101
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Lehtonen S, Silvestro D, Karger DN, Scotese C, Tuomisto H, Kessler M, Peña C, Wahlberg N, Antonelli A. Environmentally driven extinction and opportunistic origination explain fern diversification patterns. Sci Rep 2017; 7:4831. [PMID: 28684788 PMCID: PMC5500532 DOI: 10.1038/s41598-017-05263-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/25/2017] [Indexed: 01/16/2023] Open
Abstract
Combining palaeontological and neontological data offers a unique opportunity to investigate the relative roles of biotic and abiotic controls of species diversification, and the importance of origination versus extinction in driving evolutionary dynamics. Ferns comprise a major terrestrial plant radiation with an extensive evolutionary history providing a wealth of modern and fossil data for modelling environmental drivers of diversification. Here we develop a novel Bayesian model to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories. We estimate the impact of different factors on fern diversification over the past 400 million years by analysing a comprehensive dataset of fossil occurrences and complement these findings by analysing a large molecular phylogeny. We show that origination and extinction rates are governed by fundamentally different processes: originations depend on within-group diversity but are largely unaffected by environmental changes, whereas extinctions are strongly affected by external factors such as climate and geology. Our results indicate that the prime driver of fern diversity dynamics is environmentally driven extinction, with origination being an opportunistic response to diminishing ecospace occupancy.
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Affiliation(s)
- Samuli Lehtonen
- Herbarium, Biodiversity Unit, University of Turku, 20014, Turku, Finland.
- Department of Biology, University of Turku, 20014, Turku, Finland.
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg, 413 19, Sweden.
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Gothenburg, Sweden.
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.
| | - Dirk Nikolaus Karger
- Department of Biology, University of Turku, 20014, Turku, Finland
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland
| | | | - Hanna Tuomisto
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland
| | - Carlos Peña
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Niklas Wahlberg
- Department of Biology, University of Turku, 20014, Turku, Finland
- Department of Biology, Lund University, Lund, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg, 413 19, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Gothenburg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
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102
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Insights into evolution in Andean Polystichum (Dryopteridaceae) from expanded understanding of the cytosolic phosphoglucose isomerase gene. Mol Phylogenet Evol 2017; 112:36-46. [PMID: 28411162 DOI: 10.1016/j.ympev.2017.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 03/08/2017] [Accepted: 04/10/2017] [Indexed: 12/19/2022]
Abstract
Cytosolic phosphoglucose isomerase (pgiC) is an enzyme essential to glycolysis found universally in eukaryotes, but broad understanding of variation in the gene coding for pgiC is lacking for ferns. We used a substantially expanded representation of the gene for Andean species of the fern genus Polystichum to characterize pgiC in ferns relative to angiosperms, insects, and an amoebozoan; assess the impact of selection versus neutral evolutionary processes on pgiC; and explore evolutionary relationships of selected Andean species. The dataset of complete sequences comprised nine accessions representing seven species and one hybrid from the Andes and Serra do Mar. The aligned sequences of the full data set comprised 3376 base pairs (70% of the entire gene) including 17 exons and 15 introns from two central areas of the gene. The exons are highly conserved relative to angiosperms and retain substantial homology to insect pgiC, but intron length and structure are unique to the ferns. Average intron size is similar to angiosperms; intron number and location in insects are unlike those of the plants we considered. The introns included an array of indels and, in intron 7, an extensive microsatellite array with potential utility in analyzing population-level histories. Bayesian and maximum-parsimony analysis of 129 variable nucleotides in the Andean polystichums revealed that 59 (1.7% of the 3376 total) were phylogenetically informative; most of these united sister accessions. The phylogenetic trees for the Andean polystichums were incongruent with previously published cpDNA trees for the same taxa, likely the result of rapid evolutionary change in the introns and contrasting stability in the exons. The exons code a total of seven amino-acid substitutions. Comparison of non-synonymous to synonymous substitutions did not suggest that the pgiC gene is under selection in the Andes. Variation in pgiC including two additional accessions represented by incomplete sequences provided new insights into reticulate relationships among Andean taxa.
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103
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Nitta JH, Meyer J, Taputuarai R, Davis CC. Life cycle matters:
DNA
barcoding reveals contrasting community structure between fern sporophytes and gametophytes. ECOL MONOGR 2017. [DOI: 10.1002/ecm.1246] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Joel H. Nitta
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria Harvard University Cambridge Massachusetts 02138 USA
| | - Jean‐Yves Meyer
- Délégation à la Recherche Government of French Polynesia B.P. 20981 Papeete, Tahiti French Polynesia
| | - Ravahere Taputuarai
- Association Te Rau Ati Ati a Tau a Hiti Noa Tu B.P. 11553 Mahina, Tahiti French Polynesia
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria Harvard University Cambridge Massachusetts 02138 USA
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104
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Roda F, Mendes FK, Hahn MW, Hopkins R. Genomic evidence of gene flow during reinforcement in Texas Phlox. Mol Ecol 2017; 26:2317-2330. [DOI: 10.1111/mec.14041] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Federico Roda
- Department of Organismic and Evolutionary Biology; The Arnold Arboretum of Harvard University; 1300 Centre Street Boston MA 02131 USA
| | - Fábio K. Mendes
- Department of Biology; Indiana University; 1001 E. Third Street Bloomington IN 47405 USA
| | - Matthew W. Hahn
- Department of Biology; Indiana University; 1001 E. Third Street Bloomington IN 47405 USA
- School of Informatics and Computing; Indiana University; 1001 E. Third Street Bloomington IN 47405 USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology; The Arnold Arboretum of Harvard University; 1300 Centre Street Boston MA 02131 USA
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105
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Gachet MS, Schubert A, Calarco S, Boccard J, Gertsch J. Targeted metabolomics shows plasticity in the evolution of signaling lipids and uncovers old and new endocannabinoids in the plant kingdom. Sci Rep 2017; 7:41177. [PMID: 28120902 PMCID: PMC5264637 DOI: 10.1038/srep41177] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/16/2016] [Indexed: 12/28/2022] Open
Abstract
The remarkable absence of arachidonic acid (AA) in seed plants prompted us to systematically study the presence of C20 polyunsaturated fatty acids, stearic acid, oleic acid, jasmonic acid (JA), N-acylethanolamines (NAEs) and endocannabinoids (ECs) in 71 plant species representative of major phylogenetic clades. Given the difficulty of extrapolating information about lipid metabolites from genetic data we employed targeted metabolomics using LC-MS/MS and GC-MS to study these signaling lipids in plant evolution. Intriguingly, the distribution of AA among the clades showed an inverse correlation with JA which was less present in algae, bryophytes and monilophytes. Conversely, ECs co-occurred with AA in algae and in the lower plants (bryophytes and monilophytes), thus prior to the evolution of cannabinoid receptors in Animalia. We identified two novel EC-like molecules derived from the eicosatetraenoic acid juniperonic acid, an omega-3 structural isomer of AA, namely juniperoyl ethanolamide and 2-juniperoyl glycerol in gymnosperms, lycophytes and few monilophytes. Principal component analysis of the targeted metabolic profiles suggested that distinct NAEs may occur in different monophyletic taxa. This is the first report on the molecular phylogenetic distribution of apparently ancient lipids in the plant kingdom, indicating biosynthetic plasticity and potential physiological roles of EC-like lipids in plants.
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Affiliation(s)
- María Salomé Gachet
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Alexandra Schubert
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Serafina Calarco
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Science, University of Geneva, University of Lausanne, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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106
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High temperature and UV-C treatments affect stilbenoid accumulation and related gene expression levels in Gnetum parvifolium. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2016.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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107
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Pastore AI, Scherer BP. Changes in community phylogenetic structure in a North American forest chronosequence. Ecosphere 2016. [DOI: 10.1002/ecs2.1592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Abigail I. Pastore
- Department of Biological Science Florida State University Tallahassee Florida 32306 USA
| | - Brendan P. Scherer
- Department of Biological Science Florida State University Tallahassee Florida 32306 USA
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108
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A 4000-species dataset provides new insight into the evolution of ferns. Mol Phylogenet Evol 2016; 105:200-211. [DOI: 10.1016/j.ympev.2016.09.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/03/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023]
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109
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Lee J, Cho CH, Park SI, Choi JW, Song HS, West JA, Bhattacharya D, Yoon HS. Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants. BMC Biol 2016; 14:75. [PMID: 27589960 PMCID: PMC5010701 DOI: 10.1186/s12915-016-0299-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0299-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Suk Song
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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110
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Mushegian A, Shipunov A, Elena SF. Changes in the composition of the RNA virome mark evolutionary transitions in green plants. BMC Biol 2016; 14:68. [PMID: 27524491 PMCID: PMC4983792 DOI: 10.1186/s12915-016-0288-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/25/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The known plant viruses mostly infect angiosperm hosts and have RNA or small DNA genomes. The only other lineage of green plants with a relatively well-studied virome, unicellular chlorophyte algae, is mostly infected by viruses with large DNA genomes. Thus RNA viruses and small DNA viruses seem to completely displace large DNA virus genomes in late branching angiosperms. To understand better the expansion of RNA viruses in the taxonomic span between algae and angiosperms, we analyzed the transcriptomes of 66 non-angiosperm plants characterized by the 1000 Plants Genomes Project. RESULTS We found homologs of virus RNA-dependent RNA polymerases in 28 non-angiosperm plant species, including algae, mosses, liverworts (Marchantiophyta), hornworts (Anthocerotophyta), lycophytes, a horsetail Equisetum, and gymnosperms. Polymerase genes in algae were most closely related to homologs from double-stranded RNA viruses leading latent or persistent lifestyles. Land plants, in addition, contained polymerases close to the homologs from single-stranded RNA viruses of angiosperms, capable of productive infection and systemic spread. For several polymerases, a cognate capsid protein was found in the same library. Another virus hallmark gene family, encoding the 30 K movement proteins, was found in lycophytes and monilophytes but not in mosses or algae. CONCLUSIONS The broadened repertoire of RNA viruses suggests that colonization of land and growth in anatomical complexity in land plants coincided with the acquisition of novel sets of viruses with different strategies of infection and reproduction.
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Affiliation(s)
- Arcady Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 4201 Wilson Boulevard, Arlington, VA, 22230, USA.
| | - Alexey Shipunov
- Department of Biology, Minot State University, 500 University Avenue West, Minot, ND, 58707, USA
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022, València, Spain
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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111
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Strömberg CAE, Di Stilio VS, Song Z. Functions of phytoliths in vascular plants: an evolutionary perspective. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12692] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Caroline A. E. Strömberg
- Department of Biology University of Washington Seattle WA 98195 USA
- Burke Museum of Natural History & Culture University of Washington Seattle WA 98195 USA
| | | | - Zhaoliang Song
- Department of Biology University of Washington Seattle WA 98195 USA
- Institute of the Surface‐Earth System Science Research Tianjin University Tianjin 300072 China
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112
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Eguchi S, Tamura MN. Evolutionary timescale of monocots determined by the fossilized birth-death model using a large number of fossil records. Evolution 2016; 70:1136-44. [DOI: 10.1111/evo.12911] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 03/25/2016] [Accepted: 03/27/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Satoshi Eguchi
- Department of Botany, Graduate School of Science; Kyoto University, Kitashirakawa-oiwake-cho; Sakyo-ku Kyoto 606-8502 Japan
| | - Minoru N. Tamura
- Department of Botany, Graduate School of Science; Kyoto University, Kitashirakawa-oiwake-cho; Sakyo-ku Kyoto 606-8502 Japan
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113
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Gastauer M, Meira-Neto JAA. An enhanced calibration of a recently released megatree for the analysis of phylogenetic diversity. BRAZ J BIOL 2016; 76:619-28. [DOI: 10.1590/1519-6984.20814] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 03/31/2015] [Indexed: 11/22/2022] Open
Abstract
Abstract Dated or calibrated phylogenetic trees, in which branch lengths correspond to evolutionary divergence times between nodes, are important requirements for computing measures of phylogenetic diversity or phylogenetic community structure. The increasing knowledge about the diversification and evolutionary divergence times of vascular plants requires a revision of the age estimates used for the calibration of phylogenetic trees by the bladj algorithm of the Phylocom 4.2 package. Comparing the recently released megatree R20120829.new with two calibrated vascular plant phylogenies provided in the literature, we found 242 corresponding nodes. We modified the megatree (R20120829mod.new), inserting names for all corresponding nodes. Furthermore, we provide files containing age estimates from both sources for the updated calibration of R20120829mod.new. Applying these files consistently in analyses of phylogenetic community structure or diversity serves to avoid erroneous measures and ecological misinterpretation.
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Affiliation(s)
- M. Gastauer
- Universidade Federal de Viçosa, Brazil; Centro de Ciências Ambientais Floresta-Escola, Brazil
| | - J. A. A. Meira-Neto
- Universidade Federal de Viçosa, Brazil; Centro de Ciências Ambientais Floresta-Escola, Brazil
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114
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Rose JP, Kriebel R, Sytsma KJ. Shape analysis of moss (Bryophyta) sporophytes: Insights into land plant evolution. AMERICAN JOURNAL OF BOTANY 2016; 103:652-62. [PMID: 26944353 DOI: 10.3732/ajb.1500394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/08/2016] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY The alternation of generations life cycle represents a key feature of land-plant evolution and has resulted in a diverse array of sporophyte forms and modifications in all groups of land plants. We test the hypothesis that evolution of sporangium (capsule) shape of the mosses-the second most diverse land-plant lineage-has been driven by differing physiological demands of life in diverse habitats. This study provides an important conceptual framework for analyzing the evolution of a single, homologous character in a continuous framework across a deep expanse of time, across all branches of the tree of life. METHODS We reconstruct ancestral sporangium shape and ancestral habitat on the largest phylogeny of mosses to date, and use phylogenetic generalized least squares regression to test the association between habitat and sporangium shape. In addition, we examine the association between shifts in sporangium shape and species diversification. RESULTS We demonstrate that sporangium shape is convergent, under natural selection, and associated with habitat type, and that many shifts in speciation rate are associated with shifts in sporangium shape. CONCLUSIONS Our results suggest that natural selection in different microhabitats results in the diversity of sporangium shape found in mosses, and that many increasing shifts in speciation rate result in changes in sporangium shape across their 480 million year history. Our framework provides a way to examine if diversification shifts in other land plants are also associated with massive changes in sporophyte form, among other morphological traits.
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Affiliation(s)
- Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706
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115
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Wang Q, Mao KS. Puzzling rocks and complicated clocks: how to optimize molecular dating approaches in historical phytogeography. THE NEW PHYTOLOGIST 2016; 209:1353-1358. [PMID: 26355284 DOI: 10.1111/nph.13676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Qian Wang
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Kang-Shan Mao
- Key Laboratory for Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
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116
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Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Sci Rep 2016; 6:21361. [PMID: 26892537 PMCID: PMC4759575 DOI: 10.1038/srep21361] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/19/2016] [Indexed: 11/08/2022] Open
Abstract
The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817-1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681-879) Ma], Nemaliophycidae [ca. 661 (597-736) Ma], Corallinophycidae [ca. 579 (543-617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442-580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.
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117
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Schneeberger K. Plant genic methylation: Conserved for 400 million years. NATURE PLANTS 2016; 2:16003. [PMID: 27249198 DOI: 10.1038/nplants.2016.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Korbinian Schneeberger
- Research Group Leader for Genome Plasticity and Computational Genetics at the Max Planck Institute for Plant Breeding Research, Cologne, Germany
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118
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McTaggart AR, Shivas RG, van der Nest MA, Roux J, Wingfield BD, Wingfield MJ. Host jumps shaped the diversity of extant rust fungi (Pucciniales). THE NEW PHYTOLOGIST 2016; 209:1149-1158. [PMID: 26459939 DOI: 10.1111/nph.13686] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 08/26/2015] [Indexed: 06/05/2023]
Abstract
The aim of this study was to determine the evolutionary time line for rust fungi and date key speciation events using a molecular clock. Evidence is provided that supports a contemporary view for a recent origin of rust fungi, with a common ancestor on a flowering plant. Divergence times for > 20 genera of rust fungi were studied with Bayesian evolutionary analyses. A relaxed molecular clock was applied to ribosomal and mitochondrial genes, calibrated against estimated divergence times for the hosts of rust fungi, such as Acacia (Fabaceae), angiosperms and the cupressophytes. Results showed that rust fungi shared a most recent common ancestor with a mean age between 113 and 115 million yr. This dates rust fungi to the Cretaceous period, which is much younger than previous estimations. Host jumps, whether taxonomically large or between host genera in the same family, most probably shaped the diversity of rust genera. Likewise, species diversified by host shifts (through coevolution) or via subsequent host jumps. This is in contrast to strict coevolution with their hosts. Puccinia psidii was recovered in Sphaerophragmiaceae, a family distinct from Raveneliaceae, which were regarded as confamilial in previous studies.
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Affiliation(s)
- Alistair R McTaggart
- Department of Microbiology and Plant Pathology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Roger G Shivas
- Department of Agriculture and Forestry, Queensland Plant Pathology Herbarium, GPO Box 267, Brisbane, Qld, 4001, Australia
| | - Magriet A van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Jolanda Roux
- Department of Plant Sciences, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
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Takuno S, Ran JH, Gaut BS. Evolutionary patterns of genic DNA methylation vary across land plants. NATURE PLANTS 2016; 2:15222. [PMID: 27249194 DOI: 10.1038/nplants.2015.222] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 12/18/2015] [Indexed: 05/18/2023]
Abstract
Little is known about patterns of genic DNA methylation across the plant kingdom or about the evolutionary processes that shape them. To characterize gene-body methylation (gbM) within exons, we have gathered single-base resolution methylome data that span the phylogenetic breadth of land plants. We find that a basal land plant, Marchantia polymorpha, lacks any evident signal of gbM within exons, but conifers have high levels of both CG and CHG (where H is A, C or T) methylation in expressed genes. To begin to understand the evolutionary forces that shape gbM, we first tested for correlations in methylation levels across orthologues(1,2). Genic CG methylation levels, but not CHG or CHH levels, are correlated across orthologues for species as distantly related as ferns and angiosperms. Hence, relative levels of CG methylation are a consistent property across genes, even for species that diverged ∼400 million years ago(3,4). In contrast, genic CHG methylation correlates with genome size, suggesting that the host epigenetic response to transposable elements also affects genes. Altogether, our data indicate that the evolutionary forces acting on DNA methylation vary substantially across species, genes and methylation contexts.
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Affiliation(s)
- Shohei Takuno
- SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, California 92697-2525, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, California 92697-2525, USA
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Gibbs AJ, Wood J, Garcia-Arenal F, Ohshima K, Armstrong JS. Tobamoviruses have probably co-diverged with their eudicotyledonous hosts for at least 110 million years. Virus Evol 2015; 1:vev019. [PMID: 27774289 PMCID: PMC5014485 DOI: 10.1093/ve/vev019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A phylogeny has been calculated by maximum likelihood comparisons of the concatenated consensus protein sequences of 29 tobamoviruses shown to be non-recombinant. This phylogeny has statistically significant support throughout, including its basal branches. The viruses form eight lineages that are congruent with the taxonomy of the hosts from which each was first isolated and, with the exception of three of the twenty-nine species, all fall into three clusters that have either asterid or rosid or caryophyllid hosts (i.e. the major subdivisions of eudicotyledonous plants). A modified Mantel permutation test showed that the patristic distances of virus and host phylogenies are significantly correlated, especially when the three anomalously placed viruses are removed. When the internal branches of the virus phylogeny were collapsed the congruence decreased. The simplest explanation of this congruence of the virus and host phylogenies is that most tobamovirus lineages have co-diverged with their primary plant hosts for more than 110 million years, and only the brassica-infecting lineage originated from a major host switch from asterids to rosids. Their co-divergence seems to have been ‘fuzzy’ rather than ‘strict’, permitting viruses to switch hosts within major host clades. Our conclusions support those of a coalesence analysis of tobamovirus sequences, that used proxy node dating, but not a similar analysis of nucleotide sequences from dated samples, which concluded that the tobamoviruses originated only 100 thousand years ago.
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Affiliation(s)
- Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Jeffrey Wood
- Statistical Consulting Unit, Australian National University, Canberra, ACT 2601, Australia
| | - Fernando Garcia-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain and
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - John S Armstrong
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
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Phillips MJ. Geomolecular Dating and the Origin of Placental Mammals. Syst Biol 2015; 65:546-57. [PMID: 26658702 DOI: 10.1093/sysbio/syv115] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
In modern evolutionary divergence analysis the role of geological information extends beyond providing a timescale, to informing molecular rate variation across the tree. Here I consider the implications of this development. I use fossil calibrations to test the accuracy of models of molecular rate evolution for placental mammals, and reveal substantial misspecification associated with life history rate correlates. Adding further calibrations to reduce dating errors at specific nodes unfortunately tends to transfer underlying rate errors to adjacent branches. Thus, tight calibration across the tree is vital to buffer against rate model errors. I argue that this must include allowing maximum bounds to be tight when good fossil records permit, otherwise divergences deep in the tree will tend to be inflated by the interaction of rate errors and asymmetric confidence in minimum and maximum bounds. In the case of placental mammals I sought to reduce the potential for transferring calibration and rate model errors across the tree by focusing on well-supported calibrations with appropriately conservative maximum bounds. The resulting divergence estimates are younger than others published recently, and provide the long-anticipated molecular signature for the placental mammal radiation observed in the fossil record near the 66 Ma Cretaceous-Paleogene extinction event.
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Affiliation(s)
- Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
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Kitagawa R, Mimura M, Mori AS, Sakai A. Topographic patterns in the phylogenetic structure of temperate forests on steep mountainous terrain. AOB PLANTS 2015; 7:plv134. [PMID: 26602986 PMCID: PMC4683994 DOI: 10.1093/aobpla/plv134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/20/2015] [Indexed: 05/10/2023]
Abstract
In rugged terrain subject to active geomorphological processes, the species composition of forest communities changes along topographic gradients over short distances. However, the phylogenetic structure of forests on rugged terrain has rarely been examined. Understanding such structures provides insight into community assembly rules dependent on local environmental conditions. To this end, we tested the topographic trends of measurements of phylogenetic community structure [net relatedness index (NRI) and nearest taxon index] in a catchment covered by temperate forests with complex relief in Japan. We found that phylogenetic structure changed from over-dispersion to clustering with increasing slope inclination, change of slope aspect from south to north and decreasing soil depth. This result suggested that environmental filtering tended to restrict community composition at relatively stressful sites, whereas species interaction functioned more strongly at relatively stress-free sites. Relatively stressful sites were characterized by early-successional species that tended to assemble in certain phylogenetic clades, whereas highly competitive late-successional species associated with lower NRI at relatively stress-free sites. However, despite this significant topographic tendency, phylogenetic community structures were not statistically different from random assumptions in most plots. This obscuration of the phylogenetic structures at the plot level could be interpreted as species adapting to disturbances because they were abundant in this catchment. Accordingly, we suggest that a stochastic process was also important for this community at the plot level, although biotic and abiotic environmental filtering controlled the vegetation structure in the catchment, where disturbances occur frequently because of geomorphological mountain denudation processes owing to active crustal movements and abundant rainfall.
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Affiliation(s)
- Ryo Kitagawa
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Makiko Mimura
- Department of BioEnvironmental Sciences, Tamagawa University, 6-1-1 Tamagawa gakuen, Machida, Tokyo 194-8610, Japan
| | - Akira S Mori
- Environment and Information Sciences, Yokohama National University, 79-1 Tokiwadai, Hodogaya Ward, Yokohama 240-8501, Japan
| | - Akiko Sakai
- Environment and Information Sciences, Yokohama National University, 79-1 Tokiwadai, Hodogaya Ward, Yokohama 240-8501, Japan
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Huang Y, Ji X, Su T, Wang L, Deng C, Li W, Luo H, Zhou Z. Fossil seeds of Euryale (Nymphaeaceae) indicate a lake or swamp environment in the late Miocene Zhaotong Basin of southwestern China. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0870-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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125
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Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015; 91:98-122. [DOI: 10.1016/j.ympev.2015.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/01/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
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126
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Barthet MM, Moukarzel K, Smith KN, Patel J, Hilu KW. Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae. BMC Evol Biol 2015. [PMID: 26416561 DOI: 10.1186/s12862-015-0491-491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. RESULTS Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. CONCLUSION These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Keenan Moukarzel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Kayla N Smith
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
| | - Jaimin Patel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Khidir W Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
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127
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Barthet MM, Moukarzel K, Smith KN, Patel J, Hilu KW. Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae. BMC Evol Biol 2015; 15:210. [PMID: 26416561 PMCID: PMC4587860 DOI: 10.1186/s12862-015-0491-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/20/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The plastid maturase MatK has been implicated as a possible model for the evolutionary "missing link" between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. RESULTS Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. CONCLUSION These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Keenan Moukarzel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Kayla N Smith
- Department of Biology, Coastal Carolina University, Conway, SC, 29526, USA.
| | - Jaimin Patel
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
| | - Khidir W Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA.
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128
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The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift. Proc Natl Acad Sci U S A 2015; 112:11600-5. [PMID: 26324894 DOI: 10.1073/pnas.1507072112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Adaptive radiations play key roles in the generation of biodiversity and biological novelty, and therefore understanding the factors that drive them remains one of the most important challenges of evolutionary biology. Although both intrinsic innovations and extrinsic ecological opportunities contribute to diversification bursts, few studies have looked at the synergistic effect of such factors. Here we investigate the Teloschistales (Ascomycota), a group of >1,000 lichenized species with variation in species richness and phenotypic traits that hinted at a potential adaptive radiation. We found evidence for a dramatic increase in diversification rate for one of four families within this order--Teloschistaceae--which occurred ∼ 100 Mya (Late Cretaceous) and was associated with a switch from bark to rock and from shady to sun-exposed habitats. This adaptation to sunny habitats is likely to have been enabled by a contemporaneous key novel phenotypic innovation: the production in both vegetative structure (thallus) and fruiting body (apothecia) of anthraquinones, secondary metabolites known to protect against UV light. We found that the two ecological factors (sun exposure and rock substrate) and the phenotypic innovation (anthraquinones in the thallus) were all significant when testing for state-dependent shifts in diversification rates, and together they seem likely to be responsible for the success of the Teloschistaceae, one of the largest lichen-forming fungal lineages. Our results support the idea that adaptive radiations are driven not by a single factor or key innovation, but require a serendipitous combination of both intrinsic biotic and extrinsic abiotic and ecological factors.
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129
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Legendre F, Nel A, Svenson GJ, Robillard T, Pellens R, Grandcolas P. Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence. PLoS One 2015; 10:e0130127. [PMID: 26200914 PMCID: PMC4511787 DOI: 10.1371/journal.pone.0130127] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/18/2015] [Indexed: 12/03/2022] Open
Abstract
Understanding the origin and diversification of organisms requires a good phylogenetic estimate of their age and diversification rates. This estimate can be difficult to obtain when samples are limited and fossil records are disputed, as in Dictyoptera. To choose among competing hypotheses of origin for dictyopteran suborders, we root a phylogenetic analysis (~800 taxa, 10 kbp) within a large selection of outgroups and calibrate datings with fossils attributed to lineages with clear synapomorphies. We find the following topology: (mantises, (other cockroaches, (Cryptocercidae, termites)). Our datings suggest that crown-Dictyoptera-and stem-mantises-would date back to the Late Carboniferous (~ 300 Mya), a result compatible with the oldest putative fossil of stem-dictyoptera. Crown-mantises, however, would be much more recent (~ 200 Mya; Triassic/Jurassic boundary). This pattern (i.e., old origin and more recent diversification) suggests a scenario of replacement in carnivory among polyneopterous insects. The most recent common ancestor of (cockroaches + termites) would date back to the Permian (~275 Mya), which contradicts the hypothesis of a Devonian origin of cockroaches. Stem-termites would date back to the Triassic/Jurassic boundary, which refutes a Triassic origin. We suggest directions in extant and extinct species sampling to sharpen this chronological framework and dictyopteran evolutionary studies.
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Affiliation(s)
- Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - André Nel
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Gavin J. Svenson
- Department of Invertebrate Zoology, Cleveland Museum of Natural History, Cleveland, Ohio, United States of America
| | - Tony Robillard
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Roseli Pellens
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Philippe Grandcolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
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130
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Chomicki G, Renner SS. Phylogenetics and molecular clocks reveal the repeated evolution of ant-plants after the late Miocene in Africa and the early Miocene in Australasia and the Neotropics. THE NEW PHYTOLOGIST 2015; 207:411-424. [PMID: 25616013 DOI: 10.1111/nph.13271] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/04/2014] [Indexed: 06/04/2023]
Abstract
Ant-plant symbioses involve over 110 ant species in five subfamilies that are facultative or obligate occupants of stem, leaf or root domatia formed by hundreds of ant-plant species. The phylogenetic distribution and geological ages of these associations, and the frequency of gains or losses of domatium, are largely unknown. We compiled an up-to-date list of ant domatium-bearing plants, estimated their probable true number from model-based statistical inference, generated dated phylogenies that include c. 50% of ant-plant lineages, and traced the occurrence of domatia and extrafloral nectaries on a 1181-species tree, using likelihood and Bayesian methods. We found 681 vascular plants with domatia (159 genera in 50 families) resulting from minimally 158 inferred domatium origins and 43 secondary losses over the last 19 Myr. The oldest African ant-plant symbioses are younger than those in Australasia and the Neotropics. The best statistical model suggests that the true number of myrmecophytes may approach 1140 species. The phylogenetic distribution of ant-plants shows that domatia evolved from a range of pre-adapted morphological structures and have been lost frequently, suggesting that domatia have no generalizable effect on diversification. The Miocene origin of ant-plant symbioses is consistent with inferred changes in diet and behaviour during ant evolution.
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Affiliation(s)
- Guillaume Chomicki
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, 80638, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, 80638, Germany
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131
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Silvestro D, Cascales‐Miñana B, Bacon CD, Antonelli A. Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. THE NEW PHYTOLOGIST 2015; 207:425-436. [PMID: 25619401 PMCID: PMC4949670 DOI: 10.1111/nph.13247] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/23/2014] [Indexed: 05/18/2023]
Abstract
Plants have a long evolutionary history, during which mass extinction events dramatically affected Earth's ecosystems and its biodiversity. The fossil record can shed light on the diversification dynamics of plant life and reveal how changes in the origination-extinction balance have contributed to shaping the current flora. We use a novel Bayesian approach to estimate origination and extinction rates in plants throughout their history. We focus on the effect of the 'Big Five' mass extinctions and on estimating the timing of origin of vascular plants, seed plants and angiosperms. Our analyses show that plant diversification is characterized by several shifts in origination and extinction rates, often matching the most important geological boundaries. The estimated origin of major plant clades predates the oldest macrofossils when considering the uncertainties associated with the fossil record and the preservation process. Our findings show that the commonly recognized mass extinctions have affected each plant group differently and that phases of high extinction often coincided with major floral turnovers. For instance, after the Cretaceous-Paleogene boundary we infer negligible shifts in diversification of nonflowering seed plants, but find significantly decreased extinction in spore-bearing plants and increased origination rates in angiosperms, contributing to their current ecological and evolutionary dominance.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental SciencesUniversity of GothenburgCarl Skottsbergs gata 22BSE‐413 19GöteborgSweden
| | - Borja Cascales‐Miñana
- CNRSUMR Botanique et Bioinformatique de l'Architecture des Plantes (AMAP)MontpellierF‐34000France
- Present address: PPPDépartement de GéologieUniversité de LiègeAllée du 6 AoûtB18 Sart TilmanB4000LiègeBelgium
| | - Christine D. Bacon
- Department of Biological and Environmental SciencesUniversity of GothenburgCarl Skottsbergs gata 22BSE‐413 19GöteborgSweden
- Laboratório de Biología Molecular (CINBIN)Department of BiologyUniversidad Industrial de SantanderBucaramangaColombia
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of GothenburgCarl Skottsbergs gata 22BSE‐413 19GöteborgSweden
- Gothenburg Botanical GardenCarl Skottsbergs gata 22ASE‐413 19GöteborgSweden
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132
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Magallón S, Gómez-Acevedo S, Sánchez-Reyes LL, Hernández-Hernández T. A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. THE NEW PHYTOLOGIST 2015; 207:437-453. [PMID: 25615647 DOI: 10.1111/nph.13264] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/21/2014] [Indexed: 05/03/2023]
Abstract
The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135-130 million yr ago (Ma); Pentapetalae is 126-121 Ma; and Rosidae (123-115 Ma) preceded Asteridae (119-110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.
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Affiliation(s)
- Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sandra Gómez-Acevedo
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luna L Sánchez-Reyes
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation. Proc Natl Acad Sci U S A 2015; 112:6407-12. [PMID: 25941377 DOI: 10.1073/pnas.1416679112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bat-moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼ 26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18-14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.
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Ksepka DT, Parham JF, Allman JF, Benton MJ, Carrano MT, Cranston KA, Donoghue PCJ, Head JJ, Hermsen EJ, Irmis RB, Joyce WG, Kohli M, Lamm KD, Leehr D, Patané JL, Polly PD, Phillips MJ, Smith NA, Smith ND, Van Tuinen M, Ware JL, Warnock RCM. The Fossil Calibration Database—A New Resource for Divergence Dating. Syst Biol 2015; 64:853-9. [DOI: 10.1093/sysbio/syv025] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/22/2015] [Indexed: 01/10/2023] Open
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Edwards D, Kenrick P. The early evolution of land plants, from fossils to genomics: a commentary on Lang (1937) 'On the plant-remains from the Downtonian of England and Wales'. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140343. [PMID: 25750238 PMCID: PMC4360123 DOI: 10.1098/rstb.2014.0343] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the 1920s, the botanist W. H. Lang set out to collect and investigate some very unpromising fossils of uncertain affinity, which predated the known geological record of life on land. His discoveries led to a landmark publication in 1937, 'On the plant-remains from the Downtonian of England and Wales', in which he revealed a diversity of small fossil organisms of great simplicity that shed light on the nature of the earliest known land plants. These and subsequent discoveries have taken on new relevance as botanists seek to understand the plant genome and the early evolution of fundamental organ systems. Also, our developing knowledge of the composition of early land-based ecosystems and the interactions among their various components is contributing to our understanding of how life on land affects key Earth Systems (e.g. carbon cycle). The emerging paradigm is one of early life on land dominated by microbes, small bryophyte-like organisms and lichens. Collectively called cryptogamic covers, these are comparable with those that dominate certain ecosystems today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.
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Affiliation(s)
- Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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136
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Lind C, Dreyer I, López-Sanjurjo EJ, von Meyer K, Ishizaki K, Kohchi T, Lang D, Zhao Y, Kreuzer I, Al-Rasheid KAS, Ronne H, Reski R, Zhu JK, Geiger D, Hedrich R. Stomatal guard cells co-opted an ancient ABA-dependent desiccation survival system to regulate stomatal closure. Curr Biol 2015; 25:928-35. [PMID: 25802151 DOI: 10.1016/j.cub.2015.01.067] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 01/14/2015] [Accepted: 01/22/2015] [Indexed: 01/12/2023]
Abstract
During the transition from water to land, plants had to cope with the loss of water through transpiration, the inevitable result of photosynthetic CO2 fixation on land [1, 2]. Control of transpiration became possible through the development of a new cell type: guard cells, which form stomata. In vascular plants, stomatal regulation is mediated by the stress hormone ABA, which triggers the opening of the SnR kinase OST1-activated anion channel SLAC1 [3, 4]. To understand the evolution of this regulatory circuit, we cloned both ABA-signaling elements, SLAC1 and OST1, from a charophyte alga, a liverwort, and a moss, and functionally analyzed the channel-kinase interactions. We were able to show that the emergence of stomata in the last common ancestor of mosses and vascular plants coincided with the origin of SLAC1-type channels capable of using the ancient ABA drought signaling kinase OST1 for regulation of stomatal closure.
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Affiliation(s)
- Christof Lind
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Ingo Dreyer
- Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón (Madrid), Spain; Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Enrique J López-Sanjurjo
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Katharina von Meyer
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Kimitsune Ishizaki
- Laboratory of Plant Molecular Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takayuki Kohchi
- Laboratory of Plant Molecular Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, BIOSS Centre for Biological Signalling Studies, and FRIAS Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Ines Kreuzer
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Hans Ronne
- Department of Microbiology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, BIOSS Centre for Biological Signalling Studies, and FRIAS Freiburg Institute for Advanced Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Dietmar Geiger
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany.
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, 97082 Würzburg, Germany
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137
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Massoni J, Couvreur TLP, Sauquet H. Five major shifts of diversification through the long evolutionary history of Magnoliidae (angiosperms). BMC Evol Biol 2015; 15:49. [PMID: 25887386 PMCID: PMC4377182 DOI: 10.1186/s12862-015-0320-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/24/2015] [Indexed: 11/13/2022] Open
Abstract
Background With 10,000 species, Magnoliidae are the largest clade of flowering plants outside monocots and eudicots. Despite an ancient and rich fossil history, the tempo and mode of diversification of Magnoliidae remain poorly known. Using a molecular data set of 12 markers and 220 species (representing >75% of genera in Magnoliidae) and six robust, internal fossil age constraints, we estimate divergence times and significant shifts of diversification across the clade. In addition, we test the sensitivity of magnoliid divergence times to the choice of relaxed clock model and various maximum age constraints for the angiosperms. Results Compared with previous work, our study tends to push back in time the age of the crown node of Magnoliidae (178.78-126.82 million years, Myr), and of the four orders, Canellales (143.18-125.90 Myr), Piperales (158.11-88.15 Myr), Laurales (165.62-112.05 Myr), and Magnoliales (164.09-114.75 Myr). Although families vary in crown ages, Magnoliidae appear to have diversified into most extant families by the end of the Cretaceous. The strongly imbalanced distribution of extant diversity within Magnoliidae appears to be best explained by models of diversification with 6 to 13 shifts in net diversification rates. Significant increases are inferred within Piperaceae and Annonaceae, while the low species richness of Calycanthaceae, Degeneriaceae, and Himantandraceae appears to be the result of decreases in both speciation and extinction rates. Conclusions This study provides a new time scale for the evolutionary history of an important, but underexplored, part of the tree of angiosperms. The ages of the main clades of Magnoliidae (above the family level) are older than previously thought, and in several lineages, there were significant increases and decreases in net diversification rates. This study is a new robust framework for future investigations of trait evolution and of factors influencing diversification in this group as well as angiosperms as a whole. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0320-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julien Massoni
- Laboratoire Ecologie, Systématique, Evolution, Université Paris-Sud, CNRS UMR 8079, 91405, Orsay, France.
| | - Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, 911, avenue Agropolis, BP 64501, Cedex 5, F-34394, Montpellier, France. .,Département des Sciences Biologiques, Université de Yaoundé I, Ecole Normale Supérieure, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon.
| | - Hervé Sauquet
- Laboratoire Ecologie, Systématique, Evolution, Université Paris-Sud, CNRS UMR 8079, 91405, Orsay, France.
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138
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Chen KH, Miadlikowska J, Molnár K, Arnold AE, U'Ren JM, Gaya E, Gueidan C, Lutzoni F. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales. Mol Phylogenet Evol 2015; 85:117-30. [PMID: 25701073 DOI: 10.1016/j.ympev.2015.01.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/10/2014] [Accepted: 01/20/2015] [Indexed: 01/26/2023]
Abstract
Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.
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Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | | | - Katalin Molnár
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
| | - Jana M U'Ren
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
| | - Ester Gaya
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Cécile Gueidan
- Australia National Herbarium, CSIRO, GPO Box 1600, Canberra, ACT 2601, Australia
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139
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Zheng Y, Wiens JJ. Do missing data influence the accuracy of divergence-time estimation with BEAST? Mol Phylogenet Evol 2015; 85:41-9. [PMID: 25681677 DOI: 10.1016/j.ympev.2015.02.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/26/2015] [Accepted: 02/01/2015] [Indexed: 10/24/2022]
Abstract
Time-calibrated phylogenies have become essential to evolutionary biology. A recurrent and unresolved question for dating analyses is whether genes with missing data cells should be included or excluded. This issue is particularly unclear for the most widely used dating method, the uncorrelated lognormal approach implemented in BEAST. Here, we test the robustness of this method to missing data. We compare divergence-time estimates from a nearly complete dataset (20 nuclear genes for 32 species of squamate reptiles) to those from subsampled matrices, including those with 5 or 2 complete loci only and those with 5 or 8 incomplete loci added. In general, missing data had little impact on estimated dates (mean error of ∼5Myr per node or less, given an overall age of ∼220Myr in squamates), even when 80% of sampled genes had 75% missing data. Mean errors were somewhat higher when all genes were 75% incomplete (∼17Myr). However, errors increased dramatically when only 2 of 9 fossil calibration points were included (∼40Myr), regardless of missing data. Overall, missing data (and even numbers of genes sampled) may have only minor impacts on the accuracy of divergence dating with BEAST, relative to the dramatic effects of fossil calibrations.
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Affiliation(s)
- Yuchi Zheng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-088, USA.
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-088, USA.
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140
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Vanneste K, Maere S, Van de Peer Y. Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0353. [PMID: 24958926 PMCID: PMC4071526 DOI: 10.1098/rstb.2013.0353] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Genome sequencing has demonstrated that besides frequent small-scale duplications, large-scale duplication events such as whole genome duplications (WGDs) are found on many branches of the evolutionary tree of life. Especially in the plant lineage, there is evidence for recurrent WGDs, and the ancestor of all angiosperms was in fact most likely a polyploid species. The number of WGDs found in sequenced plant genomes allows us to investigate questions about the roles of WGDs that were hitherto impossible to address. An intriguing observation is that many plant WGDs seem associated with periods of increased environmental stress and/or fluctuations, a trend that is evident for both present-day polyploids and palaeopolyploids formed around the Cretaceous–Palaeogene (K–Pg) extinction at 66 Ma. Here, we revisit the WGDs in plants that mark the K–Pg boundary, and discuss some specific examples of biological innovations and/or diversifications that may be linked to these WGDs. We review evidence for the processes that could have contributed to increased polyploid establishment at the K–Pg boundary, and discuss the implications on subsequent plant evolution in the Cenozoic.
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Affiliation(s)
- Kevin Vanneste
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute (GRI), University of Pretoria, 0028 Pretoria, South Africa
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141
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Sohn JC, Labandeira CC, Davis DR. The fossil record and taphonomy of butterflies and moths (Insecta, Lepidoptera): implications for evolutionary diversity and divergence-time estimates. BMC Evol Biol 2015; 15:12. [PMID: 25649001 PMCID: PMC4326409 DOI: 10.1186/s12862-015-0290-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/15/2015] [Indexed: 11/22/2022] Open
Abstract
Background It is conventionally accepted that the lepidopteran fossil record is significantly incomplete when compared to the fossil records of other, very diverse, extant insect orders. Such an assumption, however, has been based on cumulative diversity data rather than using alternative statistical approaches from actual specimen counts. Results We reviewed documented specimens of the lepidopteran fossil record, currently consisting of 4,593 known specimens that are comprised of 4,262 body fossils and 331 trace fossils. The temporal distribution of the lepidopteran fossil record shows significant bias towards the late Paleocene to middle Eocene time interval. Lepidopteran fossils also record major shifts in preservational style and number of represented localities at the Mesozoic stage and Cenozoic epoch level of temporal resolution. Only 985 of the total known fossil specimens (21.4%) were assigned to 23 of the 40 extant lepidopteran superfamilies. Absolute numbers and proportions of preservation types for identified fossils varied significantly across superfamilies. The secular increase of lepidopteran family-level diversity through geologic time significantly deviates from the general pattern of other hyperdiverse, ordinal-level lineages. Conclusion Our statistical analyses of the lepidopteran fossil record show extreme biases in preservation type, age, and taxonomic composition. We highlight the scarcity of identified lepidopteran fossils and provide a correspondence between the latest lepidopteran divergence-time estimates and relevant fossil occurrences at the superfamily level. These findings provide caution in interpreting the lepidopteran fossil record through the modeling of evolutionary diversification and in determination of divergence time estimates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0290-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jae-Cheon Sohn
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA. .,Department of Paleobiology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA. .,Department of Entomology, University of Maryland, College Park, MD, USA.
| | - Conrad C Labandeira
- Department of Paleobiology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA. .,Department of Entomology, University of Maryland, College Park, MD, USA. .,College of Life Sciences, Capital Normal University, Beijing, China.
| | - Donald R Davis
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.
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142
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Povilus RA, Losada JM, Friedman WE. Floral biology and ovule and seed ontogeny of Nymphaea thermarum, a water lily at the brink of extinction with potential as a model system for basal angiosperms. ANNALS OF BOTANY 2015; 115:211-26. [PMID: 25497514 PMCID: PMC4551091 DOI: 10.1093/aob/mcu235] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Nymphaea thermarum is a member of the Nymphaeales, of one of the most ancient lineages of flowering plants. This species was only recently described and then declared extinct in the wild, so little is known about its reproductive biology. In general, the complete ontogeny of ovules and seeds is not well documented among species of Nymphaea and has never been studied in the subgenus Brachyceras, the clade to which N. thermarum belongs. METHODS Flowers and fruits were processed for brightfield, epifluorescence and confocal microscopy. Flower morphology, with emphasis on the timing of male and female functions, was correlated with key developmental stages of the ovule and the female gametophyte. Development of the seed tissues and dynamics of polysaccharide reserves in the endosperm, perisperm and embryo were examined. KEY RESULTS Pollen release in N. thermarum starts before the flower opens. Cell walls of the micropylar nucellus show layering of callose and cellulose in a manner reminiscent of transfer cell wall patterning. Endosperm development is ab initio cellular, with micropylar and chalazal domains that embark on distinct developmental trajectories. The surrounding maternal perisperm occupies the majority of seed volume and accumulates starch centrifugally. In mature seeds, a minute but fully developed embryo is surrounded by a single, persistent layer of endosperm. CONCLUSIONS Early male and female function indicate that N. thermarum is predisposed towards self-pollination, a phenomenon that is likely to have evolved multiple times within Nymphaea. While formation of distinct micropylar and chalazal developmental domains in the endosperm, along with a copious perisperm, characterize the seeds of most members of the Nymphaeales, seed ontogenies vary between and among the constituent families. Floral biology, life history traits and small genome size make N. thermarum uniquely promising as an early-diverging angiosperm model system for genetic and molecular studies.
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Affiliation(s)
- Rebecca A Povilus
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA and Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA 02131, USA
| | - Juan M Losada
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA and Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA 02131, USA Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA and Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA 02131, USA
| | - William E Friedman
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA and Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA 02131, USA Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA and Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA 02131, USA
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143
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Gibbs AJ, Nguyen HD, Ohshima K. The 'emergence' of turnip mosaic virus was probably a 'gene-for-quasi-gene' event. Curr Opin Virol 2015; 10:20-6. [PMID: 25559881 DOI: 10.1016/j.coviro.2014.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 11/18/2022]
Abstract
Turnip mosaic potyvirus is a virus of brassicas that emerged from a lineage of monocotyledon-infecting potyviruses about 1000 years ago. In vivo and in silico studies all indicate that sites, primarily in its protein 3 (P3) and cylindrical inclusion protein (CI) genes, but also its small 6 kDa 2 protein (6K2) and genome-linked viral protein (VPg) genes, control host specificity in a dynamic way. It is most likely that non-unique combinations of transient viral genomic single nucleotide polymorphisms (SNPs), not all of them non-synonymous, allowed the host switch to occur. These SNPs were probably ephemeral and replaced over time by other combinations as the population subsequently diverged within, and adapted to, the brassica host population.
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Affiliation(s)
- Adrian J Gibbs
- Australian National University Emeritus Faculty, Canberra, ACT 2601, Australia.
| | - Huy Duc Nguyen
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan; Department of Plant Pathology, Faculty of Agronomy, Vietnam National University of Agriculture, Trauquy, Gialam, Hanoi, Viet Nam
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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144
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Cardona-Correa C, Ecker A, Graham LE. Direction of illumination controls gametophyte orientation in seedless plants and related algae. PLANT SIGNALING & BEHAVIOR 2015; 10:e1051277. [PMID: 26237278 PMCID: PMC4883941 DOI: 10.1080/15592324.2015.1051277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
Abstract
The environmental influences that determine dorsiventral or axial gametophyte orientation are unknown for most modern seedless plants. To fill this gap, an experimental laboratory system was employed to evaluate the relative effects of light direction and gravity on body orientation of the dorsiventral green alga Coleochaete orbicularis, and gametophytes of liverworts Blasia pusilla and Marchantia polymorpha, early-diverging moss Sphagnum compactum, and fern Ceratopteris richardii, the latter functioning as experimental control. Replicate clonal cultures were experimentally illuminated only from above, only from below, or from multiple directions, with the same near-saturation PAR level for periods brief enough to minimize nutrient limitation effects, and orientation of new growth was evaluated. For all species tested, direction of illumination exerted stronger control over gametophyte body orientation than gravity. When illuminated only from below: 1) axial Sphagnum gametophores that had initially grown into an overlying air space inverted growth by 180°, burrowing into the substrate; 2) new growth of dorsiventral Blasia, Marchantia, and Ceratopteris gametophytes-whose ventral rhizoids initially penetrated agar substrate and dorsal surfaces initially faced overlying airspace-twisted 180° so that ventral surfaces bearing rhizoids faced overlying air space and rhizoids extended into the air; and 3) Coleochaete lost typical dorsiventral organization and diagnostic dorsal hairs. Direction of illumination also exerted stronger control over orientation of liverwort new growth than surface contact did. These results indicate that early land plants likely inherited light-directed gametophyte body orientation from ancestral streptophyte algae and suggest a mechanism for reorientation of gametophyte-dominant land plants after spatial disturbance.
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Affiliation(s)
| | - Alice Ecker
- Department of Botany; University of Wisconsin-Madison; Madison, WI USA
| | - Linda E Graham
- Department of Botany; University of Wisconsin-Madison; Madison, WI USA
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145
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Losada JM, Herrero M, Hormaza JI, Friedman WE. Arabinogalactan proteins mark stigmatic receptivity in the protogynous flowers of Magnolia virginiana (Magnoliaceae). AMERICAN JOURNAL OF BOTANY 2014; 101:1963-75. [PMID: 25366861 DOI: 10.3732/ajb.1400280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY Factors affecting floral receptivity in angiosperms remain opaque, but recent studies suggest that the acquisition of stigmatic receptivity associated with cell-wall-related arabinogalactan proteins (AGPs) may be a widespread feature of flowering plants. Here, the time during which a stigma is receptive is evaluated and related to the secretion of AGPs in Magnolia virginiana, a protogynous member of an early-divergent angiosperm clade (magnoliids) with a clearly discernible female receptive phase. METHODS Magnolia virginiana flower phenology was documented, and histochemical changes in the stigma before and after pollination were examined. Stigmatic receptivity was evaluated in relation to the secretion of AGPs detected in whole mounts and immunolocalized in sectioned stigmas. KEY RESULTS Protogynous Magnolia flowers had a precise window of stigmatic receptivity, which is concomitant with the secretion of two AGPs labeled for different epitopes. After pollen germination and tube growth, these two AGPs could no longer be detected in the stigmas, suggesting that these AGPs interact with the growing male gametophytes and could be markers of stigmatic receptivity. CONCLUSIONS These results show that the period of stigmatic receptivity is finely coordinated with the secretion of two arabinogalactan proteins on stigmas of flowers of M. virginiana. This first report of AGP presence in stigmatic tissues in a member of the magnoliids, together with recently described similar patterns in eudicots, monocots, and members of early-divergent lineages of flowering plants, suggests an ancient and widespread role for AGPs on stigmatic receptivity in angiosperms.
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Affiliation(s)
- Juan M Losada
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138 USA Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, Massachusetts 02131 USA
| | - Maria Herrero
- Department of Pomology, Aula Dei Experimental Station-CSIC, 1005 Avda. Montañana, Zaragoza, Spain 50059
| | - Jose I Hormaza
- Department of Subtropical Fruits, Instituto de Hortofruticultura Subtropical y Mediterránea "la Mayora," (IHSM la Mayora-CSIC-UMA), Algarrobo-Costa, Málaga, Spain 29750
| | - William E Friedman
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138 USA Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, Massachusetts 02131 USA
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146
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Peele HM, Guan N, Fogelqvist J, Dixelius C. Loss and retention of resistance genes in five species of the Brassicaceae family. BMC PLANT BIOLOGY 2014; 14:298. [PMID: 25365911 PMCID: PMC4232680 DOI: 10.1186/s12870-014-0298-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/20/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Plants have evolved disease resistance (R) genes encoding for nucleotide-binding site (NB) and leucine-rich repeat (LRR) proteins with N-terminals represented by either Toll/Interleukin-1 receptor (TIR) or coiled-coil (CC) domains. Here, a genome-wide study of presence and diversification of CC-NB-LRR and TIR-NB-LRR encoding genes, and shorter domain combinations in 19 Arabidopsis thaliana accessions and Arabidopsis lyrata, Capsella rubella, Brassica rapa and Eutrema salsugineum are presented. RESULTS Out of 528 R genes analyzed, 12 CC-NB-LRR and 17 TIR-NB-LRR genes were conserved among the 19 A. thaliana genotypes, while only two CC-NB-LRRs, including ZAR1, and three TIR-NB-LRRs were conserved when comparing the five species. The RESISTANCE TO LEPTOSPHAERIA MACULANS 1 (RLM1) locus confers resistance to the Brassica pathogen L. maculans the causal agent of blackleg disease and has undergone conservation and diversification events particularly in B. rapa. On the contrary, the RLM3 locus important in the immune response towards Botrytis cinerea and Alternaria spp. has recently evolved in the Arabidopsis genus. CONCLUSION Our genome-wide analysis of the R gene repertoire revealed a large sequence variation in the 23 cruciferous genomes. The data provides further insights into evolutionary processes impacting this important gene family.
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Affiliation(s)
- Hanneke M Peele
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Na Guan
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Johan Fogelqvist
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
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147
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Lu Y, Ran JH, Guo DM, Yang ZY, Wang XQ. Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes. PLoS One 2014; 9:e107679. [PMID: 25222863 PMCID: PMC4164646 DOI: 10.1371/journal.pone.0107679] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/19/2014] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.
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Affiliation(s)
- Ying Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Dong-Mei Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zu-Yu Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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148
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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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149
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Vanneste K, Baele G, Maere S, Van de Peer Y. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res 2014; 24:1334-47. [PMID: 24835588 PMCID: PMC4120086 DOI: 10.1101/gr.168997.113] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 05/16/2014] [Indexed: 02/02/2023]
Abstract
Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous-Paleogene (K-Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K-Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.
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Affiliation(s)
- Kevin Vanneste
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven B-3000, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0002, South Africa
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150
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One or three species in Megadenia (Brassicaceae): insight from molecular studies. Genetica 2014; 142:337-50. [PMID: 25027851 DOI: 10.1007/s10709-014-9778-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
Abstract
Megadenia Maxim. is a small genus of the Brassicaceae endemic to East Asia with three disjunct areas of distribution: the eastern edge of the Qinghai-Tibetan Plateau, the Eastern Sayan Mountains in southern Siberia, and Chandalaz Ridge in the southern Sikhote-Alin Mountains. Although distinct species (M. pygmaea Maxim., M. bardunovii Popov, and M. speluncarum Vorob., Vorosch. and Gorovoj) have been described from each area, they have lately been reduced to synonymy with M. pygmaea due to high morphological similarity. Here, we present the first molecular study of Megadenia. Using the sequences of 11 noncoding regions from the cytoplasmic (chloroplast and mitochondrial) and nuclear genomes, we assessed divergence within the genus and explored the relationships between Megadenia and Biscutella L. Although M. bardunovii, M. speluncarum, and M. pygmaea were found to be indiscernible with regard to the nuclear and mitochondrial markers studied, our data on the plastid genome revealed their distinctness and a clear subdivision of the genus into three lineages matching the three described species. All of the phylogenetic analyses of the chloroplast DNA sequences provide strong support for the inclusion of Megadenia and Biscutella in the tribe Biscutelleae. A dating analysis shows that the genus Megadenia is of Miocene origin and diversification within the genus, which has led to the three extant lineages, most likely occurred during the Early-Middle Pleistocene, in agreement with the vicariance pattern. Given the present-day distribution, differences in habitat preferences and in some anatomical traits, and lack of a direct genealogical relationship, M. pygmaea, M. bardunovii, and M. speluncarum should be treated as distinct species or at least subspecies.
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