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A surprising number of recent Bayesian phylogenetic analyses contain branch-length estimates that are several orders of magnitude longer than corresponding maximum-likelihood estimates. The levels of divergence implied by such branch lengths are unreasonable for studies using biological data and are known to be false for studies using simulated data. We(More)
As larger, more complex data sets are being used to infer phylogenies, accuracy of these phylogenies increasingly requires models of evolution that accommodate heterogeneity in the processes of molecular evolution. We investigated the effect of improper data partitioning on phylogenetic accuracy, as well as the type I error rate and sensitivity of Bayes(More)
Although an increasing number of phylogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes(More)
Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, have rigorously tested hypotheses regarding the specific factors driving divergence of taxa. Here, we test explicit speciation hypotheses by correlating geologic events with(More)
We studied the importance of proper model assumption in the context of Bayesian phylogenetics by examining >5,000 Bayesian analyses and six nested models of nucleotide substitution. Model misspecification can strongly bias bipartition posterior probability estimates. These biases were most pronounced when rate heterogeneity was ignored. The type of bias(More)
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of(More)
Although the trilling chorus frogs (subclade within Pseudacris: Hylidae) have been important in studies of speciation, continental patterns of genetic diversity within and among species have not been elucidated. As a result, this North American clade has been the subject of substantial taxonomic debate. In this study, we examined the phylogenetic(More)
We study the form of the clines in a female mating preference and male display trait using simulations of a hybrid zone. Allopatric populations of two species are connected by demes in a stepping stone arrangement. Results show that reproductive character displacement (a pattern of increased prezygotic isolation in sympatry compared with allopatry) may or(More)
The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled(More)
Recent empirical studies suggest that genes involved in speciation are often sex-linked. We derive a general analytic model of reinforcement to study the effects of sex linkage on reinforcement under three forms of selection against hybrids: one-locus, two-locus, and ecological incompatibilities. We show that the pattern of sex linkage can have a large(More)