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- Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)Publication . Lu, Limin; Cox, C. J.; Mathews, Sarah; Wang, Wei; Wen, Jun; Chen, ZhiduanEvolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep-level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep-level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned model usually performed the worst. For a data set with conflicting signals, however, the unpartitioned model outperformed models that included more partitions, demonstrating some limitations to the effectiveness of concatenation for these data. For a transcriptome data set, fast coalescent methods (STAR and MP-EST) and a Bayesian concordance approach yielded congruent topologies with trees from the concatenated analyses and previous studies. Our results highlight that well-resolved gene trees are critical for the effectiveness of coalescent-based methods. Future efforts to improve the accuracy of phylogenomic analyses should emphasize the development of newmethods that can accommodate multiple biological processes and tolerate missing data while remaining computationally tractable. (C) The Willi Hennig Society 2017.
- Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)Publication . Shaw, A. Jonathan; Devos, Nicolas; Liu, Yang; Cox, C. J.; Goffinet, B.; Flatberg, Kjell Ivar; Shaw, BlankaBackground and Aims Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently under-way. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.Methods We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium.Key Results Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include > 90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium.Conclusions Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.
- 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.
- 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.
- 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.
- The archaebacterial origin of eukaryotesPublication . Cox, C. J.; Foster, P. G.; Hirt, R. P.; Harris, S. R.; Embley, T. M.The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. Here, we have investigated the relative support for each hypothesis from analysis of 53 genes spanning the 3 domains, including essential components of the eukaryotic nucleic acid replication, transcription, and translation apparatus. As an important component of our analysis, we investigated the fit between model and data with respect to composition. Compositional heterogeneity is a pervasive problem for reconstruction of ancient relationships, which, if ignored, can produce an incorrect tree with strong support. To mitigate its effects, we used phylogenetic models that allow for changing nucleotide or amino acid compositions over the tree and data. Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life.
- The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methodsPublication . Foster, P. G.; Cox, C. J.; Martin Embley, T.The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.
- 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.
- Evolutionary conservation of TFIIH subunits: Implications for the use of zebrafish as a model to study TFIIH function and regulationPublication . Silva, IAL; Cox, C. J.; Leite, Ricardo; Cancela, Leonor; Conceição, N.Transcriptional factor IIH (TFIIH) is involved in cell cycle regulation, nucleotide excision repair, and gene transcription. Mutations in three of its subunits, XPB, XPD, and TTDA, lead to human recessive genetic disorders such as trichothiodystrophy and xeroderma pigmentosum, the latter of which is sometimes associated with Cockayne's syndrome. In the present study, we investigate the sequence conservation of TFIIH subunits among several teleost fish species and compare their characteristics and putative regulation by transcription factors to those of human and zebrafish. We report the following findings: (i) comparisons among protein sequences revealed a high sequence identity for each TFIIH subunit analysed; (ii) among transcription factors identified as putative regulators, OCT1 and AP1 have the highest binding-site frequencies in the promoters of TFIIH genes, and (iii) TFIIH genes have alternatively spliced isoforms. Finally, we compared the protein primary structure in human and zebrafish of XPD and XPB – twoimportant ATP-dependent helicases that catalyse the unwinding of the DNA duplex at promoters during transcription – highlighting the conservation of domain regions such as the helicase domains. Our study suggests that zebrafish, a widely used model for many human diseases, could also act as an important model to study the function of TFIIH complex in repair and transcription regulation in humans.
- 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.