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Herting J, Stützel T. Evolution of the coniferous seed scale. ANNALS OF BOTANY 2022; 129:753-760. [PMID: 34932788 PMCID: PMC9292595 DOI: 10.1093/aob/mcab154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/18/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND The Florin model is the commonly accepted theory of coniferous seed scale evolution. It describes the derivation of extant seed scale morphology from the morphology of fossil conifers via the reduction of complex to simple axillary structures. In this framework the seed scale is composed of a reduced lateral shoot with fertile and sterile appendages which are interpreted as leaf homologues. SCOPE The Florin model has three crucial problems that we address here: (1) the original derivation series does not take the ontogeny of extant conifers into account, (2) it cannot explain the morphology of all extant conifers and (3) Taxaceae were originally excluded. Examination of seed cones of extant conifers shows that ovules occur in three different positions in the cone: in an axillary position, replacing a leaf or terminating the cone axis. By interpreting the fertile appendage or seed-bearing structure as a leaf, not all positions are possible. The exclusion of Taxaceae from conifers is in stark contrast to recent molecular phylogenetic studies, which include Taxaceae in conifers as sister to Cupressaceae. Therefore, the Florin model does not offer an adequate explanation for taxaceous morphology. CONCLUSION We conclude that the seed-bearing structure of conifers cannot be interpreted as homologous to a leaf. In the interpretation we present here, the seed-bearing structure is the modified funiculus of the ovule, multiples of which laterally fuse to form the seed scale. The seed scales of all extant conifers can be derived from a Cunninghamia-like morphology via fusion and reduction of individual funiculi.
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Affiliation(s)
| | - Thomas Stützel
- Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Evolution und Biodiversität der Pflanzen, Universitätsstraße 150, 44801 Bochum, Germany
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Asaf S, Khan AL, Jan R, Khan A, Khan A, Kim KM, Lee IJ. The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence. THE PLANT GENOME 2021; 14:e20130. [PMID: 34505399 DOI: 10.1002/tpg2.20130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 05/25/2023]
Abstract
Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales-other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, Univ. of Nizwa, Nizwa, 616, Oman
| | - Abdul Latif Khan
- Dep. of Biotechnology, College of Technology, Univ. of Houston, Houston, TX, 77204, USA
| | - Rahmatullah Jan
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord Univ., Bodø, 8049, Norway
| | - Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, 79409, USA
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
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Bainard JD, Newmaster SG, Budke JM. Genome size and endopolyploidy evolution across the moss phylogeny. ANNALS OF BOTANY 2020; 125:543-555. [PMID: 31777923 PMCID: PMC7102977 DOI: 10.1093/aob/mcz194] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 11/27/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Compared with other plant lineages, bryophytes have very small genomes with little variation across species, and high levels of endopolyploid nuclei. This study is the first analysis of moss genome evolution over a broad taxonomic sampling using phylogenetic comparative methods. We aim to determine whether genome size evolution is unidirectional as well as examine whether genome size and endopolyploidy are correlated in mosses. METHODS Genome size and endoreduplication index (EI) estimates were newly generated using flow cytometry from moss samples collected in Canada. Phylogenetic relationships between moss species were reconstructed using GenBank sequence data and maximum likelihood methods. Additional 1C-values were compiled from the literature and genome size and EI were mapped onto the phylogeny to reconstruct ancestral character states, test for phylogenetic signal and perform phylogenetic independent contrasts. KEY RESULTS Genome size and EI were obtained for over 50 moss taxa. New genome size estimates are reported for 33 moss species and new EIs are reported for 20 species. In combination with data from the literature, genome sizes were mapped onto a phylogeny for 173 moss species with this analysis, indicating that genome size evolution in mosses does not appear to be unidirectional. Significant phylogenetic signal was detected for genome size when evaluated across the phylogeny, whereas phylogenetic signal was not detected for EI. Genome size and EI were not found to be significantly correlated when using phylogenetically corrected values. CONCLUSIONS Significant phylogenetic signal indicates closely related mosses have more similar genome sizes and EI values. This study supports that DNA content in mosses is defined by small genomes that are highly endopolyploid, suggesting strong selective pressure to maintain these features. Further research is needed to understand the functional significance of DNA content evolution in mosses.
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Affiliation(s)
- Jillian D Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-food Canada, Swift Current, SK, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Steven G Newmaster
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Jessica M Budke
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
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Medina-Villarreal A, González-Astorga J, Espinosa de los Monteros A. Evolution of Ceratozamia cycads: A proximate-ultimate approach. Mol Phylogenet Evol 2019; 139:106530. [DOI: 10.1016/j.ympev.2019.106530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022]
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Farhat P, Hidalgo O, Robert T, Siljak-Yakovlev S, Leitch IJ, Adams RP, Bou Dagher-Kharrat M. Polyploidy in the Conifer Genus Juniperus: An Unexpectedly High Rate. FRONTIERS IN PLANT SCIENCE 2019; 10:676. [PMID: 31191584 PMCID: PMC6541006 DOI: 10.3389/fpls.2019.00676] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/06/2019] [Indexed: 05/02/2023]
Abstract
Recent research suggests that the frequency of polyploidy may have been underestimated in gymnosperms. One notable example is in the conifer genus Juniperus, where there are already a few reports of polyploids although data are still missing for most species. In this study, we evaluated the extent of polyploidy in Juniperus by conducting the first comprehensive screen across nearly all of the genus. Genome size data from fresh material, together with chromosome counts, were used to demonstrate that genome sizes estimated from dried material could be used as reliable proxies to uncover the extent of ploidy diversity across the genus. Our analysis revealed that 16 Juniperus taxa were polyploid, with tetraploids and one hexaploid being reported. Furthermore, by analyzing the genome size and chromosome data within a phylogenetic framework we provide the first evidence of possible lineage-specific polyploidizations within the genus. Genome downsizing following polyploidization is moderate, suggesting limited genome restructuring. This study highlights the importance of polyploidy in Juniperus, making it the first conifer genus and only the second genus in gymnosperms where polyploidy is frequent. In this sense, Juniperus represents an interesting model for investigating the genomic and ecological consequences of polyploidy in conifers.
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Affiliation(s)
- Perla Farhat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Oriane Hidalgo
- Royal Botanic Gardens Kew, Richmond, United Kingdom
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Unitat Associada CSIC, Barcelona, Spain
| | - Thierry Robert
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
- Biology Department, Sorbonne Université, Paris, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | | | - Robert P. Adams
- Biology Department, Baylor University, Waco, TX, United States
| | - Magda Bou Dagher-Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
- *Correspondence: Magda Bou Dagher-Kharrat
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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Li H, Leavengood JM, Chapman EG, Burkhardt D, Song F, Jiang P, Liu J, Zhou X, Cai W. Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs. Proc Biol Sci 2017; 284:20171223. [PMID: 28878063 PMCID: PMC5597834 DOI: 10.1098/rspb.2017.1223] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/25/2017] [Indexed: 01/27/2023] Open
Abstract
Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats.
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Affiliation(s)
- Hu Li
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - John M Leavengood
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Eric G Chapman
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Daniel Burkhardt
- Naturhistorisches Museum, Augustinergasse 2, 4001 Basel, Switzerland
| | - Fan Song
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Pei Jiang
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jinpeng Liu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Wanzhi Cai
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
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Puttick MN, Clark J, Donoghue PCJ. Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms. Proc Biol Sci 2017; 282:20152289. [PMID: 26631568 PMCID: PMC4685785 DOI: 10.1098/rspb.2015.2289] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.
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Affiliation(s)
- Mark N Puttick
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - James Clark
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW, Rieseberg LH, Barker MS. Early genome duplications in conifers and other seed plants. SCIENCE ADVANCES 2015; 1:e1501084. [PMID: 26702445 PMCID: PMC4681332 DOI: 10.1126/sciadv.1501084] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/14/2015] [Indexed: 05/18/2023]
Abstract
Polyploidy is a common mode of speciation and evolution in angiosperms (flowering plants). In contrast, there is little evidence to date that whole genome duplication (WGD) has played a significant role in the evolution of their putative extant sister lineage, the gymnosperms. Recent analyses of the spruce genome, the first published conifer genome, failed to detect evidence of WGDs in gene age distributions and attributed many aspects of conifer biology to a lack of WGDs. We present evidence for three ancient genome duplications during the evolution of gymnosperms, based on phylogenomic analyses of transcriptomes from 24 gymnosperms and 3 outgroups. We use a new algorithm to place these WGD events in phylogenetic context: two in the ancestry of major conifer clades (Pinaceae and cupressophyte conifers) and one in Welwitschia (Gnetales). We also confirm that a WGD hypothesized to be restricted to seed plants is indeed not shared with ferns and relatives (monilophytes), a result that was unclear in earlier studies. Contrary to previous genomic research that reported an absence of polyploidy in the ancestry of contemporary gymnosperms, our analyses indicate that polyploidy has contributed to the evolution of conifers and other gymnosperms. As in the flowering plants, the evolution of the large genome sizes of gymnosperms involved both polyploidy and repetitive element activity.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Anthony E. Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Moira Scascitelli
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Corresponding author. E-mail:
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Liu J, Zhou W, Gong X. Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China. FRONTIERS IN PLANT SCIENCE 2015; 6:696. [PMID: 26442013 PMCID: PMC4562272 DOI: 10.3389/fpls.2015.00696] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/21/2015] [Indexed: 06/02/2023]
Abstract
Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.
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Affiliation(s)
- Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Wei Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Yunnan Key Laboratory for Wild Plant ResourcesKunming, China
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Condamine FL, Nagalingum NS, Marshall CR, Morlon H. Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. BMC Evol Biol 2015; 15:65. [PMID: 25884423 PMCID: PMC4449600 DOI: 10.1186/s12862-015-0347-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/02/2015] [Indexed: 01/21/2023] Open
Abstract
Background Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0347-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique), Route de Saclay, 91128, Palaiseau, France. .,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Göteborg, Sweden.
| | - Nathalie S Nagalingum
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, NSW, 2000, Australia.
| | - Charles R Marshall
- Department of Integrative Biology and Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA, 94720-4780, USA.
| | - Hélène Morlon
- CNRS, UMR 8197 Institut de Biologie de l'École Normale Supérieure, 46 rue d'Ulm, 75005, Paris, France.
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Jiao Y, Paterson AH. Polyploidy-associated genome modifications during land plant evolution. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0355. [PMID: 24958928 DOI: 10.1098/rstb.2013.0355] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more 'particulate' understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.
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Affiliation(s)
- Yuannian Jiao
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30606, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30606, USA
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Duarte LDS, Bergamin RS, Marcilio-Silva V, Seger GDDS, Marques MCM. Phylobetadiversity among forest types in the Brazilian Atlantic Forest complex. PLoS One 2014; 9:e105043. [PMID: 25121495 PMCID: PMC4133375 DOI: 10.1371/journal.pone.0105043] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 07/20/2014] [Indexed: 11/18/2022] Open
Abstract
Phylobetadiversity is defined as the phylogenetic resemblance between communities or biomes. Analyzing phylobetadiversity patterns among different vegetation physiognomies within a single biome is crucial to understand the historical affinities between them. Based on the widely accepted idea that different forest physiognomies within the Southern Brazilian Atlantic Forest constitute different facies of a single biome, we hypothesize that more recent phylogenetic nodes should drive phylobetadiversity gradients between the different forest types within the Atlantic Forest, as the phylogenetic divergence among those forest types is biogeographically recent. We compiled information from 206 checklists describing the occurrence of shrub/tree species across three different forest physiognomies within the Southern Brazilian Atlantic Forest (Dense, Mixed and Seasonal forests). We analyzed intra-site phylogenetic structure (phylogenetic diversity, net relatedness index and nearest taxon index) and phylobetadiversity between plots located at different forest types, using five different methods differing in sensitivity to either basal or terminal nodes (phylogenetic fuzzy weighting, COMDIST, COMDISTNT, UniFrac and Rao's H). Mixed forests showed higher phylogenetic diversity and overdispersion than the other forest types. Furthermore, all forest types differed from each other in relation phylobetadiversity patterns, particularly when phylobetadiversity methods more sensitive to terminal nodes were employed. Mixed forests tended to show higher phylogenetic differentiation to Dense and Seasonal forests than these latter from each other. The higher phylogenetic diversity and phylobetadiversity levels found in Mixed forests when compared to the others likely result from the biogeographical origin of several taxa occurring in these forests. On one hand, Mixed forests shelter several temperate taxa, like the conifers Araucaria and Podocarpus. On the other hand, tropical groups, like Myrtaceae, are also very representative of this forest type. We point out to the need of more attention to Mixed forests as a conservation target within the Brazilian Atlantic Forest given their high phylogenetic uniqueness.
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Affiliation(s)
- Leandro Da Silva Duarte
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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14
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Augusto L, Davies TJ, Delzon S, De Schrijver A. The enigma of the rise of angiosperms: can we untie the knot? Ecol Lett 2014; 17:1326-38. [PMID: 24975818 DOI: 10.1111/ele.12323] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/02/2014] [Accepted: 06/10/2014] [Indexed: 11/29/2022]
Abstract
Multiple hypotheses have been put forward to explain the rise of angiosperms to ecological dominance following the Cretaceous. A unified scheme incorporating all these theories appears to be an inextricable knot of relationships, processes and plant traits. Here, we revisit these hypotheses, categorising them within frameworks based on plant carbon economy, resistance to climatic stresses, nutrient economy, biotic interactions and diversification. We maintain that the enigma remains unresolved partly because our current state of knowledge is a result of the fragmentary nature of palaeodata. This lack of palaeodata limits our ability to draw firm conclusions. Nonetheless, based on consistent results, some inferences may be drawn. Our results indicate that a complex multidriver hypothesis may be more suitable than any single-driver theory. We contend that plant carbon economy and diversification may have played an important role during the early stages of gymnosperms replacement by angiosperms in fertile tropical sites. Plant tolerance to climatic stresses, plant nutrition, biotic interactions and diversification may have played a role in later stages of angiosperm expansion within temperate and harsh environments. The angiosperm knot remains partly tied, but to unravel it entirely will only be feasible if new discoveries are made by scientific communities.
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Affiliation(s)
- L Augusto
- INRA, Bordeaux Sciences Agro, UMR 1391 ISPA, Villenave d'Ornon, 33882, France
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15
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Evolution and biogeography of gymnosperms. Mol Phylogenet Evol 2014; 75:24-40. [DOI: 10.1016/j.ympev.2014.02.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022]
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16
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Yessoufou K, Bamigboye SO, Daru BH, van der Bank M. Evidence of constant diversification punctuated by a mass extinction in the African cycads. Ecol Evol 2013; 4:50-8. [PMID: 24455160 PMCID: PMC3894887 DOI: 10.1002/ece3.880] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 10/12/2013] [Accepted: 10/14/2013] [Indexed: 11/29/2022] Open
Abstract
The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated.
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Affiliation(s)
- Kowiyou Yessoufou
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Samuel O Bamigboye
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Barnabas H Daru
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg P. O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
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17
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Wehe A, Burleigh JG, Eulenstein O. Efficient algorithms for knowledge-enhanced supertree and supermatrix phylogenetic problems. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:1432-1441. [PMID: 24407302 DOI: 10.1109/tcbb.2012.162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phylogenetic inference is a computationally difficult problem, and constructing high-quality phylogenies that can build upon existing phylogenetic knowledge and synthesize insights from new data remains a major challenge. We introduce knowledge-enhanced phylogenetic problems for both supertree and supermatrix phylogenetic analyses. These problems seek an optimal phylogenetic tree that can only be assembled from a user-supplied set of, possibly incompatible, phylogenetic relationships. We describe exact polynomial time algorithms for the knowledge-enhanced versions of the NP-hard Robinson Foulds, gene duplication, duplication and loss, and deep coalescence supertree problems. Further, we demonstrate that our algorithms can rapidly improve upon results of local search heuristics for these problems. Finally, we introduce a knowledge-enhanced search heuristic that can be applied to any discrete character data set using the maximum parsimony (MP) phylogenetic problem. Although this approach is not guaranteed to find exact solutions, we show that it also can improve upon solutions from commonly used MP heuristics.
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Affiliation(s)
- André Wehe
- University of Florida, Gainesville and Iowa State University, Ames
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18
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Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA. Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PLoS One 2013; 8:e72439. [PMID: 24023741 PMCID: PMC3762812 DOI: 10.1371/journal.pone.0072439] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/10/2013] [Indexed: 12/22/2022] Open
Abstract
Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (JLW); (KAS)
| | - Brian Y. Lin
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Jacob J. Zieve
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - William M. Dougherty
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Pedro J. Martínez-García
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Maxim Koriabine
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Ann Holtz-Morris
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Pieter deJong
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Marc Crepeau
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Steven L. Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - David B. Neale
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Kristian A. Stevens
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- * E-mail: (JLW); (KAS)
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Källman T, Chen J, Gyllenstrand N, Lagercrantz U. A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species. PLANT PHYSIOLOGY 2013; 162:741-54. [PMID: 23580593 PMCID: PMC3668067 DOI: 10.1104/pp.113.214643] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/29/2013] [Indexed: 05/18/2023]
Abstract
Small RNAs (sRNAs), including microRNA (miRNA) and short-interfering RNA (siRNA), are important in the regulation of diverse biological processes. Comparative studies of sRNAs from plants have mainly focused on miRNA, even though they constitute a mere fraction of the total sRNA diversity. In this study, we report results from an in-depth analysis of the sRNA population from the conifer spruce (Picea abies) and compared the results with those of a range of plant species. The vast majority of sRNA sequences in spruce can be assigned to 21-nucleotide-long siRNA sequences, of which a large fraction originate from the degradation of transcribed sequences related to nucleotide-binding site-leucine-rich repeat-type resistance genes. Over 90% of all genes predicted to contain either a Toll/interleukin-1 receptor or nucleotide-binding site domain showed evidence of siRNA degradation. The data further suggest that this phased degradation of resistance-related genes is initiated from miRNA-guided cleavage, often by an abundant 22-nucleotide miRNA. Comparative analysis over a range of plant species revealed a huge variation in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and nonvascular plants, while particularly high frequencies were observed in spruce, grape (Vitis vinifera), and poplar (Populus trichocarpa). This divergent pattern might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding nucleotide-binding site-leucine-rich repeat gene families. Alternatively, it might reflect variation in a counter-counter defense mechanism between plant species.
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Ramu A, Kahveci T, Burleigh JG. A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. BMC Bioinformatics 2012; 13:256. [PMID: 23033843 PMCID: PMC3543182 DOI: 10.1186/1471-2105-13-256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 09/05/2012] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. RESULTS We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods. CONCLUSIONS Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses.
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Affiliation(s)
- Avinash Ramu
- Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA
| | - Tamer Kahveci
- Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA
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