Statistical inferences in phylogeography

In conventional phylogeographic studies, historical demographic processes are elucidated from the geographical distribution of individuals represented on an inferred gene tree. However, the interpretation of gene trees in this context can be difficult as the same demographic/geographical process can randomly lead to multiple different genealogies. Likewise, the same gene trees can arise under different demographic models. This problem has led to the emergence of many statistical methods for making phylogeographic inferences. A popular phylogeographic approach based on nested clade analysis is challenged by the fact that a certain amount of the interpretation of the data is left to the subjective choices of the user, and it has been argued that the method performs poorly in simulation studies. More rigorous statistical methods based on coalescence theory have been developed. However, these methods may also be challenged by computational problems or poor model choice. In this review, we will describe the development of statistical methods in phylogeographic analysis, and discuss some of the challenges facing these methods.

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Background: Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results: Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion: The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents

Covariation in the structural composition of the gut microbiome and the spectroscopically derived metabolic phenotype (metabotype) of a rodent model for obesity were investigated using a range of multivariate statistical tools. Urine and plasma samples from three strains of 10-week-old male Zucker rats (obese (fa/fa, n = 8), lean (fal-, n = 8) and lean (-/-, n = 8)) were characterized via high-resolution H-1 NMR spectroscopy, and in parallel, the fecal microbial composition was investigated using fluorescence in situ hydridization (FISH) and denaturing gradient gel electrophoresis (DGGE) methods. All three Zucker strains had different relative abundances of the dominant members of their intestinal microbiota (FISH), with the novel observation of a Halomonas and a Sphingomonas species being present in the (fa/fa) obese strain on the basis of DGGE data. The two functionally and phenotypically normal Zucker strains (fal- and -/-) were readily distinguished from the (fa/fa) obese rats on the basis of their metabotypes with relatively lower urinary hippurate and creatinine, relatively higher levels of urinary isoleucine, leucine and acetate and higher plasma LDL and VLDL levels typifying the (fa/fa) obese strain. Collectively, these data suggest a conditional host genetic involvement in selection of the microbial species in each host strain, and that both lean and obese animals could have specific metabolic phenotypes that are linked to their individual microbiomes.

Inverse effectiveness, multisensory integration, and the bodily self: some statistical considerations

A recent report in Consciousness and Cognition provided evidence from a study of the rubber hand illusion (RHI) that supports the multisensory principle of inverse effectiveness (PoIE). I describe two methods of assessing the principle of inverse effectiveness ('a priori' and 'post-hoc'), and discuss how the post-hoc method is affected by the statistical artefact of,regression towards the mean'. I identify several cases where this artefact may have affected particular conclusions about the PoIE, and relate these to the historical origins of 'regression towards the mean'. Although the conclusions of the recent report may not have been grossly affected, some of the inferential statistics were almost certainly biased by the methods used. I conclude that, unless such artefacts are fully dealt with in the future, and unless the statistical methods for assessing the PoIE evolve, strong evidence in support of the PoIE will remain lacking. (C) 2009 Elsevier Inc. All rights reserved.

Evaluating the potential for statistical decadal predictions of sea surface temperatures with a perfect model approach

We explore the potential for making statistical decadal predictions of sea surface temperatures (SSTs) in a perfect model analysis, with a focus on the Atlantic basin. Various statistical methods (Lagged correlations, Linear Inverse Modelling and Constructed Analogue) are found to have significant skill in predicting the internal variability of Atlantic SSTs for up to a decade ahead in control integrations of two different global climate models (GCMs), namely HadCM3 and HadGEM1. Statistical methods which consider non-local information tend to perform best, but which is the most successful statistical method depends on the region considered, GCM data used and prediction lead time. However, the Constructed Analogue method tends to have the highest skill at longer lead times. Importantly, the regions of greatest prediction skill can be very different to regions identified as potentially predictable from variance explained arguments. This finding suggests that significant local decadal variability is not necessarily a prerequisite for skillful decadal predictions, and that the statistical methods are capturing some of the dynamics of low-frequency SST evolution. In particular, using data from HadGEM1, significant skill at lead times of 6–10 years is found in the tropical North Atlantic, a region with relatively little decadal variability compared to interannual variability. This skill appears to come from reconstructing the SSTs in the far north Atlantic, suggesting that the more northern latitudes are optimal for SST observations to improve predictions. We additionally explore whether adding sub-surface temperature data improves these decadal statistical predictions, and find that, again, it depends on the region, prediction lead time and GCM data used. Overall, we argue that the estimated prediction skill motivates the further development of statistical decadal predictions of SSTs as a benchmark for current and future GCM-based decadal climate predictions.

Integrated cytokine and metabolic analysis of pathological responses to parasite exposure in rodents

Parasitic infections cause a myriad of responses in their mammalian hosts, on immune as well as on metabolic level. A multiplex panel of cytokines and metabolites derived from four parasite-rodent models, namely, Plasmodium berghei-mouse, Trypanosoma brucei brucei-mouse, Schistosoma mansoni-mouse, and Fasciola hepatica-rat were statistically coanalyzed. 1H NMR spectroscopy and multivariate statistical analysis were used to characterize the urine and plasma metabolite profiles in infected and noninfected animals. Each parasite generated a unique metabolic signature in the host. Plasma cytokine concentrations were obtained using the ‘Meso Scale Discovery’ multi cytokine assay platform. Multivariate data integration methods were subsequently used to elucidate the component of the metabolic signature which is associated with inflammation and to determine specific metabolic correlates with parasite-induced changes in plasma cytokine levels. For example, the relative levels of acetyl glycoproteins extracted from the plasma metabolite profile in the P. berghei-infected mice were statistically correlated with IFN-γ, whereas the same cytokine was anticorrelated with glucose levels. Both the metabolic and the cytokine data showed a similar spatial distribution in principal component analysis scores plots constructed for the combined murine data, with samples from all infected animals clustering according to the parasite species and whereby the protozoan infections (P. berghei and T. b. brucei) grouped separately from the helminth infection (S. mansoni). For S. mansoni, the main infection-responsive cytokines were IL-4 and IL-5, which covaried with lactate, choline, and D-3-hydroxybutyrate. This study demonstrates that the inherently differential immune response to single and multicellular parasites not only manifests in the cytokine expression, but also consequently imprints on the metabolic signature, and calls for in-depth analysis to further explore direct links between immune features and biochemical pathways.

The development of soil organic matter in restored biodiverse Jarrah forests of South-Western Australia as determined by ASE and GCMS

Background, aim and scope Soil organic matter (SOM) is known to increase with time as landscapes recover after a major disturbance; however, little is known about the evolution of the chemistry of SOM in reconstructed ecosystems. In this study, we assessed the development of SOM chemistry in a chronosequence (space for time substitution) of restored Jarrah forest sites in Western Australia. Materials and methods Replicated samples were taken at the surface of the mineral soil as well as deeper in the profile at sites of 1, 3, 6, 9, 12, and 17 years of age. A molecular approach was developed to distinguish and quantify numerous individual compounds in SOM. This used accelerated solvent extraction in conjunction with gas chromatography mass spectrometry. A novel multivariate statistical approach was used to assess changes in accelerated solvent extraction (ASE)-gas chromatography-mass spectrometry (GCMS) spectra. This enabled us to track SOM developmental trajectories with restoration time. Results Results showed total carbon concentrations approached that of native forests soils by 17 years of restoration. Using the relate protocol in PRIMER, we demonstrated an overall linear relationship with site age at both depths, indicating that changes in SOM chemistry were occurring. Conclusions The surface soils were seen to approach native molecular compositions while the deeper soil retained a more stable chemical signature, suggesting litter from the developing diverse plant community has altered SOM near the surface. Our new approach for assessing SOM development, combining ASE-GCMS with illuminating multivariate statistical analysis, holds great promise to more fully develop ASE for the characterisation of SOM.

On the statistical estimation of diffusion processes: a survey

Data available on continuos-time diffusions are always sampled discretely in time. In most cases, the likelihood function of the observations is not directly computable. This survey covers a sample of the statistical methods that have been developed to solve this problem. We concentrate on some recent contributions to the literature based on three di§erent approaches to the problem: an improvement of the Euler-Maruyama discretization scheme, the use of Martingale Estimating Functions and the application of Generalized Method of Moments (GMM).

On the statistical estimation of diffusion processes - a partial survey

Data available on continuous-time diffusions are always sampled discretely in time. In most cases, the likelihood function of the observations is not directly computable. This survey covers a sample of the statistical methods that have been developed to solve this problem. We concentrate on some recent contributions to the literature based on three di§erent approaches to the problem: an improvement of the Euler-Maruyama discretization scheme, the employment of Martingale Estimating Functions, and the application of Generalized Method of Moments (GMM).

Organização de uma bateria de testes para seleção de candidatos ao ensino técnico de 2. grau

O trabalho aqui apresentado relata um estudo exploratório na área de Educação Técnico-Industrial de segundo grau, cujo objetivo consistiu em selecionar, dentre vários testes, os que fossem melhores preditores do aproveitamento acadêmico dentro da formarão profissional, para formar parte da bateria de testes que serão utilizadas na seleção dos candidatos aos cursos oferecidos pelo Colégio Técnico Nacional para a formação de técnicos de nível médio. o estudo em apreço, realizado mediante a colaboração entre o Departamento de Educação Técnica e o Departamento de Orientação Educacional e Vocacional, ambos do Ministério de Educa9ão e Cultura do Paraguai, é parte do projeto de expansão da orientação no nível de Formação Técnico-Industrial e Formação Profissional do qual um dos objetivos é controlar a qualidade da matricula a fim de evitar a evasão e favorecer o maior aproveitamento destes cursos oferecidos a este nível, o que será possível através da implantarão, em todos os Colégios desde tipo, de medidas de avaliação de aptidões e interesses para o desenvolvimento dos recursos humanos dos países em desenvolvimento. Partiu-se de uma análise minuciosa dos programas de estudo das matérias que compunham a bagagem de cada especialidade, com a finalidade de realizar uma lista de aptidões e traços que compõe a especificação profissional de cada especialidade. Foram experimentados 13 testes psicométricos, um de interesses ocupacionais e dois de personalidade. Dos quais após submetidos ao tratamento estadístico para conhecer sua precisão e validade em relação a um critério (o rendimento acadêmico nas matérias da especialidade) foram selecionados os seguintes testes: I N V de Pierre Weil, Raciocínio espacial Ribakow, Rapidez e exatidão no cálculo da bateria CEPA, Teste de Destreza Manual e Atenção distribuída e o Raciocínio Mecânico do DAT por ser os de melhor índice de precisão e validade (elevada correlação com as mate rias profissionais das especialidades). Este estudo se constitui no passo inicial para a elaboração de outros sistemas de seleção de matrícula baseados em provas pSicol6gicas, organizados pela Unidade de Psicometria e Psicologia Escolar de Dpto. de Orientação Educativa e Vocacional do M. E. C.

Ecomorfologia de dez espécies de peixes marinhos mais abundantes de Galinhos/RN

Ecomorphology is a science based on the idea that morphological differences among species could be associated with distinct biological and environmental pressures suffered by them. These differences can be studied employing morphological and biometric indexes denominated Ecomorphological attributes , representing standards that express characteristics of the individual in relation to its environment, and can be interpreted as indicators of life habits or adaptations suffered due its occupation of different habitats. This work aims to contribute for the knowledge of the ecomorphology of the Brazilian marine ichthyofauna, specifically from Galinhos, located at Rio Grande do Norte state. 10 different species of fish were studied, belonging the families Gerreidae (Eucinostomus argenteus), Haemulidae (Orthopristis ruber,Pomadasyscorvinaeformis,Haemulonaurolineatum,Haemulonplumieri,Haemulonsteindachneri), Lutjanidae (Lutjanus synagris), Paralichthyidae (Syaciummicrurum), Bothidae (Bothus ocellatus) and Tetraodontidae (Sphoeroidestestudineus), which were obtained during five collections, in the period time of September/2004 to April/2005, utilizing three special nets. The ecomorphological study was performed at the laboratory. Eight to ten samples of each fish specie were measured. Fifteen morphological aspects were considered to calculate twelve ecomorphological attributes. Multivariate statistical analysis methods such as Principal Component Analysis (PCA) and Cluster Analysis were done to identify ecmorphological patterns to describe the data set obtained. As results, H.aurolineatumwas the most abundant specie found (23,03%) and S.testudineusthe less one with 0,23%. The 1st Principal component showed variation of 60,03% with influence of the ecomorphological attribute related to body morphology, while the 2nd PC with 23,25% variation had influence of the ecomorphological attribute related to oral morphology. The Cluster Analiysis promoted the identification of three distinct groups Perciformes, Pleuronectiformes and Tetraodontiformes. Based on the obtained data, considering morphological characters differences among the species studied, we suggest that all of them live at the medium (E.argenteus,O.rubber, P.corvinaeformis,H.aurolineatum,H.plumieri,H.steindachneri,L.synagris) and bottom (S.micrurum,B.ocellatus,S.testudineus) region of column water.

Emprego formal na região nordeste brasileira: seus efeitos na inclusão social

This work aims to study the problem of the formal job in the Brazilian Northeast region and its effect in the social inclusion, taking for base the analysis of variables defined in the Atlas of Social Exclusion, which is based on the 2000 Brazilian Census, choosing the county as unit of analysis. As methodological options, an exploratory data analysis was performed, followed by multivariate statistical techniques, such as weighted multiple regression analysis, cluster analysis and exploratory analysis of spatial data. The results pointed out to low rates of formal job for the active age population as well as low indexes of social inclusion in the Northeast region of Brazil. A strong association of the formal job with the indicators of social inclusion under investigation, was evidenced (schooling, inequality, poverty, youth and income form government transfers), as well as a strong association of the formal job with the new index of social inclusion (IIS), modified from the IES. At the Federative Units, in which better levels of formal job had been found, good indexes of social inclusion are also observed. Highlights for the state of the Rio Grande do Norte, with the best conditions of life, and for the states of the Maranhão and Piauí, with the worst conditions. The situation of the Northeast region, facing the indicators under study, is very precarious, claiming for the necessity of emphasizing programs and governmental actions, specially directed to the raise of formal job levels of the region, reflecting, thus, in improvements on the income inequality, as well as in the social inclusion of the population of Northeastern natives.

Discrimination of geomorphic surfaces with multivariate analysis of soil attributes in sandstone - basalt lithosequence

O conceito de superfície geomórfica permite uma interligação entre os diferentes ramos da ciência do solo, tais como geologia, geomorfologia e pedologia. Esta associação favorece a compreensão da distribuição espacial dos solos na paisagem, e torna possível compreender o comportamento dos atributos do solo, que estão principalmente relacionadas com a estratigrafia e formas do relevo. Assim, este estudo visa à aplicação da estatística multivariada para categorizar superfícies geomórficas em uma litossequência arenito-basalto, de modo a fornecer uma base para a avaliação do solo em áreas afins. A área de estudo está localizada no município de Pereira Barreto, São Paulo, Brasil. A área escolhida possui 530 hectares, onde foram localizadas e mapeadas três superfícies geomórficas (I, II e III). Na área, 134 amostras foram coletadas nas profundidades de 0,0-0,2 m e 0,8-1,0 m, foram determinados os conteúdos de areia, silte e argila, pH em CaCl2, conteúdo de MO, P, Ca, Mg, K, Al e H+Al. Com base nos resultados, foram realizadas a análise univariada e multivariada de variância, clusters e principal componente, a fim de comparar as três superfícies geomórficas. A análise estatística univariada dos atributos do solo não foi eficiente na identificação das três superfícies geomórficas. Utilizando-se os atributos físicos e químicos do solo, as técnicas estatísticas multivariada permitiram à separação dos três grupos de corpos naturais do solo que foram equivalentes as três superfícies geomórficas mapeadas. Estes resultados são interessantes, pois demonstram a viabilidade da utilização de classificação numérica das superfícies geomórficas para ajudar no mapeamento de solo.

Análise de desempenho de vendas em telecomunicações utilizando técnicas de mineração de dados

Nowadays, telecommunications is one of the most dynamic and strategic areas in the world. Organizations are always seeking to find new management practices within an ever increasing competitive environment where resources are getting scarce. In this scenario, data obtained from business and corporate processes have even greater importance, although this data is not yet adequately explored. Knowledge Discovery in Databases (KDD) appears then, as an option to allow the study of complex problems in different areas of management. This work proposes both a systematization of KDD activities using concepts from different methodologies, such as CRISP-DM, SEMMA and FAYYAD approaches and a study concerning the viability of multivariate regression analysis models to explain corporative telecommunications sales using performance indicators. Thus, statistical methods were outlined to analyze the effects of such indicators on the behavior of business productivity. According to business and standard statistical analysis, equations were defined and fit to their respective determination coefficients. Tests of hypotheses were also conducted on parameters with the purpose of validating the regression models. The results show that there is a relationship between these development indicators and the amount of sales