Systematics of the Oswaldoi Complex (Anopheles, Nyssorhynchus) in South America

Abstract Background Effective malaria control relies on accurate identification of those Anopheles mosquitoes responsible for the transmission of Plasmodium parasites. Anopheles oswaldoi s.l. has been incriminated as a malaria vector in Colombia and some localities in Brazil, but not ubiquitously throughout its Neotropical range. This evidence together with variable morphological characters and genetic differences supports that An. oswaldoi s.l. compromises a species complex. The recent fully integrated redescription of An. oswaldoi s.s. provides a solid taxonomic foundation from which to molecularly determine other members of the complex. Methods DNA sequences of the Second Internal Transcribed Spacer (ITS2 - rDNA) (n = 192) and the barcoding region of the Cytochrome Oxidase I gene (COI - mtDNA) (n = 110) were generated from 255 specimens of An. oswaldoi s.l. from 33 localities: Brazil (8 localities, including the lectotype series of An. oswaldoi), Ecuador (4), Colombia (17), Trinidad and Tobago (1), and Peru (3). COI sequences were analyzed employing the Kimura-two-parameter model (K2P), Bayesian analysis (MrBayes), Mixed Yule-Coalescent model (MYC, for delimitation of clusters) and TCS genealogies. Results Separate and combined analysis of the COI and ITS2 data sets unequivocally supported four separate species: two previously determined (An. oswaldoi s.s. and An. oswaldoi B) and two newly designated species in the Oswaldoi Complex (An. oswaldoi A and An. sp. nr. konderi). The COI intra- and inter-specific genetic distances for the four taxa were non-overlapping, averaging 0.012 (0.007 to 0.020) and 0.052 (0.038 to 0.064), respectively. The concurring four clusters delineated by MrBayes and MYC, and four independent TCS networks, strongly confirmed their separate species status. In addition, An. konderi of Sallum should be regarded as unique with respect to the above. Despite initially being included as an outgroup taxon, this species falls well within the examined taxa, suggesting a combined analysis of these taxa would be most appropriate. Conclusions: Through novel data and retrospective comparison of available COI and ITS2 DNA sequences, evidence is shown to support the separate species status of An. oswaldoi s.s., An. oswaldoi A and An. oswaldoi B, and at least two species in the closely related An. konderi complex (An. sp. nr. konderi, An. konderi of Sallum). Although An. oswaldoi s.s. has never been implicated in malaria transmission, An. oswaldoi B is a confirmed vector and the new species An. oswaldoi A and An. sp. nr. konderi are circumstantially implicated, most likely acting as secondary vectors.

Molecular phylogeography of tick-borne encephalitis virus in central Europe

In order to obtain a better understanding of tick-borne encephalitis virus (TBEV) strain movements in central Europe the E gene sequences of 102 TBEV strains collected from 1953 to 2011 at 38 sites in the Czech Republic, Slovakia, Austria and Germany were determined. Bayesian analysis suggests a 350-year history of evolution and spread in central Europe of two main lineages, A and B. In contrast to the east to west spread at the Eurasian continent level, local central European spreading patterns suggest historic west to east spread followed by more recent east to west spread. The phylogenetic and network analyses indicate TBEV ingressions from the Czech Republic and Slovakia into Germany via landscape features (Danube river system), biogenic factors (birds, red deer) and anthropogenic factors. The identification of endemic foci showing local genetic diversity is of paramount importance to the field as these will be a prerequisite for in-depth analysis of focal TBEV maintenance and long-distance TBEV spread.

Mediterranean brachiopods: morphological, ecological and phylogenetic aspects

The Brachiopoda of the Marine Protected Area “Secche di Tor Paterno”, Central Tyrrhenian Sea, have been investigated in order to give a first glance of the diversity of the brachiopods of this area and provide a new report on the Mediterranean Brachiopod fauna. Four species were reported: Novocrania anomala (Müller, 1776), Megathiris detruncata (Gmelin, 1790), Joania cordata (Risso,1826) and Argyrotheca cuneata (Risso,1826). For all the four species a morphological analysis was carried out. For the two most abundant species, J.cordata and A. cuneata, a morphometric study, based on thickness/width and length/width scattergrams, was carried out, in order to investigate their variability. Size-frequency distributions relative to the three dimensions of the shell were also computed, aimed at a evaluation of population dynamics of these two species. The results showed that, for both species, the parameters which most determine the rise of the shell during the growth of animal are width and length and that frequency distributions are mainly bi- or plurymodal and that they are difficult to interpret, as reported by other studies. Analysis of drill holes found on the shell of some specimens of the two same species revealed a predatory origin and that three different predators are responsible for them. Partial sequences of two different genetic markers, the Internal Transcribed Spacer 1 (ITS1) and the cytochrome oxidase subunit 1 (COI), were used to investigate the phylogenetic relationship between two populations of the eurybathic brachiopod species Gryphus vitreus (Born,1778) across the strait of Gibraltar. This represents the first genetic population study on brachiopods. Results from AMOVA and Bayesian analysis performed on 31 specimens highlighted no genetic differentiation indicating a likely panmixia, dispite the lecitotrophic development of the species.

Systematics, phylogeny and biogeography of Cousinia (Asteraceae)

Die Systematik, Phylogenie und Biogeographie der Gattung Cousinia (Asteraceae, Cardueae) als größter Gattung der Tribus Cardueae mit mehr als 600 Arten wurde untersucht. Diese Dissertation umfasst drei Hauptteile: Im ersten Teil wurde die Phylogenie und Evolution des Arctium-Cousinia-Komplexes Untersucht. Dieser Gattungskomplex enthält Arctium, Cousinia, Hypacanthium und Schmalhausenia und zeigt die höchste Diversität in der Irano-Turanischen Region und in den Gebirgen Zentralasiens. Es wurden ITS und rpS4-trnT-trnL-Sequenzen für insgesamt 138 Arten generiert, darunter von 129 (von ca. 600) Arten von Cousinia. Wie in früheren Analysen bereits gefunden, ist Cousinia nicht monophyletisch. Stattdessen sind Cousinia subg. Cynaroides und subg. Hypacanthodes mit insgesamt ca. 30 Arten enger mit Arctium, Hypacanthium und Schmalhausenia (Arctioid Clade) als mit subg. Cousinia (Cousinioid Clade) verwandt. Die Arctioid und Cousiniod clades werden auch durch Pollenmorphologie und Chromosomenzahl unterstützt, wie bereits früher bekannt war. In dem Arctioid Clade entsprechen morphologische Gattungsgrenzen, basierend auf Blattform, Blattbedornung und Morphologie der Involukralblätter, nicht den in der molekularen analyse gefundenen clades. Es kann keine taxonomische Lösung für diesen Konflikt gefunden werden, und die gennanten Merkmale wurden als homoplastisch betrachtet. Obwohl die phylogenetische Auflösung in dem Cousinioid Clade schlecht ist, enthalten die ITS und rpS4-trnT-trnL-Sequenzen phylogenetische Information. So gruppierten z.B. die sechs annuellen Arten in zwei Gruppen. Schlechte phylogenetische Auflösung resultiert wahrscheinlich aus dem Mangel an Merkmalen und der großen Artenzahl in dieser artenreichen und vergleichsweise jungen (ca. 8,7 mya) Linie. Artbildung in dem Cousinioid Clade scheint hauptsächlich allopatrisch zu sein. Der zweite Teil der Dissertation untersucht die Rolle der Hybridisierung in der Evolution von Cousinia s.s. Die in der Vergangenheit publizierteten 28 Hybrid-Kombinationen und 11 Zwischenformen wurden kritisch geprüft, und zwei Hybridindividuen wurden morphologisch und molekular untersucht. Die vermutlichen oder nachgewiesenen Eltern der Hybriden und Zwischenformen wurden auf die aus einer Bayesischen Analyse der ITS-Sequenzen von 216 Arten von Cousinia und verwandten Gattungen resultierenden Phylogenie aufgetragen. Weder Hybriden zwischen dem Cousinioid Clade und anderen Haupt-Claden des Arctium-Cousinia-Komplexes noch zwischen annuellen und perennirenden Arten von Cousinia s.s. wurden beobachtet. Die Ergebnisse zeigen eindeutig, dass Hybridisierung in Cousinia möglich is, und dass ca. 10,7% der Arten an interspezifischer Hybridisierung beteiligt sind. Obwohl Hybridisierung in Cousinia s.s. stattfindet und zu den Schwierigkeiten bei der Rekonstruktion ihrer phylogenetischen Geschichte beitragen könnte, war ihre Rolle für die Entwicklung und Diversität der Gruppe offenbar gering. Im dritten Teil wird eine taxonomische Revision der C. sect. Cynaroideae präsentiert. Cousinia sect. Cynaroideae, die größte Sektion der Gattung mit 110 veröffentlichten Arten, zeichnet sich durch eine Chromosomenzahl von 2n = 24 und durch ± herablaufende Blätter und Hüllblätter mit Anhängseln aus. Sie kommt im Iran, Irak, dem Kaukasus, der Türkei, Turkmenistan, Afghanistan, Pakistan, dem Libanon und Anti-Libanon vor und hat ihre Hauptzentren der Artdiversität im westlichen und nordwestlichen Iran, im Irak und in der südöstlichen Türkei. Die Revision dieser Gruppe, hauptsächlich basierend auf der Untersuchung von ca. 2250 Herbarbögen, führte zu einer Verringerung der Artenzahl auf 31 Arten mit acht Unterarten. Alle Arten werden typifiziert und ausgeschlüsselt, und Beschreibungen, Abbildungen und Verbreitungskarten werden für jede Art angegeben.

Revision of Trogulidae Sundevall, 1833 (Arachnida: Opiliones)

The relationship and phylogeny of the western Palearctic harvestmen family Trogulidae is investigated. The traditional system of seven genera and approximately 40 species appeared to be artificially composed but a phylogenetic approach and a comprehensive revision has long been sought after. Species are poorly characterised due to their uniform morphology and species evaluation is furthermore complicated by the variability of the few characters used for species delineation. To meet these demands a molecular genetic analysis is accomplished using the nuclear 28S rRNA gene and the mitochondrial cytochrome b gene. This analysis incorporates most genera and species of Trogulidae as well as a comprehensive set of Nemastomatidae and Dicranolasmatidae as outgroup taxa. Phylogenetic results of Bayesian analysis, Maximum Parsimony, Maximum Likelihood and Neighbor Joining are compared with distributional data, morphological characters and results of canonical discriminant analysis of morphometric characters and general congruence of these data sets is shown. To demonstrate the applicability of this method the revision of two species-groups within Trogulus is set out in detail. The Trogulus hirtus species-group and the Trogulus coriziformis species-group are revised. The former is in the central and north-western Balkan Peninsula. T. tricarinatus ssp. hirtus is raised to species level and four new species are described (T. karamanorum [man.n.], T. melitensis [man.n.], T. pharensis [man.n]; T. thaleri [man.n.]). The Trogulus coriziformis species-group is confined to the western Mediterranean area. T. coriziformis, T. aquaticus are re-described, T. cristatus and T. lusitanicus are re-established and four species are described as new (T. balearicus, T. huberi, T. prietoi, T. pyrenaicus). In both species-groups two further cryptic species probably exist but were not described. The species groups are shown to represent different phylogenetic levels and this information is used for the revisional work on the genus Trogulus as well as for the generic system of Trogulidae. Family status of Dicranolasmatidae is rejected and Dicranolasma is shown to be best incorporated within Trogulidae. Calathocratus, Platybessobius and Trogulocratus appear to be polyphyletic and are best to be united within Calathocratus, the oldest name of this set. The cryptic diversity within Trogulidae, especially in Trogulus and the composed genus Calathocratus rates to 150-235% and is thereby remarkably high for a group of the generally well researched European fauna. Genetic features of the group such as heteroplasmy, the possibility of major gene rearrangements and usability of the cytochrome b gene for phylogenetic studies in Opiliones are outlined.

MULTIPLE MODEL EVALUATION ABSENT THE GOLD STANDARD VIA MODEL COMBINATION

We describe a method for evaluating an ensemble of predictive models given a sample of observations comprising the model predictions and the outcome event measured with error. Our formulation allows us to simultaneously estimate measurement error parameters, true outcome — aka the gold standard — and a relative weighting of the predictive scores. We describe conditions necessary to estimate the gold standard and for these estimates to be calibrated and detail how our approach is related to, but distinct from, standard model combination techniques. We apply our approach to data from a study to evaluate a collection of BRCA1/BRCA2 gene mutation prediction scores. In this example, genotype is measured with error by one or more genetic assays. We estimate true genotype for each individual in the dataset, operating characteristics of the commonly used genotyping procedures and a relative weighting of the scores. Finally, we compare the scores against the gold standard genotype and find that Mendelian scores are, on average, the more refined and better calibrated of those considered and that the comparison is sensitive to measurement error in the gold standard.

Statistical evaluation of alternative models of human evolution

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species approximately 141 thousand years ago (Kya), an exit out-of-Africa approximately 51 Kya, and a recent colonization of the Americas approximately 10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.

Can we constrain the interior structure of rocky exoplanets from mass and radius measurements?

Aims. We present an inversion method based on Bayesian analysis to constrain the interior structure of terrestrial exoplanets, in the form of chemical composition of the mantle and core size. Specifically, we identify what parts of the interior structure of terrestrial exoplanets can be determined from observations of mass, radius, and stellar elemental abundances. Methods. We perform a full probabilistic inverse analysis to formally account for observational and model uncertainties and obtain confidence regions of interior structure models. This enables us to characterize how model variability depends on data and associated uncertainties. Results. We test our method on terrestrial solar system planets and find that our model predictions are consistent with independent estimates. Furthermore, we apply our method to synthetic exoplanets up to 10 Earth masses and up to 1.7 Earth radii, and to exoplanet Kepler-36b. Importantly, the inversion strategy proposed here provides a framework for understanding the level of precision required to characterize the interior of exoplanets. Conclusions. Our main conclusions are (1) observations of mass and radius are sufficient to constrain core size; (2) stellar elemental abundances (Fe, Si, Mg) are principal constraints to reduce degeneracy in interior structure models and to constrain mantle composition; (3) the inherent degeneracy in determining interior structure from mass and radius observations does not only depend on measurement accuracies, but also on the actual size and density of the exoplanet. We argue that precise observations of stellar elemental abundances are central in order to place constraints on planetary bulk composition and to reduce model degeneracy. We provide a general methodology of analyzing interior structures of exoplanets that may help to understand how interior models are distributed among star systems. The methodology we propose is sufficiently general to allow its future extension to more complex internal structures including hydrogen- and water-rich exoplanets.

Agglomeration effects of informal sector: evidence from Cambodia

The presence of a large informal sector in developing economies poses the question of whether informal activity produces agglomeration externalities. This paper uses data on all the nonfarm establishments and enterprises in Cambodia to estimate the impact of informal agglomeration on the regional economic performance of formal and informal firms. We develop a Bayesian approach for a spatial autoregressive model with an endogenous explanatory variable to address endogeneity and spatial dependence. We find a significantly positive effect of informal agglomeration, where informal firms gain more strongly than formal firms. Calculating the spatial marginal effects of increased agglomeration, we demonstrate that more accessible regions are more likely than less accessible regions to benefit strongly from informal agglomeration.

The impact of foreign firms on industrial productivity : evidence from Japan

With a newly constructed dataset on foreign firms in Japan for the period 1995-2008 from firm-level surveys, this paper estimates the impact of foreign firms on industrial productivity at the regional level. A Bayesian-model averaging approach is taken to account for model uncertainty resulting from various linkages between foreign firms and domestic industries. The results show that the foreign firms may contribute to industrial efficiency directly through their above-average productivity and indirectly through positive spillovers in intra-industry and local backward linkages. Forward linkages with foreign firms may have a negative impact on industrial productivity. However, these impacts depend on the nationality and entry mode of foreign investors. Aggregating foreign firms may mask their distinctive impacts on productivity.

Diversidade e estrutura genética de populações de batata da serra (Ipomoea serrana Sim.-Bianch. & L.V. Vasconcelos) da Chapada Diamantina, Bahia, utilizando marcadores ISSR

A batata-da-serra, Ipomoea serrana Sim.-Bianch. & L.V. Vasconcelos, é uma liana endêmica da Chapada Diamantina, Bahia, cuja raiz tuberosa e consumida por populações humanas ha muitos anos. Apesar da espécie, classificada como vulnerável pela IUCN (União Internacional para a Conservação da Natureza), estar submetida à pressão antrópica devido à exploração de raízes tuberosas, para uso na alimentação, são raros os estudos com a espécie, razão pela qual e de grande importância conhecer a diversidade e estrutura genética da espécie. Estudos sobre diversidade e estrutura genética a partir de marcadores moleculares são importantes por fornecerem dados sobre impactos da exploração antrópica sobre as populações, podendo oferecer subsídio para planos de manejo e conservação de espécie. Cinco populações da Chapada Diamantina, constituindo um total de 142 indivíduos, foram investigados com quatro iniciadores Inter Simple Sequence Repeats (ISSR), resultando em 34 bandas, das quais 25 foram polimórficas. A analise dos parâmetros genéticos mostrou que as populações apresentam variabilidade moderada, com 73,8% de bandas polimórficas, 0,264 de índice de diversidade de Nei e 0,389 de índice de Shannon (valores médios). A maior parte da variação ocorreu dentro das populações (77%), estimado pela analise de variância molecular (AMOVA), enquanto que a variação entre populações foi de 23%, o que corroborou os resultados de estruturação obtidos pelo programa Structure, analise de coordenadas principais (PCoA) e agrupamento estimado pelo método Neighbor-Joining, a partir do coeficiente de dissimilaridade de Jaccard. A analise Bayesiana separou os indivíduos em quatro grupos, sendo que as populações Andaraí e Capão foram alocadas em grupos distintos, enquanto as outras três populações compartilharam indivíduos distribuídos em outros dois grupos. Este estudo, por seu caráter pioneiro com relação aos marcadores moleculares, constituiu o primeiro passo para o conhecimento da diversidade genética da espécie. Estudos futuros poderão ampliar o conhecimento sobre a espécie podendo oferecer subsidio para a elaboração de um plano de manejo para esta espécie que tem sido explorada na região.

Modelagem de dados de resposta ao item sob efeito de speededness

Em testes nos quais uma quantidade considerável de indivíduos não dispõe de tempo suciente para responder todos os itens temos o que é chamado de efeito de Speededness. O uso do modelo unidimensional da Teoria da Resposta ao Item (TRI) em testes com speededness pode nos levar a uma série de interpretações errôneas uma vez que nesse modelo é suposto que os respondentes possuem tempo suciente para responder todos os itens. Nesse trabalho, desenvolvemos uma análise Bayesiana do modelo tri-dimensional da TRI proposto por Wollack e Cohen (2005) considerando uma estrutura de dependência entre as distribuições a priori dos traços latentes a qual modelamos com o uso de cópulas. Apresentamos um processo de estimação para o modelo proposto e fazemos um estudo de simulação comparativo com a análise realizada por Bazan et al. (2010) na qual foi utilizada distribuições a priori independentes para os traços latentes. Finalmente, fazemos uma análise de sensibilidade do modelo em estudo e apresentamos uma aplicação levando em conta um conjunto de dados reais proveniente de um subteste do EGRA, chamado de Nonsense Words, realizado no Peru em 2007. Nesse subteste os alunos são avaliados por via oral efetuando a leitura, sequencialmente, de 50 palavras sem sentidos em 60 segundos o que caracteriza a presença do efeito speededness.