Browsing by Author "Shaw, A. J."
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- Circumscription, classification, and taxonomy of Amblystegiaceae (Bryopsida) inferred from nuclear and chloroplast DNA sequence data and morphologyPublication . Vanderpoorten, A.; Hedenäs, Lars; Cox, C. J.; Shaw, A. J.Results from a previous broad-scale analysis employing trnL-trnF sequence data for 168 Hypnalean and 11 Hookerialean taxa, and an analysis employing two chloroplast regions, trnL-trnF and atpB-rbcL, one nuclear region, the internal transcribed spacers of 18S-26S rDNA, plus 68 morphological characters for a reduced data set of 54 Hypnalean taxa, were used to circumscribe Amblystegiaceae. The analyses provided two well-supported main clades including taxa traditionally included in Amblystegiaceae s.l. and recognized as Amblystegiaceae s.str. [Anacamptodon, Amblystegium, Campyliadelphus, Campylium, Cratoneuron, Cratoneuropsis, Drepanocladus s.str., Gradsteinia, Hygrohypnum s.str. (including the type species, H. luridum, but excluding a number of other species previously accommodated in the genus), Hypnobartlettia, Leptodictyum, Palustriella, Pseudo-calliergon, and Serpoleskea] and Calliergonaceae stat. nov. (Calliergon, Hamatocaulis, Loeskypnum, Straminergon, and Warnstorfia). Scorpidium and "Hygrohypnum" ochraceum were closely related to Calliergonaceae but were not included in the family because of the lack of support. All these genera but Anacamptodon have previously been included in Amblystegiaceae s.l. The sporophytic features of Anacamptodon, which contrast with those of all the other members of Amblystegiaceae, are interpreted as adaptations to an epiphytic habitat and suggest, together with other recent taxonomic works in Hookeriales, that characters related to sporophytic specializations are among the most homoplastic. Several other taxa (Calliergonella, Campylophyllum, Conardia, Donrichardsia, "Hygrohypnum" smithii, Platydictya, Sanionia), previously included in Amblystegiaceae s.l., appeared more closely related to other Hypnalean families. Recircumscribed Amblystegiaceae, and several clades within the family, have no identifiable morphological synapomorphies. A new system of classification for recircumscribed Amblystegiaceae, including morphological delimitation of presented clades based on maximum likelihood reconstruction of ancestral character states, is proposed and appropriate nomenclatural changes made.
- 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.
- Divergent and reticulate evolution in closely related species of Sphagnum section SubsecundaPublication . Shaw, A. J.; Melosik, I.; Cox, C. J.; Boles, S. B.The Sphagnum subsecundum complex includes a group of closely related, morphologically intergrading species in section Subsecunda. Nucleotide sequences from six genes (four nuclear and two chloroplast) were obtained from 74 populations representing all the putative species in this complex (S. denticulatum, S. inundatum, S. lescurii, S. subsecundum) to determine if the morphologically-defined taxa represent genetically distinct units. Sampling included populations from North America, Europe, and Asia. Parsimony analyses resolved two major groups of populations, one containing only North American plants (plus one from northern Russia) and the other containing all but two of the European samples, a few from North America, and one from Japan. Two of the four morphospecies occurred in both groups. Shimodaira-Hasegawa (SH) tests indicate that monophyly of S. inundatum, S. subsecundum, and S. lescurii can be rejected, whereas monophyly of S. denticulatum cannot be rejected with our data. Intragenic recombination was detected in both groups of populations, but was substantially higher in the “American” group. Because recombination calls into question the applicability of character-based phylogenetic methods, including parsimony, molecular similarity among populations was estimated using neighbor-joining. Neighbor-joining also resolved geographically correlated groups and corroborated the conclusion that morphologically defined species do not form genetically coherent groups. Groups of populations more closely reflect geographic than morphological patterns.
- Erratum: circumscription, classification, and taxonomy of the Amblystegiaceae (Bryopsida) inferred from nuclear and chloroplast DNA sequence data and morphologyPublication . Vanderpoorten, A.; Hedenäs, Lars; Cox, C. J.; Shaw, A. J.
- Evolution of multiple paralogous adenosine kinase genes in the moss genus Hygroamblystegium: phylogenetic implicationsPublication . Vanderpoorten, A.; Shaw, A. J.; Cox, C. J.Maximum likelihood analyses of DNA sequences from two chloroplast regions, trnL–trnF and atpB–rbcL, and the internal transcribed spacers of 18S–5.8S–26S rRNA gene array, were performed to resolve species relationships within the moss genus Hygroamblystegium. Constraining morphospecies to monophyly resulted in significantly less likely trees for H. tenax, but not for the other species. The lack of support for most clades and the partial incongruence among topologies necessitated the use of another independent, more variable region, namely the adenosine kinase gene (adk). Sequences for adk were polymorphic but were present as multiple copies within individuals, making parology a problem for phylogenetic analyses. Adk evolution was reconstructed using a reconciled gene tree approach in which duplications and losses were minimized in the context of an estimate of the species tree derived from the analysis of the cp and nrDNA sequence data. Additional resolution of the species tree was then obtained by searching for reconstructions that further reduced adk duplications and losses. All the traditionally recognized morphospecies appeared to be polyphyletic in the resulting tree. Together with previous data from different molecular markers, the results support the interpretation that Hygroamblystegium represents a recent radiation in which molecular and morphological evolution have been uncoupled.
- 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.
- Global patterns in peatmoss biodiversityPublication . Shaw, A. J.; Cox, C. J.; Boles, S. B.DNA sequence data from the nuclear ribosomal internal transcribed spacers (ITS) and the trnL-trnF chloroplast DNA regions were used to quantify geographical partitioning of global biodiversity in peatmosses (Sphagnum), and to compare patterns of molecular diversity with patterns of species richness. Molecular diversity was estimated for boreal, tropical, Neotropical, nonboreal (tropical plus Southern Hemisphere), Old World and New World partitions, based on a total of 436 accessions. Diversity was partitioned among geographical regions in terms of combined nuclear and chloroplast sequence data and separately for the ITS and trnL-trnF data sets.
- 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.
- 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.
- A new species of Leskeodon (Daltoniaceae) from EcuadorPublication . Buck, W. R.; Shaw, A. J.; Cox, C. J.Leskeodon caducifolius is described from recent collections made at a single site in a cloud forest in southern Ecuador. The species is distinctive in its small, caducous leaves and elongate, porose exothecial cells.
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