Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism.

The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world's richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.

The birth-and-death evolution of multigene families revisited.

For quite some time, scientists have wondered how multigene families come into existence. Over the last several decades, a number of genomic and evolutionary mechanisms have been discovered that shape the evolution, structure and organization of multigene families. While gene duplication represents the core process, other phenomena such as pseudogene formation, gene loss, recombination and natural selection have been found to act in varying degrees to shape the evolution of gene families. How these forces influence the fate of gene duplicates has ultimately led molecular evolutionary biologists to ask the question: How and why do some duplicates gain new functions, whereas others deteriorate into pseudogenes or even get deleted from the genome? What ultimately lies at the heart of this question is the desire to understand how multigene families originate and diversify. The birth-and-death model of multigene family evolution provides a framework to answer this question. However, the growing availability of molecular data has revealed a much more complex scenario in which the birth-and-death process interacts with different mechanisms, leading to evolutionary novelty that can be exploited by a species as means for adaptation to various selective challenges. Here we provide an up-to-date review into the role of the birth-and-death model and the relevance of its interaction with forces such as genomic drift, selection and concerted evolution in generating and driving the evolution of different archetypal multigene families. We discuss the scientific evidence supporting the notion of birth-and-death as the major mechanism guiding the long-term evolution of multigene families.

BadiRate: estimating family turnover rates by likelihood-based methods.

MOTIVATION: The comparative analysis of gene gain and loss rates is critical for understanding the role of natural selection and adaptation in shaping gene family sizes. Studying complete genome data from closely related species allows accurate estimation of gene family turnover rates. Current methods and software tools, however, are not well designed for dealing with certain kinds of functional elements, such as microRNAs or transcription factor binding sites. RESULTS: Here, we describe BadiRate, a new software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. It implements two stochastic population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions. We have assessed the accuracy of BadiRate by computer simulations, and have also illustrated its functionality by analyzing a representative empirical dataset. AVAILABILITY: BadiRate software and documentation is available from http://www.ub.edu/softevol/badirate.

Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot.

The Brazilian Atlantic Forest is one of the richest biodiversity hotspots of the world. Paleoclimatic models have predicted two large stability regions in its northern and central parts, whereas southern regions might have suffered strong instability during Pleistocene glaciations. Molecular phylogeographic and endemism studies show, nevertheless, contradictory results: although some results validate these predictions, other data suggest that paleoclimatic models fail to predict stable rainforest areas in the south. Most studies, however, have surveyed species with relatively high dispersal rates whereas taxa with lower dispersion capabilities should be better predictors of habitat stability. Here, we have used two land planarian species as model organisms to analyse the patterns and levels of nucleotide diversity on a locality within the Southern Atlantic Forest. We find that both species harbour high levels of genetic variability without exhibiting the molecular footprint of recent colonization or population expansions, suggesting a long-term stability scenario. The results reflect, therefore, that paleoclimatic models may fail to detect refugia in the Southern Atlantic Forest, and that model organisms with low dispersal capability can improve the resolution of these models.

Molecular population genetics of the OBP83 genomic region in Drosophila subobscura and D. guanche: contrasting the effects of natural selection and gene arrangement expansion in the patterns of nucleotide variation.

Chromosomal inversion polymorphism play a major role in the evolutionary dynamics of populations and species because of their effects on the patterns of genetic variability in the genomic regions within inversions. Though there is compelling evidence for the adaptive character of chromosomal polymorphisms, the mechanisms responsible for their maintenance in natural populations is not fully understood. For this type of analysis, Drosophila subobscura is a good model species as it has a rich and extensively studied chromosomal inversion polymorphism system. Here, we examine the patterns of DNA variation in two natural populations segregating for chromosomal arrangements that differentially affect the surveyed genomic region; in particular, we analyse both nucleotide substitutions and insertion/deletion variations in the genomic region encompassing the odorant-binding protein genes Obp83a and Obp83b (Obp83 region). We show that the two main gene arrangements are genetically differentiated, but are consistent with a monophyletic origin of inversions. Nevertheless, these arrangements interchange some genetic information, likely by gene conversion. We also find that the frequency spectrum-based tests indicate that the pattern of nucleotide variation is not at equilibrium; this feature probably reflects the rapid increase in the frequency of the new gene arrangement promoted by positive selection (that is an adaptive change). Furthermore, a comparative analysis of polymorphism and divergence patterns reveals a relaxation of the functional constraints at the Obp83b gene, which might be associated with particular ecological or demographic features of the Canary island endemic species D. guanche.

The role of historical factors and natural selection in the evolution of breeding systems of Oxalis alpina in the Sonoran desert 'Sky Islands'.

Pleistocene climatic oscillations are known to influence the patterns of genetic diversity and the distribution of traits that are the target of selection. Here, we combine phylogeographical and ecological niche modelling (ENM) approaches to explore the influence of historical factors (Pleistocene climatic shifts) and natural selection on the evolution of distyly (two floral morphs) from tristyly (three floral morphs) of Oxalis alpina in the Sky Islands of the Sonoran Desert. Molecular data and ENM indicate that historical factors have had a strong influence on the genetic structure and the geographical distribution of reproductive systems of O. alpina. Moreover, genetic results suggest the possibility that distylous populations do not represent a monophyletic group. We propose that the combined effects of natural selection and genetic drift have influenced the tristyly-distyly transition.

Genome annotation and comparative analyses of the odorant-binding proteins and chemosensory proteins in the pea aphid Acyrthosiphon pisum.

Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are two families of small water-soluble proteins, abundant in the aqueous fluid surrounding olfactory receptor neurons in insect antennae. OBPs are involved in the first step of olfactory signal transduction, carrying airborne semiochemicals to the odorant receptors and can be classified into three groups: Classic OBPs, Plus-C OBPs and Atypical OBPs. Here, we identified and annotated genes encoding putative OBPs and CSPs in the pea aphid Acyrthosiphon pisum using bioinformatics. This identified genes encoding 13 Classic and two Plus-C OBPs and 13 CSPs. Homologous OBP sequences were also identified in nine other aphid species, allowing us to compare OBPs across several aphid and non-aphid species. We show that, although OBP sequences are divergent within a species and between different orders, there is a high similarity between orthologs within a range of aphid species. Furthermore, the phylogenetic relationships between OBP orthologs reflect the divergence of aphid evolution lineages. Our results support the 'birth-and-death' model as the major mechanism explaining aphid OBP sequence evolution, with the main force acting on the evolution being purifying selection.

Molecular evolution of the major chemosensory gene families in insects.

Chemoreception is a crucial biological process that is essential for the survival of animals. In insects, olfaction allows the organism to recognise volatile cues that allow the detection of food, predators and mates, whereas the sense of taste commonly allows the discrimination of soluble stimulants that elicit feeding behaviours and can also initiate innate sexual and reproductive responses. The most important proteins involved in the recognition of chemical cues comprise moderately sized multigene families. These families include odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), which are involved in peripheral olfactory processing, and the chemoreceptor superfamily formed by the olfactory receptor (OR) and gustatory receptor (GR) families. Here, we review some recent evolutionary genomic studies of chemosensory gene families using the data from fully sequenced insect genomes, especially from the 12 newly available Drosophila genomes. Overall, the results clearly support the birth-and-death model as the major mechanism of evolution in these gene families. Namely, new members arise by tandem gene duplication, progressively diverge in sequence and function, and can eventually be lost from the genome by a deletion or pseudogenisation event. Adaptive changes fostered by environmental shifts are also observed in the evolution of chemosensory families in insects and likely involve reproductive, ecological or behavioural traits. Consequently, the current size of these gene families is mainly a result of random gene gain and loss events. This dynamic process may represent a major source of genetic variation, providing opportunities for FUTURE specific adaptations.

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.

MOTIVATION: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser. AVAILABILITY: Freely available to academic users from: (http://www.ub.edu/dnasp).

The clinico-surgico-pathological spectrum of myxopapillary ependymomas--report of four unusal cases and review of the literature.

According to the WHO grading system, myxopapillary ependymomas are assigned to WHO Grade I. However, the clinico-pathological spectrum might be very heterogenous. Herein, we report 4 cases exhibiting lumbar tumor masses, 1 causing muscular atrophy over a 30-year period, 3 displaying clinical history of persisting lumbar pain for only several weeks. All tumors were crooked with dura and spinal roots resulting in incomplete resection in three cases. On histological examination, two tumors were almost acellular and showed polycyclic hyaline and fibrotic extracellular matrix leading to differential diagnoses of chordoma, meningioma, fibrolipoma and ependymoma. Finally, together with the immunohistochemical investigations, electron microscopy led to the diagnosis of myxopapillary ependymoma, WHO Grade I, with massive degenerative changes. The other 2 cases presented with the typical neuropathology of myxopapillary ependymomas but showed local recurrence within 1 and 13 years throughout the whole neuraxis, and in 1 case additional metastases of the 3rd ventricle. Although the morphological feature of these myxopapillary ependymomas was benign, the presented cases showed that the biological behavior of myxopapillary tumors might differ greatly and that these tumors present a serious operative and diagnostic challenge. Myxopapillary ependymomas occur most often in the lumbosacral region. Due to the anatomic complexity of the cauda equina, a complete resection can be technically challenging in this region. However, a gross total resection at the primary surgery is the most predictive factor for the outcome.

Causal probabilistic modeling for malignancy grading in pathology with explanations of dependency to the related histological features.

This work demonstrates that histological grading of brain tumors and astrocytomas can be accurately predicted and causally explained with the help of causal probabilistic models, also known as Bayesian networks (BN). Although created statistically, this allows individual identification of the grade of malignancy as an internal cause that has enabled the development of the histological features to their observed state. The BN models are built from data representing 794 cases of astrocytomas with their malignant grading and corresponding histological features. The computerized learning process is improved when pre-specified knowledge (from the pathologist) about simple dependency relations to the histological features is taken into account. We use the BN models for both grading and causal analysis. In addition, the BN models provide a causal explanation of dependency between the histological features and the grading. This can offer the biggest potential for choice of an efficient treatment, since it concentrates on the malignancy grade as the cause of pathological observations. The causal analysis shows that all ten histological features are important for the grading. The histological features are causally ordered, implying that features of first order are of higher priority, e.g. for the choice of treatment in order not to allow the malignancy to progress to a higher degree. Due to the explanations of feature relations, the causal analysis can be considered as a powerful complement to any malignancy classification tool and allows reproducible comparison of malignancy grading.

Histological heterogeneity of human glioblastomas investigated with an unsupervised neural network (SOM).

The histological variability of Glioblastomas (GB) precludes the modern assimilation of theses tumors into a single histological tumor group. As an alternative to statistical histological evaluation, we investigated 1489 human GB in order to discover whether they could be correctly classified using Self-Organizing Maps (SOM). In all tumors 50 histological features, as well as the age and sex of the patients, were examined. Four clusters of GB with a significance of 52 (maximal significance 60) were found. Cluster C1 contained 37.47% of all GB and 41.09% of all polymorphic glioblastomas (PG). Cluster C2 included 35.06% of all GB and 44.96% of all giant cell glioblastomas (GCG). Cluster C3 contained 16.45% of all GB with a significant component of astroblasts, glioblasts and oligodendroglia. Cluster C4 included 11.01% of all GB, 87.80% of the gliosarcomas (GS) and 36.72% of all GCG. Placing a series of component windows with their maps side by side allows the immediate recognition of the dependencies on variables and the determination of variables necessary to build the specific clusters. The SOM allow a realistic histological classification, comparable to the actual classification by the WHO. In addition, we found new, small subclusters of human GB which may have a clinical significance. With SOM one can learn to discriminate, discard and delete data, select histological and clinical or genetic variables that are meaningful, and consequently influence the result of patient management.

Salud intercultural: elementos para la construcción de sus bases conceptuales / Intercultural health: elements to the construction of its conceptual bases

Over the past few years, intercultural health has become an emerging issue in health policy. Intercultural health is an approach to create a better communication between patients and providers. In the short term, this approach incorporates patient's culture background in health care, improving intercultural communication strategies to generate, in the long term, a health system adapted to the medical culture of patients. This article explores the underlying concepts in the intercultural health approach, such as cultural diversity and medical systems as complex models of thoughts and behaviors.

The impact of progesterone receptor expression on relapse in the long-term clinical course of 93 benign meningiomas.

BACKGROUND: Previous clinicopathological observations have pointed towards an impact of progesterone receptor (PgR) expression on the clinical course of meningiomas. MATERIALS AND METHODS: EXpression of PgR and the proliferation marker MIB-1 was assessed by immunohistochemistry in the primary tumours of 30 cases of benign, completely resected, recurrent meningiomas and compared with 63 cases of meningioma without recurrence for 14 or more years. RESULTS: Univariate analysis showed a significantly higher risk for recurrence (odds ratio 3.533) for tumours with a low expression of PgR. A tendency for a higher risk for tumours with higher proliferation rate (odds ratio 6.889) was not significant. In 20 cases in which the primary tumour could be compared with its recurrence, no consistent changes of PgR expression were observed. CONCLUSION: Our findings support previous studies that found an association of low or absent expression of PgR with a higher risk of recurrence. This encourages attempts at a hormonal therapy for patients with PgR-positive meningioma.

Effects of thrombolysis in the evolution of right bundle-branch block complicating an acute anterior myocardial infarction.

INTRODUCTION: There is scant information about the effects of thrombolysis in the evolution of right bundle-branch block (RBBB) in the setting of acute anterior myocardial infarction. The aim of this study has been to analyse these effects and its impact on prognosis. METHODS: We studied 54 patients who presented a RBBB related to an acute anterior myocardial infarction. We defined two groups: those who received thrombolytic treatment and those who did not. We analysed the evolution of RBBB (transience, moment of onset, moment of disappearance) and its relationship with in-hospital mortality.Twenty-one patients (39%) received thrombolytic treatment (groupT) and 33 patients (61%) (group NT) did not. RESULTS: The incidence of late appearance (> 6 h) of RBBB was less frequent in group T compared with group NT (10% vs. 33%, p = 0.04). The incidence of transient block was similar in the two groups (57% vs. 45%, p ns). However, early disappearance of RBBB (in < 6 hours) was more common in group T than in group NT (33% vs. 9%, p = 0.04). Mortality was higher in patients with RBBB present at 24 h after admission) than in those with RBBB resolved in less than 24 hours (in group NT, 55% vs. 8%, p = 0.02 and in group T 50% vs. 0%, p = 0.02, respectively). CONCLUSIONS: Thrombolysis seems to influence the moment of onset and disappearance of RBBB by promoting its early disappearance and avoiding its late appearance. Disappearance of RBBB is associated with a better prognosis.

DNA variation at the rp49 gene region of Drosophila simulans: evolutionary inferences from an unusual haplotype structure.

An approximately 1.3-kb region including the rp49 gene plus its 5' and 3' flanking regions was sequenced in 24 lines of Drosophila simulans (10 from Spain and 14 from Mozambique). Fifty-four nucleotide and 8 length polymorphisms were detected. All nucleotide polymorphisms were silent: 52 in noncoding regions and 2 at synonymous sites in the coding region. Estimated silent nucleotide diversity was similar in both populations (pi = 0.016, for the total sample). Nucleotide variation revealed an unusual haplotype structure showing a subset of 11 sequences with a single polymorphism. This haplotype was present at intermediate frequencies in both the European and the African samples. The presence of such a major haplotype in a highly recombining region is incompatible with the neutral equilibrium model. This haplotype structure in both a derived and a putatively ancestral population can be most parsimoniously explained by positive selection. As the rate of recombination in the rp49 region is high, the target of selection should be close to or within the region studied.

[Massive pericardial effusion and cardiac tamponade as the presentation form of hypothyroidism]. / Derrame pericárdico masivo y taponamiento cardíaco como forma de presentación de hipotiroidismo.

We report a 43 years old female, admitted due to fatigability, asthenia and diffuse abdominal pain. On admission, obesity, slowness of thinking, bradycardia, distention of jugular veins and ascites were observed on physical examination. Laboratory showed undetectable thyroid hormone levels, a chest X ray showed bilateral pleural effusion and an enlarged heart. An echocardiography showed a massive pericardial effusion with collapse of the right atrium and dilatation of both caval veins. A pericardial tap was performed, draining 350 ml. Thyroid hormone substitution was started and after 12 months of follow up, the heart size decreased and a control echocardiogram showed a minimal pericardial effusion.

DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.

UNLABELLED: DnaSP is a Windows integrated software package for the analysis of the DNA polymorphism from nucleotide sequence data. DnaSP version 3 incorporates several methods for estimating the amount and pattern of DNA polymorphism and divergence, and for conducting neutrality tests. AVAILABILITY: For academic uses, DnaSP is available free of charge from: http://www.bio.ub.es/julio/DnaSP.html CONTACT: julio@porthos.bio.ub.es

Molecular population genetics of the rp49 gene region in different chromosomal inversions of Drosophila subobscura.

Nucleotide variation at the ribosomal protein 49 (rp49) gene region has been studied in 75 lines of Drosophila subobscura belonging to four chromosomal arrangements (Ost, O3+4, O3+4+8, and O3+4+23). The location of the rp49 gene region within the inversion loop differs among heterokaryotypes: it is very close to one of the breakpoints in heterozygotes involving Ost chromosomes, while it is in a more central position in all other heterokaryotypes. The distribution of nucleotide polymorphism in the different arrangements is consistent with a monophyletic origin of the inversions. The data also provide evidence that gene conversion and possibly double crossover are involved in shuffling nucleotide variation among gene arrangements. The analyses reveal that the level of genetic exchange is higher when the region is located in a more central position of the inverted fragment than when it is close to the breakpoints. The pairwise difference distributions as well as the negative values of Tajima's and Fu and Li's statistics further support the hypothesis that nucleotide variation within chromosomal arrangements still reflects expansion after the origin of the inversions. Under the expansion model, we have estimated the time of origin of the studied inversions.