Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.
ABSTRACT We revisit statistical tests for branches of evolutionary trees reconstructed upon molecular data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a competitive alternative to nonparametric bootstrap and Bayesian estimation of branch support. The aLRT is based on the idea of the conventional LRT, with the null hypothesis corresponding to the assumption that the inferred branch has length 0. We show that the LRT statistic is asymptotically distributed as a maximum of three random variables drawn from the chi(0)2 + chi(1)2 distribution. The new aLRT of interior branch uses this distribution for significance testing, but the test statistic is approximated in a slightly conservative but practical way as 2(l1- l2), i.e., double the difference between the maximum log-likelihood values corresponding to the best tree and the second best topological arrangement around the branch of interest. Such a test is fast because the log-likelihood value l2 is computed by optimizing only over the branch of interest and the four adjacent branches, whereas other parameters are fixed at their optimal values corresponding to the best ML tree. The performance of the new test was studied on simulated 4-, 12-, and 100-taxon data sets with sequences of different lengths. The aLRT is shown to be accurate, powerful, and robust to certain violations of model assumptions. The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003).
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ABSTRACT: Gnetum (Gnetales: Gnetaceae) constitutes an evolutionarily isolated gymnosperm clade, comprising about 40 species that inhabit tropical areas of the world. While its closest living relative, the monotypic Welwitschia, has a well-documented fossil record from the Early Cretaceous, Gnetum-like fossils are rare and poorly understood. The phylogeny of Gnetum has been studied previously but the distant relationship to outgroups and the difficulty of obtaining plant material mean it is not yet fully resolved. Most species are tropical lianas with an angiospermous vegetative habit that are difficult to find and identify. Here a new phylogeny is presented based on nuclear and chloroplast data from 58 Gnetum accessions, representing 27 putative species, and outgroup information from other seed plants. The results provide support for South American species being sister to the remaining species. The two African species constitute a monophyletic group, sister to an Asian clade, within which the two arborescent species of the genus are the earliest diverging. Estimated divergence times indicate, in contrast with previous results, that the major lineages of Gnetum diverged in the Late Cretaceous. This result is obtained regardless of tree prior used in the BEAST analyses (Yule or birth-death). Together these findings suggest a correlation between early divergence events in extant Gnetum and the breakup of Gondwana in the Cretaceous. Compared to the old stem ages of major subclades of Gnetum, crown nodes date to the Cenozoic: the Asian crown group dates to the Cretaceous-Paleogene (K-Pg) boundary, the African crown group to the mid-Paleogene, and the South American crown group to the Paleogene-Neogene boundary. Although dispersal must have contributed to the current distribution of Gnetum, e.g., within South America and from Southeast Asian islands to the East Asian mainland, dispersal has apparently not occurred across major oceans, at least not during the Cenozoic.Taxon 05/2015; 64(2):239–253. DOI:10.12705/642.12 · 3.05 Impact Factor
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ABSTRACT: Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome. However, the mechanism by which they are recognized and targeted to the exosome is not fully understood. Here we report that the MTREC complex, which has recently been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs, is also the major nuclear exosome targeting complex for CUTs and unspliced pre-mRNAs in Schizosaccharomyces pombe. The MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced pre-mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and RNA-processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of CUTs.Nature Communications 05/2015; DOI:10.1038/ncomms8050 · 10.74 Impact Factor
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ABSTRACT: Natural foci of ticks, pathogens, and vertebrate reservoirs display complex relationships that are key to the circulation of pathogens and infection dynamics through the landscape. However, knowledge of the interaction networks involved in transmission of tick-borne pathogens are limited because empirical studies are commonly incomplete or performed at small spatial scales. Here, we applied the methodology of ecological networks to quantify >14,000 interactions among ticks, vertebrates, and pathogens in the western Palearctic. These natural networks are highly structured, modular, coherent, and nested to some degree. We found that the large number of vertebrates in the network contributes to its robustness and persistence. Its structure reduces interspecific competition and allows ample but modular circulation of transmitted pathogens among vertebrates. Accounting for domesticated hosts collapses the network’s modular structure, linking groups of hosts that were previously unconnected and increasing the circulation of pathogens. This framework indicates that ticks and vertebrates interact along the shared environmental gradient, while pathogens are linked to groups of phylogenetically close reservoirs.Scientific Reports 05/2015; 5(10361). DOI:10.1038/srep10361 · 5.08 Impact Factor