Lemmon EM, Lemmon AR, Salazar GA, Wanke S. Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum. FRONTIERS IN PLANT SCIENCE 2020; 10:1761. [PMID: 32063915 PMCID: PMC7000662 DOI: 10.3389/fpls.2019.01761] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/16/2019] [Indexed: 05/12/2023]
Abstract
Universal angiosperm enrichment probe sets designed to enrich hundreds of putatively orthologous nuclear single-copy loci are increasingly being applied to infer phylogenetic relationships of different lineages of angiosperms at a range of evolutionary depths. Studies applying such probe sets have focused on testing the universality and performance of the target nuclear loci, but they have not taken advantage of off-target data from other genome compartments generated alongside the nuclear loci. Here we do so to infer phylogenetic relationships in the orchid genus Epidendrum and closely related genera of subtribe Laeliinae. Our aims are to: 1) test the technical viability of applying the plant anchored hybrid enrichment (AHE) method (Angiosperm v.1 probe kit) to our focal group, 2) mine plastid protein coding genes from off-target reads; and 3) evaluate the performance of the target nuclear and off-target plastid loci in resolving and supporting phylogenetic relationships along a range of taxonomical depths. Phylogenetic relationships were inferred from the nuclear data set through coalescent summary and site-based methods, whereas plastid loci were analyzed in a concatenated partitioned matrix under maximum likelihood. The usefulness of target and flanking non-target nuclear regions and plastid loci was assessed through the estimation of their phylogenetic informativeness. Our study successfully applied the plant AHE probe kit to Epidendrum, supporting the universality of this kit in angiosperms. Moreover, it demonstrated the feasibility of mining plastome loci from off-target reads generated with the Angiosperm v.1 probe kit to obtain additional, uniparentally inherited sequence data at no extra sequencing cost. Our analyses detected some strongly supported incongruences between nuclear and plastid data sets at shallow divergences, an indication of potential lineage sorting, hybridization, or introgression events in the group. Lastly, we found that the per site phylogenetic informativeness of the ycf1 plastid gene surpasses that of all other plastid genes and several nuclear loci, making it an excellent candidate for assessing phylogenetic relationships at medium to low taxonomic levels in orchids.
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Affiliation(s)
- Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Eric Hágsater
- Herbario AMO, Instituto Chinoin, A.C., Mexico City, Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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Wolf PG, Rowe CA, Kinosian SP, Der JP, Lockhart PJ, Shepherd LD, McLenachan PA, Thomson JA. Worldwide relationships in the fern genus Pteridium (bracken) based on nuclear genome markers. AMERICAN JOURNAL OF BOTANY 2019; 106:1365-1376. [PMID: 31545874 PMCID: PMC6856829 DOI: 10.1002/ajb2.1365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Spore-bearing plants are capable of dispersing very long distances. However, it is not known if gene flow can prevent genetic divergence in widely distributed taxa. Here we address this issue, and examine systematic relationships at a global geographic scale for the fern genus Pteridium. METHODS We sampled plants from 100 localities worldwide, and generated nucleotide data from four nuclear genes and two plastid regions. We also examined 2801 single nucleotide polymorphisms detected by a restriction site-associated DNA approach. RESULTS We found evidence for two distinct diploid species and two allotetraploids between them. The "northern" species (Pteridium aquilinum) has distinct groups at the continental scale (Europe, Asia, Africa, and North America). The northern European subspecies pinetorum appears to involve admixture among all of these. A sample from the Hawaiian Islands contained elements of both North American and Asian P. aquilinum. The "southern" species, P. esculentum, shows little genetic differentiation between South American and Australian samples. Components of African genotypes are detected on all continents. CONCLUSIONS We find evidence of distinct continental-scale genetic differentiation in Pteridium. However, on top of this is a clear signal of recent hybridization. Thus, spore-bearing plants are clearly capable of extensive long-distance gene flow; yet appear to have differentiated genetically at the continental scale. Either gene flow in the past was at a reduced level, or vicariance is possible even in the face of long-distance gene flow.
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Affiliation(s)
- Paul G. Wolf
- Department of Biology and Ecology CenterUtah State UniversityLoganUtah84322USA
- Present address:
Department of Biological SciencesUniversity of Alabama in HuntsvilleHuntsvilleAlabama35899USA
| | - Carol A. Rowe
- Department of Biology and Ecology CenterUtah State UniversityLoganUtah84322USA
| | - Sylvia P. Kinosian
- Department of Biology and Ecology CenterUtah State UniversityLoganUtah84322USA
| | - Joshua P. Der
- Department of Biological ScienceCalifornia State UniversityFullertonCalifornia92831USA
| | - Peter J. Lockhart
- Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa TongarewaPO Box 467Wellington6140New Zealand
| | | | - John A. Thomson
- National Herbarium of New South WalesRoyal Botanic Gardens and Domain TrustMrs. Macquaries RoadSydneyNew South Wales2000Australia
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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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13
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Kao TT, Pryer KM, Freund FD, Windham MD, Rothfels CJ. Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae). Mol Phylogenet Evol 2019; 138:139-155. [DOI: 10.1016/j.ympev.2019.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/15/2019] [Accepted: 05/17/2019] [Indexed: 11/24/2022]
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Cardinal-McTeague WM, Wurdack KJ, Sigel EM, Gillespie LJ. Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species. BMC Evol Biol 2019; 19:29. [PMID: 30670006 PMCID: PMC6341577 DOI: 10.1186/s12862-018-1308-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/23/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BIOGEOBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model. RESULTS Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas. CONCLUSIONS The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.
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Affiliation(s)
- Warren M. Cardinal-McTeague
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Kenneth J. Wurdack
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Billeaud Hall, Room 108, 410 E. St. Mary Blvd, Lafayette, LA 70503 USA
| | - Lynn J. Gillespie
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
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Luo D, Li Y, Zhao Q, Zhao L, Ludwig A, Peng Z. Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers. Genes (Basel) 2019; 10:E38. [PMID: 30634684 PMCID: PMC6356338 DOI: 10.3390/genes10010038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/28/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called "living fossil" species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.
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Affiliation(s)
- Dehuai Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Lianpeng Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany.
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
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Fujiwara T, Serizawa S, Watano Y. Phylogenetic analysis reveals the origins of tetraploid and hexaploid species in the Japanese Lepisorus thunbergianus (Polypodiaceae) complex. JOURNAL OF PLANT RESEARCH 2018; 131:945-959. [PMID: 30167928 DOI: 10.1007/s10265-018-1061-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 07/30/2018] [Indexed: 05/27/2023]
Abstract
The Japanese Lepisorus thunbergianus complex contains diploid and tetraploid races of L. thunbergianus and a hexaploid species, L. mikawanus. Here, we performed molecular phylogenetic analysis on this complex to delimit species and to elucidate the evolutionary origins of tetraploid and hexaploid species. Chloroplast DNA (cpDNA) phylogeny supported the monophyly of the complex. Based on a single-copy nuclear gene (PgiC) tree, the tetraploid L. thunbergianus samples could be classified into two variants: an allotetraploid of hybrid origin between diploid L. thunbergianus and Japanese L. angustus and another allotetraploid of hybrid origin between diploid L. thunbergianus and an unknown diploid race of L. tosaensis. These variants can be recognized morphologically and distinguished from their parent species. Hence, here we described these allopolyploids as new species, L. nigripes and L. kuratae, respectively. The hexaploid species L. mikawanus has three types of PgiC alleles, each of which was derived from diploid L. thunbergianus, L. tosaensis, and Japanese L. angustus, while cpDNA shows that it is included in Japanese L. thunbergianus clade. Based on the cpDNA phylogeny and PgiC nucleotide sequences, we therefore concluded that L. mikawanus is an allohexaploid that originated through hybridization between tetraploid species, L. nigripes and an unknown ancestral diploid race of L. tosaensis.
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Affiliation(s)
- Tao Fujiwara
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan.
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
| | - Shunsuke Serizawa
- Aichi Green Association, Urahata 198-1, Nagamaki, Oharu-sho, Aichi, 490-1131, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
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17
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Wolf PG, Robison TA, Johnson MG, Sundue MA, Testo WL, Rothfels CJ. Target sequence capture of nuclear-encoded genes for phylogenetic analysis in ferns. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01148. [PMID: 30131890 PMCID: PMC5991577 DOI: 10.1002/aps3.1148] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/04/2018] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one documented case. However, it not yet clear what effect such hybridization has on fern evolution, in part due to a paucity of available biparentally inherited (nuclear-encoded) markers. METHODS We designed oligonucleotide baits to capture 25 targeted, low-copy nuclear markers from a sample of 24 species spanning extant fern diversity. RESULTS Most loci were successfully sequenced from most accessions. Although the baits were designed from exon (transcript) data, we successfully captured intron sequences that should be useful for more focused phylogenetic studies. We present phylogenetic analyses of the new target sequence capture data and integrate these into a previous transcript-based data set. DISCUSSION We make our bait sequences available to the community as a resource for further studies of fern phylogeny.
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Affiliation(s)
- Paul G. Wolf
- Ecology Center and Department of BiologyUtah State UniversityLoganUtah84322USA
| | - Tanner A. Robison
- Ecology Center and Department of BiologyUtah State UniversityLoganUtah84322USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Michael A. Sundue
- Pringle HerbariumDepartment of Plant BiologyUniversity of VermontBurlingtonVermont05405USA
| | - Weston L. Testo
- Pringle HerbariumDepartment of Plant BiologyUniversity of VermontBurlingtonVermont05405USA
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative BiologyUniversity of CaliforniaBerkeleyCalifornia94720USA
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Schafran PW, Johnson G, Taylor WC, Zimmer EA, Musselman LJ. Low-copy nuclear markers in Isoëtes (Isoëtaceae) identified with transcriptomes. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1142. [PMID: 30131884 PMCID: PMC5947607 DOI: 10.1002/aps3.1142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/16/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Few genetic markers provide phylogenetic information in closely related species of Isoëtes (Isoëtaceae). We describe the development of primers for several putative low-copy nuclear markers to resolve the phylogeny of Isoëtes, particularly in the southeastern United States. METHODS AND RESULTS We identified regions of interest in Isoëtes transcriptomes based on low-copy genes in other plants. Primers were designed for these regions and tested with 16 taxa of Isoëtes and one species of Lycopodium. Parts of the pgiC, gapC, and IBR3 gene regions show phylogenetic signal within the North American and Mediterranean clades of Isoëtes. CONCLUSIONS Transcriptome data prove useful for identification and primer design of low-copy genes. Three new markers show potential for inferring phylogenies in regional clades of Isoëtes, and possibly across the entire genus.
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Affiliation(s)
- Peter W. Schafran
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20560USA
| | - Gabriel Johnson
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20560USA
| | - W. Carl Taylor
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20560USA
| | - Elizabeth A. Zimmer
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20560USA
| | - Lytton J. Musselman
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia23529USA
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Rapid allopolyploid radiation of moonwort ferns (Botrychium; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions. Mol Phylogenet Evol 2018; 120:342-353. [DOI: 10.1016/j.ympev.2017.11.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/12/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022]
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20
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Valderrama E, Richardson JE, Kidner CA, Madriñán S, Stone GN. Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae). Mol Phylogenet Evol 2018; 119:13-24. [DOI: 10.1016/j.ympev.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/17/2017] [Accepted: 10/03/2017] [Indexed: 11/25/2022]
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21
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Kuo LY, Tang TY, Li FW, Su HJ, Chiou WL, Huang YM, Wang CN. Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:486. [PMID: 29755486 PMCID: PMC5932399 DOI: 10.3389/fpls.2018.00486] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/29/2018] [Indexed: 05/19/2023]
Abstract
Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome (mitogenome) from only one fern genus. We developed a new and efficient method to examine plastome and mitogenome inheritance in a fern species-Deparia lancea (Athyriaceae, Aspleniineae, Polypodiales), and found that plastid and mitochondrial DNAs were transmitted from only the maternal parentage to a next generation. To further examine whether both organelle genomes have the same manner of inheritance in other Deparia ferns, we sequenced both plastid and mitochondrial DNA regions of inter-species hybrids, and performed phylogenetic analyses to identify the origins of organellar DNA. Evidence from our experiments and phylogenetic analyses support that both organelle genomes in Deparia are uniparentally and maternally inherited. Most importantly, our study provides the first report of mitogenome inheritance in eupolypod ferns, and the second one among all ferns.
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Affiliation(s)
- Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- *Correspondence: Li-Yaung Kuo, Yao-Moan Huang, Chun-Neng Wang,
| | - Te-Yen Tang
- Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, Cornell University, Ithaca, NY, United States
| | - Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
| | - Wen-Liang Chiou
- Taiwan Forestry Research Institute, Taipei, Taiwan
- Dr. Cecilia Koo Botanic Conservation Center, Pingtung, Taiwan
| | - Yao-Moan Huang
- Taiwan Forestry Research Institute, Taipei, Taiwan
- *Correspondence: Li-Yaung Kuo, Yao-Moan Huang, Chun-Neng Wang,
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- *Correspondence: Li-Yaung Kuo, Yao-Moan Huang, Chun-Neng Wang,
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22
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Song M, Kuo LY, Huiet L, Pryer KM, Rothfels CJ, Li FW. A novel chloroplast gene reported for flagellate plants. AMERICAN JOURNAL OF BOTANY 2018. [PMID: 29532931 DOI: 10.1002/ajb2.1010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of ycf94, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern Adiantum shastense Huiet & A.R. Sm. KEY RESULTS The ycf94 predicted protein has a distinct transmembrane domain but with no sequence homology to other proteins with known function. The nonsynonymous/synonymous substitution rate ratio of ycf94 is on par with other fern plastid protein-encoding genes, and additional homologs can be found in a few lycophyte, moss, hornwort, and liverwort plastid genomes. Homologs of ycf94 were not found in seed plants. In addition, we report a high level of RNA editing for ycf94 transcripts-a hallmark of protein-coding genes in fern plastomes. CONCLUSIONS The degree of sequence conservation, together with the presence of a distinct transmembrane domain and RNA-editing sites, suggests that ycf94 is a protein-coding gene of functional significance in ferns and, potentially, bryophytes and lycophytes. However, the origin and exact function of this gene require further investigation.
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Affiliation(s)
- Michael Song
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Li-Yaung Kuo
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Section of Plant Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Section of Plant Biology, Cornell University, Ithaca, New York, 14853, USA
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A global phylogeny of the fern genus Tectaria (Tectariaceae: Polypodiales) based on plastid and nuclear markers identifies major evolutionary lineages and suggests repeated evolution of free venation from anastomosing venation. Mol Phylogenet Evol 2017; 114:295-333. [DOI: 10.1016/j.ympev.2017.05.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/24/2017] [Accepted: 05/22/2017] [Indexed: 11/17/2022]
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Insights into evolution in Andean Polystichum (Dryopteridaceae) from expanded understanding of the cytosolic phosphoglucose isomerase gene. Mol Phylogenet Evol 2017; 112:36-46. [PMID: 28411162 DOI: 10.1016/j.ympev.2017.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 03/08/2017] [Accepted: 04/10/2017] [Indexed: 12/19/2022]
Abstract
Cytosolic phosphoglucose isomerase (pgiC) is an enzyme essential to glycolysis found universally in eukaryotes, but broad understanding of variation in the gene coding for pgiC is lacking for ferns. We used a substantially expanded representation of the gene for Andean species of the fern genus Polystichum to characterize pgiC in ferns relative to angiosperms, insects, and an amoebozoan; assess the impact of selection versus neutral evolutionary processes on pgiC; and explore evolutionary relationships of selected Andean species. The dataset of complete sequences comprised nine accessions representing seven species and one hybrid from the Andes and Serra do Mar. The aligned sequences of the full data set comprised 3376 base pairs (70% of the entire gene) including 17 exons and 15 introns from two central areas of the gene. The exons are highly conserved relative to angiosperms and retain substantial homology to insect pgiC, but intron length and structure are unique to the ferns. Average intron size is similar to angiosperms; intron number and location in insects are unlike those of the plants we considered. The introns included an array of indels and, in intron 7, an extensive microsatellite array with potential utility in analyzing population-level histories. Bayesian and maximum-parsimony analysis of 129 variable nucleotides in the Andean polystichums revealed that 59 (1.7% of the 3376 total) were phylogenetically informative; most of these united sister accessions. The phylogenetic trees for the Andean polystichums were incongruent with previously published cpDNA trees for the same taxa, likely the result of rapid evolutionary change in the introns and contrasting stability in the exons. The exons code a total of seven amino-acid substitutions. Comparison of non-synonymous to synonymous substitutions did not suggest that the pgiC gene is under selection in the Andes. Variation in pgiC including two additional accessions represented by incomplete sequences provided new insights into reticulate relationships among Andean taxa.
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Rothfels CJ, Pryer KM, Li FW. Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. THE NEW PHYTOLOGIST 2017; 213:413-429. [PMID: 27463214 DOI: 10.1111/nph.14111] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 05/27/2023]
Abstract
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
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Affiliation(s)
- Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Duke University, Durham, NC, 27705, USA
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Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae). PLoS One 2016; 11:e0160611. [PMID: 27603700 PMCID: PMC5014338 DOI: 10.1371/journal.pone.0160611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.
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Grusz AL, Rothfels CJ, Schuettpelz E. Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns. BMC Genomics 2016; 17:692. [PMID: 27577050 PMCID: PMC5006594 DOI: 10.1186/s12864-016-3034-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/22/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns-an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection. RESULTS We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution. CONCLUSIONS Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.
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Affiliation(s)
- Amanda L. Grusz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013-7012 USA
- Department of Biology, University of Minnesota Duluth, 1035 Kirby Drive, Duluth, MN 55812 USA
| | - Carl J. Rothfels
- Department of Integrative Biology, University of California Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720-2466 USA
| | - Eric Schuettpelz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013-7012 USA
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Teasdale LC, Köhler F, Murray KD, O'Hara T, Moussalli A. Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture. Mol Ecol Resour 2016; 16:1107-23. [DOI: 10.1111/1755-0998.12552] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/30/2016] [Accepted: 05/19/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Luisa C. Teasdale
- Sciences Department; Museum Victoria; 11 Nicholson Street Carlton Vic. 3053 Australia
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
| | - Frank Köhler
- Australian Museum; 6 College Street Sydney NSW 2010 Australia
| | - Kevin D. Murray
- Division of Plant Sciences; Research School of Biology; Australian National University; Canberra ACT 0200 Australia
| | - Tim O'Hara
- Sciences Department; Museum Victoria; 11 Nicholson Street Carlton Vic. 3053 Australia
| | - Adnan Moussalli
- Sciences Department; Museum Victoria; 11 Nicholson Street Carlton Vic. 3053 Australia
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Pinson JB, Schuettpelz E. Unraveling the origin of the Appalachian gametophyte, Vittaria appalachiana. AMERICAN JOURNAL OF BOTANY 2016; 103:668-676. [PMID: 27033317 DOI: 10.3732/ajb.1500522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/25/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF STUDY Ferns and lycophytes are distinct among plants in producing two free-living life stages: a long-lived sporophyte phase and a (usually) short-lived gametophyte phase. Notably, however, some species have perennial, vegetatively reproducing gametophytes. Vittaria appalachiana is one of just three species in which mature sporophytes are unknown. It has a wide range throughout the Appalachian Mountains and Plateau, where it reproduces asexually via gemmae. The origin of V. appalachiana, however, has long been a mystery, with most previous studies suggesting it may have resulted from hybridization of two closely related Vittaria species (V. graminifolia and V. lineata). METHODS A four-gene plastid data set including 32 samples of six Vittaria species, plus samples of five outgroup species, was analyzed to uncover phylogenetic relationships. Additional analyses of nuclear DET1 gene sequences allowed for the examination of hypotheses involving a hybrid origin for V. appalachiana. KEY RESULTS In the plastid phylogeny, V. appalachiana is well supported as monophyletic, but is embedded within V. graminifolia. With the exception of a single aberrant allele, this result is mirrored in the nuclear tree. CONCLUSIONS Through analyses of plastid and nuclear data sets, this study demonstrates that a hybrid origin for V. appalachiana is unlikely. Instead, it appears that this species emerged from within the V. graminifolia lineage. Further work is needed to fully elucidate the genetic structure within this group.
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Affiliation(s)
- Jerald B Pinson
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525 USA
| | - Eric Schuettpelz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012 Washington, District of Columbia 20013-7012 USA
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30
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Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae). Mol Ecol Resour 2015; 16:1124-35. [DOI: 10.1111/1755-0998.12487] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/06/2015] [Accepted: 11/05/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Roswitha Schmickl
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
| | - Aaron Liston
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Vojtěch Zeisek
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
| | - Kenneth Oberlander
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Kevin Weitemier
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Shannon C. K. Straub
- Department of Biology; Hobart and William Smith Colleges; 213 Eaton Hall Geneva NY 14456 USA
| | - Richard C. Cronn
- USDA Forest Service; Pacific Northwest Research Station; 3200 SW Jefferson Way Corvallis OR 97331 USA
| | - Léanne L. Dreyer
- Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Jan Suda
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
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Zhang N, Wen J, Zimmer EA. Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming. PLoS One 2015; 10:e0144701. [PMID: 26656830 PMCID: PMC4682771 DOI: 10.1371/journal.pone.0144701] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/22/2015] [Indexed: 11/19/2022] Open
Abstract
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study,next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina NextSeq 500 instrument [corrected]. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
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Affiliation(s)
- Ning Zhang
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013–7012, United States of America
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013–7012, United States of America
- * E-mail: (JW); (EAZ)
| | - Elizabeth A. Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013–7012, United States of America
- * E-mail: (JW); (EAZ)
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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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Granados Mendoza C, Naumann J, Samain MS, Goetghebeur P, De Smet Y, Wanke S. A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea. BMC Evol Biol 2015; 15:132. [PMID: 26141718 PMCID: PMC4491267 DOI: 10.1186/s12862-015-0416-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/09/2015] [Indexed: 12/21/2022] Open
Abstract
Background Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other “fast” evolving plastid markers. Results Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae). Conclusions While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0416-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carolina Granados Mendoza
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. .,Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510, Coyoacán, Distrito Federal, Mexico.
| | - Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany.
| | - Marie-Stéphanie Samain
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. .,Instituto de Ecología, A.C., Centro Regional del Bajío, Avenida Lázaro Cárdenas 253, 61600, Pátzcuaro, Michoacán, Mexico.
| | - Paul Goetghebeur
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Yannick De Smet
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany.
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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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Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1400115. [PMID: 25909041 PMCID: PMC4406834 DOI: 10.3732/apps.1400115] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/25/2015] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. METHODS AND RESULTS We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. CONCLUSIONS MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.
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Affiliation(s)
- Srikar Chamala
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Author for correspondence:
| | - Nicolás García
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Grant T. Godden
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Rancho Santa Ana Botanic Garden, Claremont, California, USA
| | | | - Ingrid E. Jordon-Thaden
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
- Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA
| | - Riet De Smet
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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Rothfels CJ, Johnson AK, Hovenkamp PH, Swofford DL, Roskam HC, Fraser-Jenkins CR, Windham MD, Pryer KM. Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago. Am Nat 2015; 185:433-42. [DOI: 10.1086/679662] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
SUMMARY AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. AVAILABILITY AND IMPLEMENTATION AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub (www.github.com/AliView). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview CONTACT anders.larsson@ebc.uu.se SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236, Sweden
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38
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Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J, Burge DO, Pokorny L, Larsson A, Chen T, Weststrand S, Thomas P, Carpenter E, Zhang Y, Tian Z, Chen L, Yan Z, Zhu Y, Sun X, Wang J, Stevenson DW, Crandall-Stotler BJ, Shaw AJ, Deyholos MK, Soltis DE, Graham SW, Windham MD, Langdale JA, Wong GKS, Mathews S, Pryer KM. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A 2014; 111:6672-7. [PMID: 24733898 PMCID: PMC4020063 DOI: 10.1073/pnas.1319929111] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
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Affiliation(s)
- Fay-Wei Li
- Department of Biology, Duke University, Durham, NC 27708
| | - Juan Carlos Villarreal
- Systematic Botany and Mycology, Department of Biology, University of Munich, 80638 Munich, Germany
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Carl J. Rothfels
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Michael Melkonian
- Botany Department, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany
| | | | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland
| | - Erin M. Sigel
- Department of Biology, Duke University, Durham, NC 27708
| | - Joshua P. Der
- Department of Biology and
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Jarmila Pittermann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | | | | | - Anders Larsson
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Tao Chen
- Fairy Lake Botanical Garden, Shenzhen, Guangdong 518004, China
| | - Stina Weststrand
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Philip Thomas
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | | | | | - Li Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Ying Zhu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | | | - Michael K. Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Douglas E. Soltis
- Florida Museum of Natural History
- Department of Biology, and
- Genetics Institute, University of Florida, Gainesville, FL 32611
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | | | - Jane A. Langdale
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1; and
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Rothfels CJ, Schuettpelz E. Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Driven by Selection. Syst Biol 2013; 63:31-54. [DOI: 10.1093/sysbio/syt058] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
| | - Eric Schuettpelz
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; 2Department of Zoology, University of British Columbia, #4200-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; 3Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403, USA; and 4Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA
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