Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea

Nucleotide sequences of the nuclear c-mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe's [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages within the superfamily, as well as genera membership in major lineages was also assessed. Analyses suggest that Bombycillidae is not a part of Muscicapoidea, and there is strongly supported evidence to suggest that Turdinae is not part of the Muscicapidae, but is instead sister to a Sturnidae+Cinclidae clade. This clade is in turn sister to Muscicapidae (Muscicapini+Saxicolini). Of the 49 Turdinae and Muscicapidae genera that we included in our analyses, 10 (20%) are shown to be misclassified to subfamily or tribe. Our results place one current Saxicolini genus in Turdinae, two Saxicolini genera in Muscicapini, and five Turdinae and two Muscicapini genera in Saxicolini; these relationships are supported with 100% Bayesian support. Our analyses suggest that c-mos was only marginally useful in resolving these "deep" phylogenetic relationships.     

On the systematics of the fungus gnat subfamily Mycetophilinae (Diptera): a combined morphological and molecular approach

The phylogenetic relationships within the fungus gnat subfamily Mycetophilinae (Diptera) are addressed using a combined morphological and molecular approach. Twenty-four species, representing nine genera of the tribe Mycetophilini and 15 genera of the tribe Exechiini, were included in the study. Analyses include nucleotide sequences of mitochondrial (cytochrome oxidase I and 16S), and nuclear (18S and 28S rDNA) genes, in addition to 65 morphological characters. A combined parsimony analysis, including all characters, supports the monophyly of the subfamily Mycetophilinae and two of its tribes, Exechiini and Mycetophilini. There is also statistical support for a Mycetophila- group and a Phronia- group within the tribe Mycetophilini. The Phronia- group includes the genera Phronia , Macrobrachius and Trichonta . The Mycetophila- group includes the genera Mycetophila , Epicypta , Platurocypta , Sceptonia and Zygomyia . A Bayesian analysis based on the nucleotide sequences alone also support these clades within Mycetophilini except for the position of Dynatosoma which is recovered as the sister taxon to the Phronia- group. A somewhat different pattern, however, is observed for the tribe Exechiini – neither molecular data nor the combined data set support unambiguously any intergeneric relationships within Exechiini.     

An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference

The objective of this study was to obtain a quantitative assessment of the monophyly of morning glory taxa, specifically the genus Ipomoea and the tribe Argyreieae. Previous systematic studies of morning glories intimated the paraphyly of Ipomoea by suggesting that the genera within the tribe Argyreieae are derived from within Ipomoea; however, no quantitative estimates of statistical support were developed to address these questions. We applied a Bayesian analysis to provide quantitative estimates of monophyly in an investigation of morning glory relationships using DNA sequence data. We also explored various approaches for examining convergence of the Markov chain Monte Carlo (MCMC) simulation of the Bayesian analysis by running 18 separate analyses varying in length. We found convergence of the important components of the phylogenetic model (the tree with the maximum posterior probability, branch lengths, the parameter values from the DNA substitution model, and the posterior probabilities for clade support) for these data after one million generations of the MCMC simulations. In the process, we identified a run where the parameter values obtained were often outside the range of values obtained from the other runs, suggesting an aberrant result. In addition, we compared the Bayesian method of phylogenetic analysis to maximum likelihood and maximum parsimony. The results from the Bayesian analysis and the maximum likelihood analysis were similar for topology, branch lengths, and parameters of the DNA substitution model. Topologies also were similar in the comparison between the Bayesian analysis and maximum parsimony, although the posterior probabilities and the bootstrap proportions exhibited some striking differences. In a Bayesian analysis of three data sets (ITS sequences, waxy sequences, and ITS + waxy sequences) no supoort for the monophyly of the genus Ipomoea, or for the tribe Argyreieae, was observed, with the estimate of the probability of the monophyly of these taxa being less than 3.4 x 10(-7).     

Phylogeny of the plant bug subfamily Mirinae (Hemiptera: Heteroptera: Cimicomorpha: Miridae) based on total evidence analysis

The first comprehensive phylogenetic analyses of the most diverse subfamily of plant bugs, Mirinae, is presented in this study, for 110 representative taxa based on total evidence analysis. A total of 85 morphological characters and 3898 bp of mitochondrial (16S, COI) and nuclear (18S, 28S) sequences were analysed for each partitioned and combined dataset based on parsimony, maximum likelihood and Bayesian inference. Major results obtained in this study include monophyly of the tribe Mecistoscelini. The largest tribe, Mirini, was recovered as polyphyletic, and Stenodemini was recovered as paraphyletic. The clade of Stenodemini + Mecistoscelini is the sister group of the remaining Mirinae. The monophyly of two complexes composed of superficially similar genera were tested; the Lygus complex was recovered as nonmonophyletic, and the Adelphocoris–Creontiades–Megacoelum complex was confirmed to be monophyletic. The generic relationships of the main clades within each tribe based on the phylogeny, as well as their supported morphological characters, are discussed.     

Phylogeny of haplo–diploid,fungus‐growing ambrosia beetles (Curculionidae: Scolytinae: Xyleborini) inferred from molecular and morphological data

Cognato, A. I., Hulcr, J., Dole, S. A. & Jordal, B. H. (2010). Phylogeny of haplo‐diploid, fungus‐growing ambrosia beetles (Curculionidae: Scolytinae: Xyleborini) inferred from molecular and morphological data. —Zoologica Scripta, 40, 174–186. The ambrosia beetle tribe Xyleborini currently contains 30 genera and approximately 1200 species which are distributed throughout worldwide forests with most diversity located in the tropics. They also represent the most invasive scolytines in North America. Despite economic concerns and biological curiosity with this group, a comprehensive understanding of generic boundaries and the evolutionary relationship among species is lacking. In this study, we include 155 xyleborine species representing 23 genera in parsimony and Bayesian analyses using 3925 nucleotides from mitochondrial (COI) and nuclear genomes (28S, ArgK, CAD, EF‐1α) and 39 morphological characters. The phylogenies resulting from the parsimony analyses, which treated gap positions either as missing or fifth character states, and the Bayesian analysis were generally similar. Clades with high support or posterior probabilities were found in all trees, while those with low support were not recovered by all analyses. Fourteen of the 23 genera were monophyletic although not all relationships among the genera were resolved. We show monophyly of several species groups associated with particular morphological and biological characters and suggest recognition of these groups as genera. Most interesting was the monophyly of South and Central American species representing several genera. This finding suggests recent and fast radiation of xyleborines in the New World accompanied by morphological and biological diversification.     

A re-evaluation of relationships in the Metastriata (Acari: Parasitiformes: Ixodidae)

A systematic analysis of generic/subgeneric relationships in the ixodid lineage Metastriata was conducted based on 82 structural and developmental characters, 15 of which have multiple states. Results of the analysis show considerable agreement with current classifications of the Ixodidae, including good support for monophyly of the Metastriata, the genera Ixodes and Haemaphysalis, and the grouping of Hoogstraal's Rhipicephalinae and Hyalomminae, and fair support for the genus Hyalomma. Our results differ from these classifications most notably by rejecting monophyly of the genera Aponomma and Amblyomma. Instead, the analysis provides weak support for a hypothesis in which the basal two to three lineages in the Metastriata are all composed of Aponomma species, and in which a fourth lineage within that genus, Aponomma elaphense, clusters with Amblyomma quadricavum to form a more derived lineage. Resolution is insufficient to support or reject monophyly of the genera Dermacentor and Rhipicephalus, or to resolve the position of the genus Haemaphysalis relative to the other Metastriata. Overall resolution within the Rhipicephalinae/Hyalomminae is quite good, but it is quite poor among the Amblyomminae and Haemaphysalinae. These results are similar to the results of recent 16S and 18S rDNA based molecular analyses. There are few indications of host specificity among the lineages analysed. The basal metastriate lineages contain a large number of squamate associates, but the pattern is not sufficiently clear to reject the hypothesis that these ticks will feed on all available vertebrate hosts. On the other hand, nearly all of the basal taxa are Australian. This suggests a possible origin of the Metastriata in Australia, with subsequent dispersal to other parts of the world.     

Identifying clades in Asian Annonaceae: monophyletic genera in the polyphyletic Miliuseae

The tribe Miliuseae (Annonaceae) comprises six genera distributed in Asia: Alphonsea, Mezzettia, Miliusa, Orophea, Platymitra, and Phoenicanthus. A phylogenetic study to investigate the putative monophyly of the tribe and the intergeneric relationships is presented here. Nucleotide sequences of the plastid gene rbcL, trnL intron, and trnL-trnF intergenic spacer were analyzed from 114 Annonaceae taxa, including 24 Miliuseae species and two outgroups using maximum parsimony and Bayesian inference. The two data sets (rbcL and the trnL-trnF regions) were analyzed separately and in combination. Miliuseae were found to be polyphyletic due to the position of Mezzettia and are part of a large, predominantly Asian and Central-American clade (miliusoid clade). Although intergeneric relationships were poorly resolved, all genera, except Polyalthia, were monophyletic, supporting previous generic delimitation based on morphology. A group of three Polyalthia species seems the most likely sister group of Miliusa. Several infrageneric groups of Miliusa, Orophea, and Polyalthia are supported by both molecular and morphological data. No morphological synapomorphies have yet been found for the miliusoid clade. Molecular clades within the miliusoid clade, however, can be characterized by size and the shape of the outer petals, number of ovules per carpel, and the size of the fruits.     

Phylogeny of Coreopsideae (Asteraceae) using ITS sequences suggests lability in reproductive characters

Relationships among the 21 genera within the tribe Coreopsideae (Asteraceae) remain poorly resolved despite phylogenetic studies using morphological and anatomical traits. Recent molecular phylogenies have also indicated that some Coreopsideae genera are not monophyletic. We used internal transcribed spacer (ITS) sequences from representatives of 19 genera, as well as all major lineages in those genera that are not monophyletic, to examine phylogenetic relationships within this group. To examine the affects of alignment and method of analysis on our conclusions, we obtained alignments using five different parameters and analyzed all five alignments with distance, parsimony, and Bayesian methods. The method of analysis had a larger impact on relationships than did alignments, although different analytical methods gave very similar results. Although not all relationships could be resolved, a number of well-supported lineages were found, some in conflict with earlier hypotheses. We did not find monophyly in Bidens, Coreopsis, and Coreocarpus, though other genera were monophyletic for the taxa we included. Morphological and anatomical traits which have been used previously to resolve phylogenetic relationships in this group were mapped onto the well-supported nodes of the ITS phylogeny. This analysis indicated that floral and fruit characters, which have been used extensively in phylogenetic studies in the Coreopsideae, show a higher degree of evolutionary lability in this group than the more highly conserved vegetative and photosynthetic traits.     

A multilocus perspective on the phylogenetic relationships and diversification of rodents of the tribe Abrotrichini (Cricetidae: Sigmodontinae)

Abrotrichini is a recently defined and diagnosed tribe of Sigmodontinae with a complex taxonomy. Abrotrichine genera, Abrothrix (including Chroeomys), Chelemys, Geoxus, Notiomys and Pearsonomys, are mostly distributed in the central and southern Andes and adjacent lowlands and show terrestrial and fossorial habits. Recent studies have evidenced some incongruence between current taxonomy and abrotrichine phylogeny, such as the polyphyly of Chelemys and paraphyly of Geoxus respect to Pearsonomys. We used DNA sequence data of six loci (one mitochondrial and five nuclear) to resolve the relationships within the tribe. Independent and combined analyses of these loci were carried out using parsimony, maximum likelihood and Bayesian inference. Estimates of divergence time of the main lineages of abrotrichines were calculated with a molecular clock using as calibration, a fossil recently found. The concatenated data set increased the resolution and defined the relationships within the tribe. Our phylogenetic analyses corroborate that Abrothrix is sister of a clade containing the long‐clawed abrotrichines. We recovered two main clades within Abrothrix that match morphologic variation and geographic distribution of its species. In addition, we corroborated the lack of monophyly of Chelemys and the lack of monophyly of Geoxus. We discuss different taxonomic scenarios to abrotrichine classification reflects the phylogenetic relationships obtained in this study. Our molecular clock estimated the Abrotrichini crown age to be around the early Pliocene (4.4 Ma) and suggest that the tribe diversified over a short period of time.     

Evaluating the monophyly and phylogenetic relationships of Brassolini genera (Lepidoptera, Nymphalidae)

Abstract.  This study uses 80 morphological characters and cladistic analysis to evaluate the monophyly and phylogenetic relationships of 18 genera that constitute the butterfly tribe Brassolini. Most characters derive from genitalia, confirming previous generic definitions based mainly on wing characters, and showing that 16 of 18 genera are monophyletic. Mimoblepia Casagrande, syn.n. was subsumed within Opoptera Aurivillius to address the paraphyly of the latter, but resolution of the status of Aponarope Casagrande requires further study. The results suggest that the Brassolini includes six suprageneric groups/clades. Although this study verifies some genus-level relationships put forward over 100 years ago, some new hypotheses of relationships are proposed. Tracing larval host plant use onto the Brassolini phylogeny indicates that species in this tribe retain the use of Arecaceae and Poaceae from their 'satyroid' ancestors.     

Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data

Despite intensive morphological and molecular studies of Onagraceae, relationships within the family are not fully understood. One drawback of previous analyses is limited sampling within the large tribe Onagreae. In addition, the monophyly of two species-rich genera in Onagreae, Camissonia and Oenothera, has never been adequately tested. To understand relationships within Onagraceae, test the monophyly of these two genera, and ascertain the affinities of the newly discovered genus Megacorax, we conducted parsimony and maximum likelihood analyses with rbcL and ndhF sequence data for 24 taxa representing all 17 Onagraceae genera and two outgroup Lythraceae. Results strongly support a monophyletic Onagraceae, with Ludwigia as the basal lineage and a sister-taxon relationship between Megacorax and Lopezia. Gongylocarpus is supported as sister to Epilobieae plus the rest of Onagreae, although relationships within the latter clade have limited resolution. Thus, we advocate placement of Gongylocarpus in a monogeneric tribe, Gongylocarpeae. Most relationships within Onagreae are weakly resolved, suggesting a rapid diversification of this group in western North America. Neither Camissonia nor Oenothera appears to be monophyletic; however, increased taxon sampling is needed to clarify those relationships. Morphological characters generally agree with the molecular data, providing further support for relationships.     

Phylogeny of the bees of the family Apidae based on larval characters with focus on the origin of cleptoparasitism (Hymenoptera: Apiformes)

Abstract.  Fifty-four genera of the bee family Apidae comprising almost all tribes were analysed based on 77 traditional and one new character of the mature larvae. Nine, especially cleptoparasitic species, were newly added. Analyses were performed by maximum parsimony and Bayesian inference. Trees inferred from the analysis of the complete dataset were rooted by taxa from the families Melittidae and Megachilidae. Unrooted trees inferred from the analysis of the partial dataset (excluding outgroup taxa) are also presented to preclude possible negative effects of the outgroup on the topology of the ingroup. Only the subfamily Nomadinae was statistically well supported. The monophyly of the subfamilies Xylocopinae and Apinae was not topologically recovered. The monophyly of the tribe Tetrapediini was supported, and this tribe was found to be related to xylocopine taxa. At the very least, larval morphology suggests that Tetrapedia is not a member of the subfamily Apinae. Our analyses support the monophyly of the Eucerine line (Emphorini, Eucerini, Exomalopsini, Tapinotaspidini) and of the Apine line (Anthophorini, Apini, Bombini, Centridini, Euglossini, Meliponini). All analyses support the monophyly of totally cleptoparasitic tribes of the subfamily Apinae. We named this group the Melectine line (Ericrocidini, Isepeolini, Melectini, Osirini, Protepeolini, Rhathymini). In previous studies all these cleptoparasitic tribes were considered independent evolutionary lineages. Our results suggest that their similarities with hosts in morphology and pattern are probably the result of convergence and host–parasite co-evolution than phylogenetic affinity. According to the present analysis, the cleptoparasitism has evolved independently only six times within the family Apidae.     

Using molecules and morphology to infer the phylogenetic relationships and evolutionary history of the Dirini (Nymphalidae: Satyrinae), a tribe of butterflies endemic to Southern Africa

The first empirically supported phylogenetic hypothesis of relationships for the southern African endemic butterfly tribe Dirini is presented. Data derived from the morphology and ecology of the adults and immature stages (33 characters), and portions of the mitochondrial gene cytochrome oxidase I (COI) and the nuclear genes elongation factor 1α (EF1α) and wingless (WG) (totalling 1734 bp) were used to infer the relationships of the in‐group genera. An expanded molecular dataset using four genera from the Nymphalini and Satyrini to root the tree, and three genera from the Melanitini to test the monophyly of the tribe, was analysed using parsimony and Bayesian methods. Estimates of divergence times were calculated using two fossil calibrations under a relaxed molecular clock model. The monophyly of the tribe and each in‐group genus were strongly supported. Key findings are the sister‐taxon relationship of Aeropetes and Tarsocera, the apparent simultaneous or nearly simultaneous radiation of four lineages, the polyphyly of the species within Torynesis, and the apparent trans‐Atlantic dispersal of the ancestors of Manataria about 40 Ma. Estimates of divergence times indicate that the tribe has undergone two major radiations since its origin: the first when they left forest habitats in the mid–late Oligocene, shortly after the radiation of the grasses (Poaceae), and the second in the early‐middle Pliocene, coinciding with the aridification of southern Africa and the spread of conditions that favoured C₄ grasses over the C₃ grasses that dirine larvae prefer to eat. The high species diversity within the tribe appears to be partly a taxonomic artefact that may have resulted from the misinterpretation of climate‐related phenotypic variation within extant species. Relocation and breeding experiments should test this hypothesis.     

Molecular phylogenetics and generic assessment in the tribe Morindeae (Rubiaceae–Rubioideae): How to circumscribe Morinda L. to be monophyletic?

Most of the species of the family Rubiaceae with flowers arranged in head inflorescences are currently classified in three distantly related tribes, Naucleeae (subfamily Cinchonoideae) and Morindeae and Schradereae (subfamily Rubioideae). Within Morindeae the type genus Morinda is traditionally and currently circumscribed based on its head inflorescences and syncarpous fruits (syncarps). These characters are also present in some members of its allied genera, raising doubts about the monophyly of Morinda. We perform Bayesian phylogenetic analyses using combined nrETS/nrITS/trnT-F data for 67 Morindeae taxa and five outgroups from the closely related tribes Mitchelleae and Gaertnereae to rigorously test the monophyly of Morinda as currently delimited and assess the phylogenetic value of head inflorescences and syncarps in Morinda and Morindeae and to evaluate generic relationships and limits in Morindeae. Our analyses demonstrate that head inflorescences and syncarps in Morinda and Morindeae are evolutionarily labile. Morinda is highly paraphyletic, unless the genera Coelospermum, Gynochthodes, Pogonolobus, and Sarcopygme are also included. Morindeae comprises four well-supported and morphologically distinct major lineages: Appunia clade, Morinda clade (including Sarcopygme and the lectotype M. royoc), Coelospermum clade (containing Pogonolobus and Morinda reticulata), and Gynochthodes–Morinda clade. Four possible alternatives for revising generic boundaries are presented to establish monophyletic units. We favor the recognition of the four major lineages of Morindeae as separate genera, because this classification reflects the occurrence of a considerable morphological diversity in the tribe and the phylogenetic and taxonomic distinctness of its newly delimited genera.     

Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing to (i) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae, and Cypereae; (ii) define the limits of Fuireneae s.s., and (iii) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognize as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr. nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub-Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognized tribes and genera are provided.     

Phylogeny of xanthopygine rove beetles (Coleoptera) based on six molecular loci

The rove beetle subtribe Xanthopygina (Coleoptera: Staphylinidae: Staphylininae: Staphylinini) is a species‐rich group of 27 neotropical genera that contains some of the largest and most brightly coloured of all staphylinid beetles. The monophyly of the subtribe has never been tested before, using a large dataset of taxa and genes. Bayesian and maximum likelihood analyses are used on individual genes (COI, 28S rDNA, wingless, arginine kinase, CAD and topoisomerase I) and the partitioned concatenated dataset to test for monophyly and examine the relationships among Xanthopygina genera. Xanthopygina (excluding Philothalpus) are shown to be a monophyletic group with strong support values. The genus Philothalpus is removed from Xanthopygina and placed in the tribe Staphylinini as incertae sedis. Four distinct clades of Xanthopygina genera are recognized. The origin of Xanthopygina is hypothesized to be in the Late Cretaceous or later and the origin of myrmecophilous adaptations is discussed.     

Phylogenetic relationships,subdivision, and biogeography of the cyprinid tribe Labeonini (sensu ) (Teleostei: Cypriniformes), with comments on the implications of lips and associated structures in the labeonin classification

The Labeonini (sensu Rainboth, 1991) is a tribe of the subfamily Cyprininae, the largest subfamily of Cypriniformes. With around 400 species in 34 genera, this tribe is widely distributed in the freshwaters of tropical Africa and Asia. Most species are adapted to fast-flowing streams and rivers, and exhibit unique morphological modifications associated with their lips and other structures around the mouth. The monophyly of this tribe has been tested and generally accepted in previous morphological and molecular studies. The major objectives of this study were to reconstruct the phylogenetic relationships within the tribe Labeonini, test its monophyly and explore the taxonomic subdivisions, intrarelationships and biogeography of the group. The value of the morphological characters associated with the lips and other associated structures in the taxonomic classification of labeonins was also discussed. Nucleotide sequences (3867 bp) of four unlinked nuclear loci were obtained from 51 species in 18 Labeonini genera from throughout the range of the tribe. Maximum parsimony, partitioned maximum likelihood and partitioned Bayesian analyses were used for phylogenetic inference from combined and separate gene data sets. Based on our results, the monophyly of Labeonini was well supported. Two major clades could be recovered within the tribe. Three subclades could further be recognized from the first clade. These clades/subclades are not consistent with groupings of any of previous workers using either morphological or molecular characters for phylogenetic inference. Only five currently recognized genera in this analysis are monophyletic. The similarity between some lips and associated structures (e.g. suctorial discs) of labeonins may due to convergence or parallelism instead of common ancestry. Labeonins of Southeast Asia, India and China are closely related to each other; the multiple clades of African taxa do not form a single monophyletic group, indicating multiple, independent dispersal events of labeonins into Africa from Asia.     

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.