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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [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: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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Draper I, Garilleti R, Calleja JA, Flagmeier M, Mazimpaka V, Vigalondo B, Lara F. Insights Into the Evolutionary History of the Subfamily Orthotrichoideae (Orthotrichaceae, Bryophyta): New and Former Supra-Specific Taxa So Far Obscured by Prevailing Homoplasy. FRONTIERS IN PLANT SCIENCE 2021; 12:629035. [PMID: 33841460 PMCID: PMC8034389 DOI: 10.3389/fpls.2021.629035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Mosses of the subfamily Orthotrichoideae represent one of the main components of the cryptogam epiphytic communities in temperate areas. During the last two decades, this taxonomical group has undergone an extensive revision that has led to its rearrangement at the generic level. However, their phylogenetic relationships and inferences on the evolutionary patterns that have driven the present diversity have little advanced. In this study, we present a dated molecular phylogenetic reconstruction at the subfamily level, including 130 samples that represent the 12 genera currently recognized within the subfamily, and the analysis of four molecular markers: ITS2, rps4, trnG, and trnL-F. We also analyze 13 morphological characters of systematic value to infer their origin and diagnostic utility within the subfamily. The phylogenetic reconstruction yields three main clades within the subfamily, two of which correspond to the tribe Zygodonteae, and one to Orthotricheae. Within Zygodonteae, the genus Zygodon results to be a polyphyletic artificial assembly, and we propose to separate a new genus named Australoria. Conversely, our results do not support the separation of Pentastichella and Pleurorthotrichum at the genus level and we therefore propose to include Pleurorthotrichum in Pentastichella. Regarding Orthotricheae, our analyses clearly allow the distinction of two subtribes: Orthotrichinae and Lewinskyinae. Within the latter, Ulota results a polyphyletic entity, and therefore we propose the segregation of a separate new genus named Atlantichella. Dating analyses allow us to conclude that the split of the tribes within Orthotrichoideae dates from the Middle Jurassic, while the diversification of Orthotrichum and Zygodon probably started during the Late Cretaceous. However, most of the extant genera of this subfamily seem to be younger, and apparently its highest diversification burst took place during the Oligocene. Finally, the analysis of the morphological traits reveals that most of the characters previously used to separate genera and here tested are homoplastic, which has hindered the taxonomical and systematic proposals for decades. However, even if there are no exclusive characters, all of the genera can be defined by the combination of a few characters.
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Affiliation(s)
- Isabel Draper
- Centro de Investigación en Biodiversidad y Cambio Global, Madrid, Spain
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ricardo Garilleti
- Departamento de Botánica y Geología, Facultad de Farmacia, Universidad de Valencia, Burjassot, Spain
| | - Juan Antonio Calleja
- Centro de Investigación en Biodiversidad y Cambio Global, Madrid, Spain
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maren Flagmeier
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Vicente Mazimpaka
- Centro de Investigación en Biodiversidad y Cambio Global, Madrid, Spain
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Beatriz Vigalondo
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Lara
- Centro de Investigación en Biodiversidad y Cambio Global, Madrid, Spain
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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3
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Ignatov MS, Spirina UN, Kolesnikova MA, Larraín J, Ignatova EA. Cell Division Patterns in the Peristomial Layers of the Moss Genus Costesia: Two Hypotheses and a Third Solution. FRONTIERS IN PLANT SCIENCE 2020; 11:536862. [PMID: 33013962 PMCID: PMC7498844 DOI: 10.3389/fpls.2020.536862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The Chilean endemic genus Costesia belongs to the Gigaspermaceae, one of the most basal groups of arthrodontous mosses. While none of the species in this family has a peristome, earlier stages of sporophyte development often disclose its basic structure. The study of Costesia sporophytes at the early stages of development was conducted to identify possible similarities with Diphyscium, the genus sister to Gigaspermaceae plus all other arthrodontous mosses in the moss phylogenetic tree. Diphyscium shares a strongly unequal cell division pattern with the Dicranidae. In groups more closely related to Diphyscium, as it is the case of Costesia, this pattern is not known. Our study of Costesia found only irregular presence of slightly unequal cell divisions that may then be considered as a plesiomorphic state in peristomate mosses. The most frequently present pattern revealed in Costesia is common with the Polytrichaceae, a more basal moss group with nematodontous peristomes.
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Affiliation(s)
- Michael S. Ignatov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia
| | - Ulyana N. Spirina
- Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Tver State University, Tver, Russia
| | | | - Juan Larraín
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Elena A. Ignatova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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4
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Kirbis A, Waller M, Ricca M, Bont Z, Neubauer A, Goffinet B, Szövényi P. Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica. FRONTIERS IN PLANT SCIENCE 2020; 11:747. [PMID: 32587596 PMCID: PMC7299128 DOI: 10.3389/fpls.2020.00747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 05/03/2023]
Abstract
Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators.
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Affiliation(s)
- Alexander Kirbis
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Mariana Ricca
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Zoe Bont
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
- *Correspondence: Péter Szövényi,
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5
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Flores JR, Suárez GM, Hyvönen J. Reassessing the role of morphology in bryophyte phylogenetics: Combined data improves phylogenetic inference despite character conflict. Mol Phylogenet Evol 2019; 143:106662. [PMID: 31676419 DOI: 10.1016/j.ympev.2019.106662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022]
Abstract
Morphological data has gained renewed attention and has been shown to be crucial in clarifying the phylogenetic relationship in a wide range of taxa. In the last decades, phylogenetic analyses of sequence-level data have radically modified the systematic schemes within bryophytes (early non-vascular land plants) and have revealed a widespread pattern of conflict with morphology-based classifications. Yet, a comprehensive evaluation of character conflict has not yet been performed in the context of combined matrices. In this study, we evaluate the impact of morphology on bryophyte phylogeny following a total-evidence approach across 10 published matrices. The analysed matrices span a wide range of bryophytes, taxonomic levels, gene sampling and number of morphological characters and taxa. Data conflict was addressed by measuring: (i) the topological congruence between individual partitions, (ii) changes in support values of the combined data relative to the molecular partition and (iii) clade stability. The association between these measures and the number of morphological characters per taxon (Nc/T ratio) and the proportion of non-fixed characters (i.e., inapplicable, polymorphic and missing data) was explored. In the individual partition analyses, the Nc/T ratio correlated positively with the topological congruence in six to seven datasets depending on the weighting scheme. The proportion of non-fixed cells had a minor influence on congruence between data partitions. The number of characters and proportion of non-fixed data varied significantly between morphological datasets that improved congruence between data types. This variation suggests that morphological datasets affect the results of combined analyses in different ways, depending on the taxa studied. Combined analyses revealed that, despite the low congruence values between partitions, integrating data types improves support values and stability. However, while non-fixed data had no negative effect on support values, stability was reduced as the proportion of non-fixed cells increased. Nc/T ratio was negatively associated with support values and it showed ambiguous responses in stability evaluations. Overall, the results indicate that adding morphology may contribute to the inference of phylogenetic relationships of bryophytes despite character conflict. Our findings suggest that merely comparing (a) morphology-based classifications with molecular phylogenies or (b) the outcome from individual data partitions can misestimate data conflict. These findings imply that analyses of combined data may provide conservative assessments of data conflict and, eventually, lead to an improved sampling of morphological characters in large-scale analyses of bryophytes.
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Affiliation(s)
- Jorge R Flores
- Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, FI-00014 Helsinki, Finland.
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (CONICET-FML), Miguel Lillo 251, 4000 San Miguel de Tucumán, Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo - Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 San Miguel de Tucumán, Tucumán, Argentina
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, FI-00014 Helsinki, Finland
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6
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Flores JR, Catalano SA, Muñoz J, Suárez GM. Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification. Cladistics 2018; 34:517-541. [PMID: 34706484 DOI: 10.1111/cla.12225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/26/2022] Open
Abstract
The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT-psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long-held assumption that morphology may render spurious or low-quality results in this taxonomic group is challenged. The morphological trends previously proposed are re-evaluated in light of the new phylogenetic scheme.
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Affiliation(s)
- Jorge R Flores
- Unidad Ejecutora Lillo (UEL; FML-CONICET), Miguel Lillo 251, S.M. de Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, S.M. de Tucumán, 4000, Argentina
| | - Santiago A Catalano
- Unidad Ejecutora Lillo (UEL; FML-CONICET), Miguel Lillo 251, S.M. de Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, S.M. de Tucumán, 4000, Argentina
| | - Jesus Muñoz
- Real Jardín Botánico (RJB - CSIC), Plaza de Murillo 2, Madrid, 28014, Spain
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (UEL; FML-CONICET), Miguel Lillo 251, S.M. de Tucumán, 4000, Argentina.,Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, S.M. de Tucumán, 4000, Argentina
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7
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Boreotropical range expansion and long-distance dispersal explain two amphi-Pacific tropical disjunctions in Sabiaceae. Mol Phylogenet Evol 2018; 124:181-191. [DOI: 10.1016/j.ympev.2018.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 11/15/2022]
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8
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Medina R, Johnson M, Liu Y, Wilding N, Hedderson TA, Wickett N, Goffinet B. Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae. Mol Phylogenet Evol 2017; 120:240-247. [PMID: 29222063 DOI: 10.1016/j.ympev.2017.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/02/2017] [Accepted: 12/04/2017] [Indexed: 11/19/2022]
Abstract
Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.
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Affiliation(s)
- Rafael Medina
- University of Connecticut, Ecology and Evolutionary Biology, 75 N Eagleville Rd., Storrs, 06269 CT, USA; Augustana College, Department of Biology, 639 38th St. Rock, Island, 61201 IL, USA.
| | - Matthew Johnson
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022 USA; Texas Tech University, Department of Biological Sciences, 2901 Main Street, Lubbock, 79409 TX, USA
| | - Yang Liu
- University of Connecticut, Ecology and Evolutionary Biology, 75 N Eagleville Rd., Storrs, 06269 CT, USA; Key Laboratory of Southern Subtropical Plant Diversity, Shenzhen Fairy Lake Botanical Garden, Shenzhen 518004, China
| | - Nicholas Wilding
- University of La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410 Saint-Pierre, France; Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, 7701 Rondebosch, South Africa
| | - Terry A Hedderson
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, 7701 Rondebosch, South Africa
| | - Norman Wickett
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022 USA
| | - Bernard Goffinet
- University of Connecticut, Ecology and Evolutionary Biology, 75 N Eagleville Rd., Storrs, 06269 CT, USA.
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9
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Szövényi P, Ullrich KK, Rensing SA, Lang D, van Gessel N, Stenøien HK, Conti E, Reski R. Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens. Genome Biol Evol 2017; 9:1528-1546. [PMID: 28549175 PMCID: PMC5507605 DOI: 10.1093/gbe/evx098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2017] [Indexed: 12/15/2022] Open
Abstract
A long-term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support. Here, we test this hypothesis by analyzing synonymous codon usage bias of genes in the model moss Physcomitrella patens frequently undergoing haploid selfing. In line with population genetic theory, we found that the effect of natural selection on synonymous codon usage bias is very weak. Our conclusion is supported by four independent lines of evidence: 1) Very weak or nonsignificant correlation between gene expression and codon usage bias, 2) no increased codon usage bias in more broadly expressed genes, 3) no evidence that codon usage bias would constrain synonymous and nonsynonymous divergence, and 4) predominant role of genetic drift on synonymous codon usage predicted by a model-based analysis. These findings show striking similarity to those observed in AT-rich genomes with weak selection for optimal codon usage and GC content overall. Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P. patens.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Switzerland
| | - Kristian K. Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany
- Present address: Max-Planck-Insitut für Evolutionsbiologie, Plön, Germany
| | - Stefan A. Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Germany
- BIOSS—Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Daniel Lang
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | | | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Switzerland
| | - Ralf Reski
- BIOSS—Centre for Biological Signalling Studies, University of Freiburg, Germany
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
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10
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Lu L, Cox CJ, Mathews S, Wang W, Wen J, Chen Z. Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae). Cladistics 2017; 34:57-77. [DOI: 10.1111/cla.12191] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2017] [Indexed: 12/25/2022] Open
Affiliation(s)
- Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Cymon J. Cox
- Centro de Ciências do Mar Universidade do Algarve Gambelas Faro 8005‐319 Portugal
| | - Sarah Mathews
- CSIRO National Research Collections Australian National Herbarium Canberra ACT 2601 Australia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Jun Wen
- Department of Botany National Museum of Natural History MRC166, Smithsonian Institution Washington DC 20013‐7012 USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China
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11
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Budke JM, Goffinet B. Comparative Cuticle Development Reveals Taller Sporophytes Are Covered by Thicker Calyptra Cuticles in Mosses. FRONTIERS IN PLANT SCIENCE 2016; 7:832. [PMID: 27379125 PMCID: PMC4906049 DOI: 10.3389/fpls.2016.00832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/27/2016] [Indexed: 05/18/2023]
Abstract
The calyptra is a maternal structure that protects the sporophyte offspring from dehydration, and positively impacts sporophyte survival and fitness in mosses. We explore the relationship between cuticle protection and sporophyte height as a proxy for dehydration stress in Funariaceae species with sporophytes across a range of sizes. Calyptrae and sporophytes from four species were collected from laboratory-grown populations at two developmental stages. Tissues were embedded, sectioned, and examined using transmission electron microscopy. Cuticle thickness was measured from three epidermal cells per organ for each individual and compared statistically. All four species have cuticles consisting of a cuticle proper and a cuticular layer on the calyptra and sporophyte at both developmental stages. Across species, shorter sporophytes are associated with smaller calyptra and thinner calyptra cuticles, whereas taller sporophytes are associated with larger calyptra and thicker calyptra cuticles. Independent of size, young sporophytes have a thin cuticle that thickens later during development, while calyptrae have a mature cuticle produced early during development that persists throughout development. This study adds to our knowledge of maternal effects influencing offspring survival in plants. Released from the pressures to invest in protection for their sporophyte offspring, maternal resources can be allocated to other processes that support sporophyte reproductive success. Using a comparative developmental framework enables us to broaden our understanding of cuticle development across species and provides structural evidence supporting the waterproofing role of the moss calyptra.
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Affiliation(s)
- Jessica M. Budke
- Department of Plant Biology, University of California, Davis, DavisCA, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, StorrsCT, USA
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12
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Xiang KL, Wu SD, Yu SX, Liu Y, Jabbour F, Erst AS, Zhao L, Wang W, Chen ZD. The First Comprehensive Phylogeny of Coptis (Ranunculaceae) and Its Implications for Character Evolution and Classification. PLoS One 2016; 11:e0153127. [PMID: 27044035 PMCID: PMC4820238 DOI: 10.1371/journal.pone.0153127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 03/24/2016] [Indexed: 11/19/2022] Open
Abstract
Coptis (Ranunculaceae) contains 15 species and is one of the pharmaceutically most important plant genera in eastern Asia. Understanding of the evolution of morphological characters and phylogenetic relationships within the genus is very limited. Here, we present the first comprehensive phylogenetic analysis of the genus based on two plastid and one nuclear markers. The phylogeny was reconstructed using Bayesian inference, as well as maximum parsimony and maximum likelihood methods. The Swofford-Olsen-Waddell-Hillis and Bayesian tests were used to assess the strength of the conflicts between traditional taxonomic units and those suggested by the phylogenetic inferences. Evolution of morphological characters was inferred using Bayesian method to identify synapomorphies for the infrageneric lineages. Our data recognize two strongly supported clades within Coptis. The first clade contains subgenus Coptis and section Japonocoptis of subgenus Metacoptis, supported by morphological characters, such as traits of the central leaflet base, petal color, and petal shape. The second clade consists of section Japonocoptis of subgenus Metacoptis. Coptis morii is not united with C. quinquefolia, in contrast with the view that C. morii is a synonym of C. quinquefolia. Two varieties of C. chinensis do not cluster together. Coptis groenlandica and C. lutescens are reduced to C. trifolia and C. japonica, respectively. Central leaflet base, sepal shape, and petal blade carry a strong phylogenetic signal in Coptis, while leaf type, sepal and petal color, and petal shape exhibit relatively higher levels of evolutionary flexibility.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng-Dan Wu
- College of Life Sciences, Shanxi Normal University, Linfen, 041004, China
| | - Sheng-Xian Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269–3043, United States of America
| | - Florian Jabbour
- Muséum national d’Histoire naturelle, Institut de Systématique, Evolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, Paris, 75005, France
| | - Andrey S. Erst
- Central Siberian Botanical Garden of the Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia
- Laboratory of Systematics and Phylogeny of Plants, National Research Tomsk State University, prospekt Lenina 36, Tomsk, 634050, Russia
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- * E-mail:
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Carter BE, Shaw B, Shaw AJ. Endemism in the moss flora of North America. AMERICAN JOURNAL OF BOTANY 2016; 103:769-779. [PMID: 27056933 DOI: 10.3732/ajb.1500484] [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: 11/15/2015] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Identifying regions of high endemism is a critical step toward understanding the mechanisms underlying diversification and establishing conservation priorities. Here, we identified regions of high moss endemism across North America. We also identified lineages that contribute disproportionately to endemism and document the progress of efforts to inventory the endemic flora. METHODS To understand the documentation of endemic moss diversity in North America, we tabulated species publication dates to document the progress of species discovery across the continent. We analyzed herbarium specimen data and distribution data from the Flora of North America project to delineate major regions of moss endemism. Finally, we surveyed the literature to assess the importance of intercontinental vs. within-continent diversification for generating endemic species. KEY RESULTS Three primary regions of endemism were identified and two of these were further divided into a total of nine subregions. Overall endemic richness has two peaks, one in northern California and the Pacific Northwest, and the other in the southern Appalachians. Description of new endemic species has risen steeply over the last few decades, especially in western North America. Among the few studies documenting sister species relationships of endemics, recent diversification appears to have played a larger role in western North America, than in the east. CONCLUSIONS Our understanding of bryophyte endemism continues to grow rapidly. Large continent-wide data sets confirm early views on hotspots of endemic bryophyte richness and indicate a high rate of ongoing species discovery in North America.
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Affiliation(s)
- Benjamin E Carter
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Blanka Shaw
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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14
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Fedosov VE, Fedorova AV, Ignatova EA, Bobrova VK, Troitsky AV. RPS4 and NAD5 sequences indicate the polyphyly of ditrichaceae and parallelisms in the evolution of haplolepidous mosses. Mol Biol 2015. [DOI: 10.1134/s0026893315060072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Afoninia, a new moss genus of Funariaceae from Transbaikalia (East Siberia, Russia). ACTA ACUST UNITED AC 2015. [DOI: 10.15298/arctoa.24.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Church SH, Ryan JF, Dunn CW. Automation and Evaluation of the SOWH Test with SOWHAT. Syst Biol 2015; 64:1048-58. [PMID: 26231182 PMCID: PMC4604836 DOI: 10.1093/sysbio/syv055] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/24/2015] [Indexed: 01/31/2023] Open
Abstract
The Swofford–Olsen–Waddell–Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in log-likelihood between two topologies to a null distribution of differences in log-likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but it is sensitive to model misspecification, it is computationally burdensome to perform, and its implementation requires the investigator to make several decisions that each have the potential to affect the outcome of the test. We analyzed the effects of multiple factors using seven data sets to which the SOWH test was previously applied. These factors include a number of sample replicates, likelihood software, the introduction of gaps to simulated data, the use of distinct models of evolution for data simulation and likelihood inference, and a suggested test correction wherein an unresolved “zero-constrained” tree is used to simulate sequence data. To facilitate these analyses and future applications of the SOWH test, we wrote SOWHAT, a program that automates the SOWH test. We find that inadequate bootstrap sampling can change the outcome of the SOWH test. The results also show that using a zero-constrained tree for data simulation can result in a wider null distribution and higher p-values, but does not change the outcome of the SOWH test for most of the data sets tested here. These results will help others implement and evaluate the SOWH test and allow us to provide recommendations for future applications of the SOWH test. SOWHAT is available for download from https://github.com/josephryan/SOWHAT.
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Affiliation(s)
- Samuel H Church
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA;
| | - Joseph F Ryan
- Whitney Laboratory for Marine Biosciences, St. Augustine, Florida, USA; and Sars International Centre For Marine Molecular Biology, Bergen, Norway
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
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17
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Lewis PO, Holder MT, Swofford DL. Phycas: Software for Bayesian Phylogenetic Analysis. Syst Biol 2015; 64:525-31. [DOI: 10.1093/sysbio/syu132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022] Open
Affiliation(s)
- Paul O. Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA; 2Department of Ecology and Evolution, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA; and 3Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
| | - Mark T. Holder
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA; 2Department of Ecology and Evolution, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA; and 3Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
| | - David L. Swofford
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA; 2Department of Ecology and Evolution, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA; and 3Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
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18
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Beike AK, von Stackelberg M, Schallenberg-Rüdinger M, Hanke ST, Follo M, Quandt D, McDaniel SF, Reski R, Tan BC, Rensing SA. Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex. BMC Evol Biol 2014; 14:158. [PMID: 25015729 PMCID: PMC4227049 DOI: 10.1186/1471-2148-14-158] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 07/04/2014] [Indexed: 11/10/2022] Open
Abstract
Background The moss Physcomitrella patens (Hedw.) Bruch & Schimp. is an important experimental model system for evolutionary-developmental studies. In order to shed light on the evolutionary history of Physcomitrella and related species within the Funariaceae, we analyzed the natural genetic diversity of the Physcomitrium-Physcomitrella species complex. Results Molecular analysis of the nuclear single copy gene BRK1 reveals that three Physcomitrium species feature larger genome sizes than Physcomitrella patens and encode two expressed BRK1 homeologs (polyploidization-derived paralogs), indicating that they may be allopolyploid hybrids. Phylogenetic analyses of BRK1 as well as microsatellite simple sequence repeat (SSR) data confirm a polyphyletic origin for three Physcomitrella lineages. Differences in the conservation of mitochondrial editing sites further support hybridization and cryptic speciation within the Physcomitrium-Physcomitrella species complex. Conclusions We propose a revised classification of the previously described four subspecies of Physcomitrella patens into three distinct species, namely Physcomitrella patens, Physcomitrella readeri and Physcomitrella magdalenae. We argue that secondary reduction of sporophyte complexity in these species is due to the establishment of an ecological niche, namely spores resting in mud and possible spore dispersal by migratory birds. Besides the Physcomitrium-Physcomitrella species complex, the Funariaceae are host to their type species, Funaria hygrometrica, featuring a sporophyte morphology which is more complex. Their considerable developmental variation among closely related lineages and remarkable trait evolution render the Funariaceae an interesting group for evolutionary and genetic research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Stefan A Rensing
- Faculty of Biology, University of Freiburg, Schänzlestr, 1, 79104 Freiburg, Germany.
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19
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Bell NE, Boore JL, Mishler BD, Hyvönen J. Organellar genomes of the four-toothed moss, Tetraphis pellucida. BMC Genomics 2014; 15:383. [PMID: 24884426 PMCID: PMC4035505 DOI: 10.1186/1471-2164-15-383] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/08/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage. RESULTS Assembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes). CONCLUSIONS Structural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.
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Affiliation(s)
- Neil E Bell
- />Botanical Museum, Finnish Museum of Natural History, University of Helsinki, PO Box 7, FI-00014 Helsinki, Finland
- />Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, FI-00014 Helsinki, Finland
| | - Jeffrey L Boore
- />Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720-3140 USA
| | - Brent D Mishler
- />Department of Integrative Biology and University and Jepson Herbaria, University of California, 1001 Valley Life Sciences Bldg, Berkeley, CA 94720-2465 USA
| | - Jaakko Hyvönen
- />Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, FI-00014 Helsinki, Finland
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20
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Szövényi P, Devos N, Weston DJ, Yang X, Hock Z, Shaw JA, Shimizu KK, McDaniel SF, Wagner A. Efficient purging of deleterious mutations in plants with haploid selfing. Genome Biol Evol 2014; 6:1238-52. [PMID: 24879432 PMCID: PMC4041004 DOI: 10.1093/gbe/evu099] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In diploid organisms, selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of selfing known as intragametophytic selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.
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Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandInstitute of Systematic Botany, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandMTA-ELTE-MTM Ecology Research Group, ELTE, Biological Institute, Hungary
| | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Zsófia Hock
- Institute of Systematic Botany, University of Zurich, Switzerland
| | | | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | | | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandBioinformatics Institute, Agency for Science, Technology and Research (A*STAR), SingaporeThe Santa Fe Institute, Santa Fe NM
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21
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Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses. Mol Phylogenet Evol 2013; 66:1089-94. [DOI: 10.1016/j.ympev.2012.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 11/19/2022]
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22
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Liu Y, Moskwa NL, Goffinet B. Development of eight mitochondrial markers for Funariaceae (Musci) and their amplification success in other mosses. AMERICAN JOURNAL OF BOTANY 2012; 99:e62-e65. [PMID: 22275765 DOI: 10.3732/ajb.1100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY In comparison to the wide use of chloroplast markers, few mitochondrial markers are available for phylogenetic studies in bryophytes. We investigated the phylogenetic suitability of several mtDNA markers within the Funariaceae and across mosses. METHODS AND RESULTS By comparing mitochondrial genomes of two mosses, eight regions with higher substitution rates were identified and sequenced for three species in the Funariaceae and one outgroup taxon. Variations in the substitution rate of these new loci were compared to previously used markers. Thirty-four samples representing all major moss lineages were targeted to assess the universality of the newly designed primers. CONCLUSIONS The new markers provided similar or more sequence variations in Funariaceae compared to previously developed mtDNA markers. Five out of eight loci were amplified in 70% of other taxa, indicating that these markers may be suitable for phylogenetic studies in other moss lineages.
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Affiliation(s)
- Yang Liu
- Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, University of Connecticut, Storrs, Connecticut 06269-3043, USA.
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23
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Pokorny L, Ho BC, Frahm JP, Quandt D, Shaw AJ. Phylogenetic analyses of morphological evolution in the gametophyte and sporophyte generations of the moss order Hookeriales (Bryopsida). Mol Phylogenet Evol 2012; 63:351-64. [PMID: 22266481 DOI: 10.1016/j.ympev.2012.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/03/2012] [Accepted: 01/09/2012] [Indexed: 10/14/2022]
Abstract
Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. In this study we reconstruct relationships among mosses that are or have been included in the Hookeriales based on sequences from five gene regions, and reconstruct morphological evolution of six sporophyte and gametophyte traits that have been used to differentiate families and genera. We found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. This study addresses the general issue of morphological reversals to ancestral states, and resolves novel relationships in the Hookeriales.
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Affiliation(s)
- L Pokorny
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27708-0338, USA.
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24
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Budke JM, Goffinet B, Jones CS. The cuticle on the gametophyte calyptra matures before the sporophyte cuticle in the moss Funaria hygrometrica (Funariaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:14-22. [PMID: 22210839 DOI: 10.3732/ajb.1100311] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY In vascular plants, leaf primordia prevent desiccation of the shoot apical meristem. Lacking leaves, the undifferentiated moss sporophyte apex is covered by the calyptra, a cap of maternal gametophyte tissue that is hypothesized to function in desiccation protection. Herein, we compare cuticle development on the calyptra and sporophyte to assess the calyptra's potential to protect the sporophyte from desiccation. As the first comprehensive study of moss sporophyte cuticle development, this research broadens our perspectives on cuticle development and evolution across embryophytes. METHODS Calyptrae and sporophytes at nine developmental stages were collected from a laboratory-grown population of the moss Funaria hygrometrica. Tissues were embedded, sectioned, then examined using transmission electron microscopy. Epidermal cells were measured for thickness of the cuticle layers, cell wall thickness, and lumen size. KEY RESULTS The calyptra cuticle develops precociously and reaches maturity before the sporophyte cuticle. Calyptrae are covered by a four-layered cuticle at all stages, whereas sporophyte cuticle maturation is delayed until sporangium formation. The development and thickening of the sporophyte cuticle occurs in an acropetal wave. CONCLUSIONS A multilayered calyptra cuticle at the earliest developmental stages is consistent with its ability to protect the immature sporophyte from desiccation. Young sporophytes lack a complex cuticle and thus may require protection, whereas in older sporophytes a mature cuticle develops. The moss calyptra is not a vestigial structure, but rather the calyptra's role in preventing desiccation offers a functional explanation for calyptra retention during the 450 Myr of moss evolution.
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Affiliation(s)
- Jessica M Budke
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, 06269-3043, USA.
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