Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution

In this study, mitochondrial sequences were used to investigate the relationships among the major lineages of Arthropoda. The data matrix used for the analyses includes 84 taxa and 3918 nucleotides representing six mitochondrial protein-coding genes (atp6 and 8, cox1-3, and nad2). The analyses of nucleotide composition show that a reverse strand-bias, i.e., characterized by an excess of T relative to A nucleotides and of G relative to C nucleotides, was independently acquired in six different lineages of Arthropoda: (1) the honeybee mite (Varroa), (2) Opisthothelae spiders (Argiope, Habronattus, and Ornithoctonus), (3) scorpions (Euscorpius and Mesobuthus), (4) Hutchinsoniella (Cephalocarid), (5) Tigriopus (Copepod), and (6) whiteflies (Aleurodicus and Trialeurodes). Phylogenetic analyses confirm that these convergences in nucleotide composition can be particularly misleading for tree reconstruction, as unrelated taxa with reverse strand-bias tend to group together in MP, ML, and Bayesian analyses. However, the use of a specific model for minimizing effects of the bias, the "Neutral Transition Exclusion" (NTE) model, allows Bayesian analyses to rediscover most of the higher taxa of Arthropoda. Furthermore, the analyses of branch lengths suggest that three main factors explain accelerated rates of substitution: (1) genomic rearrangements, including duplication of the control region and gene translocation, (2) parasitic lifestyle, and (3) small body size. The comparisons of Bayesian Bootstrap percentages show that the support for many nodes increases when taxa with long branches are excluded from the analyses. It is therefore recommended to select taxa and genes of the mitochondrial genome for inferring phylogenetic relationships among arthropod lineages. The phylogenetic analyses support the existence of a major dichotomy within Arthropoda, separating Pancrustacea and Paradoxopoda. Basal relationships between Pancrustacean lineages are not robust, and the question of Hexapod monophyly or polyphyly cannot be answered with the available mitochondrial sequences. Within Paradoxopoda, Chelicerata and Myriapoda are each found to be monophyletic, and Endeis (Pycnogonida) is, surprisingly, associated with Acari.     

Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition

The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.     

Inferring speciation times under an episodic molecular clock

We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates among lineages. The method can use heterogeneous data from multiple gene loci and accommodate multiple fossil calibrations. Uncertainties in fossil calibrations are described using flexible statistical distributions. The prior for divergence times for nodes lacking fossil calibrations is specified by use of a birth-death process with species sampling. The prior for lineage-specific substitution rates is specified using either a model with autocorrelated rates among adjacent lineages (based on a geometric Brownian motion model of rate drift) or a model with independent rates among lineages specified by a log-normal probability distribution. We develop an infinite-sites theory, which predicts that when the amount of sequence data approaches infinity, the width of the posterior credibility interval and the posterior mean of divergence times form a perfect linear relationship, with the slope indicating uncertainties in time estimates that cannot be reduced by sequence data alone. Simulations are used to study the influence of among-lineage rate variation and the number of loci sampled on the uncertainty of divergence time estimates. The analysis suggests that posterior time estimates typically involve considerable uncertainties even with an infinite amount of sequence data, and that the reliability and precision of fossil calibrations are critically important to divergence time estimation. We apply our new algorithms to two empirical data sets and compare the results with those obtained in previous Bayesian and likelihood analyses. The results demonstrate the utility of our new algorithms.     

Modeling compositional heterogeneity

Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.     

Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within 'Amoebozoa' upon removal of varying rate classes of SSU-rDNA

Placing amoeboid lineages on the eukaryotic tree of life is difficult due to the paucity of comparable morphological characters and the limited molecular data available for many groups. This situation has led to the lumping of distantly related lineages into large inclusive groups, such as Sarcodina, that do not reflect evolutionary relationships. Previous analyses of molecular markers with limited taxon sampling reveal members of Sarcodina are scattered in five of the six proposed supergroups. We have used multigene analyses to place seven diverse amoeboid lineages-two Nolandella spp., Rhizamoeba sp., Pessonella sp., Arcella hemisphaerica, Arachnula sp. and Trichosphaerium sp.-on the eukaryotic tree of life. Bayesian analysis of the concatenated data of the four genes sequenced (SSU-rDNA, actin, alpha-tubulin and beta-tubulin), including diverse representatives of eukaryotes, indicates that all seven taxa group within the 'Amoebozoa' supergroup. We further performed separate analyses of the well-sampled SSU-rDNA and actin genes using Bayesian and Maximum Likelihood analyses to assess the positions of our newly characterized taxa. In the case of SSU-rDNA, we performed extensive analyses with removal of the fastest rates classes to evaluate the stability and resolution of various taxonomic hypotheses within 'Amoebozoa'. Five of our seven amoeboid lineages fall within well-supported clades that are corroborated by morphology. In contrast, the positions of Arachnula sp. and Trichosphaerium sp. in the SSU-rDNA gene trees are unstable and vary by analyses. Placement of these taxa will require additional data from slowly evolving genes combined with taxon-rich phylogenetic analyses. Finally, the analyses without the fastest rate classes demonstrate that SSU-rDNA has a limited signal for deep relationships within the 'Amoebozoa'.     

Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8-kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.     

Systematics of the Pezizomycetes--the operculate discomycetes

The Pezizomycetes (order Pezizales) is an early diverging lineage within the Pezizomycotina. A shared derived character, the operculate ascus, supports the Pezizales as monophyletic, although functional opercula have been lost in certain taxa. Phylogenetic relationships within Pezizales were studied using parsimony and Bayesian analyses of partial SSU and LSU rDNA sequences from 100 taxa representing 82 genera and 13 of the 15 families currently recognized. Three primary lineages are identified that more or less correspond to the A, B and C lineages resolved in previous analyses using SSU rDNA: (A) Ascobolaceae and Pezizaceae; (B) Discinaceae-Morchellaceae and Helvellaceae-Tuberaceae; (C) Ascodesmidaceae, Glaziellaceae, Pyronemataceae, Sarcoscyphaceae and Sarcosomataceae. In contrast the monotypic Rhizinaceae and Caloscyphaceae are resolved as two independent lineages. Bayesian analyses support a relationship among Rhizina and two species of Psilopezia (Pyronemataceae). Only lineage C is highly supported. The B and C lineages form a strongly supported monophyletic group. None of these lineages corresponds to earlier proposed suborders. The A and B lineages are supported by certain morphological features (e.g. ascus bluing reaction in iodine, cytology of spores and paraphyses, septal pore structures and excipulum structure); these characters have been subject to homoplasy. Lineage C is the largest and most heterogeneous, and no unifying morphological features support its recognition. The Pyronemataceae, in which almost half of the species in the order are found, is not monophyletic because the Ascodesmidaceae and Glaziellaceae are nested within it. The relationships among all families in the C lineage remain uncertain. The origin of various forms of ascomata, including hypogeous forms (truffles and truffle-like), epigeous cleistothecia, simple reduced apothecia and highly elaborate, stipitate forms (helvelloid and morchelloid), are discussed.     

Specialist and generalist symbionts show counterintuitive levels of genetic diversity and discordant demographic histories along the Florida Reef Tract

Specialist and generalist life histories are expected to result in contrasting levels of genetic diversity at the population level, and symbioses are expected to lead to patterns that reflect a shared biogeographic history and co-diversification. We test these assumptions using mtDNA sequencing and a comparative phylogeographic approach for six co-occurring crustacean species that are symbiotic with sea anemones on western Atlantic coral reefs, yet vary in their host specificities: four are host specialists and two are host generalists. We first conducted species discovery analyses to delimit cryptic lineages, followed by classic population genetic diversity analyses for each delimited taxon, and then reconstructed the demographic history for each taxon using traditional summary statistics, Bayesian skyline plots, and approximate Bayesian computation to test for signatures of recent and concerted population expansion. The genetic diversity values recovered here contravene the expectations of the specialist–generalist variation hypothesis and classic population genetics theory; all specialist lineages had greater genetic diversity than generalists. Demography suggests recent population expansions in all taxa, although Bayesian skyline plots and approximate Bayesian computation suggest the timing and magnitude of these events were idiosyncratic. These results do not meet the a priori expectation of concordance among symbiotic taxa and suggest that intrinsic aspects of species biology may contribute more to phylogeographic history than extrinsic forces that shape whole communities. The recovery of two cryptic specialist lineages adds an additional layer of biodiversity to this symbiosis and contributes to an emerging pattern of cryptic speciation in the specialist taxa. Our results underscore the differences in the evolutionary processes acting on marine systems from the terrestrial processes that often drive theory. Finally, we continue to highlight the Florida Reef Tract as an important biodiversity hotspot.

     

A mtDNA-based phylogeny of the brown algal genus Fucus (Heterokontophyta; Phaeophyta)

Species of Fucus are among the dominant seaweeds along Northern Hemisphere shores, but taxonomic designations often are confounded by significant intraspecific morphological variability. We analyzed intra- and inter-specific phylogenetic relationships within the genus (275 individuals representing 16 taxa) using two regions of the mitochondrion: a variable intergenic spacer and a conserved portion of the 23S subunit. Bayesian ML and MP analyses verified a shallow phylogeny with two major lineages (previously reported) and resolved some intra-lineage relationships. Significant species-level paraphyly/polyphyly was observed within lineages 1A and 2. Despite higher species richness in the North Atlantic, a North Pacific origin of the genus is supported by a gradient of decreasing haplotype and nucleotide diversities in F. distichus from the North Pacific to the East Atlantic.     

A phylogeny of anisopterous dragonflies (Insecta,Odonata) using mtRNA genes and mixed nucleotide/doublet models

The application of mixed nucleotide/doublet substitution models has recently received attention in RNA‐based phylogenetics. Within a Bayesian approach, it was shown that mixed models outperformed analyses relying on simple nucleotide models. We analysed an mt RNA data set of dragonflies representing all major lineages of Anisoptera plus outgroups, using a mixed model in a Bayesian and parsimony (MP) approach. We used a published mt 16S rRNA secondary consensus structure model and inferred consensus models for the mt 12S rRNA and tRNA valine. Secondary structure information was used to set data partitions for paired and unpaired sites on which doublet or nucleotide models were applied, respectively. Several different doublet models are currently available of which we chose the most appropriate one by a Bayes factor test. The MP reconstructions relied on recoded data for paired sites in order to account for character covariance and an application of the ratchet strategy to find most parsimonious trees. Bayesian and parsimony reconstructions are partly differently resolved, indicating sensitivity of the reconstructions to model specification. Our analyses depict a tree in which the damselfly family Lestidae is sister group to a monophyletic clade Epiophlebia + Anisoptera, contradicting recent morphological and molecular work. In Bayesian analyses, we found a deep split between Libelluloidea and a clade ‘Aeshnoidea’ within Anisoptera largely congruent with Tillyard’s early ideas of anisopteran evolution, which had been based on evidently plesiomorphic character states. However, parsimony analysis did not support a clade ‘Aeshnoidea’, but instead, placed Gomphidae as sister taxon to Libelluloidea. Monophyly of Libelluloidea is only modestly supported, and many inter‐family relationships within Libelluloidea do not receive substantial support in Bayesian and parsimony analyses. We checked whether high Bayesian node support was inflated owing to either: (i) wrong secondary consensus structures; (ii) under‐sampling of the MCMC process, thereby missing other local maxima; or (iii) unrealistic prior assumptions on topologies or branch lengths. We found that different consensus structure models exert strong influence on the reconstruction, which demonstrates the importance of taxon‐specific realistic secondary structure models in RNA phylogenetics.     

Phylogeny of the Mexican coastal leopard frogs of the Rana berlandieri group based on mtDNA sequences

Phylogenetic relationships among specimens from 25 different locations for the six Mexican coastal leopard frog species of the Rana berlandieri species group were investigated using 797 bp of the mitochondrial 12S rDNA gene. Relationships among the haplotypes obtained were recovered using maximum parsimony and Bayesian analyses. Most of the clades recovered by both tree building methods are strongly supported, but conflicting clades recovered by each analysis are generally poorly supported. Both analyses reject the previously proposed subgroupings of the R. berlandieri species group. Based on the strongly supported relationships, genetic differentiation, and geographic distribution of the haplotypes examined, nine independent lineages appear to comprise the group of study. However, confirmation of the new proposed lineages will require further analyses based on other genetic markers and additional samples that cover their entire geographic distribution. Concordance was noted between Miocene-Pliocene geological and climatic events in Mexico and the relationships recovered among the lineages proposed and their geographic distribution.     

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.     

Dating the evolutionary origins of wrasse lineages (Labridae) and the rise of trophic novelty on coral reefs

We estimated ages of divergence between major labrid tribes and the timing of the evolution of trophic novelty. Sequence data for 101 labrid taxa and 14 outgroups consisting of two mitochondrial gene regions (12s, 16s), and two nuclear protein-coding genes (RAG2, TMO4c4), a combined 2567 bp of sequence, were examined using novel maximum likelihood, maximum parsimony and mixed model Bayesian inference methods. These analyses yielded well supported trees consistent with published phylogenies. Bayesian inference using five fossil calibration points estimated the minimum ages of lineages. With origins in the late Cretaceous to early tertiary, the family diversified quickly with both major lineages (hypsigenyine and julidine) present at approximately 62.7 Ma, shortly after the K/T boundary. All lineages leading to major tribes were in place by the beginning of the Miocene (23 Ma) with most diversification in extant lineages occurring within the Miocene. Optimisation of trophic information onto the chronogram revealed multiple origins of novel feeding modes with two distinct periods of innovation. The Palaeocene/Eocene saw the origins of feeding modes that are well represented in other families: gastropod feeders, piscivores and browsing herbivores. A wave of innovation in the Oligocene/Miocene resulted in specialized feeding modes, rarely seen in other groups: coral feeding, foraminifera feeding and fish cleaning. There is little evidence of a general relationship between trophic specialization and species diversity. The current trophic diversity of the Labridae is a result of the accumulation of feeding modes dating back to the K/T boundary at 65 Ma, with all major feeding modes on present day reefs already in place 7.5 million years ago.     

Multilocus and morphological analysis of south-eastern Iberian Wall lizards (Squamata,Podarcis)

The phylogenetic relationships among the wall lizards of the Podarcis hispanicus complex that inhabit the south-east (SE) of the Iberian Peninsula and other lineages of the complex remain unclear. In this study, four mitochondrial and two nuclear markers were used to study genetic relationships within this complex. The phylogenetic analyses based on mtDNA gene trees constructed with ML and BI, and a species tree using *BEAST support three divergent clades in this region: the Valencia, Galera and Albacete/Murcia lineages. These three lineages were also corroborated in species delimitation analyses based on mtDNA using bPTP, mPTP, GMYC, ABGD and BAPS. Bayesian inference species delimitation method (BPP) based on both nuclear data and a combined data set (mtDNA + nuclear) showed high posterior probabilities for these three SE lineages (≥0.94) and another Bayesian analysis (STACEY) based on combined data set recovered the same three groups in this region. Divergence time dating of the species tree provided an estimated divergence of the Galera lineage from the other SE group (Podarcis vaucheri, (Albacete/Murcia, Valencia)) at 12.48 Ma. During this period, the Betic–Rifian arc was isolated, which could have caused the isolation of the Galera form distributed to the south of the Betic Corridor. Although lizards from the Albacete/Murcia and Galera lineage are morphologically similar, they clearly represent distinct genetic lineages. The noteworthy separation of the Galera lineage enables us to conclude that this lineage must be considered as a new full species.     

Molecular phylogenetics and evolutionary history of the neotropical Satyrine Subtribe Euptychiina (Nymphalidae: Satyrinae)

The Euptychiina is one of the more diverse lineages of satyrine butterflies, represented by over 300 species. The first phylogenetic analyses of the subtribe is presented based on 2506 aligned nucleotide sequences obtained from 69 individuals spanning 28 ingroup genera and nine outgroup genera. Two genes were used, the mitochondrial gene cytochrome oxidase 1 (1268 bp) and the nuclear gene elongation factor-1alpha (1238 bp). The subtribe is never recovered as monophyletic in analyses using parsimony, maximum likelihood, or Bayesian inference. Several euptychiine genera are placed basal to the ingroup, but support is found only for Euptychia and Oressinoma. Three main lineages within the ingroup were clearly defined and many taxonomic groupings within the clades strongly supported. The majority of genera tested were paraphyletic or polyphyletic. Based on results presented here and novel host use, a close relationship of Euptychia to the Indo-Australian tribe Ragadiini is hypothesized. Origins of the group remain unclear, but the basal position of most of the Nearctic genera is discussed.     

Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA

To provide a robust phylogeny of Pezizaceae, partial sequences from two nuclear protein-coding genes, RPB2 (encoding the second largest subunit of RNA polymerase II) and beta-tubulin, were obtained from 69 and 72 specimens, respectively, to analyze with nuclear ribosomal large subunit RNA gene sequences (LSU). The three-gene data set includes 32 species of Peziza, and 27 species from nine additional epigeous and six hypogeous (truffle) pezizaceous genera. Analyses of the combined LSU, RPB2, and beta-tubulin data set using parsimony, maximum likelihood, and Bayesian approaches identify 14 fine-scale lineages within Pezizaceae. Species of Peziza occur in eight of the lineages, spread among other genera of the family, confirming the non-monophyly of the genus. Although parsimony analyses of the three-gene data set produced a nearly completely resolved strict consensus tree, with increased confidence, relationships between the lineages are still resolved with mostly weak bootstrap support. Bayesian analyses of the three-gene data, however, show support for several more inclusive clades, mostly congruent with Bayesian analyses of RPB2. No strongly supported incongruence was found among phylogenies derived from the separate LSU, RPB2, and beta-tubulin data sets. The RPB2 region appeared to be the most informative single gene region based on resolution and clade support, and accounts for the greatest number of potentially parsimony informative characters within the combined data set, followed by the LSU and the beta-tubulin region. The results indicate that third codon positions in beta-tubulin are saturated, especially for sites that provide information about the deeper relationships. Nevertheless, almost all phylogenetic signal in beta-tubulin is due to third positions changes, with almost no signal in first and second codons, and contribute phylogenetic information at the "fine-scale" level within the Pezizaceae. The Pezizaceae is supported as monophyletic in analyses of the three-gene data set, but its sister-group relationships is not resolved with support. The results advocate the use of RPB2 as a marker for ascomycete phylogenetics at the inter-generic level, whereas the beta-tubulin gene appears less useful.     

Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca)

Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five segments), 12S rRNA, cytochrome c oxidase subunit I, histone H3 and elongation factor 1alpha. The alignment has a combined length of 3995 base positions for 36 taxa, comprising 29 Caenogastropoda representing all of its major lineages and seven outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted. The results generally support monophyly of Caenogastropoda and Hypsogastropoda (Caenogastropoda excepting Architaenioglossa, Cerithioidea and Campanilioidea). Within Hypsogastropoda, maximum likelihood and Bayesian analyses identified a near basal clade of nine or 10 families lacking an anterior inhalant siphon, and Cerithiopsidae s.l. (representing Triphoroidea), where the siphon is probably derived independently from other Hypsogastropoda. The asiphonate family Eatoniellidae was usually included in the clade but was removed in one Bayesian analysis. Of the two other studied families lacking a siphon, the limpet-shaped Calyptraeidae was associated with this group in some analyses, but the tent-shaped Xenophoridae was generally associated with the siphonate Strombidae. The other studied hypsogastropods with an anterior inhalant siphon include nine families, six of which are Neogastropoda, the only traditional caenogastropod group above the superfamily-level with strong morphological support. The hypotheses that Neogastropoda are monophyletic and that the group occupies a derived position within Hypsogastropoda are both contradicted, but weakly, by the molecular analyses. Despite the addition of large amounts of new molecular data, many caenogastropod lineages remain poorly resolved or unresolved in the present analyses, possibly due to a rapid radiation of the Hypsogastropoda following the Permian-Triassic extinction during the early Mesozoic.     

Complex biogeographic history of the cuckoo-shrikes and allies (Passeriformes: Campephagidae) revealed by mitochondrial and nuclear sequence data

The Campephagidae (minivets, cuckoo-shrikes and trillers, seven genera and 81 species) represents an Old World corvid clade of tropical birds with a mixed diet that forage in different manners, i.e., flycatching, foliage-gleaning or shriking. This family has never been the focus of any phylogenetic survey, so their phylogenetic relationships and biogeographic history remain largely unknown. To address these questions, we sequenced four loci (ND2, myoglobin intron-2, GAPDH intron-11 and c-mos) for 27 species of Campephagidae. Our analyses suggest that Coracina consists of five unrelated lineages and that Lalage is paraphyletic. Our dating analyses, using a Bayesian relaxed-clock method, indicate that the split between the Indo-Malayan genus Pericrocotus and the remaining Campephagidae occurred synchronously with other splits involving Indo-Malayan corvid lineages, suggesting that several lineages of Indo-Malayan birds were isolated at the same time from their closest relatives. The African stock of cuckoo-shrikes is likely the result of three independent trans-oceanic dispersals from Australasia.     

The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters

We tested whether it is beneficial for the accuracy of phylogenetic inference to sample characters that are evolving under different sets of parameters, using both Bayesian MCMC (Markov chain Monte Carlo) and parsimony approaches. We examined differential rates of evolution among characters, differential character-state frequencies and character-state space, and differential relative branch lengths among characters. We also compared the relative performance of parsimony and Bayesian analyses by progressively incorporating more of these heterogeneous parameters and progressively increasing the severity of this heterogeneity. Bayesian analyses performed better than parsimony when heterogeneous simulation parameters were incorporated into the substitution model. However, parsimony outperformed Bayesian MCMC when heterogeneous simulation parameters were not incorporated into the Bayesian substitution model. The higher the rate of evolution simulated, the better parsimony performed relative to Bayesian analyses. Bayesian and parsimony analyses converged in their performance as the number of simulated heterogeneous model parameters increased. Up to a point, rate heterogeneity among sites was generally advantageous for phylogenetic inference using both approaches. In contrast, branch-length heterogeneity was generally disadvantageous for phylogenetic inference using both parsimony and Bayesian approaches. Parsimony was found to be more conservative than Bayesian analyses, in that it resolved fewer incorrect clades.
© The Willi Hennig Society 2006.     

Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1

Although the family Sciuridae is large and well known, phylogenetic analyses are scarce. We report on a comprehensive molecular phylogeny for the family. Two nuclear genes (c-myc and RAG1) comprising approximately 4500 bp of data (most in exons) are applied for the first time to rodent phylogenetics. Parsimony, likelihood, and Bayesian analyses of the separate gene regions and combined data reveal five major lineages and refute the conventional elevation of the flying squirrels (Pteromyinae) to subfamily status. Instead, flying squirrels are derived from one of the tree squirrel lineages. C-myc indels corroborate the sequence-based topologies. The common ancestor of extant squirrels appears to have been arboreal, confirming the fossil evidence. The results also reveal an unexpected clade of mostly terrestrial squirrels with African and Holarctic centers of diversity. We present a revised classification of squirrels. Our results demonstrate the phylogenetic utility of relatively slowly evolving nuclear exonic data even for relatively recent clades.