Data partitioning in Bayesian analysis: molecular phylogenetics of metalmark moths (Lepidoptera: Choreutidae)

In this study a multilocus phylogenetic analysis of metalmark moths (Lepidoptera: Choreutidae) focused on resolving the higher‐level phylogeny of this group is presented. Through the analysis of this dataset, I explore different data‐partitioning strategies in Bayesian phylogenetic inference, and find that a partitioning strategy can have a large influence on the results of phylogenetic analysis. Depending on how the data are partitioned, there can be significant differences in branch support. I also test for the existence of the Bayesian star tree paradox, and its importance in this dataset, and find that it appears to inflate support for the clade including Rhobonda gaurisana, Hemerophila houttuinialis, H. diva and H. felis, but plays no role in other cases where the differences between maximum‐likelihood bootstraps and Bayesian posterior probabilities are large. The results of all the phylogenetic analyses strongly suggest that including Millieriinae in Choreutidae renders the family polyphyletic. The monophyly of the other two subfamilies, Brenthiinae and Choreutinae, as well as their sister‐group relationship, is strongly supported. Similarly, the monophyly of all the genera examined except Hemerophila is also well supported. To bring the classification of Choreutidae in line with our current understanding of the phylogenetic relationships in the family, I propose to exclude Millieriinae from Choreutidae, elevate it to Millieriidae Heppner, and place it as incertae sedis within Ditrysia.     

Phylogeographic analysis of Pimoidae (Arachnida: Araneae) inferred from mitochondrial cytochrome c oxidase subunit I and nuclear 28S rRNA gene regions

Using mitochondrial DNA cytochrome c oxidase subunit I and nuclear DNA 28S rRNA data, we explored the phylogenetic relationships of the family Pimoidae (Arachnida: Araneae) and tested the North America to Asia dispersal hypothesis. Sequence data were analysed using maximum parsimony and Bayesian inference. A phylogenetic analysis suggested that vicariance, instead of dispersal, better explained the present distribution pattern of Pimoidae. Times of divergence events were estimated using penalized likelihood method. The dating analysis suggested that the emergence time of Pimoidae was approximately 140 million years ago (Ma). The divergence time of the North American and Asian species of Pimoa was approximately 110 Ma. Our phylogenetic hypothesis supports the current morphology‐based taxonomy and suggests that the cave dwelling might have played an important role in the speciation of pimoids in arid areas.     

A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders

We present a mitochondrial (mt) genome phylogeny inferring relationships within Neuropterida (lacewings, alderflies and camel flies) and between Neuropterida and other holometabolous insect orders. Whole mt genomes were sequenced for Sialis hamata (Megaloptera: Sialidae), Ditaxis latistyla (Neuroptera: Mantispidae), Mongoloraphidia harmandi (Raphidioptera: Raphidiidae), Macrogyrus oblongus (Coleoptera: Gyrinidae), Rhopaea magnicornis (Coleoptera: Scarabaeidae), and Mordella atrata (Coleoptera: Mordellidae) and compared against representatives of other holometabolous orders in phylogenetic analyses. Additionally, we test the sensitivity of phylogenetic inferences to four analytical approaches: inclusion vs. exclusion of RNA genes, manual vs. algorithmic alignments, arbitrary vs. algorithmic approaches to excluding variable gene regions and how each approach interacts with phylogenetic inference methods (parsimony vs. Bayesian inference). Of these factors, phylogenetic inference method had the most influence on interordinal relationships. Bayesian analyses inferred topologies largely congruent with morphologically‐based hypotheses of neuropterid relationships, a monophyletic Neuropterida whose sister group is Coleoptera. In contrast, parsimony analyses failed to support a monophyletic Neuropterida as Raphidioptera was the sister group of the entire Holometabola excluding Hymenoptera, and Neuroptera + Megaloptera is the sister group of Diptera, a relationship which has not previously been proposed based on either molecular or morphological data sets. These differences between analytical methods are due to the high among site rate heterogeneity found in insect mt genomes which is properly modelled by Bayesian methods but results in artifactual relationships under parsimony. Properly analysed, the mt genomic data set presented here is among the first molecular data to support traditional, morphology‐based interpretations of relationships between the three neuropterid orders and their grouping with Coleoptera.     

Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors

Background  

The typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set.     

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.     

What's old and new in molecular phylogenetics

While it is fairly easy to devise a phylogenetic tree based on molecular data, it has proven difficult to tell how reliable any such tree is. Thus while the genetic inference that humans, chimpanzees, and gorillas cluster together is widely accepted, the genetic inference that the primary division among Old World human populations is between Asia and EurAfrica is not. A molecular phylogenetic inference linking humans and chimpanzees was proposed in the 1980s based on the technique of DNA hybridization. Despite several recent publications in primary and secondary source material, much confusion still exists surrounding the work. This paper tries to clarify issues that may still be confusing to physical anthropologists, and proposes criteria upon which to judge the robusticity of a phylogenetic inference based on DNA hybridization, in light of a recent published claim of replication. The claim of replication is considered critically. Interestingly, the original DNA hybridization data may actually show a chimp-gorilla link, in harmony with other phylogenetic results.     

Using Confidence Set Heuristics During Topology Search Improves the Robustness of Phylogenetic Inference

We examine the impact of likelihood surface characteristics on phylogenetic inference. Amino acid data sets simulated from topologies with branch length features chosen to represent varying degrees of difficulty for likelihood maximization are analyzed. We present situations where the tree found to achieve the global maximum in likelihood is often not equal to the true tree. We use the program covSEARCH to demonstrate how the use of adaptively sized pools of candidate trees that are updated using confidence tests results in solution sets that are highly likely to contain the true tree. This approach requires more computation than traditional maximum likelihood methods, hence covSEARCH is best suited to small to medium-sized alignments or large alignments with some constrained nodes. The majority rule consensus tree computed from the confidence sets also proves to be different from the generating topology. Although low phylogenetic signal in the input alignment can result in large confidence sets of trees, some biological information can still be obtained based on nodes that exhibit high support within the confidence set. Two real data examples are analyzed: mammal mitochondrial proteins and a small tubulin alignment. We conclude that the technique of confidence set optimization can significantly improve the robustness of phylogenetic inference at a reasonable computational cost. Additionally, when either very short internal branches or very long terminal branches are present, confident resolution of specific bipartitions or subtrees, rather than whole-tree phylogenies, may be the most realistic goal for phylogenetic methods. [Reviewing Editor: Dr. Nicolas Galtier]     

Character-state space versus rate of evolution in phylogenetic inference

With only four alternative character states, parallelisms and reversals are expected to occur frequently when using nucleotide characters for phylogenetic inference. Greater available character‐state space has been described as one of the advantages of third codon positions relative to first and second codon positions, as well as amino acids relative to nucleotides. We used simulations to quantify how character‐state space and rate of evolution relate to one another, and how this relationship is affected by differences in: tree topology, branch lengths, rate heterogeneity among sites, probability of change among states, and frequency of character states. Specifically, we examined how inferred tree lengths, consistency and retention indices, and accuracy of phylogenetic inference are affected. Our results indicate that the relatively small increases in the character‐state space evident in empirical data matrices can provide enormous benefits for the accuracy of phylogenetic inference. This advantage may become more pronounced with unequal probabilities of change among states. Although increased character‐state space greatly improved the accuracy of topology inference, improvements in the estimation of the correct tree length were less apparent. Accuracy and inferred tree length improved most when character‐state space increased initially; further increases provided more modest improvements. © The Willi Hennig Society 2004.     

Systematics and evolution of syllids (Annelida,Syllidae)

A large, combined phylogenetic analysis (including morphological and molecular data from 18S rDNA, 16S rDNA and cytochrome c oxidase subunit I), with the highest number of species and genera of Syllidae studied to date (213 terminals), is examined. The data were explored with different parameters and optimality criteria (parsimony, likelihood, and bayesian inference). The monophyly of Syllidae and most of the traditional subfamilies is supported. The subfamily Eusyllinae is polyphyletic, as currently delineated, but it is herein reorganized and its diagnosis modified to be a valid group. Additional well supported clades arise. The phylogenetic relationships of the well known and established genera, as well as several enigmatic genera (e.g. Anguillosyllis, Paraopisthosyllis and Parahaplosyllis), the position of which in syllid taxonomy was uncertain or dubious to date, are clarified. The results corroborate previous hypotheses about the evolution of the reproductive and brooding modes. Within Syllinae, the nature of the stolon is phylogenetically informative. The classification of the whole family is revised and discussed on the basis of this phylogenetic hypothesis. © The Willi Hennig Society 2011.     

Molecular phylogeny of Geoplaninae (Platyhelminthes) challenges current classification: proposal of taxonomic actions

Despite likely being the most diverse group within the Tricladida, the systematics of land planarians (Geoplanidae) has received minor attention. The most species‐rich ingroup, the subfamily Geoplaninae, is restricted to the Neotropics. The systematics of Geoplaninae remains uncertain. Unique features supporting the genera are scanty; moreover, parts of the known species have been poorly described, making comparative studies difficult. Likewise the evolutionary relationships among land planarians remain insufficiently understood. In the present study, a phylogenetic hypothesis for selected taxa of Geoplaninae based on the molecular data is presented and discussed in the light of morphological features. Our phylogenetic inference is based on the fragments of three nuclear regions (18S, 28S rDNA and EF‐1α) and a mitochondrial marker (cytochrome oxidase I) for which we considered three optimality criteria (parsimony, maximum likelihood and Bayesian inference). Although our data provide little support for most basal nodes, our phylogenetic trees show a number of well‐supported clades, unveiling morphologically homogeneous groups. According to these results, we propose to separate Geoplana into Barreirana (formerly considered a subgenus), Cratera gen. n., Imbira gen. n., Matuxia gen. n., Obama gen. n. and Paraba gen. n., emend the diagnoses of Barreirana, Geoplana, Notogynaphallia, Pasipha and Xerapoa and review the classification of the species within these genera. For Geoplana goetschi sensu Marcus, (1951), a new name is proposed.     

Dissolving the star-tree paradox

While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy prior as a solution (or rather dissolution) of the paradox and argue that it is preferable to a data-size dependent branch lengths prior from a methodological perspective. However, while this reply dissolves the star-tree paradox, the general challenge to Bayesian confirmation theory remains unmet.     

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase‐activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.     

Exploring tree-building methods and distinct molecular data to recover a known asymmetric phage phylogeny

An experimental phylogeny was constructed using bacteriophage T7 and a propagation protocol, in the presence of the mutagen N-methyl-N′-nitro-N′-nitrosoguanidine, based on Hillis et al. [Hillis, D.M., Bull, J.J., White, M.E., Badgett, M.R., Molineux, I.J., 1992. Experimental phylogenetics, generation of a known phylogeny. Science 255, 589–592]. The topology presented in this study has a considerable variation in branch lengths and is less symmetric than the one presented by Hillis et al. [Hillis, D.M., Bull, J.J., White, M.E., Badgett, M.R., Molineux, I.J., 1992. Experimental phylogenetics, generation of a known phylogeny. Science 255, 589–592]. These features are known to present additional difficulties to phylogenetic inference methods. The performance of several phylogenetic methods (conventional and less conventional) was tested using restriction site and nucleotide data. Only methods that encompassed a molecular clock or those based on sequence signatures recovered the true phylogeny. Nevertheless a likelihood ratio test rejected the hypothesis of the existence of a molecular clock when the whole sequence data set was considered. This fact or the particular substitution pattern (mainly G → A and C → T) may be related to the unexpected performance of distance methods based on sequence signatures. To test if the results could have been predicted by simulation studies we estimated the evolution parameters from the real phylogeny and used them to simulate evolution along the same tree (parametric bootstrap). We found that simulation could predict most but not all of the problems encountered by phylogenetic inference methods in the real phylogeny. Short interior branches may be more prone to error than predicted by theoretical studies.     

Bayesian model adequacy and choice in phylogenetics

Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.     

Correlation of Functional Domains and Rates of Nucleotide Substitution in Cytochromeb

Distinguishing noise from signal presents a problem when DNA sequences are used for phylogeny reconstruction. Multiple substitutions at sites are a primary cause of noise and this is compounded by variation in substitution rates among sites. For protein-coding genes, one method used to determine if data are noisy is to assess levels of saturation of substitutions by codon position. However, this procedure may not be a fine enough filter for assessing noise. Variation in substitution rates may also be caused by constraints on change imposed by the function of the protein product. Using a structural model of the cytochromebprotein as a template, I divided cytbsequence data for species within the avian family Falconidae (falcons and caracaras) into three functional domains. Saturation of substitutions of sequences within these regions was assessed graphically. This qualitative determination of saturation was then used to differentially weight phylogenetic analysis, resulting in an hypothesis congruent with existing cladistic analyses and traditional morphology. These results demonstrate that saturation of substitutions is correlated with functional regions of cytochromeband that using this information improves phylogenetic inference.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Predicting evolutionary potential. I. Predicting the evolution of a lactose-PTS system in Escherichia coli.

Genomes contain not only information for current biological functions, but also information for potential novel functions that may allow the host to adapt to new environments. The field of experimental evolution studies that potential by selecting for novel functions and deducing the means by which the function evolved, but until now it has not attempted to predict the outcomes of such experiments. Here I present a model system that is being developed specifically to examine the issue of what kind of information is most useful in predicting how novel functions will evolve. The system is the evolution of a Lac-PTS transport system and a phospho-beta-galactosidase hydrolase system as a novel pathway for metabolism of lactose in Escherichia coli. Two kinds of information, sequence-based phylogenetic inference and biochemical activity, are considered as predictors of which E. coli genes will evolve the required new functions. Both biochemical data and phylogenetic inference predict that the cryptic celABC genes, which currently specify a PTS-beta-glucoside transport system, are most likely to evolve into a PTS-lactose transport system. Phylogenetic inference predicts that the bglA gene, which currently specifies a phospho-beta-glucosidase, is most likely to evolve into a phospho-beta-galactosidase. In contrast, biochemical data predict that the cryptic bglB gene, which also currently specifies a phospho-beta-glucosidase, is most likely to evolve into a phospho-beta-galactosidase.     

Molecular phylogenetics of cixiid planthoppers (Hemiptera: Fulgoromorpha): new insights from combined analyses of mitochondrial and nuclear genes

The planthopper family Cixiidae (Hemiptera: Fulgoromorpha) comprises approximately 160 genera and 2000 species divided in three subfamilies: Borystheninae, Bothriocerinae and Cixiinae, the later with 16 tribes. The current paper represents the first attempt to estimate phylogenetic relationships within Cixiidae based on molecular data. We use a total of 3652 bp sequence alignment of four genes: the mitochondrial coding genes Cytochrome c Oxidase subunit 1 (Cox1) and Cytochrome b (Cytb), a portion of the nuclear 18S rDNA and two non-contiguous portions of the nuclear 28S rDNA. The phylogenetic relationships of 72 terminal specimens were reconstructed using both maximum parsimony and Bayesian inference methods. Through the analysis of this empirical dataset, we also provide comparisons among different a priori partitioning strategies and the use of mixture models in a Bayesian framework. Our comparisons suggest that mixture models overcome the benefits obtained by partitioning the data according to codon position and gene identity, as they provide better accuracy in phylogenetic reconstructions. The recovered maximum parsimony and Bayesian inference phylogenies suggest that the family Cixiidae is paraphyletic in respect with Delphacidae. The paraphyly of the subfamily Cixiinae is also recovered by both approaches. In contrast to a morphological phylogeny recently proposed for cixiids, subfamilies Borystheninae and Bothriocerinae form a monophyletic group.