Burial depth distribution of fennel pondweed tubers (Potamogeton pectinatus) in relation to foraging by Bewick's swans

Deep burial in the sediment of tubers of fennel pondweed (Potamogeton pectinatus) has been explained in terms of avoidance by escape against consumption by Bewick's swans (Cygnus columbianus bewickii) in autumn. We therefore expected changes in foraging pressure to ultimately result in a change in the tuber distribution across sediment depth. A trade-off underlies this idea: deep tubers are less accessible to swans but must be larger to meet the higher energy demands of sprouting in spring. To test this prediction, we compared tuber burial depth over a gradient of foraging pressure both across space and across time. Tuber samples were obtained after aboveground plant senescence but before arrival of Bewick's swans. First, we compared the current tuber bank depth profile in a shallow lake with high foraging pressure, the Lauwersmeer, with that in two wetlands with moderate and low foraging pressure. Second, we compared the current tuber burial in the Lauwersmeer with that in the early 1980s when exploitation by swans had just started there. In accordance with our hypothesis, we found significantly deeper burial of tubers under high consumption risk compared to low consumption risk, both when comparing sites and comparing time periods. Since tubers in effect only survive to the next spring, the observed differences in burial depth among sites and over time cannot be a direct result of tuber losses due to consumption by swans. Rather, these observations suggest adaptive responses in tuber burial related to foraging pressure from Bewick's swans in the recent past. We thus propose that fennel pondweed exhibits flexible avoidance by escape, of a kind rarely described for plants, where both phenotypic plasticity and genotype sorting may contribute to the observed differences in tuber burial.

Natural selection for earlier male arrival to breeding grounds through direct and indirect effects in a migratory songbird

For migratory birds, the earlier arrival of males to breeding grounds is often expected to have fitness benefits. However, the selection differential on male arrival time has rarely been decomposed into the direct effect of male arrival and potential indirect effects through female traits. We measured the directional selection differential on male arrival time in the pied flycatcher (Ficedula hypoleuca) using data from 6 years and annual number of fledglings as the fitness proxy. Using structural equation modeling, we were able to take into account the temporal structure of the breeding cycle and the hierarchy between the examined traits. We found directional selection differentials for earlier male arrival date and earlier female laying date, as well as strong selection differential for larger clutch size. These selection differentials were due to direct selection only as indirect selection for these traits was nonsignificant. When decomposing the direct selection for earlier male arrival into direct and indirect effects, we discovered that it was almost exclusively due to the direct effect of male arrival date on fitness and not due to its indirect effects via female traits. In other words, we showed for the first time that there is a direct effect of male arrival date on fitness while accounting for those effects that are mediated by effects of the social partner. Our study thus indicates that natural selection directly favored earlier male arrival in this flycatcher population.

Aspectos de patogenicidade e relacionamento genético de isolados clínicos vaginas e anais de Candida albicans oriundos de pacientes com candidíase vulvovaginal

Vulvovaginal candidiasis (VVC) is one of the most common causes of vaginitis and affects about 75% of women of reproductive age. The majority of cases (80 to 90%) are due to C. albicans, the most virulent species of the genus Candida. Virulence attributes are scarcely investigated and the source of infection remains uncertain. Objective: This study aimed to evaluate the virulence factors and genotypes of clinical isolates of C. albicans sequentially obtained from the anus and vagina of patients with sporadic and recurrent VVC. Materials and methods: We analyzed 62 clinical isolates of C. albicans (36 vaginal and 26 anal strains). Direct examination of vaginal and anal samples and colony forming units (CFU) counts were performed. Yeasts were identified using the chromogenic media CHROMagar Candida® and by classical methodology, and phenotypically characterized regarding to virulence factors, including the ability to adhere to epithelial cells, proteinase activity, morphogenesis and biofilm formation. The genotypes of the strains were investigated with ABC genotyping, microsatellite genotyping with primer M13 and RAPD. Results: We found 100% agreement between direct examination and culture of vaginal samples. Filamentous forms were present in most of the samples of vaginal secretion, which presented CFU counts significantly higher than the samples of anal secretion. There was no statistically significant difference between virulence factors of infecting vaginal isolates and those presented by colonizing anal isolates; as well as for the comparison of the vaginal isolates from patients with different clinical conditions (sporadic or recurrent VVC). There was a decrease in the ability to adhere to HBEC, morphogenesis and biofilm formation of the vaginal isolates during the progress of infection. There was an association between the ability to express different virulence factors and the clinical manifestations presented by the patients. Genotype A was the most prevalent (93.6%), followed by genotype C (6.4%). We found maintenance of the same ABC genotype and greater prevalence of microevolution for the vaginal strains of C. albicans sequentially obtained. Vaginal and anal isolates of C. albicans obtained simultaneously from the same patient presented the same ABC genotype and high genetic relatedness. Conclusion: It is noteworthy that the proliferation of yeast and bud-to-hypha transition are important for the establishment of CVV. The expression of virulence factors is important for the pathogenesis of VVC, although it does not seem to be determinant in the transition from colonization to infection or to the installation of recurrent condition. Genotype A seems to be dominant over the others in both vaginal and anal isolates of patients with VVC. The most common scenario was microevolution of the strains of C. albicans in the vaginal environment. It is suggested that the anal reservoir constituted a possible source of vaginal infection, in most cases assessed

Molecular typing and antifungal susceptibility of clinical sequential isolates of Cryptococcus neoformans from São Paulo State, Brazil

The antifungal susceptibility profiles and the genetic variability of 83 sequential clinical isolates of Cryptococcus neoformans, including four Cryptococcus gattii isolates, obtained from 38 São Paulo AIDS patients with cryptococcal meningitis were assessed by electrophoretic karyotyping and random amplified polymorphic DNA (RAPD) analysis. The majority of the Cryptococcus neoformans isolates were highly susceptible to amphotericin B and fluconazole. Twenty percent of the minimum inhibitory concentration values for amphotericin B varied from 0.5 to 1 mu g mL(-1). For fluconazole, 22% occurred in the range 8-16 mu g mL(-1). Sequential isolates from nine patients showed a trend towards lower susceptibility to fluconazole, flucytosine, itraconazole and amphotericin B. The results of molecular typing by electrophoretic karyotyping and RAPD analysis showed the presence of 22 electrophoretic karyotypes (EK) and 15 RAPD profiles that were highly correlated. Our results provided evidence for the occurrence of genetic changes in some strains associated with microevolution during the course of infection. We also observed both microevolution and simultaneous coinfection with two distinct Cryptococcus neoformans strains in one patient. In some patients, we found changed EK- and RAPD patterns in association with increased MIC values.

Candida albicans: genotyping methods and clade related phenotypic characteristics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comparison of wing geometry data and genetic data for assessing the population structure of Aedes aegypti

Aedes aegypti is the most important vector of dengue viruses in tropical and subtropical regions. Because vaccines are still under development, dengue prevention depends primarily on vector control. Population genetics is a common approach in research involving Ae. aegypti. In the context of medical entomology, wing morphometric analysis has been proposed as a strong and low-cost complementary tool for investigating population structure. Therefore, we comparatively evaluated the genetic and phenotypic variability of population samples of Ae. aegypti from four sampling sites in the metropolitan area of Sao Paulo city, Brazil. The distances between the sites ranged from 7.1 to 50 km. This area, where knowledge on the population genetics of this mosquito is incipient, was chosen due to the thousands of dengue cases registered yearly. The analysed loci were polymorphic, and they revealed population structure (global F-ST = 0.062; p < 0.05) and low levels of gene flow (Nm = 0.47) between the four locations. Principal component and discriminant analyses of wing shape variables (18 landmarks) demonstrated that wing polymorphisms were only slightly more common between populations than within populations. Whereas microsatellites allowed for geographic differentiation, wing geometry failed to distinguish the samples. These data suggest that microevolution in this species may affect genetic and morphological characters to different degrees. In this case, wing shape was not validated as a marker for assessing population structure. According to the interpretation of a previous report, the wing shape of Ae. aegypti does not vary significantly because it is stabilised by selective pressure. (C) 2011 Elsevier B.V. All rights reserved.

CD80 and CD86 polymorphisms in populations of various ancestries: 5 new CD80 promoter alleles

CD80 and CD86 are closely linked genes on chromosome 3 that code for glycoproteins of the immunoglobulin superfamily, expressed on the surface of antigen-presenting cells. These costimulatory molecules play essential roles for stimulation and inhibition of T cells through binding to CD28 and CTLA-4 receptors. In this study, CD80 promoter and CD86 exon 8 polymorphisms were analyzed to investigate the genetic diversity and microevolution of the 2 genes. We genotyped 1,124 individuals, including Brazilians of predominantly European, mixed African and European, and Japanese ancestry, 5 Amerindian populations, and an African sample. All variants were observed in Africans, which suggests their origin in Africa before the human migrations out of that continent. Five new CD80 promoter alleles were identified and confirmed by cloning and sequencing, and promoter 2 is most likely the ancestral allele. Nucleotide -79 is monomorphic in 4 Amerindian populations, where the presence of the -79 G allele is probably the result of gene flow from non-Amerindians. (C) 2012 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Evolutionary epigenetics of modern human populations

Epigenetic variability is a new mechanism for the study of human microevolution, because it creates both phenotypic diversity within an individual and within population. This mechanism constitutes an important reservoir for adaptation in response to new stimuli and recent studies have demonstrated that selective pressures shape not only the genetic code but also DNA methylation profiles. The aim of this thesis is the study of the role of DNA methylation changes in human adaptive processes, considering the Italian peninsula and macro-geographical areas. A whole-genome analysis of DNA methylation profile across the Italian penisula identified some genes whose methylation levels differ between individuals of different Italian districts (South, Centre and North of Italy). These genes are involved in nitrogen compound metabolism and genes involved in pathogens response. Considering individuals with different macro-geographical origins (individuals of Asians, European and African ancestry) more significant DMRs (differentially methylated regions) were identified and are located in genes involved in glucoronidation, in immune response as well as in cell comunication processes. A "profile" of each ancestry (African, Asian and European) was described. Moreover a deepen analysis of three candidate genes (KRTCAP3, MAD1L and BRSK2) in a cohort of individuals of different countries (Morocco, Nigeria, China and Philippines) living in Bologna, was performed in order to explore genetic and epigenetic diversity. Moreover this thesis have paved the way for the application of DNA methylation for the study of hystorical remains and in particular for the age-estimation of individuals starting from biological samples (such as teeth or blood). Noteworthy, a mathematical model that considered methylation values of DNA extracted from cementum and pulp of living individuals can estimate chronological age with high accuracy (median absolute difference between age estimated from DNA methylation and chronological age was 1.2 years).

Strong natural selection causes microscale allozyme variation in a marine snail.

Natural selection is one of the most fundamental processes in biology. However, there is still a controversy over the importance of selection in microevolution of molecular traits. Despite the general lack of data most authors hold the view that selection on molecular characters may be important, but at lower rates than selection on most phenotypic traits. Here we present evidence that natural selection may contribute substantially to molecular variation on a scale of meters only. In populations of the marine snail Littorina saxatilis living on exposed rocky shores, steep microclines in allele frequencies between splash and surf zone groups are present in the enzyme aspartate aminotransferase (allozyme locus Aat; EC. 2.6.1.1). We followed one population over 7 years, including a period of strong natural perturbation. The surf zone part of the population dominated by the allele Aat100 was suddenly eliminated by a bloom of a toxin-producing microflagellate. Downshore migration of splash zone snails with predominantly Aat120 alleles resulted in a drastic increase in surf zone frequency of Aat120, from 0.4 to 0.8 over 2 years. Over the next four to six generations, however, the frequency of Aat120 returned to the original value. We estimated the coefficient of selection of Aat120 in the surf zone to be about 0.4. Earlier studies show similar or even sharper Aat clines in other countries. Thus, we conclude that microclinal selection is an important evolutionary force in this system.

Type 2 diabetes, but not obesity, prevalence is positively associated with ambient temperature

Acknowledgements This study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13030000), the National Science foundation of China (microevolution program NSFC91431102) and the 1000 talents program. We are grateful to members of the Molecular Energetics group in Beijing and the Energetics group in Aberdeen, UK for valuable discussion of the data and analysis. All data analysed in this paper are already available in the public domain.

Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models

Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document micro-evolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder’s equation, indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments.

Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation

Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK). TprK demonstrated remarkable variability and redundancy, intra- and interpatient, suggesting ongoing parallel adaptive diversification during human infection. Some bacterial functions (for example, flagella- and chemotaxis-associated) were systematically targeted by both inter- and intrastrain single nucleotide polymorphisms, as well as by ongoing within-patient phase variation events. Finally, patient-derived genomes possess mutations targeting a penicillin-binding protein coding gene (mrcA) that had never been reported, unveiling it as a candidate target to investigate the impact on the susceptibility to penicillin. Our findings decode the major genetic mechanisms by which T. pallidum promotes immune evasion and survival, and demonstrate the exceptional power of characterizing evolving pathogen subpopulations during human infection.