Share This Author
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.
Computer simulation is used to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony boot strap proportion (MP-BP).
Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.
A new method is presented that allows the inclusion of ambiguously aligned regions without violating homology in phylogenetic analyses by integrating previously nonaccessible characters without violating positional homology, and can improve branch length estimations when using parsimony.
Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes
Four primers for the amplification of mitochondrial DNA of lichenforming ascomycetes match the conserved regions U2, U4, and U6, respectively, of mitochondrial small subunit (SSU) ribosomal DNA (rDNA) and suggest that mitochondrial SSU rDNA may be useful for phylogenetic analyses of Lichen-formingAscomyCetes.
CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models
- M. Gil, M. S. Zanetti, S. Zoller, M. Anisimova
- BiologyMolecular biology and evolution
- 23 February 2013
A fast maximum likelihood (ML) package for phylogenetic inference, CodonPhyML offers hundreds of different codon models, the largest variety to date, for phylogeny inference by ML, and is shown to offer excellent speed and convergence properties.
Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation
This study provides evidence suggesting that L. pulmonaria is self‐incompatible and heterothallic, and gives populations with sexually reproducing individuals a higher rank in terms of conservation priority than strictly asexual populations.
Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps
Genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps are examined to provide a genomewide perspective on the distribution of adaptive genetic variation innatural plant populations from a highly diverse and heterogeneous alpine environment.
TAK1 suppresses a NEMO-dependent but NF-kappaB-independent pathway to liver cancer.
New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex
Complete concordance between phylogenetically based and morphologically based species delimitation for 15 of the 17 species from the P. canina complex is reported and it is found that morphologically and chemically distinct P. extenuata form two non-sister monophyletic entities, therefore the latter taxon should be recognized at the species level.
Hepatocyte‐specific deletion of the antiapoptotic protein myeloid cell leukemia‐1 triggers proliferation and hepatocarcinogenesis in mice
In vivo evidence is provided that increased apoptosis of hepatocytes not only impairs liver homeostasis but is also accompanied by hepatocyte proliferation and hepatocarcinogenesis, which might have implications for understanding apoptosis‐related human liver diseases.
Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions
R regressions of allele frequencies of the most strongly associated SNPs along environmental gradients are used to predict the risk of nonadaptedness (RONA), which represents the average change in allele frequency at climate‐associated loci theoretically required to match future climatic conditions.