Browsing by Author "Goffinet, B."
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- Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structurePublication . Forrest, L. L.; Wickett, N. J.; Cox, C. J.; Goffinet, B.Background and aims – Organellar genome sampling is patchy for non-vascular groups, with the earliest land plants poorly represented; currently only two liverworts, two mosses and one hornwort have sequenced, annotated plastid genomes. This is in part due to methodological difficulties that have hampered attempts to generate plastid genome data from liverworts. In this paper we present a method that overcomes some of the inherent difficulties by circumventing the need for plastid enrichment, but that also provides other valuable information from nuclear and mitochondrial regions including sequences from loci that may be phylogenetically useful, and potential population-level markers such as single nucleotide polymorphisms and microsatellites. Methods – A shotgun library developed from total genomic liverwort DNA was subjected to high-throughput pyrosequencing using the Roche 454 platform. Plastid reads were bioinformatically identified, assembled and annotated. To maximize usage of the vast number of reads generated using 454 sequencing technology, combined nuclear, mitochondrial and plastid contigs were also screened for microsatellite markers, and presumed nuclear contigs were scanned for protein domains. Key Results – This is the first plastid genome to be assembled for a leafy liverwort (i.e. Ptilidium) and also the first such genome to be sequenced using next generation technology for any bryophyte. The 119,007 base long plastid genome of Ptilidium pulcherrimum contains 88 protein-coding genes, four rRNAs and thirty tRNAs. The Inverted Repeat occurs between trn V-GAC and trn N-GUU. Functional copies of the two plastid-encoded sulphate import protein-coding genes (cysA and cysT) are absent, although pseudogenes are present in the same position that the functional genes occupy in Marchantia. Microsatellites: 197 novel potential primer pairs for P. pulcherrimum were found. Presumed nuclear Ptilidium contigs gave multiple hits to Class I transposable elements. Conclusions – The arrangement of genes is identical to the plastid of the complex thalloid liverwort Marchantia, suggesting that structural rearrangements are rare in hepatics. This dataset represents a valuable resource for novel phylogenetic and population level marker design in hepatics.
- Disentangling knots of rapid evolution: origin and diversification of the moss order HypnalesPublication . Huttunen, S.; Bell, N.; Bobrova, V. K.; Buchbender, V.; Buck, W. R.; Cox, C. J.; Goffinet, B.; Hedenäs, Lars; Ho, B. -C.; Ignatov, M. S.; Krug, M.; Kuznetsova, O.; Milyutina, I. A.; Newton, Alice; Olsson, S.; Pokorny, L.; Shaw, J. A.; Stech, M.; Troitsky, A.; Vanderpoorten, A.; Quandt, D.The Hypnales are the largest order of mosses comprising approximately 4200 species. Phylogenetic reconstruction within the group has proven to be difficult due to rapid radiation at an early stage of evolution and, consequently, relationships among clades have remained poorly resolved. We compiled data from four sequence regions, namely, nuclear ITS1–5.8S–ITS2, plastid trnL–F and rps4, and mitochondrial nad5, for 122 hypnalean species and 34 species from closely related groups. Tree topologies from both Bayesian and parsimony analyses resolve the order as monophyletic. Although inferences were made from fastevolving genes, and despite strong phylogenetic signal in the nuclear ITS1–5.8S–ITS2 data, monophyly, as well as backbone nodes within the Hypnales, remains rather poorly supported except under Bayesian inferences. Ancestral distribution based on Bayesian dispersal-vicariance analysis supports a Gondwanan origin of the Hypnales and subsequent geographical radiation in the area of the former Laurasian supercontinent. Reconstruction of historical biogeography is congruent with mainly tropical and Gondwanan distributions in the sister groups Hypnodendrales, Ptychomniales, and Hookeriales, and with the dating for the oldest pleurocarp and hypnalean fossils. We contrast groupings in the phylogenetic tree with recent classifications and other phylogenetic inferences based on molecular data, and summarise current knowledge on the evolutionary history of, and relationships among, the Hypnales.
- Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta)Publication . Goffinet, B.; Wickett, N. J.; Werner, O.; Ros, R. M.; Shaw, A. J.; Cox, C. J.Background and Aims The recent assembly of the complete sequence of the plastid genome of the model taxon Physcomitrella patens (Funariaceae, Bryophyta) revealed that a 71-kb fragment, encompassing much of the large single copy region, is inverted. This inversion of 57% of the genome is the largest rearrangement detected in the plastid genomes of plants to date. Although initially considered diagnostic of Physcomitrella patens, the inversion was recently shown to characterize the plastid genome of two species from related genera within Funariaceae, but was lacking in another member of Funariidae. The phylogenetic significance of the inversion has remained ambiguous. Methods Exemplars of all families included in Funariidae were surveyed. DNA sequences spanning the inversion break ends were amplified, using primers that anneal to genes on either side of the putative end points of the inversion. Primer combinations were designed to yield a product for either the inverted or the non-inverted architecture. Key Results The survey reveals that exemplars of eight genera of Funariaceae, the sole species of Disceliaceae and three generic representatives of Encalyptales all share the 71-kb inversion in the large single copy of the plastid genome. By contrast, the plastid genome of Gigaspermaceae (Funariales) is characterized by a gene order congruent with that described for other mosses, liverworts and hornworts, and hence it does not possess this inversion. Conclusions The phylogenetic distribution of the inversion in the gene order supports a hypothesis only weakly supported by inferences from sequence data whereby Funariales are paraphyletic, with Funariaceae and Disceliaceae sharing a common ancestor with Encalyptales, and Gigaspermaceae sister to this combined clade. To reflect these relationships, Gigaspermaceae are excluded from Funariales and accommodated in their own order, Gigaspermales order nov., within Funariideae.
- Evolution of the major moss lineages phylogenetic analyses based on multiple gene sequences and morphologyPublication . Newton, Alice; Cox, C. J.; Duckett, J. E.; Wheeler, J. A.; Goffinet, B.; Hedderson, T. A. J.; Mishler, B. D.Evolutionary relationships of mosses are still poorly understood, with family, order, and subclass circumscription and relationships remaining especially obscure. Over the past decade, a considerable body of data has accumulated, including information on morphological, developmental, anatomical, and ultrastructural characteristics, as well as nucleotide sequences for a number of nuclear and plastid genes. We have combined data from these different sources to provide an overview of the relationships of the major lineages of mosses. We analyzed a data set that includes 33 moss species and ten outgroup taxa drawn from the liverworts, hornworts, and vascular plants. Molecular data consisted of nucleotide sequences from four DNA regions, (rbcL, trnL-trnF, rps4 and 18S). Morphological data included 41 characters of which many were derived from published anatomical and ultra-structural studies. Combining morphological and molecular data in the analyses showed that mosses, including Sphagnum, Takakia, Andreaea and Andreaeobryum, form a monophyletic group, provided improved resolution of higher level relationships, and further insight into evolutionary patterns in morphology.
- Evolution of the major moss lineages: phylogenetic analyses based on multiple gene sequences and morphologyPublication . Newton, Alice; Cox, C. J.; Duckett, J. G.; Wheeler, J. A.; Goffinet, B.; Hedderson, T. A. J.; Mishler, B. D.Evolutionary relationships of mosses are still poorly understood, with family, order, and subclass circumscription and relationships remaining especially obscure.
- Extant diversity of bryophytes emerged from successive post-Mesozoic diversification burstsPublication . Laenen, B.; Shaw, B.; Schneider, H.; Goffinet, B.; Paradis, E.; Desamore, A.; Heinrichs, J.; Villarreal, J. C.; Gradstein, S. R.; McDaniel, S. F.; Long, D. G.; Forrest, L. L.; Hollingsworth, M. L.; Crandall-Stotler, B.; Davis, E. C.; Engel, J.; Von Konrat, M.; Cooper, E. D.; Patino, J.; Cox, C. J.; Vanderpoorten, A.; Shaw, A. J.Unraveling the macroevolutionary history of bryophytes, which arose soon after the origin of land plants but exhibit substantially lower species richness than the more recently derived angiosperms, has been challenged by the scarce fossil record. Here we demonstrate that overall estimates of net species diversification are approximately half those reported in ferns and similar to 30% those described for angiosperms. Nevertheless, statistical rate analyses on time-calibrated large-scale phylogenies reveal that mosses and liverworts underwent bursts of diversification since the mid-Mesozoic. The diversification rates further increase in specific lineages towards the Cenozoic to reach, in the most recently derived lineages, values that are comparable to those reported in angiosperms. This suggests that low diversification rates do not fully account for current patterns of bryophyte species richness, and we hypothesize that, as in gymnosperms, the low extant bryophyte species richness also results from massive extinctions.
- Geographical range in liverworts: does sex really matter?Publication . Laenen, Benjamin; Machac, Antonin; Gradstein, S. Robbert; Shaw, Blanka; Patino, Jairo; Desamore, Aurelie; Goffinet, B.; Cox, C. J.; Shaw, Jonathan; Vanderpoorten, AlainAimWhy some species exhibit larger geographical ranges than others remains a fundamental, but largely unanswered, question in ecology and biogeography. In plants, a relationship between range size and mating system was proposed over a century ago and subsequently formalized in Baker's Law. Here, we take advantage of the extensive variation in sexual systems of liverworts to test the hypothesis that dioecious species compensate for limited fertilization by producing vegetative propagules more commonly than monoecious species. As spores are assumed to contribute to random long-distance dispersal, whereas vegetative propagules contribute to colony maintenance and frequent short-distance dispersal, we further test the hypothesis that monoecious species exhibit larger geographical ranges than dioecious ones.LocationWorldwide.MethodsWe used comparative phylogenetic methods to assess the correlation between range size and life history traits related to dispersal, including mating systems, spore size and production of specialized vegetative propagules.ResultsNo significant correlation was found between dioecy and production of vegetative propagules. However, production of vegetative propagules is correlated with the size of geographical ranges across the liverwort tree of life, whereas sexuality and spores size are not. Moreover, variation in sexual systems did not have an influence on the correlation between geographical range and production of asexual propagules.Main conclusionsOur results challenge the long-held notion that spores, and not vegetative propagules, are involved in long-distance dispersal. Asexual reproduction seems to play a major role in shaping the global distribution patterns of liverworts, so that monoecious species do not tend to display, on average, broader distribution ranges than dioecious ones. Our results call for further investigation on the spatial genetic structure of bryophyte populations at different geographical scales depending on their mating systems to assess the dispersal capacities of spores and asexual propagules and determine their contribution in shaping species distribution ranges.
- Global patterns of moss diversity: taxonomic and molecular inferencesPublication . Shaw, A. J.; Cox, C. J.; Goffinet, B.Taxonomic and molecular data were utilized to test the hypothesis that moss diversity is greatest near the equator. Species richness estimates from 86 taxonomic checklists representing global moss diversity do not support the hypothesis that, in general, mosses are more species-rich in the tropics than at higher latitudes.
- Increased diversification rates follow shifts to bisexuality in liverwortsPublication . Laenen, Benjamin; Machac, Antonin; Gradstein, S. Robbert; Shaw, Blanka; Patino, Jairo; Desamore, Aurelie; Goffinet, B.; Cox, C. J.; Shaw, A. Jonathan; Vanderpoorten, AlainShifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism.
- Moss diversity: a molecular phylogenetic analysis of generaPublication . Cox, C. J.; Goffinet, B.; Wickett, N. J.; Boles, S. B.; Shaw, A. J.In this study we present phylogenetic and molecular phylogenetic diversity analyses of moss taxa from a total of 655 genera of mosses. Three loci were sampled: chloroplast ribosomal small protein 4, the intronic region of the mitochondrial NADH dehydogenase subunit 5, and partial sequences of the nuclear 26S ribosomal RNA. Maximum likelihood and Bayesian phylogenetic analyses were performed on individual loci and on multilocus data sets. A measure of phylogenetic diversity was calculated and constrasted among major lineages of mosses. We reveal many instances of incongruence among genomic partitions, but, overall, our analyses describe relationships largely congruent with previous studies of the major groups of mosses. Moreover, our greater sampling highlights the possible non-monophyly of many taxonomic families, particularly in the haplolepideous and pleurocarpous mosses. Comparisons of taxic and phylogenetic diversity among genera indicate that the Dicranidae (haplolepideous taxa) include about 15% of moss genera, but nearly 30% of the phylogenetic diversity. By contrast, the Hypnanae (hypnalian pleurocarps) contain about 45% of moss genera, but a lower percentage of phylogenetic diversity. Agreement between numbers of genera and phylogenetic diversity within other moss clades are remarkably consistent.
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