Regular ArticleMolecular Polytomies
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A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach
2015, Molecular Phylogenetics and EvolutionMolecular systematics and historical biogeography of the green lizards (Lacerta) in Greece: Insights from mitochondrial and nuclear DNA
2014, Molecular Phylogenetics and EvolutionA confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses
2014, Molecular Phylogenetics and EvolutionCitation Excerpt :But the reality is that for many phylogenetic studies wherein characters are sampled from multiple unlinked genes and thorough taxon sampling is achieved, this is not the case because of biological processes (lineage sorting, introgression, unrecognized paralogy problems, horizontal gene transfer; Doyle, 1992; Maddison, 1997) and/or lab artifacts (e.g., PCR artifacts, contamination, mislabeling; Bradley and Hillis, 1997; Zhang et al., 1997; Page and Charleston, 1999). Hence, investigators conducting thorough empirical phylogenetic analyses are not only faced with well-known artifacts caused by long-branch attraction (Felsenstein, 1978), heterotachy among lineages (Fitch and Markowitz, 1970; Lopez et al., 2002), convergence in nucleotide composition (Lockhart et al., 1992), and rapid radiations with few synapomorphies (Slowinski, 2001), but also with characters that do not have a single underlying phylogenetic signal. Given the factors described above, robust phylogenetic methods need to be able to accommodate some characters that do not have a single underlying phylogenetic signal, and do so in the context of non-randomly distributed missing data.
Phylogeny and divergence times of Australian Sphenomorphus group skinks (Scincidae, Squamata)
2013, Molecular Phylogenetics and EvolutionCitation Excerpt :Applying a (then) recently described methodology for detecting lineage-level polytomies (see Poe and Chubb, 2004), Skinner (2007) examined the possibility that multiple clades within the Australian Sphenomorphus group diverged effectively simultaneously; in this case, the actual evolutionary pattern may not be accurately represented by a strictly bifurcating phylogeny, or at least cannot be resolved using standard phylogenetic methods (e.g., Heled and Drummond, 2010; Poe and Chubb, 2004). An assessment of congruence between the mitochondrial DNA and nuclear intron data sets indicated a moderate level of discordance, consistent with the prediction that simultaneous divergence of three or more lineages should result in gene trees for independently assorting loci that are no more congruent than would be expected by chance (i.e., for the relevant parts of the trees; see Poe and Chubb, 2004; Slowinski, 2001). This result, in combination with the observation of very short internal branches, prompted Skinner (2007) to conclude that several clades of Australian Sphenomorphus group scincids diverged very rapidly, if not effectively simultaneously.
Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory
2013, Molecular Phylogenetics and EvolutionCitation Excerpt :Bifurcating genealogies also will differ from biological reality if there is a ‘hard polytomy’ in the species tree (i.e. multiple descendant species split simultaneously from a single common ancestor), because any given bifurcating gene tree will not recapitulate the species tree (Slowinski, 2001). The hypothesis of a hard polytomy may be assessed explicitly with many independent loci by testing for equal representation of all possible gene tree topologies at the given putatively polytomous node (Slowinski, 2001). However, if the species tree contains a hard polytomy and the descendant species differ in population size (Ne), then genealogies might strongly, yet spuriously, support a bifurcating species tree because genealogies of species with a small population will coalesce sooner (Fig. 4).
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