Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process.

Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical data sets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical data set of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical data sets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits. [Bayesian phylogenetic inference; fossil age estimates; fossilized birth-death; Lagerstätte; total-evidence.].

Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs.

The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here, we study the 19 pollinator species (Pegoscapus spp.) associated with an entire community of 16 Panamanian strangler fig species (Ficus subgenus Urostigma, section Americanae) to determine whether the previously documented history of pollinator host switching and current host sharing predicts genetic admixture among the pollinator species, as has been observed in their host figs. Specifically, we use genome-wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and introgression among the pollinator species. In all cases, we recover well-delimited pollinator species that contain high interspecific divergence. Even among pairs of pollinator species that currently reproduce within syconia of shared host fig species, we found no evidence of hybridization or introgression. This is in contrast to their host figs, where hybridization and introgression have been detected within this community, and more generally, within figs worldwide. Consistent with general patterns recovered among other obligate pollination mutualisms (e.g. yucca moths and yuccas), our results suggest that while hybridization and introgression are processes operating within the host plants, these processes are relatively unimportant within their associated insect pollinators.

Total-evidence analysis resolves the phylogenetic position of an enigmatic group of Paederinae rove beetles (Coleoptera: Staphylinidae).

Paederinae is one of the most diverse subfamilies among rove beetles, yet their evolutionary history remains poorly understood. This is attributed to the limited number of phylogenetic studies, which either sought answers at a shallower taxonomic level or included limited taxon sampling. Especially problematic is the position of the rare Neotropical tribe Cylindroxystini, morphologically one of the most puzzling groups of Paederinae. The phylogenetic position of this group within Paederinae was never understood, though its rank in the classification has already been shifted twice. We assembled molecular and morphological data matrices sampled from all currently recognized Paederinae subtribes, including both genera of Cylindroxystini, and used these data to estimate phylogenetic relationships using Bayesian inference. A total of 123 morphological characters and 4,631 bp of nuclear (28S, TP, Wg, CADA, CADC, ArgK) and mitochondrial (COI) sequences were analyzed for 76 taxa. The current tribe Cylindroxystini was resolved as a monophylum within the tribe Lathrobiini as sister to the genus Pseudolathra, and together they are sister to the so-called 'Medonina and allied taxa' clade. Based on these results, we downgraded Cylindroxystini back to the subtribal level, Cylindroxystina status reinstated, now with a known sister group. The resulting phylogeny is the largest of the subfamily Paederinae to date and lays the foundation for establishing a natural classification of the group.

Ancient crested penguin constrains timing of recruitment into seabird hotspot.

New Zealand is a globally significant hotspot for seabird diversity, but the sparse fossil record for most seabird lineages has impeded our understanding of how and when this hotspot developed. Here, we describe multiple exceptionally well-preserved specimens of a new species of penguin from tightly dated (3.36-3.06 Ma) Pliocene deposits in New Zealand. Bayesian and parsimony analyses place Eudyptes atatu sp. nov. as the sister species to all extant and recently extinct members of the crested penguin genus Eudyptes. The new species has a markedly more slender upper beak and mandible compared with other Eudyptes penguins. Our combined evidence approach reveals that deep bills evolved in both crested and stiff-tailed penguins (Pygoscelis) during the Pliocene. That deep bills arose so late in the greater than 60 million year evolutionary history of penguins suggests that dietary shifts may have occurred as wind-driven Pliocene upwelling radically restructured southern ocean ecosystems. Ancestral area reconstructions using BioGeoBEARS identify New Zealand as the most likely ancestral area for total-group penguins, crown penguins and crested penguins. Our analyses provide a timeframe for recruitment of crown penguins into the New Zealand avifauna, indicating this process began in the late Neogene and was completed via multiple waves of colonizing lineages.

Taming the BEAST-A Community Teaching Material Resource for BEAST 2.

Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines as diverse as epidemiology, developmental biology, palaeontology, ecology, and linguistics. The combination of increasingly large genetic data sets and increases in computing power is facilitating the development of more sophisticated phylogenetic and phylodynamic methods. Big data sets allow us to answer complex questions. However, since the required analyses are highly specific to the particular data set and question, a black-box method is not sufficient anymore. Instead, biologists are required to be actively involved with modeling decisions during data analysis. The modular design of the Bayesian phylogenetic software package BEAST 2 enables, and in fact enforces, this involvement. At the same time, the modular design enables computational biology groups to develop new methods at a rapid rate. A thorough understanding of the models and algorithms used by inference software is a critical prerequisite for successful hypothesis formulation and assessment. In particular, there is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software. These resources will also benefit researchers who do not have access to similar courses or training at their home institutions. Here, we introduce the "Taming the Beast" (https://taming-the-beast.github.io/) resource, which was developed as part of a workshop series bearing the same name, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.

The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth­death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ∼12.7 ∼12.7 Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed.

The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes.

A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model - also referred to as the fossilized birth-death (FBD) model - gives rise to phylogenetic trees on extant and fossil samples. The model has been mathematically analyzed and successfully applied to a range of datasets on different taxonomic levels, such as penguins, plants, and insects. However, the current mathematical treatment of this model does not allow for a group of temporally distinct fossil specimens to be assigned to the same species. In this paper, we provide a general mathematical FBD modeling framework that explicitly takes "stratigraphic ranges" into account, with a stratigraphic range being defined as the lineage interval associated with a single species, ranging through time from the first to the last fossil appearance of the species. To assign a sequence of fossil samples in the phylogenetic tree to the same species, i.e., to specify a stratigraphic range, we need to define the mode of speciation. We provide expressions to account for three common speciation modes: budding (or asymmetric) speciation, bifurcating (or symmetric) speciation, and anagenetic speciation. Our equations allow for flexible joint Bayesian analysis of paleontological and neontological data. Furthermore, our framework is directly applicable to epidemiology, where a stratigraphic range is the observed duration of infection of a single patient, "birth" via budding is transmission, "death" is recovery, and "sampling" is sequencing the pathogen of a patient. Thus, we present a model that allows for incorporation of multiple observations through time from a single patient.

Total-Evidence Dating under the Fossilized Birth-Death Process.

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.].

The fossilized birth-death process for coherent calibration of divergence-time estimates.

Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data--most commonly, fossil age estimates--are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the "fossilized birth-death" (FBD) process--a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene.

Probabilistic graphical model representation in phylogenetics.

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

A dirichlet process prior for estimating lineage-specific substitution rates.

We introduce a new model for relaxing the assumption of a strict molecular clock for use as a prior in Bayesian methods for divergence time estimation. Lineage-specific rates of substitution are modeled using a Dirichlet process prior (DPP), a type of stochastic process that assumes lineages of a phylogenetic tree are distributed into distinct rate classes. Under the Dirichlet process, the number of rate classes, assignment of branches to rate classes, and the rate value associated with each class are treated as random variables. The performance of this model was evaluated by conducting analyses on data sets simulated under a range of different models. We compared the Dirichlet process model with two alternative models for rate variation: the strict molecular clock and the independent rates model. Our results show that divergence time estimation under the DPP provides robust estimates of node ages and branch rates without significantly reducing power. Further analyses were conducted on a biological data set, and we provide examples of ways to summarize Markov chain Monte Carlo samples under this model.

A hierarchical Bayesian model for calibrating estimates of species divergence times.

In Bayesian divergence time estimation methods, incorporating calibrating information from the fossil record is commonly done by assigning prior densities to ancestral nodes in the tree. Calibration prior densities are typically parametric distributions offset by minimum age estimates provided by the fossil record. Specification of the parameters of calibration densities requires the user to quantify his or her prior knowledge of the age of the ancestral node relative to the age of its calibrating fossil. The values of these parameters can, potentially, result in biased estimates of node ages if they lead to overly informative prior distributions. Accordingly, determining parameter values that lead to adequate prior densities is not straightforward. In this study, I present a hierarchical Bayesian model for calibrating divergence time analyses with multiple fossil age constraints. This approach applies a Dirichlet process prior as a hyperprior on the parameters of calibration prior densities. Specifically, this model assumes that the rate parameters of exponential prior distributions on calibrated nodes are distributed according to a Dirichlet process, whereby the rate parameters are clustered into distinct parameter categories. Both simulated and biological data are analyzed to evaluate the performance of the Dirichlet process hyperprior. Compared with fixed exponential prior densities, the hierarchical Bayesian approach results in more accurate and precise estimates of internal node ages. When this hyperprior is applied using Markov chain Monte Carlo methods, the ages of calibrated nodes are sampled from mixtures of exponential distributions and uncertainty in the values of calibration density parameters is taken into account.

Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps.

Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (Ficus subgenus Pharmacosycea, section Pharmacosycea) and their six associated fig-pollinator wasp species (Tetrapus). Two of the five fig species, F. glabrata and F. maxima, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. By contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.

Genomic insights into the secondary aquatic transition of penguins.

Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.

Inferring processes of coevolutionary diversification in a community of Panamanian strangler figs and associated pollinating wasps.

The fig and pollinator wasp obligate mutualism is diverse (∼750 described species), ecologically important, and ancient (∼80 Ma). Once thought to be an example of strict one-to-one cospeciation, current thinking suggests genera of pollinator wasps codiversify with corresponding sections of figs, but the degree to which cospeciation or other processes contribute to the association at finer scales is unclear. Here, we use genome-wide sequence data from a community of Panamanian strangler figs and associated wasp pollinators to estimate the relative contributions of four evolutionary processes generating cophylogenetic patterns in this mutualism: cospeciation, host switching, pollinator speciation, and pollinator extinction. Using a model-based approach adapted from the study of gene family evolution, our results demonstrate the importance of host switching of pollinator wasps at this fine phylogenetic and regional scale. Although we estimate a modest amount of cospeciation, simulations reveal the number of putative cospeciation events to be consistent with what would be expected by chance. Additionally, model selection tests identify host switching as a critical parameter for explaining cophylogenetic patterns in this system. Our study demonstrates a promising approach through which the history of evolutionary association between interacting lineages can be rigorously modeled and tested in a probabilistic phylogenetic framework.

Phylogenetic Inference Using RevBayes.

Bayesian phylogenetic inference aims to estimate the evolutionary relationships among different lineages (species, populations, gene families, viral strains, etc.) in a model-based statistical framework that uses the likelihood function for parameter estimates. In recent years, evolutionary models for Bayesian analysis have grown in number and complexity. RevBayes uses a probabilistic-graphical model framework and an interactive scripting language for model specification to accommodate and exploit model diversity and complexity within a single software package. In this unit we describe how to specify standard phylogenetic models and perform Bayesian phylogenetic analyses in RevBayes. The protocols focus on the basic analysis of inferring a phylogeny from single and multiple loci, describe a hypothesis-testing approach, and point to advanced topics. Thus, this unit is a starting point to illustrate the power and potential of Bayesian inference under complex phylogenetic models in RevBayes. © 2017 by John Wiley & Sons, Inc.

Analysis and visualization of tree space.

We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring "tree islands" (sets of topologically related trees among larger sets of near-optimal trees), for comparing sets of trees obtained from bootstrapping and Bayesian sampling, for comparing trees obtained from the analysis of several different genes, and for comparing multiple Bayesian analyses. The technique was also useful as a teaching aid for illustrating the progress of a Bayesian analysis and as an exploratory tool for examining large sets of phylogenetic trees. We also identified some limitations to the method, including distortions of the multidimensional tree space into two dimensions through the MDS technique, and the definition of the MDS-defined space based on a limited sample of trees. Nonetheless, the technique is a useful approach for the analysis of large sets of phylogenetic trees.

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study.