1
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Pezzi PH, Wheeler LC, Freitas LB, Smith SD. Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae). Mol Phylogenet Evol 2024; 198:108136. [PMID: 38909873 DOI: 10.1016/j.ympev.2024.108136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.
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Affiliation(s)
- Pedro H Pezzi
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
| | - Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
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2
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Luo JJ, Shang H, Xue ZQ, Wang Y, Dai XL, Shen H, Yan YH. Genome-wide data reveal bi-direction and asymmetrical hybridization origin of a fern species Microlepia matthewii. FRONTIERS IN PLANT SCIENCE 2024; 15:1392990. [PMID: 39040506 PMCID: PMC11260791 DOI: 10.3389/fpls.2024.1392990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/20/2024] [Indexed: 07/24/2024]
Abstract
Introduction Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing Microlepia matthewii as a case study to investigate its origins of hybridization. Methods We performed double digest Genotyping-by-sequencing (dd-GBS) on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBA-BABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin. Results and discussion The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of M. hancei and M. calvescens. Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of M. matthewii cluster separately with M. hancei or M. calvescens on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that M. matthewii is a bidirectional and asymmetrical hybrid offspring of M. hancei and M. calvescens.
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Affiliation(s)
- Jun-Jie Luo
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
- Middle School Department, Songjiang Experimental School Affiliated To Shanghai University of International Business and Economics (SUIBE), Shanghai, China
| | - Hui Shang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zhi-Qing Xue
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ying Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xi-Ling Dai
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Shen
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shanghai Chenshan Science Research Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yue-Hong Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation& Research Center of Shenzhen, Shenzhen, Guangdong, China
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3
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Alfieri JM, Hingoranee R, Athrey GN, Blackmon H. Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes). J Hered 2024; 115:1-10. [PMID: 37769441 PMCID: PMC10838130 DOI: 10.1093/jhered/esad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 09/30/2023] Open
Abstract
Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among hybridizing species on reproductive isolation in the bird order Galliformes. We compiled and analyzed hybridization occurrences from literature and recorded measures of postzygotic reproductive isolation. We used a text-mining approach leveraging a historical aviculture magazine to quantify the degree of domestication across species. We obtained divergence time, morphology, habitat, and clutch size data from open sources. We found 123 species pairs (involving 77 species) with known offspring fertility (sterile, only males fertile, or both sexes fertile). We found that divergence time and clutch size were significant predictors of reproductive isolation (McFadden's Pseudo-R2 = 0.59), but not habitat or morphological mismatch. Perhaps most interesting, we found a significant relationship between domestication and reproductive compatibility after correcting for phylogeny, removing extreme values, and addressing potential biases (F1,74 = 5.43, R2 = 0.06, P-value = 0.02). We speculate that the genetic architecture and disruption in selective reproductive regimes associated with domestication may impact reproductive isolation, causing domesticated species to be more reproductively labile.
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Affiliation(s)
- James M Alfieri
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Reina Hingoranee
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, TX, USA
| | - Giridhar N Athrey
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - Heath Blackmon
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Biology, Texas A&M University, College Station, TX, USA
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Katayama N, Yamamoto T, Aiuchi S, Watano Y, Fujiwara T. Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales). FRONTIERS IN PLANT SCIENCE 2024; 14:1286320. [PMID: 38264021 PMCID: PMC10803465 DOI: 10.3389/fpls.2023.1286320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.
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Affiliation(s)
- Natsu Katayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Sakura Aiuchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Tao Fujiwara
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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Patel N, Medina R, Williams LD, Lemieux O, Goffinet B, Johnson MG. Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes. Evolution 2023; 77:2561-2575. [PMID: 37740404 DOI: 10.1093/evolut/qpad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/30/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023]
Abstract
Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. Here, we test a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called Homologizer, in the family Funariaceae. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of Physcomitrium eurystomum and one population of Physcomitrium collenchymatum. We also reveal that hybridization gave rise to Physcomitrium immersum, as well as to yet unrecognized lineages sharing the phenotype of Physcomitrium pyriforme and Physcomitrium sphaericum. Our findings demonstrate the utility of our approach when working with polyploid genomes, and its value in identifying progenitor species using target capture data.
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Affiliation(s)
- Nikisha Patel
- Biology Department, Trinity College, Hartford, CT, United States
| | - Rafael Medina
- Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Lindsay D Williams
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Olivia Lemieux
- Department of Ecology and Evolutionary Biology, University of Connecticut, Mansfield, CT, United States
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Mansfield, CT, United States
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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Zhao J, Zhou X, Fang S, Zhu Z, Li Y, Yu H, He Z. Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:2237. [PMID: 37375862 DOI: 10.3390/plants12122237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/07/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, a dataset of 26 transcriptomes (including 11 newly generated) were used to assess single-copy nuclear genes and to obtain the organelle gene sequences. Through phylotranscriptomic analysis, the phylogeny and hybridization events of Marattiaceae were explored and a robust phylogenomic framework for the evolution of Marattiaceae was provided. Using both concatenation- and coalescent-based phylogenies, the gene-tree discordance, incomplete lineage sorting (ILS) simulations, and network inference were examined. Except the low support with mitochondrial genes of Marattiaceae, nuclear genes and chloroplast genes strongly supported a sister relationship between Marattiaceae and leptosporangiate ferns. At the genus level, all phylogenetic analysis based on nuclear genes datasets recovered five genera in Marattiaceae as monophyletic with strong support. Danaea and Ptisana were the first two diverged clades in turn. Christensenia was a sister clade to the clade Marattia + Angiopteris s.l. In Angiopteris s.l., three clades (Angiopteris s.s., the Archangiopteris group, and An. sparsisora) were well identified with maximum support. The Archangiopteris group was derived from Angiopteris s.s. at ca. 18 Ma. The putative hybrid species An. sparsisora between Angiopteris s.s. and the Archangiopteris group was verified by the species network analyses and the maternal plastid genes. This study will improve our understanding for using the phylotranscriptomic method to explore phylogeny and investigate hybridization events for difficult taxa in ferns.
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Affiliation(s)
- Jing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
- School of Life Sciences, Yunnan University, East Outer Ring Road, Chenggong District, Kunming 650500, China
| | - Xinmao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Shaoli Fang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Zhangming Zhu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Yuxin Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Hong Yu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Zhaorong He
- School of Life Sciences, Yunnan University, East Outer Ring Road, Chenggong District, Kunming 650500, China
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7
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Stull GW, Pham KK, Soltis PS, Soltis DE. Deep reticulation: the long legacy of hybridization in vascular plant evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:743-766. [PMID: 36775995 DOI: 10.1111/tpj.16142] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/27/2023]
Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
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Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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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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10
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Dagilis AJ, Peede D, Coughlan JM, Jofre GI, D'Agostino ERR, Mavengere H, Tate AD, Matute DR. A need for standardized reporting of introgression: Insights from studies across eukaryotes. Evol Lett 2022; 6:344-357. [PMID: 36254258 PMCID: PMC9554761 DOI: 10.1002/evl3.294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 01/04/2023] Open
Abstract
With the rise of affordable next-generation sequencing technology, introgression-or the exchange of genetic materials between taxa-has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes. We collated a single statistic, Patterson's D, which can be used as a test for introgression across 123 studies to further assess how taxonomic group, divergence time, and sequencing technology influence reports of introgression. Overall, introgression has mostly been measured in plants and vertebrates, with less attention given to the rest of the Eukaryotes. We find that the most frequently used metrics to detect introgression are difficult to compare across studies and even more so across biological systems due to differences in study effort, reporting standards, and methodology. Nonetheless, our analyses reveal several intriguing patterns, including the observation that differences in sequencing technologies may bias values of Patterson's D and that introgression may differ throughout the course of the speciation process. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities and highlight important areas of future research that can be better assessed once this unified approach is met.
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Affiliation(s)
| | - David Peede
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - Jenn M. Coughlan
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Gaston I. Jofre
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
| | - Emmanuel R. R. D'Agostino
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Heidi Mavengere
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
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11
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Toews DPL, Rhinehart TA, Mulvihill R, Galen S, Gosser SM, Johnson T, Williamson JL, Wood AW, Latta SC. Genetic confirmation of a hybrid between two highly divergent cardinalid species: A rose-breasted grosbeak ( Pheucticus ludovicianus) and a scarlet tanager ( Piranga olivacea). Ecol Evol 2022; 12:e9152. [PMID: 35928797 PMCID: PMC9343856 DOI: 10.1002/ece3.9152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 12/04/2022] Open
Abstract
Using low-coverage whole-genome sequencing, analysis of vocalizations, and inferences from natural history, we document a first-generation hybrid between a rose-breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). These two species occur sympatrically throughout much of eastern North America, although were not previously known to interbreed. Following the field identification of a putative hybrid, we use genetic and bioacoustic data to show that a rose-breasted grosbeak was the maternal parent and a scarlet tanager was the paternal parent of the hybrid, whose song was similar to the latter species. These two species diverged >10 million years ago, and thus it is surprising to find a hybrid formed under natural conditions in the wild. Notably, the hybrid has an exceptionally heterozygous genome, with a conservative estimate of a heterozygous base every 100 bp. The observation that this hybrid of such highly divergent parental taxa has survived until adulthood serves as another example of the capacity for hybrid birds to survive with an exceptionally divergent genomic composition.
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Affiliation(s)
- David P. L. Toews
- Department of Biology, 619 Mueller LaboratoryPennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Tessa A. Rhinehart
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Robert Mulvihill
- Department of Conservation and Field ResearchNational AviaryPittsburghPennsylvaniaUSA
| | - Spencer Galen
- Biology DepartmentUniversity of ScrantonScrantonPennsylvaniaUSA
| | | | - Tom Johnson
- The Academy of Natural Sciences of Drexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Jessie L. Williamson
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Andrew W. Wood
- Department of Biology, 619 Mueller LaboratoryPennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Steven C. Latta
- Department of Conservation and Field ResearchNational AviaryPittsburghPennsylvaniaUSA
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12
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Bloesch Z, Nauheimer L, Elias Almeida T, Crayn D, Raymond Field A. HybPhaser identifies hybrid evolution in Australian Thelypteridaceae. Mol Phylogenet Evol 2022; 173:107526. [DOI: 10.1016/j.ympev.2022.107526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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13
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Irwin D, Schluter D. Hybridization and the Coexistence of Species. Am Nat 2022; 200:E93-E109. [DOI: 10.1086/720365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Buck R, Flores-Rentería L. The Syngameon Enigma. PLANTS (BASEL, SWITZERLAND) 2022; 11:895. [PMID: 35406874 PMCID: PMC9002738 DOI: 10.3390/plants11070895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 05/17/2023]
Abstract
Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.
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Affiliation(s)
- Ryan Buck
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
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15
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Hodson CN, Jaron KS, Gerbi S, Ross L. Gene-rich germline-restricted chromosomes in black-winged fungus gnats evolved through hybridization. PLoS Biol 2022; 20:e3001559. [PMID: 35213540 PMCID: PMC8906591 DOI: 10.1371/journal.pbio.3001559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 03/09/2022] [Accepted: 01/28/2022] [Indexed: 12/20/2022] Open
Abstract
Germline-restricted DNA has evolved in diverse animal taxa and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline-restricted DNA has evolved, especially in flies, in which 3 diverse families, Chironomidae, Cecidomyiidae, and Sciaridae, carry germline-restricted chromosomes (GRCs). We conducted a genomic analysis of GRCs in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which has 2 large germline-restricted "L" chromosomes. We sequenced and assembled the genome of B. coprophila and used differences in sequence coverage and k-mer frequency between somatic and germline tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene rich, and have many genes with divergent homologs on other chromosomes in the genome. We also found that 2 divergent GRCs exist in the population we sequenced. GRC genes are more similar in sequence to genes from another Dipteran family (Cecidomyiidae) than to homologous genes from Sciaridae. This unexpected finding suggests that these chromosomes likely arose in Sciaridae through hybridization with a related lineage. These results provide a foundation from which to answer many questions about the evolution of GRCs in Sciaridae, such as how this hybridization event resulted in GRCs and what features on these chromosomes cause them to be restricted to the germline.
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Affiliation(s)
- Christina N. Hodson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Kamil S. Jaron
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan Gerbi
- Division of Biology and Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Laura Ross
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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16
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May MR, Contreras DL, Sundue MA, Nagalingum NS, Looy CV, Rothfels CJ. Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity. Syst Biol 2021; 70:1232-1255. [PMID: 33760075 PMCID: PMC8513765 DOI: 10.1093/sysbio/syab020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ${\sim}$2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth-death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.].
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Affiliation(s)
- Michael R May
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
| | - Dori L Contreras
- Department of Paleontology, Perot Museum of Nature and Science, 2201 N. Field Street, Dallas TX 75201, USA
| | - Michael A Sundue
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
- The Pringle Herbarium, University of Vermont, 305 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Nathalie S Nagalingum
- Department of Botany, California Academy of Sciences, Golden Gate Park, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Cindy V Looy
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
- Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
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17
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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18
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Kinosian SP, Pearse WD, Wolf PG. Cryptic diversity in the model fern genus Ceratopteris (Pteridaceae). Mol Phylogenet Evol 2020; 152:106938. [PMID: 32791300 DOI: 10.1016/j.ympev.2020.106938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/23/2020] [Accepted: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Cryptic species are present throughout the tree of life. They are especially prevalent in ferns, because of processes such hybridization, polyploidy, and reticulate evolution. In addition, the simple morphology of ferns limits phenotypic variation and makes it difficult to detect cryptic species. The model fern genus Ceratopteris has long been suspected to harbor cryptic diversity, in particular within the highly polymorphic C. thalictroides. Yet no studies have included samples from throughout its pan-tropical range or utilized genomic sequencing, making it difficult to assess the full extent of cryptic variation within this genus. Here, we present the first multilocus phylogeny of the genus using reduced representation genomic sequencing (RADseq) and examine population structure, phylogenetic relationships, and ploidy level variation. We recover similar species relationships found in previous studies, find support for the cryptic species C. gaudichaudii as genetically distinct, and identify novel genomic variation within two of the mostly broadly distributed species in the genus, C. thalictroides and C. cornuta. Finally, we detail the utility of our approach for working on cryptic, reticulate groups of ferns. Specifically, it does not require a reference genome, of which there are very few available for ferns. RADseq is a cost-effective way to work with study groups lacking genomic resources, and to obtain the thousands of nuclear markers needed to untangle species complexes.
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Affiliation(s)
- Sylvia P Kinosian
- Ecology Center and Department of Biology, Utah State University, Logan, UT 84322, USA.
| | - William D Pearse
- Ecology Center and Department of Biology, Utah State University, Logan, UT 84322, USA; Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, UK
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Hunstville, AL 35899, USA
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19
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Larson DA, Walker JF, Vargas OM, Smith SA. A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales. AMERICAN JOURNAL OF BOTANY 2020; 107:773-789. [PMID: 32350864 DOI: 10.1002/ajb2.1469] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/12/2020] [Indexed: 05/27/2023]
Abstract
PREMISE Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. METHODS We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods, and is summarized in a consensus framework. RESULTS Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole-genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications. CONCLUSIONS We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.
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Affiliation(s)
- Drew A Larson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph F Walker
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, CB2 1LR, UK
| | - Oscar M Vargas
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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20
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Babiychuk E, Teixeira JG, Tyski L, Guimaraes JTF, Romeiro LA, da Silva EF, Dos Santos JF, Vasconcelos S, da Silva DF, Castilho A, Siqueira JO, Fonseca VLI, Kushnir S. Geography is essential for reproductive isolation between florally diversified morning glory species from Amazon canga savannahs. Sci Rep 2019; 9:18052. [PMID: 31792228 PMCID: PMC6889514 DOI: 10.1038/s41598-019-53853-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 11/06/2019] [Indexed: 11/29/2022] Open
Abstract
The variety, relative importance and eco-evolutionary stability of reproductive barriers are critical to understanding the processes of speciation and species persistence. Here we evaluated the strength of the biotic prezygotic and postzygotic isolation barriers between closely related morning glory species from Amazon canga savannahs. The flower geometry and flower visitor assemblage analyses supported pollination by the bees in lavender-flowered Ipomoea marabaensis and recruitment of hummingbirds as pollinators in red-flowered Ipomoea cavalcantei. Nevertheless, native bee species and alien honeybees foraged on flowers of both species. Real-time interspecific hybridization underscored functionality of the overlap in flower visitor assemblages, questioning the strength of prezygotic isolation underpinned by diversification in flower colour and geometry. Interspecific hybrids were fertile and produced offspring in nature. No significant asymmetry in interspecific hybridization and hybrid incompatibilities among offspring were found, indicating weak postmating and postzygotic isolation. The results suggested that despite floral diversification, the insular-type geographic isolation remains a major barrier to gene flow. Findings set a framework for the future analysis of contemporary evolution of plant-pollinator networks at the population, community, and ecosystem levels in tropical ecosystems that are known to be distinct from the more familiar temperate climate models.
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Affiliation(s)
- Elena Babiychuk
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil.
| | | | - Lourival Tyski
- Parque Zoobotânico Vale, VALE S.A., Rod. Raimundo Mascarenhas, Km 26, S/N., Núcleo Urbano de Carajás, CEP 68516-000, Parauapebas, Pará, Brazil
| | | | - Luiza Araújo Romeiro
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil
| | | | | | - Santelmo Vasconcelos
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil
| | - Delmo Fonseca da Silva
- Parque Zoobotânico Vale, VALE S.A., Rod. Raimundo Mascarenhas, Km 26, S/N., Núcleo Urbano de Carajás, CEP 68516-000, Parauapebas, Pará, Brazil
| | - Alexandre Castilho
- Gerência de Meio Ambiente, Departamento de Ferrosos Corredor Norte, Vale S.A., Rua Guamá n 60, Núcleo Urbano, CEP 68516-000, Parauapebas, Pará, Brazil
| | - José Oswaldo Siqueira
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil
| | | | - Sergei Kushnir
- Unaffiliated, Belém, Pará, Brazil.,Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12, Ireland
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21
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Mitchell N, Campbell LG, Ahern JR, Paine KC, Giroldo AB, Whitney KD. Correlates of hybridization in plants. Evol Lett 2019; 3:570-585. [PMID: 31867119 PMCID: PMC6906982 DOI: 10.1002/evl3.146] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 01/08/2023] Open
Abstract
Hybridization is a biological phenomenon increasingly recognized as an important evolutionary process in both plants and animals, as it is linked to speciation, radiation, extinction, range expansion and invasion, and allows for increased trait diversity in agricultural and horticultural systems. Estimates of hybridization frequency vary across taxonomic groups, but causes of this variation are unknown. Here, we ask on a global scale whether hybridization is linked to any of 11 traits related to plant life history, reproduction, genetic predisposition, and environment or opportunity. Given that hybridization is not evenly distributed across the plant tree of life, we use phylogenetic generalized least squares regression models and phylogenetic path analysis to detect statistical associations between hybridization and plant traits at both the family and genus levels. We find that perenniality and woodiness are each weakly associated with an increased frequency of hybridization in univariate analyses, but path analysis suggests that the direct linkage is between perenniality and increased hybridization (with woodiness having only an indirect relationship with hybridization via perenniality). Weak associations between higher rates of hybridization and higher outcrossing rates, abiotic pollination syndromes, vegetative reproductive modes, larger genomes, and less variable genome sizes are detectable in some cases but not others. We argue that correlational evidence at the global scale, such as that presented here, provides a robust framework for forming hypotheses to examine and test drivers of hybridization at a more mechanistic level.
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Affiliation(s)
- Nora Mitchell
- Department of BiologyUniversity of New MexicoAlbuquerqueNew Mexico87131
- Department of BiologyUniversity of Wisconsin–Eau ClaireEau ClaireWisconsin54701
| | - Lesley G. Campbell
- Department of Chemistry and BiologyRyerson UniversityTorontoOntarioM5B 2K3Canada
| | - Jeffrey R. Ahern
- Department of BiologyUniversity of New MexicoAlbuquerqueNew Mexico87131
| | - Kellen C. Paine
- Department of BiologyUniversity of New MexicoAlbuquerqueNew Mexico87131
| | - Aelton B. Giroldo
- Departamento de EnsinoInstituto Federal de Educação, Ciência e Tecnologia do Ceará – Campus Crateús, CrateúsBrazil
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22
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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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23
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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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24
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Adams RH, Schield DR, Castoe TA. Recent Advances in the Inference of Gene Flow from Population Genomic Data. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s40610-019-00120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Shepherd LD, Brownsey PJ, Stowe C, Newell C, Perrie LR. Genetic and morphological identification of a recurrent Dicksonia tree fern hybrid in New Zealand. PLoS One 2019; 14:e0216903. [PMID: 31107899 PMCID: PMC6527230 DOI: 10.1371/journal.pone.0216903] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/30/2019] [Indexed: 11/18/2022] Open
Abstract
Hybridization is common in many ferns and has been a significant factor in fern evolution and speciation. However, hybrids are rare between the approximately 30 species of Dicksonia tree ferns world-wide, and none are well documented. In this study we examine the relationship of a newly-discovered Dicksonia tree fern from Whirinaki, New Zealand, which does not fit the current taxonomy of the three species currently recognized in New Zealand. Our microsatellite genotyping and ddRAD-seq data indicate these plants are F1 hybrids that have formed multiple times between D. fibrosa and D. lanata subsp. lanata. The Whirinaki plants have intermediate morphology between D. fibrosa and D. lanata subsp. lanata and their malformed spores are consistent with a hybrid origin. The Whirinaki plants–Dicksonia fibrosa × D. lanata subsp. lanata–are an example of hybridization between distantly related fern lineages, with the two parent species estimated to have diverged 55–25 mya. Our chloroplast sequencing indicates asymmetric chloroplast inheritance in the Whirinaki morphology with D. lanata subsp. lanata always contributing the chloroplast genome.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- * E-mail:
| | | | | | | | - Leon R. Perrie
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
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26
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Testo WL, Sessa E, Barrington DS. The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae). THE NEW PHYTOLOGIST 2019; 222:604-613. [PMID: 30326543 DOI: 10.1111/nph.15544] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade. We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift. Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr. Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.
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Affiliation(s)
- Weston L Testo
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - David S Barrington
- Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington, VT, 05405, USA
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Clark JW, Donoghue PCJ. Whole-Genome Duplication and Plant Macroevolution. TRENDS IN PLANT SCIENCE 2018; 23:933-945. [PMID: 30122372 DOI: 10.1016/j.tplants.2018.07.006] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/29/2018] [Accepted: 07/12/2018] [Indexed: 05/18/2023]
Abstract
Whole-genome duplication (WGD) is characteristic of almost all fundamental lineages of land plants. Unfortunately, the timings of WGD events are loosely constrained and hypotheses of evolutionary consequence are poorly formulated, making them difficult to test. Using examples from across the plant kingdom, we show that estimates of timing can be improved through the application of molecular clock methodology to multigene datasets. Further, we show that phenotypic change can be quantified in morphospaces and that relative phenotypic disparity can be compared in the light of WGD. Together, these approaches facilitate tests of hypotheses on the role of WGD in plant evolution, underscoring the potential of plants as a model system for investigating the role WGD in macroevolution.
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Affiliation(s)
- James W Clark
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TH, UK.
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Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian non-sister parrot species, Platycercus adscitus and Platycercus eximius. Heredity (Edinb) 2018; 122:402-416. [PMID: 30082918 PMCID: PMC6460760 DOI: 10.1038/s41437-018-0127-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 06/23/2018] [Accepted: 06/27/2018] [Indexed: 01/27/2023] Open
Abstract
The study of hybrid zones advances understanding of the speciation process, and approaches incorporating genomic data are increasingly used to draw significant conclusions about the impact of hybridisation. Despite the progress made, the complex interplay of factors that can lead to substantially variable hybridisation outcomes are still not well understood, and many systems and/or groups remain comparatively poorly studied. Our study aims to broaden the literature on avian hybrid zones, investigating a potentially geographically and temporally complex putative hybrid zone between two native Australian non-sister parrot species, the pale-headed and eastern rosellas (Platycercus adscitus and Platycercus eximius, respectively). We analysed six plumage traits and >1400 RADseq loci and detected hybrid individuals and an unexpectedly complex geographic structure. The hybrid zone is larger than previously described due to either observer bias or its movement over recent decades. It comprises different subregions where genetic and plumage signals of admixture vary markedly in their concordance. Evidence of contemporary hybridisation (later generation and backcrossed individuals) both within and beyond the previously defined zone, when coupled with a lack of F1 hybrids and differential patterns of introgression among potentially diagnostic loci, indicates a lack of post-zygotic barriers to gene flow between species. Despite ongoing gene flow, species boundaries are likely maintained largely by strong pre-mating barriers. These findings are discussed in detail and future avenues for research into this system are proposed, which would be of benefit to the speciation and hybrid zone literature.
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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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Schrider DR, Ayroles J, Matute DR, Kern AD. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. PLoS Genet 2018; 14:e1007341. [PMID: 29684059 PMCID: PMC5933812 DOI: 10.1371/journal.pgen.1007341] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 05/03/2018] [Accepted: 03/28/2018] [Indexed: 12/30/2022] Open
Abstract
Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia. Understanding the extent to which species or diverged populations hybridize in nature is crucially important if we are to understand the speciation process. Accordingly numerous research groups have developed methodology for finding the genetic evidence of such introgression. In this report we develop a supervised machine learning approach for uncovering loci which have introgressed across species boundaries. We show that our method, FILET, has greater accuracy and power than competing methods in discovering introgression, and in addition can detect the directionality associated with the gene flow between species. Using whole genome sequences from Drosophila simulans and Drosophila sechellia we show that FILET discovers quite extensive introgression between these species that has occurred mostly from D. simulans to D. sechellia. Our work highlights the complex process of speciation even within a well-studied system and points to the growing importance of supervised machine learning in population genetics.
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Affiliation(s)
- Daniel R. Schrider
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
- * E-mail:
| | - Julien Ayroles
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, New Jersey, United States of America
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Andrew D. Kern
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
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Nydam ML, Yanckello LM, Bialik SB, Giesbrecht KB, Nation GK, Peak JL. Introgression in two species of broadcast spawning marine invertebrate. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Smith JF, Clark JL, Amaya-Márquez M, Marín-Gómez OH. Resolving incongruence: Species of hybrid origin in Columnea (Gesneriaceae). Mol Phylogenet Evol 2017; 106:228-240. [DOI: 10.1016/j.ympev.2016.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/19/2023]
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Rothfels CJ, Pryer KM, Li FW. Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. THE NEW PHYTOLOGIST 2017; 213:413-429. [PMID: 27463214 DOI: 10.1111/nph.14111] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 05/27/2023]
Abstract
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
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Affiliation(s)
- Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Duke University, Durham, NC, 27705, USA
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34
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Kuo LY, Ebihara A, Shinohara W, Rouhan G, Wood KR, Wang CN, Chiou WL. Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy. Mol Phylogenet Evol 2016; 104:123-134. [DOI: 10.1016/j.ympev.2016.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 08/06/2016] [Accepted: 08/09/2016] [Indexed: 12/14/2022]
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35
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Vaux F, Trewick SA, Morgan-Richards M. Speciation through the looking-glass. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Felix Vaux
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Steven A. Trewick
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Mary Morgan-Richards
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
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36
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Affiliation(s)
- Delbert Wiens
- White Mountain Research Center; 3000 E. Line Street Bishop CA 93514 USA
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37
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Oberlander KC, Dreyer LL, Goldblatt P, Suda J, Linder HP. Species-rich and polyploid-poor: Insights into the evolutionary role of whole-genome duplication from the Cape flora biodiversity hotspot. AMERICAN JOURNAL OF BOTANY 2016; 103:1336-47. [PMID: 27352831 DOI: 10.3732/ajb.1500474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/22/2016] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Whole-genome duplication (WGD) in angiosperms has been hypothesized to be advantageous in unstable environments and/or to increase diversification rates, leading to radiations. Under the first hypothesis, floras in stable environments are predicted to have lower proportions of polyploids than highly, recently disturbed floras, whereas species-rich floras would be expected to have higher than expected proportions of polyploids under the second. The South African Cape flora is used to discriminate between these two hypotheses because it features a hyperdiverse flora predominantly generated by a limited number of radiations (Cape clades), against a backdrop of climatic and geological stability. METHODS We compiled all known chromosome counts for species in 21 clades present in the Cape (1653 species, including 24 Cape clades), inferred ploidy levels for these species by inspection or derived from the primary literature, and compared Cape to non-Cape ploidy levels in these clades (17,520 species) using G tests. KEY RESULTS The Cape flora has anomalously low proportions of polyploids compared with global levels. This pattern is consistently observed across nearly half the clades and across global latitudinal gradients, although individual lineages seem to be following different paths to low levels of WGD and to differing degrees. CONCLUSIONS This pattern shows that the diversity of the Cape flora is the outcome of primarily diploid radiations and supports the hypothesis that WGD may be rare in stable environments.
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Affiliation(s)
- Kenneth C Oberlander
- Institute of Botany, The Czech Academy of Sciences, Průhonice, CZ-25243, Czech Republic Department Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Léanne L Dreyer
- Department Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Peter Goldblatt
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166 USA
| | - Jan Suda
- Institute of Botany, The Czech Academy of Sciences, Průhonice, CZ-25243, Czech Republic Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ - 128 01, Czech Republic
| | - H Peter Linder
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich CH8008, Switzerland
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Ezard THG, Quental TB, Benton MJ. The challenges to inferring the regulators of biodiversity in deep time. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150216. [PMID: 26977058 PMCID: PMC4810811 DOI: 10.1098/rstb.2015.0216] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2016] [Indexed: 11/12/2022] Open
Abstract
Attempts to infer the ecological drivers of macroevolution in deep time have long drawn inspiration from work on extant systems, but long-term evolutionary and geological changes complicate the simple extrapolation of such theory. Recent efforts to incorporate a more informed ecology into macroevolution have moved beyond the descriptive, seeking to isolate generating mechanisms and produce testable hypotheses of how groups of organisms usurp each other or coexist over vast timespans. This theme issue aims to exemplify this progress, providing a series of case studies of how novel modelling approaches are helping infer the regulators of biodiversity in deep time. In this Introduction, we explore the challenges of these new approaches. First, we discuss how our choices of taxonomic units have implications for the conclusions drawn. Second, we emphasize the need to embrace the interdependence of biotic and abiotic changes, because no living organism ignores its environment. Third, in the light of parts 1 and 2, we discuss the set of dynamic signatures that we might expect to observe in the fossil record. Finally, we ask whether these dynamics represent the most ecologically informative foci for research efforts aimed at inferring the regulators of biodiversity in deep time. The papers in this theme issue contribute in each of these areas.
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Affiliation(s)
- Thomas H G Ezard
- Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Tiago B Quental
- Departamento de Ecologia, Universidade de São Paulo, São Paulo, SP 05508-900, Brazil
| | - Michael J Benton
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
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Forsdyke DR. Chargaff’s GC rule. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Wolf PG, Rowe CA, Der JP, Schilling MP, Visger CJ, Thomson JA. Origins and diversity of a cosmopolitan fern genus on an island archipelago. AOB PLANTS 2015; 7:plv118. [PMID: 26487677 PMCID: PMC4662730 DOI: 10.1093/aobpla/plv118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/09/2015] [Indexed: 05/12/2023]
Abstract
Isolated oceanic islands are characterized by patterns of biological diversity different from that on nearby continental mainlands. Isolation can provide the opportunity for evolutionary divergence, but also set the stage for hybridization between related taxa arriving from different sources. Ferns disperse by haploid spores, which are produced in large numbers and can travel long distances in air currents, enabling these plants to become established on most oceanic islands. Here, we examine the origins and patterns of diversity of the cosmopolitan fern genus Pteridium (Dennstaedtiaceae; bracken) on the Galapagos Islands. We use nucleotide sequences from two plastid genes, and two nuclear gene markers, to examine phylogeography of Pteridium on the Galapagos Islands. We incorporate data from a previous study to provide a worldwide context. We also sampled new specimens from South and Central America. We used flow cytometry to estimate genome size of some accessions. We found that both plastid and nuclear haplotypes fall into two distinct clades, consistent with a two-diploid-species taxonomy of P. aquilinum and P. esculentum. As predicted, the allotetraploid P. caudatum possesses nuclear haplotypes from both diploid species. Samples from the Galapagos include P. esculentum subsp. arachnoideum, P. caudatum and possible hybrids between them. Multiple Pteridium taxa were also observed growing together at some sites. We find evidence for multiple origins of Pteridium on the Galapagos Islands and multiple origins of tetraploid P. caudatum throughout its range in Central and South America. We also posit that P. caudatum may include recent diploid hybrids, backcrosses to P. esculentum, as well as allotetraploid plants. The Galapagos Islands are positioned close to the equator where they can receive dispersing propagules from both hemispheres. This may partly explain the high levels of diversity found for this cosmopolitan fern on these islands.
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Affiliation(s)
- Paul G Wolf
- Department of Biology, Utah State University, Logan, UT 84322, USA Ecology Center, Utah State University, Logan, UT 84322, USA
| | - Carol A Rowe
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | - Joshua P Der
- Department of Biological Science, California State University, Fullerton, CA 92834, USA
| | | | - Clayton J Visger
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - John A Thomson
- National Herbarium of NSW, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
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Vaux F, Trewick SA, Morgan-Richards M. Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12665] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Felix Vaux
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Steven A. Trewick
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
| | - Mary Morgan-Richards
- Ecology Group; Institute of Agriculture and Environment; Massey University; Palmerston North New Zealand
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42
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Ranker TA, Sundue MA. Why are there so few species of ferns? TRENDS IN PLANT SCIENCE 2015; 20:402-403. [PMID: 25986968 DOI: 10.1016/j.tplants.2015.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/29/2015] [Accepted: 05/05/2015] [Indexed: 06/04/2023]
Abstract
A recent study has documented a natural hybridization event between two fern lineages that last shared a common ancestor about 60 million years ago. This is one of the deepest hybridization events ever described and has important implications for plant speciation theory.
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Affiliation(s)
- Tom A Ranker
- Department of Botany, University of Hawai'i at Mānoa, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Michael A Sundue
- Department of Botany, University of Hawai'i at Mānoa, 3190 Maile Way, Honolulu, HI 96822, USA; The Pringle Herbarium, Department of Plant Biology, The University of Vermont, 27 Colchester Ave., Burlington, VT 05405, USA
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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. AMERICAN JOURNAL OF BOTANY 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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Fern hybrid does not mind the gap. Nature 2015. [DOI: 10.1038/518276c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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