Nucleotide Substitution Model Research Articles

Detection of Bovine Papillomavirus Types, Co-Infection and a Putative New BPV11 Subtype in Cattle

The aim of this study was to evaluate the presence of different types of Bovine papillomavirus (BPV) in cattle skin lesions and to identify new viral types in Brazil. A total of 72 skin lesions were analysed from 66 different bovines by PCR using degenerate and specific primers, and subsequent sequencing. Sequencing quality was determined using Staden package with Phred 30. Similarity analysis was performed with BioEdit and BLAST programs to verify the identity with known BPV types. Phylogenetic analysis was carried out using Maximum Likelihood method with TIM3 + G as nucleotide substitution model in PAUP*, and 1000 non-parametric bootstrap replicates. Analyses revealed the presence of ten different types of BPV in the samples, with the exception of BPV7. The presence of co-infections was very high as almost all samples (89%) were co-infected. A putative new BPV11 subtype was also found in lesions from different animals. These results add significant knowledge about the prevalence and diversity of BPV infection in Brazilian cattle, which could be used in future studies aiming at the development of more specific treatment and diagnostic methods.

Advantages of a Mechanistic Codon Substitution Model for Evolutionary Analysis of Protein-Coding Sequences

BackgroundA mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated.ResultsThe present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that assuming variable mutation rates over sites lead to the overestimation of branch lengths.

Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): New insights from ssrDNA and morphology, and origin of umazuracolids from polychaete-infesting ancestors rejected

Poecilostome cyclopoids are among the most morphologically diverse copepods, having established symbiotic relationships with teleosts, elasmobranchs and invertebrate hosts belonging to no fewer than 14 marine phyla. Many parasitic lineages display radically divergent body plans and on that basis have traditionally been placed at higher taxonomic rank than they deserve. The most recent example is the monotypic family Umazuracolidae, established for a derived fish parasite with bomolochiform affinities. Phylogenetic analysis of complete ssrDNA (18S) sequences of 44 species belonging to 21 families of cyclopoid copepods shows that there is no support for the familial distinctiveness of the Umazuracolidae. Both maximum parsimony tree reconstruction and Bayesian inference, operating under the GTR + I + Γ model of nucleotide substitution, unambiguously placed Umazuracola elongatus in the Taeniacanthidae within the predominantly fish parasitic bomolochiform complex, refuting the original suggestion of a shared most recent common ancestry with polychaete symbionts. The phylogenies also revealed that the bomolochiform families and the Clausidiidae (and allies) form a monophyletic group, the clausidiiform complex, with high nodal support under both methods. Bayesian inference suggested a diphyletic origin of the “Poecilostomatoida” with the clausidiiform family-group holding a basal position while the traditional cyclopoid families form a monophyletic group in apposition to a second poecilostomatoid clade; however, maximum parsimony results were equivocal, depending on outgroup selection. Scrutiny of the morphological characters diagnosing the monotypic families Tegobomolochidae and Tuccidae demonstrated that they merely represent derived lineages within more inclusive taxa, the former being related to a group of nostril-inhabiting genera within the Bomolochidae, the latter forming the sistergroup of Taeniacanthodes within the Taeniacanthidae. The taeniacanthid genus Makrostrotos occupies a position at the base of the bomolochiform complex and is fixed as the type of a new family, Makrostrotidae. Although both morphological and molecular evidence hint that the Bomolochidae is nested within a paraphyletic Taeniacanthidae, the status quo of maintaining both families is favoured here pending additional molecular data. The bomolochiform complex, comprising the Bomolochidae, Taeniacanthidae, Telsidae and Makrostrotidae, is attributed superfamilial rank as the Bomolochoidea. A recent controversial phylogenetic analysis of the poecilostomatoid families is shown to be flawed, being based on a dataset containing imperfect or misleading information, and characters whose states were wrongly assessed.

Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)

Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.

Non-hereditary Maximum Parsimony trees

In this paper, we investigate a conjecture by Arndt von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particular (DNA) alignment necessarily has subtrees of all possible sizes which are most parsimonious for the corresponding subalignments. We answer the conjecture affirmatively for binary alignments on 5 taxa but also show how to construct examples for which Maximum Parsimony trees are not hereditary. Apart from showing that a most parsimonious tree cannot generally be reduced to a most parsimonious tree on fewer taxa, we also show that compatible most parsimonious quartets do not have to provide a most parsimonious supertree. Last, we show that our results can be generalized to Maximum Likelihood for certain nucleotide substitution models.

Confidence intervals for the substitution number in the nucleotide substitution models

In the nucleotide substitution model for molecular evolution, a major task in the exploration of an evolutionary process is to estimate the substitution number per site of a protein or DNA sequence. The usual estimators are based on the observation of the difference proportion of the two nucleotide sequences. However, a more objective approach is to report a confidence interval with precision rather than only providing point estimators. The conventional confidence intervals used in the literature for the substitution number are constructed by the normal approximation. The performance and construction of confidence intervals for evolutionary models have not been much investigated in the literature. In this article, the performance of these conventional confidence intervals for one-parameter and two-parameter models are explored. Results show that the coverage probabilities of these intervals are unsatisfactory when the true substitution number is small. Since the substitution number may be small in many situations for an evolutionary process, the conventional confidence interval cannot provide accurate information for these cases. Improved confidence intervals for the one-parameter model with desirable coverage probability are proposed in this article. A numerical calculation shows the substantial improvement of the new confidence intervals over the conventional confidence intervals.

DNA barcodes effectively identify the morphologically similar Common Opossum (Didelphis marsupialis) and Virginia Opossum (Didelphis virginiana) from areas of sympatry in Mexico

Two morphologically similar species of opossum from the genus Didelphis–Didelphis virginiana and Didelphis marsupialis–cooccur sympatrically in Mexico. High intraspecific variation complicates their morphological discrimination, under both field and museum conditions. This study aims to evaluate the utility and reliability of using DNA barcodes (short standardized genome fragments used for DNA-based identification) to distinguish these two species. Sequences of the cytochrome c oxidase subunit I (Cox1) mitochondrial gene were obtained from 12 D. marsupialis and 29 D. virginiana individuals and were compared using the neighbor-joining (NJ) algorithm with Kimura's two-parameter (K2P) model of nucleotide substitution. Average K2P distances were 1.56% within D. virginiana and 1.65% in D. marsupialis. Interspecific distances between D. virginiana and D. marsupialis varied from 7.8 to 9.3% and their barcode sequences formed distinct non-overlapping clusters on NJ trees. All sympatric specimens of both species were effectively discriminated, confirming the utility of Cox1 barcoding as a tool for taxonomic identification of these morphologically similar taxa.

Two Stationary Nonhomogeneous Markov Models of Nucleotide Sequence Evolution

The general Markov model (GMM) of nucleotide substitution does not assume the evolutionary process to be stationary, reversible, or homogeneous. The GMM can be simplified by assuming the evolutionary process to be stationary. A stationary GMM is appropriate for analyses of phylogenetic data sets that are compositionally homogeneous; a data set is considered to be compositionally homogeneous if a statistical test does not detect significant differences in the marginal distributions of the sequences. Though the general time-reversible (GTR) model assumes stationarity, it also assumes reversibility and homogeneity. We propose two new stationary and nonhomogeneous models--one constrains the GMM to be reversible, whereas the other does not. The two models, coupled with the GTR model, comprise a set of nested models that can be used to test the assumptions of reversibility and homogeneity for stationary processes. The two models are extended to incorporate invariable sites and used to analyze a seven-taxon hominoid data set that displays compositional homogeneity. We show that within the class of stationary models, a nonhomogeneous model fits the hominoid data better than the GTR model. We note that if one considers a wider set of models that are not constrained to be stationary, then an even better fit can be obtained for the hominoid data. However, the methods for reducing model complexity from an extremely large set of nonstationary models are yet to be developed.

May Phylogenetic Analysis Support Epidemiological Investigation in Identifying the Source of HIV Infection?

Editor: The human immunodeficiency virus (HIV) is characterized by great genetic heterogeneity driven by several factors, such as the lack of proofreading ability of the reverse transcriptase (RT), the rapid turnover of HIV-1 in vivo, host selective immune pressures, and recombination events during replication. In particular, HIV-1 group M subtypes are responsible for most of the infections worldwide. At the end of the year 2008, in Italy, 60,346 persons were cumulatively diagnosed with AIDS. Overall, it is estimated that 140,000/150,000 HIV-positive people live within the country. At the beginning of the epidemic the most common route of HIV transmission was needle sharing among intravenous drug users (IDUs) whereas in more recent years heterosexual contacts have become the leading cause of infection (44.7%). Phylogenetic analysis is an important way to trace epidemiological relationship in cases with dubious or unknown links. Moreover, phylogeny is also an easy way to describe and to identify groups of viral isolates forming genetically related sister clades, which appear to be more closely related to each other. We describe here a case of HIV-1 infection in a 24-year-old Italian soldier in service in Kabul, Afghanistan, where his military command was placed. The epidemiological investigation was conducted in three different phases. In September 2009, during a laboratory investigation in the Military Barracks based on demand screening, he was found to be positive for anti-HIV antibodies (by an ELISA test), which was confirmed by Western blot. The viral load was 39,882 copies/ml and the CD4 cell count was 568 cells/ml. During the month of October he was hospitalized in Catanzaro Hospital for diagnostic controls. His viral load was of 18,000 copies/ml and his CD4 cell count was 701 cells/ml. The epidemiological investigation did not identify any known risk factors for HIV infection (i.e., drug use, tattoos, homosexual or heterosexual contact, biological fluid exposure). Thus, we tried to reconstruct the epidemiological network using the pol viral sequences (1271 nucleotides) detected by a sample collected in November 2009, before starting antiretroviral therapy. RNA extraction, polymerase chain reaction (PCR) amplification, and sequences were obtained as previously described. The pol gene sequence was aligned and compared with reference sequences of the HIV-1 pol genes downloaded from the HIV Los Alamos database (htpp://hiv-web.lanl .gov) as previously described; the HIV-1 pol sequences were obtained with the Blast similarity search (using the Italian soldier’s sequence as the query sequence). HIV-1 subtype B pol sequences obtained by Blast similarity search analysis are reported in Supplementary Table 1 (Supplementary data are available online at www.liebertonline.com/aid). The tree was generated using the F84 model of substitution using both neighbor-joining (NJ) and maximum-likelihood (ML) tree building methods. The evolutionary model was chosen as the best-fitting nucleotide substitution model according to the hierarchical likelihood ratio test (HLRT) implemented with Model Test v3.0 software. The statistical robustness and reliability of the branching order within each phylogenetic tree were confirmed by bootstrap analysis using 1000 replicates for the NJ tree and with the zero branch length test for the ML tree. All calculations were performed with PAUP*4.0 software. SimPlot software version 3.2 and the split-decomposition analysis were used to investigate the recombinant. Separate phylogenetic analyses of the subalignments generated by the different break-points were also used to better investigate the supposed recombinant sequences. Phylogenetic analysis classified our pol gene sequence as a ‘‘nonpure’’ B subtype and showed that the patient’s isolate was closely related to B subtype sequences from Spain, forming a significant monophyletic cluster (bootstrap value >70%) (Fig. 1). Because our sequence was in a marginal position within the cluster, SimPlot and split-decomposition analyses were performed and our sequence was found to be a possible BFB recombinant form; however, we classified it as ‘‘BUB’’ (U for unclassified) since the F trait and the break-point of recombination were under the threshold value (70%) useful for statistical significance (Supplementary Figs. 1 and 2). The young man was enrolled in the peace military mission of the ISAF (International Security Assistance Force). In this context, soldiers from different nations (Italy, the United States,

NovelChlamydia-like Organisms as Cause of Bovine Abortions, UK

Novel<i>Chlamydia</i>-like Organisms as Cause of Bovine Abortions, UK

A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds

1. Methods that assess patterns of phylogenetic relatedness, as well as character distribution and evolution, allow one to infer the ecological processes involved in community assembly. Assuming niche conservatism, assemblages should shift from phylogenetic clustering to evenness with decreasing geographic scale because the relative importance of mechanisms that shape assemblages is hypothesized to be scale-dependent. Whereas habitat filtering is more likely to act at regional scales because of increased habitat heterogeneity that allows sorting of ecologically similar species in contrasting environments, competition is more likely to act at local scales because low habitat heterogeneity provides few opportunities for niche partitioning. 2. We used species lists to assess assemblage composition, data on ecologically-relevant traits, and a molecular phylogeny, to examine the phylogenetic structure of antbird (Thamnophilidae) assemblages at three different geographical scales: regional (ecoregions), intermediate (100-ha plots) and local (mixed-flocks). In addition, we used patterns of phylogenetic beta diversity and beta diversity to separate the factors that structure antbird assemblages at regional scales. 3. Contrary to previous findings, we found a shift from phylogenetic evenness to clustering with decreasing geographical scale. We argue that this does not reject the hypothesis that habitat filtering is the predominant force in regional community assembly, because analyses of trait evolution and structure indicated a lack of niche conservatism in antbirds. 4. In some cases, phylogenetic evenness at regional scales can be an effect of historical biogeographic processes instead of niche-based processes. However, regional patterns of beta diversity and phylogenetic beta diversity suggested that phylogenetic structure in our study cannot be explained by the history of speciation and dispersal of antbirds, further supporting the habitat-filtering hypothesis. 5. Our analyses suggested that competitive interactions might not play an important role locally, which would provide a plausible explanation for the high alpha diversity of antbirds in Amazonia. 6. Finally, we emphasize the importance of including trait information in studies of phylogenetic community structure to adequately assess the mechanisms that determine species co-existence.

Phylogenetic Trees in Bioinformatics

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.

BackgroundPseudogenes provide a record of the molecular evolution of genes. As glycolysis is such a highly conserved and fundamental metabolic pathway, the pseudogenes of glycolytic enzymes comprise a standardized genomic measuring stick and an ideal platform for studying molecular evolution. One of the glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has already been noted to have one of the largest numbers of associated pseudogenes, among all proteins.ResultsWe assembled the first comprehensive catalog of the processed and duplicated pseudogenes of glycolytic enzymes in many vertebrate model-organism genomes, including human, chimpanzee, mouse, rat, chicken, zebrafish, pufferfish, fruitfly, and worm (available at ). We found that glycolytic pseudogenes are predominantly processed, i.e. retrotransposed from the mRNA of their parent genes. Although each glycolytic enzyme plays a unique role, GAPDH has by far the most pseudogenes, perhaps reflecting its large number of non-glycolytic functions or its possession of a particularly retrotranspositionally active sub-sequence. Furthermore, the number of GAPDH pseudogenes varies significantly among the genomes we studied: none in zebrafish, pufferfish, fruitfly, and worm, 1 in chicken, 50 in chimpanzee, 62 in human, 331 in mouse, and 364 in rat. Next, we developed a simple method of identifying conserved syntenic blocks (consistently applicable to the wide range of organisms in the study) by using orthologous genes as anchors delimiting a conserved block between a pair of genomes. This approach showed that few glycolytic pseudogenes are shared between primate and rodent lineages. Finally, by estimating pseudogene ages using Kimura's two-parameter model of nucleotide substitution, we found evidence for bursts of retrotranspositional activity approximately 42, 36, and 26 million years ago in the human, mouse, and rat lineages, respectively.ConclusionOverall, we performed a consistent analysis of one group of pseudogenes across multiple genomes, finding evidence that most of them were created within the last 50 million years, subsequent to the divergence of rodent and primate lineages.

How Robust Are "Isolation with Migration" Analyses to Violations of the IM Model? A Simulation Study

Methods developed over the past decade have made it possible to estimate molecular demographic parameters such as effective population size, divergence time, and gene flow with unprecedented accuracy and precision. However, they make simplifying assumptions about certain aspects of the species' histories and the nature of the genetic data, and it is not clear how robust they are to violations of these assumptions. Here, we use simulated data sets to examine the effects of a number of violations of the "Isolation with Migration" (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IMA. We also examine the effect of having data that fit a nucleotide substitution model other than the two relatively simple models available in IMA. We find that IMA estimates are generally quite robust to small to moderate violations of the IM model assumptions, comparable with what is often encountered in real-world scenarios. In particular, population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure. Likewise, most parameter estimates are robust to significant levels of recombination when data sets are pared down to apparently nonrecombining blocks, although substantial bias is introduced to several estimates when the entire data set with recombination is included. In contrast, a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among data sets simulated under the same conditions.

Using Non-Homogeneous Models of Nucleotide Substitution to Identify Host Shift Events: Application to the Origin of the 1918 ‘Spanish’ Influenza Pandemic Virus

Nonhomogeneous Markov models of nucleotide substitution have received scant attention. Here we explore the possibility of using nonhomogeneous models to identify host shift nodes along phylogenetic trees of pathogens evolving in different hosts. It has been noticed that influenza viruses show marked differences in nucleotide composition in human and avian hosts. We take advantage of this fact to identify the host shift event that led to the 1918 ‘Spanish’ influenza. This disease killed over 50 million people worldwide, ranking it as the deadliest pandemic in recorded history. Our model suggests that the eight RNA segments which eventually became the 1918 viral genome were introduced into a mammalian host around 1882–1913. The viruses later diverged into the classical swine and human H1N1 influenza lineages around 1913–1915. The last common ancestor of human strains dates from February 1917 to April 1918. Because pigs are more readily infected with avian influenza viruses than humans, it would seem that they were the original recipient of the virus. This would suggest that the virus was introduced into humans sometime between 1913 and 1918.

Rapid Likelihood Analysis on Large Phylogenies Using Partial Sampling of Substitution Histories

Likelihood-based approaches can reconstruct evolutionary processes in greater detail and with better precision from larger data sets. The extremely large comparative genomic data sets that are now being generated thus create new opportunities for understanding molecular evolution, but analysis of such large quantities of data poses escalating computational challenges. Recently developed Markov chain Monte Carlo methods that augment substitution histories are a promising approach to alleviate these computational costs. We analyzed the computational costs of several such approaches, considering how they scale with model and data set complexity. This provided a theoretical framework to understand the most important computational bottlenecks, leading us to combine novel variations of our conditional pathway integration approach with recent advances made by others. The resulting technique ("partial sampling" of substitution histories) is considerably faster than all other approaches we considered. It is accurate, simple to implement, and scales exceptionally well with dimensions of model complexity and data set size. In particular, the time complexity of sampling unobserved substitution histories using the new method is much faster than previously existing methods, and model parameter and branch length updates are independent of data set size. We compared the performance of methods on a 224-taxon set of mammalian cytochrome-b sequences. For a simple nucleotide substitution model, partial sampling was at least 10 times faster than the PhyloBayes program, which samples substitutions in continuous time, and about 100 times faster than when using fully integrated substitution histories. Under a general reversible model of amino acid substitution, the partial sampling method was 1,600 times faster than when using fully integrated substitution histories, confirming significantly improved scaling with model state-space complexity. Partial sampling of substitutions thus dramatically improves the utility of likelihood approaches for analyzing complex evolutionary processes on large data sets.

Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design

The understanding that gene trees are often in discord with each other and with the species trees that contain them has led researchers to methods that incorporate the inherent stochasticity of genetic processes in the phylogenetic estimation procedure. Recently developed methods for species-tree estimation that not only consider the retention and sorting of ancestral polymorphism but also quantify the actual probabilities of incomplete lineage sorting are expected to provide an improvement over earlier summary-statistic based approaches that discard much of the information content of gene trees. However, these new methods have yet to be tested on truly challenging evolutionary histories such as those marked by recent rapid speciation where high levels of incomplete lineage sorting and discord among gene trees predominate. Here, we test a new maximum-likelihood method that incorporates stochastic models of both nucleotide substitution and lineage sorting for species-tree estimation. Using a simulation approach, we consider a broad range of species-tree topologies under 2 scenarios representing moderate and severe incomplete lineage sorting. We show that the maximum-likelihood method results in more accurate species trees than a summary-statistic based approach, demonstrating that information contained in discordant gene trees can be effectively extracted using a full probabilistic model. Moreover, we demonstrate that the shape of the original species tree (i.e., the relative lengths of internal branches) has a significant impact on whether the species tree is estimated accurately. In the speciation histories explored here, it is not just the recent origin of species that affects the accuracy of the estimates but the variance in relative species divergence times as well. Additionally, we show that sampling effort (number of individuals and/or loci) and sampling design (ratio of individuals to loci) are both important factors affecting the accuracy of species-tree estimates, which is again affected by the relative timing of divergence among species. The inherent difficulties of estimating relationships when species have undergone a recent radiation are discussed, and in particular, the limitations with maximum-likelihood estimates of species trees that do not consider uncertainty in the estimated gene trees of individual loci. Thus, despite substantial improvements over current summary-statistic based approaches, and the increased sophistication of procedures that incorporate the process of gene lineage coalescence, recent radiations still appear to pose daunting challenges for phylogenetics.

THE TEMPO AND MODE OF EVOLUTION OF TRANSPOSABLE ELEMENTS AS REVEALED BY MOLECULAR PHYLOGENIES RECONSTRUCTED FROM MOSQUITO GENOMES

Although many mathematical models exist predicting the dynamics of transposable elements (TEs), there is a lack of available empirical data to validate these models and inherent assumptions. Genomes can provide a snapshot of several TE families in a single organism, and these could have their demographics inferred by coalescent analysis, allowing for the testing of theories on TE amplification dynamics. Using the available genomes of the mosquitoes Aedes aegypti and Anopheles gambiae, we indicate that such an approach is feasible. Our analysis follows four steps: (1) mining the two mosquito genomes currently available in search of TE families; (2) fitting, to selected families found in (1), a phylogeny tree under the general time-reversible (GTR) nucleotide substitution model with an uncorrelated lognormal (UCLN) relaxed clock and a nonparametric demographic model; (3) fitting a nonparametric coalescent model to the tree generated in (2); and (4) fitting parametric models motivated by ecological theories to the curve generated in (3).

Phylogenetic Analysis in the Anomaly Zone

The concatenation method has been widely used as a means of combining data to estimate phylogenetic trees (Huelsenbeck et al. 1996a, 1996b; Glazko and Nei 2003). However, simulation studies have shown that the maximum likelihood (ML) estimate of the species tree for concatenated sequences may be statistically incon sistent if the gene trees are highly heterogeneous (Ko laczkowski and Thornton 2004; Kubatko and Degnan 2007). Recently, Degnan and Rosenberg (2006) defined an zone?a set of short internal branches in species trees that will generate gene trees that are discor dant with the species tree more often than gene trees that are concordant. Kubatko and Degnan (2007) went on to show that when DNA sequences are generated from gene trees simulated from species trees in the anomaly zone, as well as from species trees slightly outside this zone but still with short internal branches, the ML esti mate of the species tree for the concatenated sequences can be inconsistent, resulting in increasing certainty in the wrong species tree. These studies were all performed with a molecular clock on rooted gene and species trees within the variation realized in stochastic simulations of DNA sequences under the Jukes and Cantor (1969) model of nucleotide substitution. They applied the ML method with a clock to recover phylogenetic trees from their simulated concatenated data sets.

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test their ability to jointly improve phylogenetic and dating accuracy. We propose a software package, PhyloBayes 3, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models, as well as alternative clock relaxation processes.