Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

Transformation Based Interpolation with Generalized Representative Values

Z. Huang and Q. Shen. Transformation Based Interpolation with Generalized Representative Values. Proceedings of the 14th International Conference on Fuzzy Systems, pages 821-826.

A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data

Mark Pagel, Andrew Meade (2004). A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology, 53(4), 571-581. RAE2008

Testing Mean-Variance Efficiency in CAPM with Possibly Non-Gaussian Errors : An Exact Simulation-Based Approach

In this paper we propose exact likelihood-based mean-variance efficiency tests of the market portfolio in the context of Capital Asset Pricing Model (CAPM), allowing for a wide class of error distributions which include normality as a special case. These tests are developed in the frame-work of multivariate linear regressions (MLR). It is well known however that despite their simple statistical structure, standard asymptotically justified MLR-based tests are unreliable. In financial econometrics, exact tests have been proposed for a few specific hypotheses [Jobson and Korkie (Journal of Financial Economics, 1982), MacKinlay (Journal of Financial Economics, 1987), Gib-bons, Ross and Shanken (Econometrica, 1989), Zhou (Journal of Finance 1993)], most of which depend on normality. For the gaussian model, our tests correspond to Gibbons, Ross and Shanken’s mean-variance efficiency tests. In non-gaussian contexts, we reconsider mean-variance efficiency tests allowing for multivariate Student-t and gaussian mixture errors. Our framework allows to cast more evidence on whether the normality assumption is too restrictive when testing the CAPM. We also propose exact multivariate diagnostic checks (including tests for multivariate GARCH and mul-tivariate generalization of the well known variance ratio tests) and goodness of fit tests as well as a set estimate for the intervening nuisance parameters. Our results [over five-year subperiods] show the following: (i) multivariate normality is rejected in most subperiods, (ii) residual checks reveal no significant departures from the multivariate i.i.d. assumption, and (iii) mean-variance efficiency tests of the market portfolio is not rejected as frequently once it is allowed for the possibility of non-normal errors.

Stochastic Volatility.

This paper prepared for the Handbook of Statistics (Vol.14: Statistical Methods in Finance), surveys the subject of stochastic volatility. the following subjects are covered: volatility in financial markets (instantaneous volatility of asset returns, implied volatilities in option prices and related stylized facts), statistical modelling in discrete and continuous time and, finally, statistical inference (methods of moments, quasi-maximum likelihood, likelihood-based and bayesian methods and indirect inference).

Inférence robuste à la présence des valeurs aberrantes dans les enquêtes

Cette thèse comporte trois articles dont un est publié et deux en préparation. Le sujet central de la thèse porte sur le traitement des valeurs aberrantes représentatives dans deux aspects importants des enquêtes que sont : l’estimation des petits domaines et l’imputation en présence de non-réponse partielle. En ce qui concerne les petits domaines, les estimateurs robustes dans le cadre des modèles au niveau des unités ont été étudiés. Sinha & Rao (2009) proposent une version robuste du meilleur prédicteur linéaire sans biais empirique pour la moyenne des petits domaines. Leur estimateur robuste est de type «plugin», et à la lumière des travaux de Chambers (1986), cet estimateur peut être biaisé dans certaines situations. Chambers et al. (2014) proposent un estimateur corrigé du biais. En outre, un estimateur de l’erreur quadratique moyenne a été associé à ces estimateurs ponctuels. Sinha & Rao (2009) proposent une procédure bootstrap paramétrique pour estimer l’erreur quadratique moyenne. Des méthodes analytiques sont proposées dans Chambers et al. (2014). Cependant, leur validité théorique n’a pas été établie et leurs performances empiriques ne sont pas pleinement satisfaisantes. Ici, nous examinons deux nouvelles approches pour obtenir une version robuste du meilleur prédicteur linéaire sans biais empirique : la première est fondée sur les travaux de Chambers (1986), et la deuxième est basée sur le concept de biais conditionnel comme mesure de l’influence d’une unité de la population. Ces deux classes d’estimateurs robustes des petits domaines incluent également un terme de correction pour le biais. Cependant, ils utilisent tous les deux l’information disponible dans tous les domaines contrairement à celui de Chambers et al. (2014) qui utilise uniquement l’information disponible dans le domaine d’intérêt. Dans certaines situations, un biais non négligeable est possible pour l’estimateur de Sinha & Rao (2009), alors que les estimateurs proposés exhibent un faible biais pour un choix approprié de la fonction d’influence et de la constante de robustesse. Les simulations Monte Carlo sont effectuées, et les comparaisons sont faites entre les estimateurs proposés et ceux de Sinha & Rao (2009) et de Chambers et al. (2014). Les résultats montrent que les estimateurs de Sinha & Rao (2009) et de Chambers et al. (2014) peuvent avoir un biais important, alors que les estimateurs proposés ont une meilleure performance en termes de biais et d’erreur quadratique moyenne. En outre, nous proposons une nouvelle procédure bootstrap pour l’estimation de l’erreur quadratique moyenne des estimateurs robustes des petits domaines. Contrairement aux procédures existantes, nous montrons formellement la validité asymptotique de la méthode bootstrap proposée. Par ailleurs, la méthode proposée est semi-paramétrique, c’est-à-dire, elle n’est pas assujettie à une hypothèse sur les distributions des erreurs ou des effets aléatoires. Ainsi, elle est particulièrement attrayante et plus largement applicable. Nous examinons les performances de notre procédure bootstrap avec les simulations Monte Carlo. Les résultats montrent que notre procédure performe bien et surtout performe mieux que tous les compétiteurs étudiés. Une application de la méthode proposée est illustrée en analysant les données réelles contenant des valeurs aberrantes de Battese, Harter & Fuller (1988). S’agissant de l’imputation en présence de non-réponse partielle, certaines formes d’imputation simple ont été étudiées. L’imputation par la régression déterministe entre les classes, qui inclut l’imputation par le ratio et l’imputation par la moyenne sont souvent utilisées dans les enquêtes. Ces méthodes d’imputation peuvent conduire à des estimateurs imputés biaisés si le modèle d’imputation ou le modèle de non-réponse n’est pas correctement spécifié. Des estimateurs doublement robustes ont été développés dans les années récentes. Ces estimateurs sont sans biais si l’un au moins des modèles d’imputation ou de non-réponse est bien spécifié. Cependant, en présence des valeurs aberrantes, les estimateurs imputés doublement robustes peuvent être très instables. En utilisant le concept de biais conditionnel, nous proposons une version robuste aux valeurs aberrantes de l’estimateur doublement robuste. Les résultats des études par simulations montrent que l’estimateur proposé performe bien pour un choix approprié de la constante de robustesse.

Systematics and evolution of the genus Deuterocohnia Mez (Bromeliaceae)

The present study investigates the systematics and evolution of the Neotropical genus Deuterocohnia Mez (Bromeliaceae). It provides a comprehensive taxonomic revision as well as phylogenetic analyses based on chloroplast and nuclear DNA sequences and presents a hypothesis on the evolution of the genus. A broad morphological, anatomical, biogeographical and ecological overview of the genus is given in the first part of the study. For morphological character assessment more than 700 herbarium specimens from 39 herbaria as well as living plant material in the field and in the living collections of botanical gardens were carefully examined. The arid habitats, in which the species of Deuterocohnia grow, are reflected by the morphological and anatomical characters of the species. Important characters for species delimitation were identified, like the length of the inflorescence, the branching order, the density of flowers on partial inflorescences, the relation of the length of the primary bracts to that of the partial inflorescence, the sizes of floral bracts, sepals and petals, flower colour, the presence or absence of a pedicel, the curvature of the stamina and the petals during anthesis. After scrutinizing the nomenclatural history of the taxa belonging to Deuterocohnia – including the 1992 syonymized genus Abromeitiella – 17 species, 4 subspecies and 4 varieties are accepted in the present revision. Taxonomic changes were made in the following cases: (I) New combinations: A. abstrusa (A. Cast.) N. Schütz is re-established – as defined by Castellanos (1931) – and transfered to D. abstrusa; D. brevifolia (Griseb.) M.A. Spencer & L.B. Sm. includes accessions of the former D. lorentziana (Mez) M.A. Spencer & L.B. Sm., which are not assigned to D. abstrusa; D. bracteosa W. Till is synonymized to D. strobilifera Mez; D. meziana Kuntze ex Mez var. carmineo-viridiflora Rauh is classified as a subspecies of D. meziana (ssp. carmineo-viridiflora (Rauh) N. Schütz); D. pedicellata W. Till is classified as a subspecies of D. meziana (ssp. pedicellata (W. Till) N. Schütz); D. scapigera (Rauh & L. Hrom.) M.A. Spencer & L.B. Sm ssp. sanctae-crucis R. Vásquez & Ibisch is classified as a species (D. sanctae-crucis (R. Vásquez & Ibisch) N. Schütz); (II) New taxa: a new subspecies of D. meziana Kuntze ex Mez is established; a new variety of D. scapigera is established; (the new taxa will be validly published elsewhere); (III) New type: an epitype for D. longipetala was chosen. All other species were kept according to Spencer and Smith (1992) or – in the case of more recently described species – according to the protologue. Beside the nomenclatural notes and the detailed descriptions, information on distribution, habitat and ecology, etymology and taxonomic delimitation is provided for the genus and for each of its species. An key was constructed for the identification of currently accepted species, subspecies and varieties. The key is based on easily detectable morphological characters. The former synonymization of the genus Abromeitiella into Deuterocohnia (Spencer and Smith 1992) is re-evalutated in the present study. Morphological as well as molecular investigations revealed Deuterocohnia incl. Abromeitiella as being monophyletic, with some indications that a monophyletic Abromeitiella lineage arose from within Deuterocohnia. Thus the union of both genera is confirmed. The second part of the present thesis describes and discusses the molecular phylogenies and networks. Molecular analyses of three chloroplast intergenic spacers (rpl32-trnL, rps16-trnK, trnS-ycf3) were conducted with a sample set of 119 taxa. This set included 103 Deuterocohnia accessions from all 17 described species of the genus and 16 outgroup taxa from the remainder of Pitcairnioideae s.str. (Dyckia (8 sp.), Encholirium (2 sp.), Fosterella (4 sp.) and Pitcairnia (2 sp.)). With its high sampling density, the present investigation by far represents the most comprehensive molecular study of Deuterocohnia up till now. All data sets were analyzed separately as well as in combination, and various optimality criteria for phylogenetic tree construction were applied (Maximum Parsimony, Maximum Likelihood, Bayesian inferences and the distance method Neighbour Joining). Congruent topologies were generally obtained with different algorithms and optimality criteria, but individual clades received different degrees of statistical support in some analyses. The rps16-trnK locus was the most informative among the three spacer regions examined. The results of the chloroplast DNA analyses revealed a highly supported paraphyly of Deuterocohnia. Thus, the cpDNA trees divide the genus into two subclades (A and B), of which Deuterocohnia subclade B is sister to the included Dyckia and Encholirium accessions, and both together are sister to Deuterocohnia subclade A. To further examine the relationship between Deuterocohnia and Dyckia/Encholirium at the generic level, two nuclear low copy markers (PRK exon2-5 and PHYC exon1) were analysed with a reduced taxon set. This set included 22 Deuterocohnia accessions (including members of both cpDNA subclades), 2 Dyckia, 2 Encholirium and 2 Fosterella species. Phylogenetic trees were constructed as described above, and for comparison the same reduced taxon set was also analysed at the three cpDNA data loci. In contrast to the cpDNA results, the nuclear DNA data strongly supported the monophyly of Deuterocohnia, which takes a sister position to a clade of Dyckia and Encholirium samples. As morphology as well as nuclear DNA data generated in the present study and in a former AFLP analysis (Horres 2003) all corroborate the monophyly of Deuterocohnia, the apparent paraphyly displayed in cpDNA analyses is interpreted to be the consequence of a chloroplast capture event. This involves the introgression of the chloroplast genome from the common ancestor of the Dyckia/ Encholirium lineage into the ancestor of Deuterocohnia subclade B species. The chloroplast haplotypes are not species-specific in Deuterocohnia. Thus, one haplotype was sometimes shared by several species, where the same species may harbour different haplotypes. The arrangement of haplotypes followed geographical patterns rather than taxonomic boundaries, which may indicate some residual gene flow among populations from different Deuteroccohnia species. Phenotypic species coherence on the background of ongoing gene flow may then be maintained by sets of co-adapted alleles, as was suggested by the porous genome concept (Wu 2001, Palma-Silva et al. 2011). The results of the present study suggest the following scenario for the evolution of Deuterocohnia and its species. Deuterocohnia longipetala may be envisaged as a representative of the ancestral state within the genus. This is supported by (1) the wide distribution of this species; (2) the overlap in distribution area with species of Dyckia; (3) the laxly flowered inflorescences, which are also typical for Dyckia; (4) the yellow petals with a greenish tip, present in most other Deuterocohnia species. The following six extant lineages within Deuterocohnia might have independently been derived from this ancestral state with a few changes each: (I) D. meziana, D. brevispicata and D. seramisiana (Bolivia, lowland to montane areas, mostly reddish-greenish coloured, very laxly to very densely flowered); (II) D. strobilifera (Bolivia, high Andean mountains, yellow flowers, densely flowered); (III) D. glandulosa (Bolivia, montane areas, yellow-greenish flowers, densely flowered); (IV) D. haumanii, D. schreiteri, D. digitata, and D. chrysantha (Argentina, Chile, E Andean mountains and Atacama desert, yellow-greenish flowers, densely flowered); (V) D. recurvipetala (Argentina, foothills of the Andes, recurved yellow flowers, laxly flowered); (VI) D. gableana, D. scapigera, D. sanctae-crucis, D. abstrusa, D. brevifolia, D. lotteae (former Abromeitiella species, Bolivia, Argentina, higher Andean mountains, greenish-yellow flowers, inflorescence usually simple). Originating from the lower montane Andean regions, at least four lineages of the genus (I, II, IV, VI) adapted in part to higher altitudes by developing densely flowered partial inflorescences, shorter flowers and – in at least three lineages (II, IV, VI) – smaller rosettes, whereas species spreading into the lowlands (I, V) developed larger plants, laxly flowered, amply branched inflorescences and in part larger flowers (I).

Family-based association analysis with ordered categorical phenotypes, covariates and interactions

Genetic association analyses of family-based studies with ordered categorical phenotypes are often conducted using methods either for quantitative or for binary traits, which can lead to suboptimal analyses. Here we present an alternative likelihood-based method of analysis for single nucleotide polymorphism (SNP) genotypes and ordered categorical phenotypes in nuclear families of any size. Our approach, which extends our previous work for binary phenotypes, permits straightforward inclusion of covariate, gene-gene and gene-covariate interaction terms in the likelihood, incorporates a simple model for ascertainment and allows for family-specific effects in the hypothesis test. Additionally, our method produces interpretable parameter estimates and valid confidence intervals. We assess the proposed method using simulated data, and apply it to a polymorphism in the c-reactive protein (CRP) gene typed in families collected to investigate human systemic lupus erythematosus. By including sex interactions in the analysis, we show that the polymorphism is associated with anti-nuclear autoantibody (ANA) production in females, while there appears to be no effect in males.

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation

We describe and evaluate a new estimator of the effective population size (N-e), a critical parameter in evolutionary and conservation biology. This new "SummStat" N-e. estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N-e. Simulations of a Wright-Fisher population with known N-e show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N-e values. We also address the paucity of information about the relative performance of N-e estimators by comparing the SUMMStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated rising initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and Ne less than or equal to 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N-e. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any, potentially informative summary statistic from Population genetic data.

A little learning is a dangerous thing: an experimental demonstration of ignorance-driven inference

Studies of ignorance-driven decision making have been employed to analyse when ignorance should prove advantageous on theoretical grounds or else they have been employed to examine whether human behaviour is consistent with an ignorance-driven inference strategy (e. g., the recognition heuristic). In the current study we examine whether-under conditions where such inferences might be expected-the advantages that theoretical analyses predict are evident in human performance data. A single experiment shows that, when asked to make relative wealth judgements, participants reliably use recognition as a basis for their judgements. Their wealth judgements under these conditions are reliably more accurate when some of the target names are unknown than when participants recognize all of the names (a "less-is-more effect"). These results are consistent across a number of variations: the number of options given to participants and the nature of the wealth judgement. A basic model of recognition-based inference predicts these effects.

When does ignorance make us smart? Additional factors guiding heuristic inference

“Fast & frugal” heuristics represent an appealing way of implementing bounded rationality and decision-making under pressure. The recognition heuristic is the simplest and most fundamental of these heuristics. Simulation and experimental studies have shown that this ignorance-driven heuristic inference can prove superior to knowledge based inference (Borges, Goldstein, Ortman & Gigerenzer, 1999; Goldstein & Gigerenzer, 2002) and have shown how the heuristic could develop from ACT-R’s forgetting function (Schooler & Hertwig, 2005). Mathematical analyses also demonstrate that, under certain conditions, a “less-is-more effect” will always occur (Goldstein & Gigerenzer, 2002). The further analyses presented in this paper show, however, that these conditions may constitute a special case and that the less-is-more effect in decision-making is subject to the moderating influence of the number of options to be considered and the framing of the question.

Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation

Many modern statistical applications involve inference for complex stochastic models, where it is easy to simulate from the models, but impossible to calculate likelihoods. Approximate Bayesian computation (ABC) is a method of inference for such models. It replaces calculation of the likelihood by a step which involves simulating artificial data for different parameter values, and comparing summary statistics of the simulated data with summary statistics of the observed data. Here we show how to construct appropriate summary statistics for ABC in a semi-automatic manner. We aim for summary statistics which will enable inference about certain parameters of interest to be as accurate as possible. Theoretical results show that optimal summary statistics are the posterior means of the parameters. Although these cannot be calculated analytically, we use an extra stage of simulation to estimate how the posterior means vary as a function of the data; and we then use these estimates of our summary statistics within ABC. Empirical results show that our approach is a robust method for choosing summary statistics that can result in substantially more accurate ABC analyses than the ad hoc choices of summary statistics that have been proposed in the literature. We also demonstrate advantages over two alternative methods of simulation-based inference.

Design-based random permutation models with auxiliary information

We extend the random permutation model to obtain the best linear unbiased estimator of a finite population mean accounting for auxiliary variables under simple random sampling without replacement (SRS) or stratified SRS. The proposed method provides a systematic design-based justification for well-known results involving common estimators derived under minimal assumptions that do not require specification of a functional relationship between the response and the auxiliary variables.

Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia

Background: The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. Results: The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33-42 Ma) origin in North America. Two independent lineages (Battus and Euryades + Parides) reached South America via the GAARlandia temporary connection, and later became extinct in North America. They only began substantive diversification during the early Miocene in Amazonia. Macroevolutionary analysis supports the "museum model" of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. Conclusions: This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady accumulation of diversity over time with constant net diversification rates, a result that contrasts with previous studies on other South American butterflies.