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Chao YS, Yang YW, Sheue CR, Lai IL. Niche and phenotypic differentiation in fern hybrid speciation, a case study of Pteris fauriei (Pteridaceae). ANNALS OF BOTANY 2024; 134:71-84. [PMID: 38470192 DOI: 10.1093/aob/mcae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/11/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND AND AIMS Niche differentiation is a crucial issue in speciation. Although it has a well-known role in adaptive processes of hybrid angiosperms, it is less understood in hybrid ferns. Here, we investigate whether an intermediate ecological niche of a fern hybrid is a novel adaptation that provides insights into fern hybrid speciation. METHODS Pteris fauriei (Pteridaceae) is a natural hybrid fern, occurring in environments between its parent species. The maternal Pteris minor is found in sunny areas, but the habitat of the paternal Pteris latipinna is shady. We combined data from morphology, leaf anatomy and photosynthetic traits to explore adaptation and differentiation, along with measuring the environmental features of their niches. We also performed experiments in a common garden to understand ecological plasticity. KEY RESULTS The hybrid P. fauriei was intermediate between the parent species in stomatal density, leaf anatomical features and photosynthetic characteristics in both natural habitats and a common garden. Interestingly, the maternal P. minor showed significant environmental plasticity and was more similar to the hybrid P. fauriei in the common garden, suggesting that the maternal species experiences stress in its natural habitats but thrives in environments similar to those of the hybrid. CONCLUSIONS Based on the similar niche preferences of the hybrid and parents, we propose hybrid superiority. Our results indicate that the hybrid P. fauriei exhibits greater fitness and can compete with and occupy the initial niches of the maternal P. minor. Consequently, we suggest that the maternal P. minor has experienced a niche shift, elucidating the pattern of niche differentiation in this hybrid group. These findings offer a potential explanation for the frequent occurrence of hybridization in ferns and provide new insights into fern hybrid speciation, enhancing our understanding of fern diversity.
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Affiliation(s)
- Yi-Shan Chao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Yao-Wei Yang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chiou-Rong Sheue
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Global Change Biology Research Center, National Chung Hsing University, Taichung, Taiwan
| | - I-Ling Lai
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Moore‐Pollard ER, Jones DS, Mandel JR. Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11568. [PMID: 38369976 PMCID: PMC10873820 DOI: 10.1002/aps3.11568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/30/2023] [Accepted: 11/12/2023] [Indexed: 02/20/2024]
Abstract
Premise A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. Methods We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 Packera taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support. Results We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061. Discussion Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.
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Affiliation(s)
- Erika R. Moore‐Pollard
- Department of Biological SciencesUniversity of Memphis3700 Walker Ave.MemphisTennessee38152USA
| | - Daniel S. Jones
- Department of Biological SciencesAuburn University101 Rouse Life SciencesAuburnAlabama36849USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of Memphis3700 Walker Ave.MemphisTennessee38152USA
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Ptáček J, Ekrt L, Hornych O, Urfus T. Interploidy gene flow via a 'pentaploid bridge' and ploidy reduction in Cystopteris fragilis fern complex (Cystopteridaceae: Polypodiales). PLANT REPRODUCTION 2023; 36:321-331. [PMID: 37532893 DOI: 10.1007/s00497-023-00476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
KEY MESSAGE Our results indicate the existence of interploidy gene flow in Cystopteris fragilis, resulting in sexual triploid and diploid gametophytes from pentaploid parents. Similar evolutionary dynamics might operate in other fern complexes and need further investigation. Polyploidization and hybridization are a key evolutionary processes in ferns. Here, we outline an interploidy gene flow pathway operating in the polyploid Cystopteris fragilis complex. The conditions necessary for the existence of this pathway were tested. A total of 365 C. fragilis individuals were collected covering representatives of all three predominant ploidy levels (tetraploid, pentaploid, and hexaploid), cultivated, had their ploidy level estimated by flow cytometry, and their spores collected. The spores, as well as gametophytes and sporophytes established from them, were analysed by flow cytometry. Spore abortion rate was also estimated. In tetraploids, we observed the formation of unreduced (tetraploid) spores (ca 2%). Collected pentaploid individuals indicate ongoing hybridization between ploidy levels. Pentaploids formed up to 52% viable spores, ca 79% of them reduced, i.e. diploid and triploid. Reduced spores formed viable gametophytes, and, in the case of triploids, filial hexaploid sporophytes, showing evidence of sexual reproduction. Some tetraploid sporophytes reproduce apomictically (based on uniform ploidy of their metagenesis up to filial sporophytes). Triploid and diploid gametophytes from pentaploid parents are able to mate among themselves, or with "normal" reduced gametophytes from the sexual tetraploid sporophytes (the dominant ploidy level in the sporophytes in this populations), to produce tetraploid, pentaploid, and hexaploid sporophytes, allowing for geneflow from the pentaploids to both the tetraploid and hexaploid populations. Similar evolutionary dynamics might operate in other fern complexes and need further investigation.
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Affiliation(s)
- Jan Ptáček
- Department of Botany, Faculty of Science, Charles University, Benátská 2, , 128 00, Praha, Czech Republic
| | - Libor Ekrt
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Ondřej Hornych
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Benátská 2, , 128 00, Praha, Czech Republic.
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Rutherford S, Rossetto M, Bragg JG, Wan JSH. Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex. AMERICAN JOURNAL OF BOTANY 2023; 110:e16245. [PMID: 37747108 DOI: 10.1002/ajb2.16245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
PREMISE Species delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups, species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take into account complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar "species" within the eucalypts. METHODS Multiple populations of each recognized scribbly gum species were sampled over a wide region across climates, and genomewide scans were used to resolve species boundaries. RESULTS None of the taxa were completely divergent, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time, blurring species boundaries. CONCLUSIONS Our results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that high-throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and be used as a standard practice for disentangling species complexes.
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Affiliation(s)
- Susan Rutherford
- Department of Environmental Science, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Department of Environmental and Sustainability Sciences, The Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, NJ, USA
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Justin S H Wan
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
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Kim HT, Park SH, Kim JS. Dynamic hybridization between two spleenworts, Asplenium incisum and Asplenium ruprechtii in Korea. FRONTIERS IN PLANT SCIENCE 2023; 14:1116040. [PMID: 37476173 PMCID: PMC10354290 DOI: 10.3389/fpls.2023.1116040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/31/2023] [Indexed: 07/22/2023]
Abstract
Natural hybridization between Asplenium incisum and A. ruprechtii has been observed in Northeast Asia and its allotetraploid species, A. castaneoviride, was reported. However, the hybridization process between the parental species and the origin of the allotetraploid taxon remains obscure. Additionally, the systematic affinities of the recently described hybrid A. bimixtum, considered to have originated from the hybridization of A. ruprechtii, A. trichomanes, and A. incisum, is unresolved owing to its similarity to A. castaneoviride. The goals of this study were to (1) investigate the hybridization between A. ruprechtii and A. incisum; (2) verify the origin of A. castaneoviride occurring in Korea, whether it independently arose from 2x sterile hybrids; and (3) elucidate the reliability of identifying A. bimixtum. Three genotypes, A. incisum, A. ruprechtii, and their hybrid, were identified based on the nuclear gene pgiC sequence and finally divided them into six types by ploidy levels: diploid A. incisum, A. ruprechtii, and four hybrid types (diploid A. × castaneoviride, triploid A. × castaneoviride, allotetraploid A. castaneoviride, and A. bimixtum). In the analyses of plastid DNA, all hybrids had an A. ruprechtii-type rbcL gene. In addition, the four plastomes of A. ruprechtii and the hybrids had high pairwise sequence identities greater than 98.48%. They increased up to 99.88% when a large deletion of A. x castaneoriviride (2x) collected from Buramsan populations was ignored. Notably, this large deletion was also found in triploid A. × castaneoviride and allotetraploid A. castaneoviride in the same populations. Sequence data of the nuclear and plastid genes showed that hybridization is unidirectional, and A. ruprechtii is the maternal parent. The large deletion of rpoC2-rps2 commonly found in the different ploidy hybrids of the Buramsan population suggests that the allotetraploid A. castaneoviride can be created independently from sterile hybrids. We assume that both polyploidization driving allopolyploidy and minority cytotype exclusion took place independently in the population, since A castaenoviride co-occurs with A. ruprechtii in small populations. Furthermore, it was also observed that an enlarged noncoding region in fern organelle (ENRIFO) of the plastome was found in the genus Asplenium.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Ecological and Environmental System, Kyungpook National University, Sangju, Republic of Korea
| | - Sang Hee Park
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jung Sung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
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Yi H, Dong S, Yang L, Wang J, Kidner C, Kang M. Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns. Mol Phylogenet Evol 2023; 184:107801. [PMID: 37088242 DOI: 10.1016/j.ympev.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.
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Affiliation(s)
- Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Shiying Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Catherine Kidner
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK; Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China.
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Freyman WA, Johnson MG, Rothfels CJ. homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
| | - Matthew G. Johnson
- Department of Biological Sciences Texas Tech University Lubbock Texas USA
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology University of California Berkeley California USA
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Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, Davis JI, Zomlefer WB, Stevenson DW, Graham SW, Givnish TJ, Leebens-Mack J, dePamphilis CW. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. FRONTIERS IN PLANT SCIENCE 2022; 13:876779. [PMID: 36483967 PMCID: PMC9723157 DOI: 10.3389/fpls.2022.876779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Eric K. Wafula
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Saravanaraj Ayyampalayam
- Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Joel R. McNeal
- Department of Ecology, Evolution, and Organismal Biology, Biology Kennesaw State University, Kennesaw, GA, United States
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Matthieu Villegente
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Department of Statistics, University of Wisconsin–Madison, Madison, WI, United States
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jerrold I. Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | | | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
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Testo WL, de Gasper AL, Molino S, Galán JMGY, Salino A, Dittrich VADO, Sessa EB. Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family. AMERICAN JOURNAL OF BOTANY 2022; 109:1579-1595. [PMID: 36063431 DOI: 10.1002/ajb2.16062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. METHODS We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. RESULTS Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. CONCLUSIONS Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.
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Affiliation(s)
- Weston L Testo
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76102, USA
- Department of Science and Education, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - André L de Gasper
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, Rua Antônio da Veiga, 140, Victor Konder, CEP 89030-903, Blumenau, SC, Brazil
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | - Sonia Molino
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - José María Gabriel Y Galán
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - Alexandre Salino
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | | | - Emily B Sessa
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
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Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. An open and continuously updated fern tree of life. FRONTIERS IN PLANT SCIENCE 2022; 13:909768. [PMID: 36092417 PMCID: PMC9449725 DOI: 10.3389/fpls.2022.909768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/12/2022] [Indexed: 05/31/2023]
Abstract
Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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11
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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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12
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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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13
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Suissa JS, Kinosian SP, Schafran PW, Bolin JF, Taylor WC, Zimmer EA. Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex. Mol Phylogenet Evol 2021; 166:107332. [PMID: 34687842 DOI: 10.1016/j.ympev.2021.107332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western North American Isoëtes, to understand the role of hybridization and high-level polyploidy in generating and maintaining novel diversity. To uncover these processes, we use restriction-site associated DNA sequencing (RADseq), multiple alleles of a single low-copy nuclear marker, whole plastomes, cytology (genome size estimates and chromosome counts), and reproductive status (fertile or sterile). With this dataset, we show that hybridization occurs easily between species in this complex and is bidirectional between identical, but not different, cytotypes. Furthermore, we show that fertile allopolyploids appear to have formed repeatedly from sterile homoploid and interploid hybrids. We propose that low prezygotic reproductive barriers and a high frequency of whole-genome duplication allow for high-level polyploid systems to generate novel lineages, and that these mechanisms may be important in shaping extant Isoëtes diversity.
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Affiliation(s)
- Jacob S Suissa
- The Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; The Arnold Arboretum of Harvard University, Boston, MA, USA; Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Sylvia P Kinosian
- Department of Biology & Ecology Center, Utah State University, Logan, UT, USA
| | - Peter W Schafran
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Boyce Thompson Institute, Ithaca, NY, USA
| | - Jay F Bolin
- Department of Biology, Catawba College, Salisbury, NC, USA
| | - W Carl Taylor
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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14
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Wang J, Dong S, Yang L, Harris A, Schneider H, Kang M. Allopolyploid Speciation Accompanied by Gene Flow in a Tree Fern. Mol Biol Evol 2021; 37:2487-2502. [PMID: 32302390 DOI: 10.1093/molbev/msaa097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid speciation as an evolutionary process in fern lineages remains poorly understood. Here, we employ flow cytometry, phylogeny, genomewide single nucleotide polymorphism data sets, and admixture and coalescent modeling to show that the scaly tree fern, Gymnosphaera metteniana is a naturally occurring allotetraploid species derived from hybridization between the diploids, G. denticulata and G. gigantea. Moreover, we detected ongoing gene flow between the hybrid species and its progenitors, and we found that G. gigantea and G. metteniana inhabit distinct niches, whereas climatic niches of G. denticulata and G. metteniana largely overlap. Taken together, these results suggest that either some degree of intrinsic genetic isolation between the hybrid species and its parental progenitors or ecological isolation over short distances may be playing an important role in the evolution of reproductive barriers. Historical climate change may have facilitated the origin of G. metteniana, with the timing of hybridization coinciding with a period of intensification of the East Asian monsoon during the Pliocene and Pleistocene periods in southern China. Our study of allotetraploid G. metteniana represents the first genomic-level documentation of hybrid speciation in scaly tree ferns and, thus, provides a new perspective on evolution in the lineage.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Shiyong Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Aj Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Department of Biology, Oberlin College, Oberlin, OH
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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15
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Cruz-Nicolás J, Villarruel-Arroyo A, Gernandt DS, Fonseca RM, Aguirre-Planter E, Eguiarte LE, Jaramillo-Correa JP. Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics. Mol Phylogenet Evol 2021; 160:107125. [PMID: 33636326 DOI: 10.1016/j.ympev.2021.107125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022]
Abstract
Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80 K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of πa/πs and Ka/Ks with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.
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Affiliation(s)
- Jorge Cruz-Nicolás
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Alfredo Villarruel-Arroyo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, AP 70-233, Mexico City CDMX 04510, Mexico
| | - Rosa María Fonseca
- Laboratorio de Plantas Vasculares, Facultad de Ciencias, Universidad Nacional Autónoma de México, AP 70-282, Mexico City CDMX 04510, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico.
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16
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Gorrer DA, Ramos Giacosa JP, Giudice GE. Palynological analysis of the genus Dryopteris Adans. (Dryopteridaceae) in Argentina. AN ACAD BRAS CIENC 2020; 92 Suppl 2:e20181052. [PMID: 32813768 DOI: 10.1590/0001-3765202020181052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/02/2019] [Indexed: 11/21/2022] Open
Abstract
The spore morphology and wall ultrastructure of Dryopteris filix-mas, D. patula and D. wallichiana from Argentina were studied using light microscope, scanning and transmission electron microscope. The study was carried out with herbarium material from Argentine institutions. Equatorial diameters, polar diameters and laesura length were measured. The spores are monoletes with a rugate ornamentation. The folds are short to long, inflate, irregular in shape and size, and varying from subglobose to elongate. The perispore surface is rugulate. The exospore of all the species analyzed is two-layered in section. Simple and branched channels are also present. The perispore is composed of two layers, the inner one forms the ornamentation and the outer covers all the outer and inner surfaces. Some abnormalities, such as globose, triangular or twisted spores were observed. The morphology and ultrastructure of the species are very similar. The differences observed are related to the length and thickness of the perispore folds. The characteristics of these spores would not provide relevant information to differentiate species or sections within the genus, but can provide information for phylogenetic studies as well as for alterations in the biological cycles.
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Affiliation(s)
- Daniel A Gorrer
- Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, CABA, Argentina
| | - Juan P Ramos Giacosa
- Consejo Nacional de Investigaciones Científicas y Técnicas/CONICET, CABA, Argentina
| | - Gabriela E Giudice
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
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17
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Slager DL, Epperly KL, Ha RR, Rohwer S, Wood C, Van Hemert C, Klicka J. Cryptic and extensive hybridization between ancient lineages of American crows. Mol Ecol 2020; 29:956-969. [PMID: 32034818 DOI: 10.1111/mec.15377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/30/2019] [Accepted: 02/05/2020] [Indexed: 01/02/2023]
Abstract
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.
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Affiliation(s)
- David L Slager
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Kevin L Epperly
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Renee R Ha
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Sievert Rohwer
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Chris Wood
- Burke Museum of Natural History and Culture, Seattle, WA, USA
| | | | - John Klicka
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
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18
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Hornych O, Ekrt L, Riedel F, Koutecký P, Košnar J. Asymmetric hybridization in Central European populations of the Dryopteris carthusiana group. AMERICAN JOURNAL OF BOTANY 2019; 106:1477-1486. [PMID: 31634425 DOI: 10.1002/ajb2.1369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Hybridization is a key process in plant speciation. Despite its importance, there is no detailed study of hybridization rates in fern populations. A proper estimate of hybridization rates is needed to understand factors regulating hybridization. METHODS We studied hybridization in the European Dryopteris carthusiana group, represented by one diploid and two tetraploid species and their hybrids. We sampled ~100 individuals per population in 40 mixed populations of the D. carthusiana group across Europe. All plants were identified by measuring genome size (DAPI staining) using flow cytometry. To determine the maternal parentage of hybrids, we sequenced the chloroplast region trnL-trnF of all taxa involved. RESULTS We found hybrids in 85% of populations. Triploid D. ×ambroseae occurred in every population that included both parent species and is most abundant when the parent species are equally abundant. By contrast, tetraploid D. ×deweveri was rare (15 individuals total) and triploid D. ×sarvelae was absent. The parentage of hybrid taxa is asymmetric. Despite expectations from previous studies, tetraploid D. dilatata is the predominant male parent of its triploid hybrid. CONCLUSIONS This is a thorough investigation of hybridization rates in natural populations of ferns. Hybridization rates differ greatly even among closely related fern taxa. In contrast to angiosperms, our data suggest that hybridization rates are highest in balanced parent populations and support the notion that some ferns possess very weak barriers to hybridization. Our results from sequencing cpDNA challenge established notions about the correlation of ploidy level and mating tendencies.
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Affiliation(s)
- Ondřej Hornych
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Libor Ekrt
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Felix Riedel
- Botanischer Garten der Universität Potsdam, Maulbeerallee 3, Potsdam, D-14469, Germany
- Arboretum der Humboldt-Universität zu Berlin, Späthstrasse 80/81, Berlin, D-12437, Germany
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Jiří Košnar
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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19
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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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20
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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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21
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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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Krinitsina AA, Belenikin MS, Churikova OA, Kuptsov3 SV, Antipin MI, Logacheva MD, Speranskaya AS. The systematic position of Dryopteris blanfordii subsp. nigrosquamosa (Ching) Fraser-Jenkins within the genus Dryopteris Adans. PHYTOKEYS 2017; 90:89-112. [PMID: 29391852 PMCID: PMC5784233 DOI: 10.3897/phytokeys.90.14745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Dryopteris blanfordii (C.Hope) C.Chr. is a member of the Dryopteridaceae, growing in high altitude Picea or Abies forests (2900-3500 m) in China and India. Phylogenetic relationships between D. blanfordii subsp. nigrosquamosa and closely related species of Dryopteris were investigated using a combined analysis of multiple molecular data sets (the protein-coding region of rbcL and matK genes and intergenic spacers psbA-trnH, trnP-petG, rps4-trnS, trnL-trnF and rbcL-accD). An assumption about the position of D. blanfordii subsp. nigrosquamosa within Dryopteris was made by using the Maximum Likelihood and Bayesian Inference approach and chloroplast marker sequences of Dryopteris species from GenBank. The results demonstrated that Asian taxa D. blanfordii subsp. nigrosquamosa and D. laeta as well as two American species D. arguta and D. marginalis belong to the same clade, all four of them being part of Dryopteris section Dryopteris.
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Affiliation(s)
- Anastasiya A. Krinitsina
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Maxim S. Belenikin
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141700
| | - Olga A. Churikova
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Sergey V. Kuptsov3
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Maxim I. Antipin
- Botanical Garden, Lomonosov Moscow State University, Leninskie gory, Moscow, Russia, 119899
| | - Maria D. Logacheva
- Department of Evolutional Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, 1, 40, Moscow, Russia, 119992
| | - Anna S. Speranskaya
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
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Vargas OM, Ortiz EM, Simpson BB. Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium). THE NEW PHYTOLOGIST 2017; 214:1736-1750. [PMID: 28333396 DOI: 10.1111/nph.14530] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 02/19/2017] [Indexed: 05/21/2023]
Abstract
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
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Affiliation(s)
- Oscar M Vargas
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University Ave, Ann Arbor, MI, 48109, USA
| | - Edgardo M Ortiz
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Beryl B Simpson
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
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A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals. Mol Phylogenet Evol 2016; 98:324-36. [DOI: 10.1016/j.ympev.2016.02.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/15/2016] [Accepted: 02/20/2016] [Indexed: 11/18/2022]
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25
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Guo YY, Luo YB, Liu ZJ, Wang XQ. Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in South-East Asia. Mol Ecol 2015; 24:2838-55. [PMID: 25847454 DOI: 10.1111/mec.13189] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 03/29/2015] [Accepted: 03/31/2015] [Indexed: 01/19/2023]
Abstract
South-East Asia covers four of the world's biodiversity hotspots, showing high species diversity and endemism. Owing to the successive expansion and contraction of distribution and the fragmentation by geographical barriers, the tropical flora greatly diversified in this region during the Tertiary, but the evolutionary tempo and mode of species diversity remain poorly investigated. Paphiopedilum, the largest genus of slipper orchids comprising nearly 100 species, is mainly distributed in South-East Asia, providing an ideal system for exploring how plant species diversity was shaped in this region. Here, we investigated the evolutionary history of this genus with eight cpDNA regions and four low-copy nuclear genes. Discordance between gene trees and network analysis indicates that reticulate evolution occurred in the genus. Ancestral area reconstruction suggests that vicariance and long-distance dispersal together led to its current distribution. Diversification rate variation was detected and strongly correlated with the species diversity in subg. Paphiopedilum (~80 species). The shift of speciation rate in subg. Paphiopedilum was coincident with sea-level fluctuations in the late Cenozoic, which could have provided ecological opportunities for speciation and created bridges or barriers for gene flow. Moreover, some other factors (e.g. sympatric distribution, incomplete reproductive barriers and clonal propagation) might also be advantageous for the formation and reproduction of hybrid species. In conclusion, our study suggests that the interplay of reticulate evolution and sea-level fluctuations has promoted the diversification of the genus Paphiopedilum and sheds light into the evolution of Orchidaceae and the historical processes of plant species diversification in South-East Asia.
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Affiliation(s)
- Yan-Yan Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China.,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, No. 889, Wangtong Road, Shenzhen, 518114, China.,Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, No. 889, Wangtong Road, Shenzhen, 518114, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China
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Hori K, Tono A, Fujimoto K, Kato J, Ebihara A, Watano Y, Murakami N. Reticulate evolution in the apogamous Dryopteris varia complex (Dryopteridaceae, subg. Erythrovariae, sect. Variae) and its related sexual species in Japan. JOURNAL OF PLANT RESEARCH 2014; 127:661-84. [PMID: 25064510 DOI: 10.1007/s10265-014-0652-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/04/2014] [Indexed: 05/27/2023]
Abstract
Apogamous fern species are often difficult to distinguish from related species because of their continuous morphological variations. To clarify the genetic relationships among the members of the Dryopteris varia complex, we analyzed the nucleotide sequences of the plastid gene rbcL and the nuclear gene PgiC. We also analyzed the diploid sexual species D. caudipinna and D. chinensis, which have not been included in the complex, but were recently shown to be closely related to the complex in a molecular phylogenetic study. The PgiC sequences of the diploid sexual species, D. varia, D. saxifraga, D. sp. 'protobissetiana' (undescribed diploid sexual species), D. caudipinna, and D. chinensis, were well differentiated and hence designated A, B, C, D, and E, respectively. Thus, the PgiC constitution of apogamous species in the complex was as follows: D. bissetiana, B + C; D. kobayashii, B + C + E); D. pacifica, A + C, A + B + C, or A + C + D; D. sacrosancta, A + C + E; and D. saxifragivaria, B + C. These results suggest that these apogamous species are formed by hybridizations of species including not only the three diploid sexual species of the D. varia complex (A, B, and C) but also the two diploid sexual species D. caudipinna (D) and D. chinensis (E), which do not belong to the complex.
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Affiliation(s)
- Kiyotaka Hori
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan,
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Zheng X, Cai D, Potter D, Postman J, Liu J, Teng Y. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences. Mol Phylogenet Evol 2014; 80:54-65. [PMID: 25083939 DOI: 10.1016/j.ympev.2014.07.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 07/10/2014] [Accepted: 07/17/2014] [Indexed: 11/28/2022]
Abstract
Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus.
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Affiliation(s)
- Xiaoyan Zheng
- Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Horticulture and Landscape, College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| | - Danying Cai
- Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Daniel Potter
- Department of Plant Sciences, University of California, Mail Stop 2, Davis, CA 95616-8780, USA
| | - Joseph Postman
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR 97333, USA
| | - Jing Liu
- Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuanwen Teng
- Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Phylogeny of a genomically diverse group of elymus (poaceae) allopolyploids reveals multiple levels of reticulation. PLoS One 2013; 8:e78449. [PMID: 24302986 PMCID: PMC3840256 DOI: 10.1371/journal.pone.0078449] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/11/2013] [Indexed: 11/19/2022] Open
Abstract
The grass tribe Triticeae (=Hordeeae) comprises only about 300 species, but it is well known for the economically important crop plants wheat, barley, and rye. The group is also recognized as a fascinating example of evolutionary complexity, with a history shaped by numerous events of auto- and allopolyploidy and apparent introgression involving diploids and polyploids. The genus Elymus comprises a heterogeneous collection of allopolyploid genome combinations, all of which include at least one set of homoeologs, designated St, derived from Pseudoroegneria. The current analysis includes a geographically and genomically diverse collection of 21 tetraploid Elymus species, and a single hexaploid species. Diploid and polyploid relationships were estimated using four molecular data sets, including one that combines two regions of the chloroplast genome, and three from unlinked nuclear genes: phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I. Four gene trees were generated using maximum likelihood, and the phylogenetic placement of the polyploid sequences reveals extensive reticulation beyond allopolyploidy alone. The trees were interpreted with reference to numerous phenomena known to complicate allopolyploid phylogenies, and introgression was identified as a major factor in their history. The work illustrates the interpretation of complicated phylogenetic results through the sequential consideration of numerous possible explanations, and the results highlight the value of careful inspection of multiple independent molecular phylogenetic estimates, with particular focus on the differences among them.
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Relationships and origins of the Dryopteris varia (L.) Kuntze species complex (Dryopteridaceae) in Korea inferred from nuclear and chloroplast DNA sequences. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Roy T, Chang TH, Lan T, Lindqvist C. Phylogeny and biogeography of New World Stachydeae (Lamiaceae) with emphasis on the origin and diversification of Hawaiian and South American taxa. Mol Phylogenet Evol 2013; 69:218-38. [DOI: 10.1016/j.ympev.2013.05.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/25/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022]
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Shaw AJ, Shaw B, Johnson MG, Higuchi M, Arikawa T, Ueno T, Devos N. Origins, genetic structure, and systematics of the narrow endemic peatmosses (Sphagnum): S. guwassanense and S. triseriporum (Sphagnaceae). AMERICAN JOURNAL OF BOTANY 2013; 100:1202-1220. [PMID: 23720430 DOI: 10.3732/ajb.1200630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Sphagnum dominates vast expanses of wetland habitats throughout the northern hemisphere and species delimitation within the genus is important because floristic changes associated with a warming global climate may have measureable impacts on large-scale ecological processes. Most northern hemisphere peatmoss species (Sphagnum) have circumboreal ranges, but the Japanese species generally known as S. calymmatophyllum is endemic to Honshu Island. This prompted a population genetic and phylogenetic analysis to resolve the origin(s), population structure, and phylogenetic relationships of this morphologically variable species. • METHODS Sixty plants collected from Mt. Gassan and Mt. Hakkoda were genotyped for 12 microsatellite loci. Two plastid loci and three anonymous nuclear loci were sequenced in a subset of the plants, plus representatives from 10 closely related species. • KEY RESULTS Gametophytes exhibited fixed or nearly fixed heterozygosity at 9-10 of the 12 microsatellite loci. Two genetic groups were resolved by the microsatellite data, individuals showed no evidence of admixture, and the two groups of plants differ in morphology. They are heterozygous for different sets of alleles. The two taxa share plastid DNA sequences with two species that are common in Alaska. • CONCLUSIONS Two taxa were distinguished: S. guwassanense and S. triseriporum. Both are allopolyploids; they originated independently from different but closely related progenitors. The maternal progenitor was likely either S. orientale or S. inexspectatum. The two allopolyploid taxa are heterozygous for (different) private microsatellite alleles, and one progenitor could be extinct.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA.
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Isomura N, Iwao K, Fukami H. Possible natural hybridization of two morphologically distinct species of Acropora (Cnidaria, Scleractinia) in the Pacific: fertilization and larval survival rates. PLoS One 2013; 8:e56701. [PMID: 23457605 PMCID: PMC3573024 DOI: 10.1371/journal.pone.0056701] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/13/2013] [Indexed: 11/18/2022] Open
Abstract
Natural hybridization of corals in the Indo-Pacific has been considered rather rare. However, field studies have observed many corals with intermediate interspecific or unusual morphologies. Given that the existence of F1 hybrids with intermediate interspecific morphologies has been proven in the Caribbean, hybrids may also inhabit the Indo-Pacific and occur more frequently than expected. In this study, we focused on two morphologically different species, Acropora florida and A. intermedia, and performed crossing experiments at Akajima Island, Japan. Results showed that these species could hybridize in both directions via eggs and sperm, but that fertilization rates significantly differed according to which species provided eggs. These results are similar to those reported from the Caribbean. Although all embryos developed normally to the planular larval stage, the developmental processes of some hybrid embryos were delayed by approximately 1 h compared with conspecific embryos, suggesting that fertilization occurred 1 h later in interspecific crosses than in intraspecific crosses. More successful hybridization could occur under conditions with low numbers of conspecific colonies. Additionally, a comparison of survival rates between hybrid and intraspecific larvae revealed that intra- and interspecific larvae produced from eggs of A. florida survived for significantly longer than those produced from eggs of A. intermedia. Considering these data, under specific conditions, hybrids can be expected to be produced and survive in nature in the Pacific. Furthermore, we identified one colony with intermediate morphology between A. florida and A. intermedia in the field. This colony was fertilized only by eggs of A. florida, with high fertilization rates, suggesting that this colony would be a hybrid of these two species and might be backcrossed.
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Affiliation(s)
- Naoko Isomura
- Department of Bioresources Engineering, Okinawa National College of Technology, Nago-City, Okinawa, Japan
| | - Kenji Iwao
- Akajima Marine Science Laboratory, Zamamison, Okinawa, Japan
| | - Hironobu Fukami
- Department of Marine Biology and Environmental Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- * E-mail:
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Warnow T. Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. MODELS AND ALGORITHMS FOR GENOME EVOLUTION 2013. [DOI: 10.1007/978-1-4471-5298-9_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Zhang LB, Zhang L, Dong SY, Sessa EB, Gao XF, Ebihara A. Molecular circumscription and major evolutionary lineages of the fern genus Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:180. [PMID: 22971160 PMCID: PMC3483261 DOI: 10.1186/1471-2148-12-180] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 09/04/2012] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The fern genus Dryopteris (Dryopteridaceae) is among the most common and species rich fern genera in temperate forests in the northern hemisphere containing 225-300 species worldwide. The circumscription of Dryopteris has been controversial and various related genera have, over the time, been included in and excluded from Dryopteris. The infrageneric phylogeny has largely remained unclear, and the placement of the majority of the supraspecific taxa of Dryopteris has never been tested using molecular data. RESULTS In this study, DNA sequences of four plastid loci (rbcL gene, rps4-trnS spacer, trnL intron, trnL-F spacer) were used to reconstruct the phylogeny of Dryopteris. A total of 122 accessions are sampled in our analysis and they represent 100 species of the expanded Dryopteris including Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema. All four subgenera and 19 sections currently recognized in Dryopteris s.s. are included. One species each of Arachniodes, Leptorumohra, and Lithostegia of Dryopteridaceae are used as outgroups. Our study confirms the paraphyly of Dryopteris and provides the first strong molecular evidence on the monophyly of Acrophorus, Diacalpe, Dryopsis, Nothoperanema, and Peranema. However, all these monophyletic groups together with the paraphyletic Acrorumohra are suggested to be merged into Dryopteris based on both molecular and morphological evidence. Our analysis identified 13 well-supported monophyletic groups. Each of the 13 clades is additionally supported by morphological synapomophies and is inferred to represent a major evolutionary lineage in Dryopteris. In contrast, monophyly of the four subgenera and 15 out of 19 sections currently recognized in Dryopteris s.s is not supported by plastid data. CONCLUSIONS The genera, Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema, should all be merged into Dryopteris. Most species of these genera share a short rhizome and catadromic arrangement of frond segments, unlike the sister genus of Dryopteris s.l., Arachniodes, which has anadromic arrangement of frond segments. The non-monophyly of the 19 out of the 21 supraspecific taxa (sections, subgenera) in Dryopteris strongly suggests that the current taxonomy of this genus is in need of revision. The disagreement between the previous taxonomy and molecular results in Dryopteris may be due partly to interspecific hybridization and polyplodization. More morphological studies and molecular data, especially from the nuclear genome, are needed to thoroughly elucidate the evolutionary history of Dryopteris. The 13 well-supported clades identified based on our data represent 13 major evolutionary lineages in Dryopteris that are also supported by morphological synapomophies.
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Affiliation(s)
- Li-Bing Zhang
- The ECORES Lab, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, P. R China
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Liang Zhang
- The ECORES Lab, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, P. R China
| | - Shi-Yong Dong
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Emily B Sessa
- Botany Department, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, 53706-1313, USA
| | - Xin-Fen Gao
- The ECORES Lab, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan, 610041, P. R China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba-shi, Ibaraki, 305-0005, Japan
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Sessa EB, Zimmer EA, Givnish TJ. Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:104. [PMID: 22748145 PMCID: PMC3509404 DOI: 10.1186/1471-2148-12-104] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called "semicristata" hypothesis, contention over the group's history has continued in several recent, conflicting studies. RESULTS Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the "semicristata" hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. CONCLUSIONS This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis, including the existence of a missing diploid progenitor, and allow us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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