Browsing by Author "Boles, S. B."
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- 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.
- 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.
- 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.
- Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?Publication . Shaw, A. J.; Devos, N.; Cox, C. J.; Boles, S. B.; Shaw, B.; Buchanan, A. M.; Cave, L.; Seppelt, R.Global climate changes sometimes spark biological radiations that can feed back to effect significant ecological impacts. Northern Hemisphere peatlands dominated by living and dead peatmosses (Sphagnum) harbor almost 30% of the global soil carbon pool and have functioned as a net carbon sink throughout the Holocene, and probably since the late Tertiary. Before that time, northern latitudes were dominated by tropical and temperate plant groups and ecosystems.
- Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta)Publication . Shaw, A. J.; Cox, C. J.; Goffinet, B.; Buck, W. R.; Boles, S. B.Pleurocarpous mosses, characterized by lateral female gametangia and highly branched, interwoven stems, comprise three orders and some 5000 species, or almost half of all moss diversity. Recent phylogenetic analyses resolve the Ptychomniales as sister to the Hypnales plus Hookeriales. Species richness is highly asymmetric with approximately 100 Ptychomniales, 750 Hookeriales, and 4400 Hypnales. Chloroplast DNA (cpDNA) sequences were obtained to compare partitioning of molecular diversity among the orders with estimates of species richness, and to test the hypothesis that either the Hookeriales or Hypnales underwent a period (or periods) of exceptionally rapid diversification. Levels of biodiversity were quantified using explicitly historical ‘‘phylogenetic diversity’’ and nonhistorical estimates of standing sequence diversity. Diversification rates were visualized using lineage-through-time (LTT) plots, and statistical tests of alternative diversification models were performed using the methods of Paradis (1997). The effects of incomplete sampling on the shape of LTT plots and performance of statistical tests were investigated using simulated phylogenies with incomplete sampling. Despite a much larger number of accepted species, the Hypnales contain lower levels of (cpDNA) biodiversity than their sister group, the Hookeriales, based on all molecular measures. Simulations confirm previous results that incomplete sampling yields diversification patterns that appear to reflect a decreasing rate through time, even when the true phylogenies were simulated with constant rates. Comparisons between simulated results and empirical data indicate that a constant rate of diversification cannot be rejected for the Hookeriales. The Hypnales, however, appear to have undergone a period of exceptionally rapid diversification for the earliest 20% of their history.
- Phylogenetic relationships among Sphagnum sections: Hemitheca, Isocladus, and SubsecundaPublication . Shaw, J. A.; Cox, C. J.; Boles, S. B.Sphagnum macrophyllum, S. pylaesii, and S. cyclophyllum are morphologically atypical in the genus Sphagnum and their systematic placement has been a source of controversy. The first is generally classified in the mono-specific section Isocladus, and the second as section Hemitheca. Sphagnum cyclophyllum is classified in the section Subsecunda, but several authors have hypothesized a close relationship between all three species. Nucleotide sequences from eight nuclear and chloroplast loci were obtained to test hypotheses about relationships among these taxa. Phylogenetic analyses resolve these species (along with S. microcarpum, closely related to S. cyclophyllum) in a well-supported monophyletic group within the section Subsecunda. Sphagnum macrophyllum is sister to S. cyclophyllum, S. microcarpum, and S. pylaesii. Sphagnum cyclophyllum and S. microcarpum form a clade that is sister to S. pylaesii. Two mutually monophyletic groups of populations are resolved within S. pylaesii, one including the European populations and the other including populations from eastern North America and South America. The European populations are almost identical at the nucleotide sequence level whereas the American populations are genetically diverse. Short, delicate pseudopodia; exceptionally large opercula; and an absence or near absence of pseudostomata appear to be synapomorphies for the clade containing S. macrophyllum, S. microcarpum, S. cyclophyllum, and S. pylaesii.
- Phylogenetic relationships among the mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomic compartmentsPublication . Cox, C. J.; Goffinet, B.; Jonathan Shaw, A.; Boles, S. B.Nucleotide sequences fromeight nuclear, chloroplast, andmitochondrial genes were obtained from30mosses (plus four outgroup liverworts) in order to resolve phylogenetic relationships among the major clades of division Bryophyta. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood (ML), and Bayesian inference. Inferences were compared from Bayesian analyses using homogeneous and several heterogeneous models. Estimates of clade con dence were based on bootstrap analyses, posterior probabilities (in Bayesian analyses) and novel combined approaches. Most ingroup relationships were congruent among analyses, but support for individual clades depended on the analytical approach. Increasingly parameterized models of nucleotide substitution in the likelihood analyses provided signi cantly higher goodness-of- t to the data. The results suggest that 1) the Bryophyta, including Sphagnum and Takakia, are monophyletic, 2) Andreaea and Andreaeobryum form a monophyletic group, 3) Oedipodium grif thianum is sister to all other operculate taxa, 4) mosses with nematodontous peristomes are paraphyletic and basal to arthrodontous mosses, 5) Diphyscium is sister to all other arthrodontous mosses, 6) Encalypta is sister to the Funariaceae, and 6) mosses with diplolepideousalternate peristomes form a monophyletic group. Implications of the phylogenetic hypothesis formorphological evolution in mosses include 1) a pseudopodium has arisen independently in Sphagnum and Andreaea, 2) the mucilage hairs of Andreaeobryum and Takakia are non-homologous, 3) the stomata found in Sphagnum are not homologous to those of other mosses, and 4) that stomata were absent in the ancestor of all mosses.
- Phylogeny, species delimitation, and recombination in Sphagnum section AcutifoliaPublication . Shaw, A. J.; Cox, C. J.; Boles, S. B.Nucleotide sequences for six nuclear loci and one chloroplast region were used to reconstruct phylogenetic relationships in Sphagnum section Acutifolia. The combined data matrix, which includes 136 accessions (129 ingroup taxa and seven outgroups) and 5126 nucleotide sites, was analyzed using Bayesian inference. Most of the individual morphospecies commonly recognized in the section were represented by multiple populations, in some cases by up to 16 accessions from throughout the Northern Hemisphere. Results of the combined seven-locus analysis resolved many of the species as monophyletic, but the deeper nodes were generally without support. Separate analyses of single-locus data sets revealed significant conflicts, indicating gene flow among both closely and more distantly related species within the section. The sequence data allowed likely parentage to be identified for several species of hybrid origin, and identified individual accessions that appear to be genetic admixtures. Taxonomic conclusions that can be made from the analyses include: 1. Sphagnum wulfianum and S. aongstroemii should both be included in section Acutifolia, 2. S. subtile cannot be separated from S. capillifolium, and the two should be synonymized, 3. S. capillifolium and S. rubellum each contain a monophyletic core of populations and should be retained as separate species, but 4. S. rubellum cannot be separated from S. andersonianum and S. bartlettianum and the three should be merged, 5. S. tenerum is highly differentiated from S. capillifolium and should be treated as a separate species, 6. interspecific mixed ancestry is demonstrated for S. russowii (a likely allopolyploid), S. skyense, S. arcticum, and S. olafii. Interspecific recombination appears to be rather common in section Acutifolia, yet species, for the most part, maintain cohesiveness.
- Polarity of peatmoss (Sphagnum) evolution: who says bryophytes have no roots?Publication . Shaw, A. J.; Cox, C. J.; Boles, S. B.The class Sphagnopsida (Bryophyta) includes two genera: Ambuchanania and Sphagnum. Ambuchanania contains just one rare species known from two Tasmanian localities, but Sphagnum comprises a speciose clade of mosses that dominates many wetland ecosystems, especially in the boreal zone of the Northern Hemisphere. Recent phylogenetic analyses have resolved well-supported clades within Sphagnum, but polarizing Sphagnum evolution has been problematic because the genus is so isolated that it is difficult to determine homologies between morphological and/or molecular traits within Sphagnum with those of any potential outgroup. DNA sequences from 16 genomic regions representing the mitochondrial, chloroplast, and nuclear genomes (ca. 16 kilobases) were obtained from 24 species of Sphagnum plus one species each from Takakia and Andreaea in order to resolve a rooted phylogeny. Two tropical species, S. sericeum and S. lapazense, were resolved as sister to the rest of the genus and are extremely divergent from all other sphagna. The main Sphagnum lineage consists of two clades; one includes the sections Sphagnum, Rigida, and Cuspidata, and the other includes Subsecunda, Acutifolia, and Squarrosa. The placement of section Subsecunda is weakly supported, but other nodes are strongly supported by maximum parsimony, maximum likelihood, and Bayesian analyses. In addition to homogeneous Bayesian analyses, heterogeneous models were employed to account for different patterns of nucleotide substitution among genomic regions.