Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae)

We suggest a new phylogenetic hypothesis for the tripunctata radiation based on sequences of mitochondrial genes. Phylogenetic trees were reconstructed by parsimony, maximum likelihood and Bayesian methods. We performed tests for hypotheses of monophyly for taxonomic groups and other specific hypotheses. Results reject the monophyly for the tripunctata group whereas monophyly is not rejected for the tripunctata radiation and other specific groups within the radiation. Although most of the basal nodes were unresolved we were able to identify four clusters within the tripunctata radiation. These results suggest the collection of additional data before a proper taxonomic revision could be proposed.     

Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models.

In recent years, likelihood ratio tests (LRTs) based on DNA and protein sequence data have been proposed for testing various evolutionary hypotheses. Because conducting an LRT requires an evolutionary model of nucleotide or amino acid substitution, which is almost always unknown, it becomes important to investigate the robustness of LRTs to violations of assumptions of these evolutionary models. Computer simulation was used to examine performance of LRTs of the molecular clock, transition/transversion bias, and among-site rate variation under different substitution models. The results showed that when correct models are used, LRTs perform quite well even when the DNA sequences are as short as 300 nt. However, LRTs were found to be biased under incorrect models. The extent of bias varies considerably, depending on the hypotheses tested, the substitution models assumed, and the lengths of the sequences used, among other things. A preliminary simulation study also suggests that LRTs based on parametric bootstrapping may be more sensitive to substitution models than are standard LRTs. When an assumed substitution model is grossly wrong and a more realistic model is available, LRTs can often reject the wrong model; thus, the performance of LRTs may be improved by using a more appropriate model. On the other hand, many factors of molecular evolution have not been considered in any substitution models so far built, and the possibility of an influence of this negligence on LRTs is often overlooked. The dependence of LRTs on substitution models calls for caution in interpreting test results and highlights the importance of clarifying the substitution patterns of genes and proteins and building more realistic models.     

Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda)

Phylogenetic analysis conducted on a 784-bp fragment of 82 actin gene sequences of 44 coleoid cephalopod taxa, along with results obtained from genomic Southern blot analysis, confirmed the presence of at least three distinct actin loci in coleoids. Actin isoforms were characteri zed through phylogenetic analysis of representative cephalopod sequences from each of the three isoforms, along with translated actin cDNA sequences from a diverse array of metazoan taxa downloaded from GenBank. One of the three isoforms found in cephalopods was closely related to actin sequences expressed in the muscular tissues of other molluscs. A second isoform was most similar to cytoplasmic-specific actin amino acid sequences. The muscle type actins of molluscs were found to be distinct from those of arthropods, suggesting at least two independent derivations of muscle actins in the protostome lineage, although statistical support for this conclusion was lacking. Parsimony and maximum-likelihood analyses of two of the isoforms from which >30 orthologous coleoid sequences had been obtained (one of the cytoplasmic actins and the muscle actin) supported the monophyly of several higher-level coleoid taxa. These included the superorders Octopodiformes and Decapodiformes, the order Octopoda, the octopod suborder Incirrata, and the teuthoid suborder Myopsida. The monophyly of several taxonomic groups within the Decapodiformes was not supported, including the orders Teuthoidea and Sepioidea and the teuthoid suborder Oegopsida. Parametric bootstrap analysis conducted on the simulated cytoplasmic actin data set provided statistical support to reject the monophyly of the Sepioidea. Although parametric bootstrap analysis of the muscle actin isoform did not reject sepioid monophyly at the 5% level, the results (rejection at P: = 0.068) were certainly suggestive of sepioid nonmonophyly.     

Assessing tillage disturbance on assemblages of ground beetles (Coleoptera: Carabidae) by using a range of ecological indices

Many ecological studies have used diversity indices to assess the impact of environmental disturbance. In particular, ground beetles have been advocated as a good group for assessing disturbance. Most studies on various organisms have used only one or two indices. For our study of the impact of tillage disturbance on carabid beetles in farm fields in southern Ontario, Canada, we used seven different diversity indices (richness, Shannon–Wiener, Berger–Parker, Q-statistic, Margalef, and evenness). Few studies have used deviation from diversity abundance models as a measure of disturbance; however, we use three that are applicable to our data (geometric, log-normal and log-series). The indices and models were used to test the null hypothesis that there is no change in diversity with increasing tillage disturbance, and that there is no difference in diversity with different crops or years. We were not able to reject the null hypothesis that there is any diversity difference among farms. We also found that there was no single diversity index or model that was better than any other at detecting disturbance. These results are supplemented by a meta-analysis of 45 published data sets for the same taxon but in different habitats. The meta-analysis supports the conclusions from our field research that diversity indices and models are not useful for detecting the possible effect of disturbance on assemblages of carabid beetles.     

Least and most powerful phylogenetic tests to elucidate the origin of the seed plants in the presence of conflicting signals under misspecified models

Several tests of molecular phylogenies have been proposed over the last decades, but most of them lead to strikingly different P-values. I propose that such discrepancies are principally due to different forms of null hypotheses. To support this hypothesis, two new tests are described. Both consider the composite null hypothesis that all the topologies are equidistant from the true but unknown topology. This composite hypothesis can either be reduced to the simple hypothesis at the least favorable distribution (frequentist significance test [FST]) or to the maximum likelihood topology (frequentist hypothesis test [FHT]). In both cases, the reduced null hypothesis is tested against each topology included in the analysis. The tests proposed have an information-theoretic justification, and the distribution of their test statistic is estimated by a nonparametric bootstrap, adjusting P-values for multiple comparisons. I applied the new tests to the reanalysis of two chloroplast genes, psaA and psbB, and compared the results with those of previously described tests. As expected, the FST and the FHT behaved approximately like the Shimodaira-Hasegawa test and the bootstrap, respectively. Although the tests give overconfidence in a wrong tree when an overly simple nucleotide substitution model is assumed, more complex models incorporating heterogeneity among codon positions resolve some conflicts. To further investigate the influence of the null hypothesis, a power study was conducted. Simulations showed that FST and the Shimodaira-Hasegawa test are the least powerful and FHT is the most powerful across the parameter space. Although the size of all the tests is affected by misspecification, the two new tests appear more robust against misspecification of the model of evolution and consistently supported the hypothesis that the Gnetales are nested within gymnosperms.     

Evolutionary genetics of the accessory gene regulator (agr) locus in Staphylococcus aureus

The accessory gene regulator (agr) locus influences the expression of many virulence genes in the human pathogen Staphylococcus aureus. Four allelic groups of agr, which generally inhibit the regulatory activity of each other, have been identified within the species. Interference in virulence gene expression caused by different agr groups has been suggested to be a mechanism for isolating bacterial populations and a fundamental basis for subdividing the species. To test the hypothesis that the species is phylogenetically structured according to agr groups, we mapped agr groups onto a clone phylogeny inferred from partial sequences of 14 genes from 27 genetically diverse strains. Shimodaira-Hasegawa and parametric bootstrap tests rejected the hypotheses that the species is subdivided into three or five monophyletic agr groups but failed to reject the hypothesis that the species is subdivided into two groups that each consist of multiple clonal complexes and multiple agr groups. Additional evidence for agr recombination is found from clustered polymorphisms in complete agr sequences. However, agr recombination has not occurred frequently or randomly through time, because the topology and branch lengths of the clone phylogeny are reflected within each agr group. To account for these observations, we propose a new evolutionary model that involves a genetically polymorphic ancestral population of S. aureus that horizontally transferred agr groups between two subspecies groups near the time that these subspecies groups diverged.     

Model misspecification and probabilistic tests of topology: evidence from empirical data sets

Probabilistic tests of topology offer a powerful means of evaluating competing phylogenetic hypotheses. The performance of the nonparametric Shimodaira-Hasegawa (SH) test, the parametric Swofford-Olsen-Waddell-Hillis (SOWH) test, and Bayesian posterior probabilities were explored for five data sets for which all the phylogenetic relationships are known with a very high degree of certainty. These results are consistent with previous simulation studies that have indicated a tendency for the SOWH test to be prone to generating Type 1 errors because of model misspecification coupled with branch length heterogeneity. These results also suggest that the SOWH test may accord overconfidence in the true topology when the null hypothesis is in fact correct. In contrast, the SH test was observed to be much more conservative, even under high substitution rates and branch length heterogeneity. For some of those data sets where the SOWH test proved misleading, the Bayesian posterior probabilities were also misleading. The results of all tests were strongly influenced by the exact substitution model assumptions. Simple models, especially those that assume rate homogeneity among sites, had a higher Type 1 error rate and were more likely to generate misleading posterior probabilities. For some of these data sets, the commonly used substitution models appear to be inadequate for estimating appropriate levels of uncertainty with the SOWH test and Bayesian methods. Reasons for the differences in statistical power between the two maximum likelihood tests are discussed and are contrasted with the Bayesian approach.     

Pitfalls of hypothesis tests and model selection on bootstrap samples: Causes and consequences in biometrical applications

The bootstrap method has become a widely used tool applied in diverse areas where results based on asymptotic theory are scarce. It can be applied, for example, for assessing the variance of a statistic, a quantile of interest or for significance testing by resampling from the null hypothesis. Recently, some approaches have been proposed in the biometrical field where hypothesis testing or model selection is performed on a bootstrap sample as if it were the original sample. P‐values computed from bootstrap samples have been used, for example, in the statistics and bioinformatics literature for ranking genes with respect to their differential expression, for estimating the variability of p‐values and for model stability investigations. Procedures which make use of bootstrapped information criteria are often applied in model stability investigations and model averaging approaches as well as when estimating the error of model selection procedures which involve tuning parameters. From the literature, however, there is evidence that p‐values and model selection criteria evaluated on bootstrap data sets do not represent what would be obtained on the original data or new data drawn from the overall population. We explain the reasons for this and, through the use of a real data set and simulations, we assess the practical impact on procedures relevant to biometrical applications in cases where it has not yet been studied. Moreover, we investigate the behavior of subsampling (i.e., drawing from a data set without replacement) as a potential alternative solution to the bootstrap for these procedures.     

Reconciling gene trees with organism history: the mtDNA phylogeography of three Nesotes species (Coleoptera: Tenebrionidae) on the western Canary Islands

The processes of island colonization and speciation are investigated through mtDNA studies on Canary Island beetles. The genus Nesotes (Coleoptera: Tenebrionidae) is represented by 19 endemic species on the Canary Islands, the majority of which are single island endemics. Nesotes conformis is the most widespread, occurring on Gran Canaria, Tenerife, La Palma and El Hierro. Nesotes conformis forms a paraphyletic assemblage, with a split between Gran Canaria and the other three islands. Nesotes conformis of the western Canary Islands cluster with Nesotes altivagans and Nesotes elliptipennis from Tenerife. Fifty‐two individuals from this western islands species complex have been sequenced for 675 base pairs of the mtDNA cytochrome oxidase II gene, representing Tenerife, La Palma and El Hierro. A neighbour joining analysis of maximum likelihood distances resulted in three distinct mtDNA lineages for N. conformis, two of which also include mitotypes of N. altivagans and N. elliptipennis. Through application of parametric bootstrap tests, we are able to reject hypotheses of monophyly for both N. conformis and N. altivagans. Nesotes altivagans and N. elliptipennis are poorly separated morphologically and mtDNA sequence data adds support to this being one species with a highly variable morphology. We propose that N. altivagans/N. elliptipennis is recently derived from two ancestral mtDNA lineages within N. conformis from the Teno region of Tenerife. We further propose colonization of the younger islands of La Palma and El Hierro by N. conformis from a mitochondrial lineage within the Teno massif (colonization; diversification; mitochondrial DNA; Canary Islands; Coleoptera).     

A new method for characterizing replacement rate variation in molecular sequences. Application of the Fourier and wavelet models to Drosophila and mammalian proteins

We propose models for describing replacement rate variation in genes and proteins, in which the profile of relative replacement rates along the length of a given sequence is defined as a function of the site number. We consider here two types of functions, one derived from the cosine Fourier series, and the other from discrete wavelet transforms. The number of parameters used for characterizing the substitution rates along the sequences can be flexibly changed and in their most parameter-rich versions, both Fourier and wavelet models become equivalent to the unrestricted-rates model, in which each site of a sequence alignment evolves at a unique rate. When applied to a few real data sets, the new models appeared to fit data better than the discrete gamma model when compared with the Akaike information criterion and the likelihood-ratio test, although the parametric bootstrap version of the Cox test performed for one of the data sets indicated that the difference in likelihoods between the two models is not significant. The new models are applicable to testing biological hypotheses such as the statistical identity of rate variation profiles among homologous protein families. These models are also useful for determining regions in genes and proteins that evolve significantly faster or slower than the sequence average. We illustrate the application of the new method by analyzing human immunoglobulin and Drosophilid alcohol dehydrogenase sequences.     

Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae)

In an effort to improve our knowledge of the phylogenetic relationships among species and genera of the subfamily Sarcophaginae, we analysed data from three mitochondrial gene fragments. Sequence data for portions of the genes cytochrome oxidase I (COI), cytochrome oxidase II (COII) and dehydrogenase subunit 4 (ND4) were obtained from 43 species of Sarcophagidae representing 15 genera. We used a Bayesian approach to simultaneously choose how best to partition the data and which substitution model to apply to each partition. Phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods. Our results are consistent with monophyly of the subfamily Sarcophaginae (posterior probability 1; bootstrap support 93%), as well as with monophyly of several genera within the Sarcophaginae (including Sarcophaga s.l.; posterior probability 1; bootstrap support 97%). We found support for a sister‐group relationship between Ravinia Robineau‐Desvoidy and Oxysarcodexia Townsend, which has been hypothesised by past authors on the basis of morphological similarities, although this was supported only in the Bayesian analyses (posterior probability 0. 81–0. 98), and for some novel supra‐generic clades. Contrary to a recent morphological hypothesis, we do not find Helicobia Coquillett to be nested within Sarcophaga Meigen; our data suggest, but do not strongly support, a hypothesis that Peckia Robineau‐Desvoidy is the sister group to Sarcophaga.     

Novel relationships among hyloid frogs inferred from 12S and 16S mitochondrial DNA sequences

Advanced frogs (Neobatrachia) are usually divided into two taxa, Ranoidea (the firmisternal frogs) and Hyloidea (all other neobatrachians). We investigated phylogenetic relationships among several groups of Hyloidea using 12S and 16S rRNA mitochondrial gene sequences and tested explicit relationships of certain problematic hyloid taxa using a sample of 93 neobatrachians. Parsimony, maximum likelihood, and Bayesian inference methods suggest that both the Ranoidea and Hyloidea are well-supported monophyletic groups. We reject three hypotheses using parametric bootstrap simulation: (1) Dendrobatidae lies within the Ranoidea; (2) The group containing Hylidae, Pseudidae, and Centrolenidae is monophyletic; and (3) Brachycephalus is part of Bufonidae.     

Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae

Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford–Olsen–Waddell–Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco-heterotrophic plants. © The Willi Hennig Society 2009.     

Bilaterian Phylogeny Based on Analyses of a Region of the Sodium–Potassium ATPase β-Subunit Gene

Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the subunit of the nuclear-encoded sodium–potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject monophyly for Arthropoda and Nemertea but are unable to reject deuterostome monophyly. Overall, the sodium–potassium ATPase -subunit gene appears to be useful for deep-level studies of metazoan phylogeny.     

Adding mitochondrial sequence data (16S rRNA and cytochrome c oxidase subunit I) to the phylogeny of centipedes (Myriapoda: Chilopoda): an analysis of morphology and four molecular loci

Relationships within Chilopoda (centipedes) are assessed based on 222 morphological characters, complete 18S rRNA sequences for 70 chilopod terminals, the D3 region of 28S rRNA for 65 terminals, 16S rRNA sequences for 54 terminals and cytochrome c oxidase subunit I sequences for 45 terminals. Morphological and molecular data for seven orders of Diplopoda are used to root cladograms for Chilopoda. Analyses use direct character optimization for 15 gap and substitution models. The Pleurostigmophora and Epimorpha s.l. hypotheses are largely stable to parameter variation for the combined data; the latter clade is formalized as the new taxon Phylactometria. The combined data include parameter sets that support either the monophyly of Epimorpha s.str. (=Scolopendromorpha + Geophilomorpha) or Craterostigmus + Geophilomorpha; the former derives its support from morphology and the nuclear ribosomal genes. Monophyly of Lithobiomorpha and the sister group relationship between Lithobiidae and Henicopidae are stable for morphological and combined data, and are also resolved for the molecular data for 14 of 15 parameter sets. The fundamental split in Scolopendromorpha is between Cryptopidae and Scolopendridae sensu Attems. Blind scolopendromorphs unite as a clade in most molecular and combined analyses, including those that minimize incongruence between data partitions. Geophilomorpha divides into Placodesmata and Adesmata under nine of 15 explored parameter sets.     

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

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

Molecular systematics of Scaphirhynchinae: an assessment of North American and Central Asian Freshwater Sturgeon Species

The sturgeon subfamily Scaphirhynchinae contains two genera of obligate freshwater sturgeon: Scaphirhynchus and Pseudoscaphirhynchus, from North America and Central Asia, respectively. Both genera contain morphologically variable species. A novel data set containing multiple individuals representing four diagnosable morphological variants for two species of Pseudoscaphirhynchus, P. hermanni and P. kaufmanni, was generated. These data were used to test taxonomic hypotheses of monophyly for the subfamily Scaphirhynchinae, monophyly of both Scaphirhynchus and Pseudoscaphirhynchus, monophyly of P. hermanni and P. kaufmanni, and monophyly of the recognized morphological variants. Monophyly of the subfamily Scaphirhynchinae is consistently rejected by all phylogenetic reconstruction methodologies with the molecular character set while monophyly of both river sturgeon genera is robustly supported. The molecular data set also rejects hypotheses of monophyly for sampled species of Pseudoscaphirhynchus as well as monophyly for the recognized intraspecific morphological variants. Interestingly both Scaphirhynchus and Pseudoscaphirhynchus demonstrate the same general pattern in reconstructed topologies; a lack of phylogenetic structure in the clade with respect to recognized diversity. Despite rejection of monophyly for the subfamily Scaphirhynchinae with molecular data, reconstructed hypotheses from morphological character sets consistently support monophyly for this subfamily. Disparities among the data sets, as well as reasons for rejection of monophyly for Scaphirhynchinae and species of Scaphirhynchus and Pseudoscaphirhynchus with molecular characters are examined and a decreased rate of molecular evolution is found to be most consistent with the data.     

Testing biogeographical hypotheses in space and time: faunal relationships of the putative ancient Lake Egˇirdir in Asia Minor

Aim The aims of this study are to establish a multi‐locus phylogeny‐based hypothesis for the biogeographical relationship of gastropods from the putative ancient Lake Egˇirdir, to test the respective null hypothesis, to estimate the timing of biogeographical events based on independent molecular clock approaches, and to interpret the data with respect to the putative ancient character of Lake Egˇirdir. Location Lake Egˇirdir, western Taurus Lake District, Turkey. Methods DNA sequences from the putatively only extant endemic taxon of Lake Egˇirdir, Falsipyrgula pfeiferi, as well as representatives of other pyrgulinid genera from Europe and western Asia are used for phylogenetic analyses based on Bayesian inference. The respective null hypothesis is tested utilizing parametric bootstrapping. The timing of evolutionary events is estimated based on two independent molecular clock approaches, which involve the modelling of judicious errors associated with branch‐length calculations and calibration points. Results Bayesian inference indicates a very close relationship between the Lake Egˇirdir and Ponto‐Caspian taxa. Parametric bootstrapping rejects the null hypothesis that these taxa are not monophyletic (P ≤ 0.01). The alternative hypothesis, namely monophyly of the Ponto‐Caspian and Egˇirdir taxa, can therefore be accepted. The two independent molecular clock approaches show diversion times for the Ponto‐Caspian/Egˇirdir taxa of 0.42 ± 0.18 and 0.43 ± 0.63 Ma. Main conclusions The present study shows that there is no close biogeographical affiliation between the probably only remaining endemic taxon of Lake Egˇirdir and taxa from central Europe or the Balkan region. Instead, there is a very close and relatively young (i.e. late Pleistocene) biogeographical relationship with the Ponto‐Caspian pyrgulinids. However, fossil and comparative data from other invertebrates indicate that biogeographical connections between Lake Egˇirdir and the Ponto‐Caspian region existed during various time periods, i.e. the Miocene/Pliocene, early Pleistocene, and late Pleistocene. Acknowledging the still‐restricted knowledge of the evolutionary history of the lake, the data presented here do not reject the putative ancient status of Lake Egˇirdir. Future studies utilizing endemic taxa of other lakes in the region need to show whether the western Taurus Lake District represents a melting pot of Pleistocene refuge biodiversity from different regions, and whether the admixture of divergent lineages has created a genetically distinct set of taxa that would warrant the designation of the area as a unique biogeographical subregion.     

Phylogeny of the Carnivora (Mammalia): Congruence vs Incompatibility among Multiple Data Sets

The purpose of this study was to determine the higher-level phylogenetic relationships among Carnivora, using a conditional data combination (CDC) approach to analyzing multiple data sets. New nucleotide sequences (851 base pairs from intron I of the transthyretin gene) among 22 representatives of the 11 families of Carnivora were generated and analyzed in concert with, and comparison to, other mitochondrial and morphological character data. Conditional data combination analyses of the four independent data sets (transthyretin intron I, cytochromeb,partial 12S rRNA, and morphology) indicate that the phylogenetic results derived from each generally agree, with two exceptions. The first exception, signal heterogeneity in comparisons involving transthyretin and morphology, provides an example where phylogenetic conclusions drawn from total evidence analyses may differ from conclusions drawn from CDC analyses. The second exception demonstrates that while a CDC method may reject the null hypothesis of homogeneity for a particular partition, including that partition in combined analyses, may nevertheless provide an overall increase in phylogenetic signal, in terms of nodal support for most associations, without altering the topology derived from the combined homogeneous data partitions. Phylogenetic reconstruction among the feliform families supports a sister-group relationship between the hyaenas (Hyaenidae) and mongooses (Herpestidae) and places the African palm civet (Nandinia) as basal to all other living Feliformia. Among the caniform families, CDC analyses strongly support the previously enigmatic red panda (Ailurus) as a monotypic lineage that is sister to Musteloideasensu stricto(mustelids plus procyonids), in addition to pinniped monophyly and a sister-group relationship between the walrus and sea lions.     

Estimation of false discovery rates in multiple testing: application to gene microarray data

Testing for significance with gene expression data from DNA microarray experiments involves simultaneous comparisons of hundreds or thousands of genes. If R denotes the number of rejections (declared significant genes) and V denotes the number of false rejections, then V/R, if R > 0, is the proportion of false rejected hypotheses. This paper proposes a model for the distribution of the number of rejections and the conditional distribution of V given R, V / R. Under the independence assumption, the distribution of R is a convolution of two binomials and the distribution of V / R has a noncentral hypergeometric distribution. Under an equicorrelated model, the distributions are more complex and are also derived. Five false discovery rate probability error measures are considered: FDR = E(V/R), pFDR = E(V/R / R > 0) (positive FDR), cFDR = E(V/R / R = r) (conditional FDR), mFDR = E(V)/E(R) (marginal FDR), and eFDR = E(V)/r (empirical FDR). The pFDR, cFDR, and mFDR are shown to be equivalent under the Bayesian framework, in which the number of true null hypotheses is modeled as a random variable. We present a parametric and a bootstrap procedure to estimate the FDRs. Monte Carlo simulations were conducted to evaluate the performance of these two methods. The bootstrap procedure appears to perform reasonably well, even when the alternative hypotheses are correlated (rho = .25). An example from a toxicogenomic microarray experiment is presented for illustration.