How accurate is the current picture of human genetic variation?

Our understanding of the distribution of worldwide human genomic diversity has greatly increased over recent years thanks to the availability of large data sets derived from short tandem repeats (STRs), insertion deletion polymorphisms (indels) and single nucleotide polymorphisms (SNPs). A concern, however, is that the current picture of worldwide human genomic diversity may be inaccurate because of biases in the selection process of genetic markers (so-called 'ascertainment bias'). To evaluate this problem, we first compared the distribution of genomic diversity between these three types of genetic markers in the populations from the HGDP-CEPH panel for evidence of bias or incongruities. In a second step, using a very relaxed set of criteria to prevent the intrusion of bias, we developed a new set of unbiased STR markers and compared the results against those from available panels. Contrarily to recent claims, our results show that the STR markers suffer from no discernible bias, and can thus be used as a baseline reference for human genetic diversity and population differentiation. The bias on SNPs is moderate compared to that on the set of indels analysed, which we recommend should be avoided for work describing the distribution of human genetic diversity or making inference on human settlement history.

Evolution of intraspecific variation : a comparative phylogenetic approach

Understanding the evolution of intraspecific variance is a major research question in evolutionary biology. While its importance to processes operating at individual and population levels is well-documented, much less is known about its role in macroevolutionary patterns. Nevertheless, both experimental and theoretical evidence suggest that the intraspecific variance is susceptible to selection, can transform into interspecific variation and, therefore, is crucial for macroevolutionary processes. The main objectives of this thesis were: (l) to investigate which factors impact evolution of intraspecific variation in Polygonaceae and determine if evolution of intraspecific variation influences species diversification; and (2) to develop a novel comparative phylogenetic method to model evolution of intraspecific variation. Using the buckwheat family, Polygonaceae, as a study system, I demonstrated which life-history and ecological traits are relevant to the evolution of intraspecific variation. I analyzed how differential intraspecific variation drives species diversification patterns. I showed with computer simulations the shortcomings of existing comparative methods with respect to intraspecific variation. I developed a novel comparative model that readily incorporates the intraspecific variance into phylogenetic comparative methods. The obtained results are complimentary, because they affect both empirical and methodological aspects of comparative analysis. Overall, I highlight that intraspecific variation is an important contributor to the macroevolutionary patterns and it should be explicitly considered in the comparative phylogenetic analysis. - En biologie évolutive comprendre l'évolution de la variance intraspécifique est un axe de recherche majeur. Bien que l'importance de cette variation soit bien documentée au niveau individuel et populationnel, on en sait beaucoup moins sur son rôle au niveau macroévolutif. Néanmoins, des preuves expérimentales et théoriques suggèrent que la variance intraspécifique est sensible à la sélection et peut se transformer en variation interspécifique. Par conséquent, elle est cruciale pour mieux comprendre les processus macroévolutifs. Les principaux objectifs de ma thèse étaient : (i) d'enquêter sur les facteurs qui affectent l'évolution de la variation intraspécifique chez les Polygonaceae et de déterminer si l'évolution de cette dernière influence la diversification des espèces, et (2) de développer une nouvelle méthode comparative permettant de modéliser l'évolution de la variation intraspécifique dans un cadre phylogénétique. En utilisant comme système d'étude la famille du sarrasin, les Polygonacées, je démontre que les traits d'histoire de vie sont pertinents pour comprendre l'évolution de la variation intraspécifique. J'ai également analysé l'influence de la variation intraspécifique au niveau de la diversification des espèces. J'ai ensuite démontré avec des données simulées les limites des méthodes comparatives existantes vis à vis de la variation intraspécifique. Finalement, j'ai développé un modèle comparatif qui intègre facilement la variance intraspécifique dans les méthodes comparatives phylogénétiques existantes. Les résultats obtenus lors de ma thèse sont complémentaires car ils abordent aspects empiriques et méthodologiques de l'analyse comparative. En conclusion, je souligne que la variation intraspécifique est un facteur important en macroévolution et qu'elle doit être explicitement considérée lors d'analyses comparatives phylogénétiques.

Isotopic variation across the Audubon's-myrtle warbler hybrid zone.

Differences in seasonal migratory behaviours are thought to be an important component of reproductive isolation in many organisms. Stable isotopes have been used with success in estimating the location and qualities of disjunct breeding and wintering areas. However, few studies have used isotopic data to estimate the movements of hybrid offspring in species that form hybrid zones. Here, we use stable hydrogen to estimate the wintering locations and migratory patterns of two common and widespread migratory birds, Audubon's (Setophaga auduboni) and myrtle (S. coronata) warblers, as well as their hybrids. These two species form a narrow hybrid zone with extensive interbreeding in the Rocky Mountains of British Columbia and Alberta, Canada, which has been studied for over four decades. Isotopes in feathers grown on the wintering grounds or early on migration reveal three important patterns: (1) Audubon's and myrtle warblers from allopatric breeding populations winter in isotopically different environments, consistent with band recovery data and suggesting that there is a narrow migratory transition between the two species, (2) most hybrids appear to overwinter in the south-eastern USA, similar to where myrtle warblers are known to winter, and (3) some hybrid individuals, particularly those along the western edge of the hybrid zone, show Audubon's-like isotopic patterns. These data suggest there is a migratory divide between these two species, but that it is not directly coincident with the centre of the hybrid zone in the breeding range. We interpret these findings and discuss them within the context of previous research on hybrid zones, speciation and migratory divides.

Polymorphism, inter-population and inter-specific variation in Nyssomyia intermedia (Lutz & Neiva) and Nyssomyia neivai (Pinto) (Diptera, Psychodidae, Phlebotominae)

Nyssomyia intermedia (Lutz & Neiva) and Nyssomyia neivai (Pinto) are morphologically very close and both present great variation in some structures. The objective of this study is a description of the variation among the females of these species in populations from the States of Minas Gerais and São Paulo. The morphological structures studied were the number of horizontal teeth in the cibarium and the number of rings and the shape of the terminal knob of the spermathecae. The spermatheca rings are significantly more numerous in N. intermedia than in N. neivai and the simple shape of the terminal knob predominated in both species. Regarding the cibarium, eight to eleven teeth have been found in both species, with up to twelve teeth in the latter. The number of horizontal teeth and the shape of the terminal knob of the spermathecae were variable throughout the populations of both species and all structures were polymorphic in the populations studied.

Evolution in subdivided plant populations: concepts, recent advances and future directions.

SUMMARY: Research into the evolution of subdivided plant populations has long involved the study of phenotypic variation across plant geographic ranges and the genetic details underlying that variation. Genetic polymorphism at different marker loci has also allowed us to infer the long- and short-term histories of gene flow within and among populations, including range expansions and colonization-extinction dynamics. However, the advent of affordable genome-wide sequences for large numbers of individuals is opening up new possibilities for the study of subdivided populations. In this review, we consider what the new tools and technologies may allow us to do. In particular, we encourage researchers to look beyond the description of variation and to use genomic tools to address new hypotheses, or old ones afresh. Because subdivided plant populations are complex structures, we caution researchers away from adopting simplistic interpretations of their data, and to consider the patterns they observe in terms of the population genetic processes that have given rise to them; here, the genealogical framework of the coalescent will continue to be conceptually and analytically useful.

The HSR on chromosome 1 of the house mouse, Mus domesticus: distribution and frequency in Switzerland.

A total of 357 house mice (Mus domesticus) from 83 localities uniformly distributed throughout Switzerland were screened for the presence of a homogenously staining region (HSR) on chromosome 1. Altogether 47 mice from 11 localities were HSR/+ or HSR/HSR. One sample of 11 individuals all had an HSR/HSR karyotype. Almost all mice with the variant were collected from the Rhone valley (HSR frequency: 61%) and Val Bregaglia (HSR frequency: 81%). For samples from most of the area of Switzerland, the HSR was absent. There was no strong association between the geographic distribution of the HSR and the areas of occurrence of metacentrics. However, at Chiggiogna the HSR was found on Rb (1.3). Possible explanations for the HSR polymorphism are discussed.

Survey on batch-to-batch variation in spray paints: a collaborative study

This study represents the most extensive analysis of batch-to-batch variations in spray paint samples to date. The survey was performed as a collaborative project of the ENFSI (European Network of Forensic Science Institutes) Paint and Glass Working Group (EPG) and involved 11 laboratories. Several studies have already shown that paint samples of similar color but from different manufacturers can usually be differentiated using an appropriate analytical sequence. The discrimination of paints from the same manufacturer and color (batch-to-batch variations) is of great interest and these data are seldom found in the literature. This survey concerns the analysis of batches from different color groups (white, papaya (special shade of orange), red and black) with a wide range of analytical techniques and leads to the following conclusions. Colored batch samples are more likely to be differentiated since their pigment composition is more complex (pigment mixtures, added pigments) and therefore subject to variations. These variations may occur during the paint production but may also occur when checking the paint shade in quality control processes. For these samples, techniques aimed at color/pigment(s) characterization (optical microscopy, microspectrophotometry (MSP), Raman spectroscopy) provide better discrimination than techniques aimed at the organic (binder) or inorganic composition (fourier transform infrared spectroscopy (FTIR) or elemental analysis (SEM - scanning electron microscopy and XRF - X-ray fluorescence)). White samples contain mainly titanium dioxide as a pigment and the main differentiation is based on the binder composition (Csingle bondH stretches) detected either by FTIR or Raman. The inorganic composition (elemental analysis) also provides some discrimination. Black samples contain mainly carbon black as a pigment and are problematic with most of the spectroscopic techniques. In this case, pyrolysis-GC/MS represents the best technique to detect differences. Globally, Py-GC/MS may show a high potential of discrimination on all samples but the results are highly dependent on the specific instrumental conditions used. Finally, the discrimination of samples when data was interpreted visually as compared to statistically using principal component analysis (PCA) yielded very similar results. PCA increases sensitivity and could perform better on specific samples, but one first has to ensure that all non-informative variation (baseline deviation) is eliminated by applying correct pre-treatments. Statistical treatments can be used on a large data set and, when combined with an expert's opinion, will provide more objective criteria for decision making.

Seasonal and spatial species richness variation of dung beetle (Coleoptera, Scarabaeidae s. str.) in the Atlantic Forest of southeastern Brazil

The knowledge on Atlantic Forest scarab beetle fauna is quite limited. This biome is strongly degraded and these insects can be used as bioindicators since they are sensitive to forest destruction and show distinct organizational patterns in forest fragments or in areas that have been deteriorated by human activity. Thus, a study of the Scarabaeidae (sensu stricto) dung beetles fauna that inhabit Serra do Japi, São Paulo, Brazil (23º12'-23º22' S and 46º53'-47º03'W) was carried out; the monthly species richness was analyzed in six areas during one year and the vegetation's structural physiognomy was described. The areas included a conserved and a degraded valley, a northward and a southward hillside, a hilltop, and an area of secondary forest growing under eucalyptus trees. The specimens were collected using four pitfall traps baited with human feces, which remained at each spot during 48 hours. Between September, 1997 and August, 1998, 3524 individuals of 39 species were collected; the most abundant were: Canthidium trinodosum, Eurysternus cyanescens, Uroxys kratochvili, Scybalocanthon nigriceps, Uroxys lata, Canthonella sp., Dichotomius assifer, Deltochilum furcatum, Canthidium sp.2, Canthon latipes, Deltochilum rubripenne, Eurysternus sp., and Dichotomius sp.1. The number of individuals and species was greater in the hot, rainy season, when there was a correlation between the number of species and the mean annual temperature [r²= 0.69; p<0.01]. The lower winter richness was most pronounced in the conserved valley, while richness remained relatively constant in the degraded valley; abundance was much higher in the degraded valley. The cluster analysis showed that the valleys and hillsides are the most similar in relation to species composition and abundance, yet different from the secondary forest with eucalypts and the hilltop.

Morphological and physiological variation between queens and workers of Protonectarina sylveirae (de Saussure) (Hymenoptera, Vespidae, Epiponini)

Morphological and physiological variation between queens and workers of Protonectarina sylveirae (de Saussure) (Hymenoptera, Vespidae, Epiponini). The Neotropical swarm-founding wasps, Epiponini, range from the absence of morphological differentiation between castes to highly distinct castes. We measured eight body parts of females of two colonies of Protonectarina sylveirae (de Saussure, 1854). ANOVA and Discriminant Analysis evidenced significant differences between castes, as previously observed by other authors for other species of Epiponini. However, some females previously categorized as queens, were actually workers, supported by our statistic analyses. These individuals showed intermediate morphological features between queens and workers, having distinct patterns of hairs and clypeal spots. The castes of P. sylveirae are distinct, however intermediate individuals may be found in colonies promoting social flexibility.

The three phases of the ensemble forecasting of niche models: geographic range and shifts in climatically suitable areas of Utetheisa ornatrix (Lepidoptera, Arctiidae)

Species' geographic ranges are usually considered as basic units in macroecology and biogeography, yet it is still difficult to measure them accurately for many reasons. About 20 years ago, researchers started using local data on species' occurrences to estimate broad scale ranges, thereby establishing the niche modeling approach. However, there are still many problems in model evaluation and application, and one of the solutions is to find a consensus solution among models derived from different mathematical and statistical models for niche modeling, climatic projections and variable combination, all of which are sources of uncertainty during niche modeling. In this paper, we discuss this approach of ensemble forecasting and propose that it can be divided into three phases with increasing levels of complexity. Phase I is the simple combination of maps to achieve a consensual and hopefully conservative solution. In Phase II, differences among the maps used are described by multivariate analyses, and Phase III consists of the quantitative evaluation of the relative magnitude of uncertainties from different sources and their mapping. To illustrate these developments, we analyzed the occurrence data of the tiger moth, Utetheisa ornatrix (Lepidoptera, Arctiidae), a Neotropical moth species, and modeled its geographic range in current and future climates.

Inter- and intra-individual variation of oxytocin secretion in oestrous mares exposed to stallions

The neuro-peptide hormone oxytocin regulates several reproductive mechanisms in mammals, such as uterine contractions during parturition and milk ejection in the lactating mammary gland. Oxytocin may also influence behavior and behavioral strategies, e.g. pair bonding, social recognition, maternal behavior, trust building, or anxiety. Teasing oestrous mares by a stallion provokes the release of oxytocin. We therefore tested whether such elevated oxytocin levels reveal possible mate preferences as determined in typical preference tests.

Genome-wide association analysis of copy number variation in recurrent depressive disorder.

Large, rare copy number variants (CNVs) have been implicated in a variety of psychiatric disorders, but the role of CNVs in recurrent depression is unclear. We performed a genome-wide analysis of large, rare CNVs in 3106 cases of recurrent depression, 459 controls screened for lifetime-absence of psychiatric disorder and 5619 unscreened controls from phase 2 of the Wellcome Trust Case Control Consortium (WTCCC2). We compared the frequency of cases with CNVs against the frequency observed in each control group, analysing CNVs over the whole genome, genic, intergenic, intronic and exonic regions. We found that deletion CNVs were associated with recurrent depression, whereas duplications were not. The effect was significant when comparing cases with WTCCC2 controls (P=7.7 × 10(-6), odds ratio (OR) =1.25 (95% confidence interval (CI) 1.13-1.37)) and to screened controls (P=5.6 × 10(-4), OR=1.52 (95% CI 1.20-1.93). Further analysis showed that CNVs deleting protein coding regions were largely responsible for the association. Within an analysis of regions previously implicated in schizophrenia, we found an overall enrichment of CNVs in our cases when compared with screened controls (P=0.019). We observe an ordered increase of samples with deletion CNVs, with the lowest proportion seen in screened controls, the next highest in unscreened controls and the highest in cases. This may suggest that the absence of deletion CNVs, especially in genes, is associated with resilience to recurrent depression.

Genetic variability of a population of Aedes aegypti from Paraná, Brazil, using the mitochondrial ND4 gene

Genetic variability of a population of Aedes aegypti from Paraná, Brazil, using the mitochondrial ND4 gene. To analyze the genetic variability of populations of Aedes aegypti, 156 samples were collected from 10 municipalities in the state of Paraná, Brazil. A 311 base pairs (bp) region of the NADH dehydrogenase subunit 4 (ND4) mitochondrial gene was examined. An analysis of this fragment identified eight distinct haplotypes. The mean genetic diversity was high (h = 0.702; p = 0.01556). AMOVA analysis indicated that most of the variation (67%) occurred within populations and the F ST value (0.32996) was highly significant. F ST values were significant in most comparisons among cities. The isolation by distance was not significant (r = -0.1216 and p = 0, 7550), indicating that genetic distance is not related to geographic distance. Neighbor-joining analysis showed two genetically distinct groups within Paraná. The DNA polymorphism and AMOVA data indicate a decreased gene flow in populations from Paraná, which can result in increased vectorial competence.

Short term variation in the vertical distribution of copepods off the coast of northern Peru

Analiza los datos colectados de la clorofila frente al Peru cerca de 9°S. Determinandose la profundidad a la que se enuentran y la concentración de oxigeno durante el dia y la noche.

Local-scale spatial variation in diversity of social wasps in an Amazonian rain forest in Caxiuanã, Pará, Brazil (Hymenoptera, Vespidae, Polistinae)

Polistine wasps are important in Neotropical ecosystems due to their ubiquity and diversity. Inventories have not adequately considered spatial attributes of collected specimens. Spatial data on biodiversity are important for study and mitigation of anthropogenic impacts over natural ecosystems and for protecting species. We described and analyzed local-scale spatial patterns of collecting records of wasp species, as well as spatial variation of diversity descriptors in a 2500-hectare area of an Amazon forest in Brazil. Rare species comprised the largest fraction of the fauna. Close range spatial effects were detected for most of the more common species, with clustering of presence-data at short distances. Larger spatial lag effects could also be identified in some species, constituting probably cases of exogenous autocorrelation and candidates for explanations based on environmental factors. In a few cases, significant or near significant correlations were found between five species (of Agelaia, Angiopolybia, and Mischocyttarus) and three studied environmental variables: distance to nearest stream, terrain altitude, and the type of forest canopy. However, association between these factors and biodiversity variables were generally low. When used as predictors of polistine richness in a linear multiple regression, only the coefficient for the forest canopy variable resulted significant. Some level of prediction of wasp diversity variables can be attained based on environmental variables, especially vegetation structure. Large-scale landscape and regional studies should be scheduled to address this issue.