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.

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.

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).

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.

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.

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.

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.

Evidence of extensive genetic exchange in the rp49 region among polymorphic chromosome inversions in Drosophila subobscura.

Restriction map variation in 107 lines extracted from two natural populations of Drosophila subobscura was investigated with seven four-nucleotide-recognizing enzymes in a 1.6-kb region including the rp49 gene, that is located very close to the proximal breakpoint of inversion O3. Fourteen restriction site and 8 length polymorphisms, resulting in 73 haplotypes, have been identified. Estimated heterozygosity per nucleotide, pi = 0.0045, is comparable to the average nucleotide variation observed in Drosophila melanogaster. Because of the location of the rp49 region in D. subobscura, variation in three different gene arrangements-Ost, O3 + 4 and O3 + 4 + 8-has been compared. Out of 14 restriction site polymorphisms, 3 are shared by Ost, O3 + 4 and O3 + 4 + 8, and 3 additional ones are shared by Ost and O3 + 4, evidencing extensive genetic exchange among these polymorphic inversions. In agreement with previous data, the higher level of variation of O3 + 4 (as measured by haplotype diversity and nucleotide variation) suggests that O3 + 4 may be ancestral in relationship to extant gene arrangements.

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.

The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data.

DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for population DNA sequence data. Two length distributions are defined in the model: (1) that of the observed tract lengths and (2) that of the true tract lengths. If the latter follows a geometric distribution, the relationship between both distributions depends on two basic parameters: psi, which measures the probability of detecting a converted site, and phi, the parameter of the geometric distribution, from which the average true tract length, 1/(1-phi), can be estimated. Expressions are provided for estimating phi by the method of the moments and that of the maximum likelihood. The robustness of the model is examined by computer simulation. The present methods have been applied to the published rp49 sequences of Drosophila subobscura. Maximum likelihood estimate of phi for this data set is 0.9918, which represents an average conversion tract length of 122 bp. Only a small percentage of extant conversion events is detected.

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.

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.

Hypothalamic modulation of growth hormone secretion in the rhesus monkey: evidence from intracerebroventricular infusions of glucose, free fatty acid, and ketone bodies.

To evaluate the hypothalamus as a possible site of metabolic modulation of GH secretion, we studied the GH response to insulin hypoglycemia (IHG) and nicotinic acid (NA)-induced FFA depression in the absence and presence of third ventricular (ivt) infusions of glucose, oleic acid (Ol-Ac), or beta-hydroxybutyrate (beta OHB). Four rhesus monkeys had been prepared for chronic remote iv and ivt infusions as well as blood sampling from the adjacent room. Statistical evaluation used a two-way analysis of variance and individual comparisons with Tukey's Studentized range test. The GH response (area under the curve +/- SE) to IHG was significantly reduced by a concomitant ivt glucose infusion (control, 1.0 +/- 0.1; IHG, 12.1 +/- 3.3; IHG plus ivt glucose, 7.0 +/- 1.2 microgram/L.120 min). The GH response to FFA depression was significantly reduced by ivt Ol-Ac or beta OHB infusion (control, 6.0 +/- 1.0; NA, 51.5 +/- 4.1; Na plus Ol-Ac, 81.2 +/- 1.3; NA plus beta OHB, 38.6 +/- 3.5 microgram/L.300 min). Introcerebroventricular infusions of glucose, Ol-Ac, or beta OHB alone had no effect on plasma GH, glucose, FFA, or beta OHB concentrations. These results provide evidence for a hypothalamic site of metabolic modulation of GH secretion in the rhesus monkey. This does not exclude an additional effect directly at the pituitary gland.

HLA-DR expression is associated with excellent prognosis in squamous cell carcinoma of the larynx.

We studied class II antigen expression and tumor-infiltrating leukocytes (TIL) in tissue sections of 69 squamous cell carcinomas of the larynx and 24 lymph node metastases in the neck. HLA-DR expression was found only in eight well-differentiated, highly keratinizing squamous cell carcinomas comprising seven of the verrucous variety and one ventriculosaccular tumor. None of the metastases was positive for DR antigen. Neither primary tumors nor autologous metastases stained for DP or DQ antigens. DR-positive tumors shared a peculiar pattern of TIL composed mainly of T cells, most of which belonged to the cytotoxic/suppressor subset, and B cells. These neoplasms had in common a slow rate of growth, and are considered low-grade carcinomas in the literature. We conclude from our study that HLA-DR expression seems to characterize tumors with a prominent infiltrate and an excellent prognosis.

The neuropathology and epidemiology of AIDS. A Berlin experience. A review of 200 cases.

The brains of 200 patients who died with Acquired Immunodeficiency Syndrome (AIDS) from Berlin were examined retrospectively. This study was specifically intended to evaluate and document the prevalence of neuropathologic abnormalities, establishing the frequency of the various types of structural lesions, their combinations, their relative incidence, and the risk factors involved in different age groups. The data were compared and contrasted with the findings reported from other parts of the world and other German cities. It was found that the mean age of this group of patients was 41.4 years old, 75% were homosexual/bisexuals (H/B) and 18.5% were drug abusers (DA). Only 5.5% were women. Brain parenchymal changes, called in this report, HIV-related encephalopathy (HIVRE), characterized by vacuolization or spongy changes and astrocytosis in the subcortical white matter, and occasionally in gray matter, were found in 67 patients (33.5%). Drug abusers had a higher incidence of HIVRE (59.5%) compared with homosexual/bisexuals (28%). This is statistically significant (p < 0.0005). CMV encephalitis was found in 26 patients (13%) (8% of the drug abusers in contrast to 13% in the homosexual/bisexuals group). Primary central nervous system lymphoma (PCNSL) was seen in 28 patients (14%) regardless of the risk factor involved. 20 (13%) of the 150 H/B and 3 (8%) of the 37 DA had CMV encephalitis. Of the 150 H/B, 24 (16%) had PCNSL compared with only 4 of 37 (11%) of the DA. A significant incidence of opportunistic infections, both protozoal and viral was found in all groups. Cerebral toxoplasmosis occurred in 68 patients (34%). Microglial (phagocytic) nodules, probably related to CMV or cerebral Toxoplasmosis, were observed in 40 cases (20%). Diffuse microglial proliferation was noted in 104 patients (52%). Cerebral cryptococcosis was found in three patients. Progressive multifocal leukoencephalopathy was seen in 16 patients (8%). Various combinations of CNS pathological processes were found in 44 of the patients (22%). These include concomitant infections with Toxoplasma gondii and HIVRE in 13 patients; Toxoplasmosis and PCNSL in 8 patients; Toxoplasmosis with CMV and HIVRE in 4 patients; Toxoplasmosis with CMV in 2 patients; Toxoplasmosis with PCNSL and CMV in 2 patients; Toxoplasmosis with PCNSL and HIVRE in 2 patients and Toxoplasmosis with PML and HIVRE in 2 patients; Cerebral CMV with PCNSL and HIVRE in 4 patients; Cerebral CMV with HIVRE in 2 patients; PML with PCNSL in one patient; PML with HIVRE in 2 patients; and PML with PCNSL and HIVRE in one patient. Cerebrovascular lesions were found in 34 patients (17%).(ABSTRACT TRUNCATED AT 400 WORDS)

Myelin basic protein (MBP) in human gliomas: a study of twenty-five cases.

Twenty five gliomas (5 oligodendrogliomas, 8 oligoastrocytomas, 5 astrocytomas grades I-II, and 7 malignant astrocytomas-glioblastomas) were studied with the immunohistochemical technique avidin-biotin complex (ABC) for myelin basic protein (MBP). We found four patterns of positivity with variable degrees and frequencies in the different types of tumors. We believe this method can help in the diagnosis of non-characteristic gliomas, particularly oligoastrocytomas.

Disseminated melanomatosis of the central nervous system and other organs: a case report.

This case represents an example of clinically occult, disseminated neoplastic disease with almost asymptomatic but severe involvement of the central nervous system. The only helpful diagnostic investigation appeared to be cerebrospinal fluid cytology. Extensive post mortem examination was inconclusive as to whether the widespread CNS involvement with melanoma was primary or secondary.

Cerebral lymphoma in AIDS. Clinical, radiological, neuropathological and immunopathological study.

Neuropathological findings from 8 individual cases of cerebral lymphomas in AIDS patients with consideration of the clinical, radiological, immunopathological, and other pertinent data selected from a series of 80 patients between 1985 and 1989 were studied. A wide variation in pathology was noted among our cases. It has been shown that lymphoma as a neuropathological diagnosis can coexist with a wide range of other characteristics, including toxoplasmosis, glial nodules, neuronophagia, degeneration, bleeding, hypoxia, progressive multifocal leucoencephalopathy, and myelopathy, although none of these attributes appeared more than casually interrelated. In general, the late-stage manifestations of lymphoma as were observed in this study, tended to be poorly localized, often simultaneously meningeal, perivascular, and diffuse in character. An important distinction between cerebral lymphomas of AIDS and non-AIDS patients is the highly atypical, clinically unreliable computer tomographic signals observed in several of our cases. Five of the six immunopathological investigations showed a preponderance of B-cell markers, corresponding in toto to high-grade non-Hodgkin lymphoma. One case exhibited immunohistological markers typical of Hodgkin's lymphoma (antibody CD-30). Of 6 obtainable serum specimens from our 8 cases, 4 showed high (greater than 2000) IgG titers against the EBNA-1 antigen of Epstein-Barr virus (EBV), of these three had IgM titers further supporting viral reactivation. One showed a normal IgG titer, yet with a significantly raised IgM titer.