Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards

Partitioned Bayesian analyses of ∼ 2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean-lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2ln Bayes factor > 10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces” + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine” clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces” is polyphyletic and we make necessary taxonomic change

Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards

Abstract.-Partitioned Bayesian analyses of ∼2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean −lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2ln Bayes factor >10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes

Phylogenetic insights on evolutionary novelties in lizards and snakes: sex, birth, bodies, niches

Abstract Squamate reptiles (lizards and snakes) are a diverse clade in which there appear to have been multiple origins of many remarkable traits, including (a) parthenogenetic reproduction, (b) viviparity, (c) snake-like, limb-reduced body form, (d ) herbivory, and (e) venom. These repeated transitions make squamates an outstanding/excellent system for addressing many fundamental questions in evolutionary biology. For example, they are the only vertebrate group with true parthenogenesis (with at least 40 separate origins), they have more origins of viviparity than any other group of vertebrates, and they have undergone dramatic changes in body form (lizard-like to snake-like) dozens of times. New molecular phylogenies for squamates have overturned many traditional hypotheses and taxonomies based on morphology and are now revealing exciting new insights into the evolution of many of these traits at both higher and lower taxonomic levels. In this review, we summarize many of these new insights and outline important areas for future research

Eumeces managuae

Number of Pages: 2Integrative BiologyGeological Science

Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification

The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth–death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time. The HiSSE model also allows researchers to test state-dependent models against appropriate state-independent null models that have the same number of parameters as the state-dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state-dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states

Figure S2. Ancestral state reconstruction of viviparity for Liolaemidae using the uncorrected sample fraction

Figure S2. Ancestral state reconstruction of viviparity for Liolaemidae using the uncorrected sample fraction from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars)

Fig. S8. Macrostomatan phenotype reconstruction on constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny

Fig. S8. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist

Data from: Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of feeding morphology and limb reduction

Bayesian divergence time analyses were used to simultaneously infer the phylogenetic relationships and date the major clades of snakes including several important fossils that have not previously been included in divergence dating analyses as terminal taxa. We also explored the effect of using fossilized birth–death (FBD) and uniform tree priors for divergence dating with terminal calibrations. Nonclock and relaxed clock analyses of the combined morphology and molecular data set supported previous molecular phylogenetic hypotheses for the major clades of snakes, including the paraphyly of the traditionally recognized Scolecophidia and Macrostomata. Tip-dating analyses using either a uniform tree prior or FBD prior that assume that all fossils are tips and that extant lineages are randomly sampled resulted in older ages than those inferred using a FBD prior assuming diversified sampling of extant lineages and those estimated by previous studies. We used Bayesian ancestral state reconstruction methods to map the evolution of the ability to consume large prey and the loss of limbs onto our inferred time-calibrated phylogeny. We found strong support for early evolution of the ability to consume large prey, indicating multiple independent losses of this ability. We also found strong support for retention of external hindlimbs until relatively late in snake evolution, indicating multiple independent losses of hindlimbs

Fig. S5. Limb reconstruction on constrained, diversified FBD Tetrapodophis excluded phylogeny.

Fig. S5. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of fully-developed hind limbs (blue), reduced limbs (yellow), and completely lost limbs (red) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist. The phylogeny is plotted without Diablophis or Portugalophis because of issues visualizing branch lengths when these taxa were included, but they were included in the trees used for ancestral state reconstruction