Polymorphism of the Human Immunodeficiency Virus Type 1 in Brazil: genetic characterization of the nef gene and implications for vaccine design

Most of the Brazilian HIV-1 samples have been characterized based on the structural genes (env, gag and pol) and no data concerning the variability of the accessory genes such as nef have been available so far. Considering the role of the nef on virus biology and the inclusion of this region in some HIV/AIDS vaccine products under testing, the purpose of this study was to document the genetic diversity of the nef gene in third-four HIV-1 Brazilian samples previously subtyped based on the env C2-V3 region. Although only few non-subtype B samples have already been analyzed so far, the cytotoxic Tlymphocyte epitopes encoded in this region were relatively conserved among the subtypes, with some amino acid signatures mainly in the subtype C samples. Considering the increasing of the non-B HIV-1 subtypes worldwide, in special the subtype C, more data should be generated concerning the genetic and antigenic variability of these subtypes, as well as the study of the impact of such polymorphism in HIV/AIDS vaccine design and testing.     

Sampling HIV Intrahost Genealogies Based on a Model of Acute Stage CTL Response

Cytotoxic T lymphocytes (CTLs) play an important role in the immune response to HIV during the acute stage of infection, but the effect of CTLs on HIV intrahost genetic diversity is poorly understood. We introduce a model of CTL attack during the acute stage. Assuming this model, we develop a method to sample HIV intrahost genealogies. Using our sampling approach, we characterize the evolutionary forces that shape HIV genealogies. In particular, we show that early mutation events can have significant impact on HIV genealogies and that certain types of CTL attack are best at controlling HIV genetic diversity. Our sampler represents a first step toward using HIV genetic data to infer properties of CTL attack.     

Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification

Background

The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes.

Results

All HIV full-length genomes available in public databases were analysed (n?=?2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes.

Conclusions

With this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts.

     

Fertilization and defoliation frequency affect genetic diversity of Festuca pratensis Huds. in permanent grasslands

Permanent pastures and meadows are species-rich vegetation systems that play an important role in the ecology and agriculture of temperate climates. Intensive management reduces species diversity and may also influence the genetic diversity within individual species and populations. The objective of this study was to assess genetic variability of meadow fescue, an important component of species-rich grasslands, and to determine whether fertilization and defoliation frequency influence genetic variability within natural populations. Genetic diversity of six natural populations and three cultivars of Festuca pratensis was investigated using randomly amplified polymorphic DNA (RAPD) markers and agronomic traits. Samples of natural populations were taken from two unrelated long-term experiments, where treatments had been applied for 11–38 years. RAPD analysis detected a clear genetic distinction of the cultivars from the natural populations. Genetic variability within cultivars was lower than within natural populations. Analysis of molecular variance ( AMOVA ) showed a significant effect of management on genetic variability. Fertilization and frequent defoliation led to a reduction in genetic variability within natural populations. Analysis of agronomic traits was only partially congruent with the results of RAPD analysis. This study shows that significant genetic variability exists within cultivars and natural populations of Festuca pratensis and can be reduced by intensive management.     

Genetic assessment of population restorations of the critically endangered Silene hifacensis in the Iberian Peninsula

In order to preserve endangered plant populations and recover their evolutionary potential and ecological behavior, some restoration measures generally involve the reinforcement of the population size in existing natural populations or the reintroduction of new populations. Genetic monitoring of both natural and restored populations can provide an assessment of restoration protocol success in establishing populations that maintain levels of genetic diversity similar to those in natural populations. The highly threatened Spanish species Silene hifacensis (Caryophyllaceae) has only three natural reduced mainland populations in the Iberian Peninsula, following decline and extinction that occurred during the late 20th century. Preterit restoration strategies were essentially based on the implantation of new populations and reinforcement of certain existing populations using transplants mostly cultivated in greenhouses. In the present contribution, levels and patterns of genetic variability within natural and restored populations of Silene hifacensis were assessed using the molecular technique AFLP. Our results pointed out significant genetic diversity differences across the three existing natural populations though their population fragmentation and progressive loss of individuals have not had an impact on the global genetic diversity of this species. For restored populations, their levels of genetic diversity were similar and even higher than in natural populations. As a result, the past restoration protocols were successful in capturing similar and even higher levels of genetic diversity than those observed within natural pools. However, inbreeding processes have been detected for two restored populations. Finally, the main source of plant material for the long-time restored transplants appears to be the natural population of Cova de les Cendres. This study demonstrates, once again, how genetic markers are useful tools to be taken in consideration for endangered plant species conservation plans.     

Levels of genetic polymorphism: marker loci versus quantitative traits.

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species.     

Evidence of parasite-mediated disruptive selection on genetic diversity in a wild fish population

Identifying the processes maintaining genetic variability in wild populations is a major concern in conservation and evolutionary biology. Parasite-mediated selection may strongly affect genetic variability in wild populations. The inbreeding depression theory predicts that directional selection imposed by parasites should act against the most inbred hosts, thus favouring genetic diversity in wild populations. We have tested this prediction by evaluating the strength and shape of the relationship between the load of a harmful fin-feeder ectoparasite ( Tracheliastes polycolpus ) and the genome-wide genetic diversity (i.e. heterozygosity measured at a set of 15 microsatellites) of its fish host, the rostrum dace ( Leuciscus leuciscus ). Contrary to expectation, we found a nonlinear relationship between host genetic diversity and ectoparasite load, with hosts that were either homozygous or heterozygous harbouring significantly fewer parasites than hosts with an intermediate level of heterozygosity. This relationship suggests that parasites could increase the variance of global heterozygosity in this host population through disruptive selection on genetic diversity. Moreover, when genetic diversity was measured at each locus separately, we found two very strong positive associations between host genetic diversity and the ectoparasite load. This latter result has three main implications: (i) genome-wide effect cannot alone explain the nonlinear relationship between global heterozygosity and ectoparasite load, (ii) negative non-additive allelic interactions (i.e. underdominance) may be a mechanism for resisting ectoparasite infection, and (iii) ectoparasites may favour homozygosity at some loci in this host population.     

Genetic variability in geographic populations of the natterjack toad (Bufo calamita)

Across altitudinal and latitudinal gradients, the proportion of suitable habitats varies, influencing the individual dispersal that ultimately can produce differentiation among populations. The natterjack toad (Bufo calamita) is distributed across a wide geographic range that qualifies the species as interesting for a geographic analysis of its genetic variability. Five populations of B. calamita in the Sierra de Gredos (Spain) were studied in an altitudinal gradient ranging from 750 to 2270 m using microsatellite markers. In addition, we analyzed the latitudinal genetic variation in B. calamita within a global European distribution using genetic diversity parameters (mean number of alleles per locus [M(a)] and expected heterozygosity [H(E)]) obtained from our results and those published in the literature. The low level of genetic differentiation found between populations of B. calamita (F(st) ranging from 0.0115 to 0.1018) and the decreases in genetic diversity with altitude (M(a) from 13.6 to 8.3, H(E) from 0.82 to 0.74) can be interpreted by the combined effects of discontinuous habitat, produced mainly by the high slopes barriers and geographic distance. In the latitudinal gradient, genetic diversity decreases from south to north as a consequence of the colonization of the species from the Pleistocene refugium. We conclude that the genetic variability in B. calamita along its wide altitudinal and latitudinal geographic distribution mainly reflects the colonization history of the species after the last glacial period.     

Non-random distribution of individual genetic diversity along an environmental gradient

Improving our knowledge of the links between ecology and evolution is especially critical in the actual context of global rapid environmental changes. A critical step in that direction is to quantify how variation in ecological factors linked to habitat modifications might shape observed levels of genetic variability in wild populations. Still, little is known on the factors affecting levels and distribution of genetic diversity at the individual level, despite its vital underlying role in evolutionary processes. In this study, we assessed the effects of habitat quality on population structure and individual genetic diversity of tree swallows (Tachycineta bicolor) breeding along a gradient of agricultural intensification in southern Québec, Canada. Using a landscape genetics approach, we found that individual genetic diversity was greater in poorer quality habitats. This counter-intuitive result was partly explained by the settlement patterns of tree swallows across the landscape. Individuals of higher genetic diversity arrived earlier on their breeding grounds and settled in the first available habitats, which correspond to intensive cultures. Our results highlight the importance of investigating the effects of environmental variability on individual genetic diversity, and of integrating information on landscape structure when conducting such studies.     

Landscape structure and the genetic effects of a population collapse

Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift.     

Phylogeography of the European spiny lobster (Palinurus elephas): Influence of current oceanographical features and historical processes

The European spiny lobster (Palinurus elephas) is a suitable model organism to study the effects of past history and current oceanographic processes on the genetic diversity and population structure of marine species with a long-lived larval phase. A portion of the COI gene was sequenced in 227 individuals from 11 localities, covering most of the present distribution of the species. Divergence was found between Atlantic and Mediterranean regions, which could be explained by restricted gene flow between populations. Moreover, a principal component analysis detected differences within basins. The existence of genetic differentiation between Brittany and Ireland–Scotland populations could be accounted for by the large effect of the Gulf Stream, while mesoscale processes suffered by the incoming Atlantic waters could be responsible of genetic differentiation within the Mediterranean. Furthermore, historical processes could be responsible for a reduction on the overall genetic variability of P. elephas. The haplotypic distribution found in P. elephas, with the presence of one abundant haplotype and a large number of closely related haplotypes, is typical of species experiencing reduction in variability and subsequent expansions. Climatic fluctuations related to glacial cycles could explain the present level of variability and nucleotide diversity found. Interestingly, these glacial events do not seem to have the same impact in other species of the same genus. Our results indicate that recent glacial events could have had a lower impact on Palinurus mauritanicus, a congeneric species that presents an overlapping distribution area but is found in cooler waters than P. elephas.     

Diversifying mechanisms in the on‐farm evolution of crop mixtures

While modern agriculture relies on genetic homogeneity, diversifying practices associated with seed exchange and seed recycling may allow crops to adapt to their environment. This socio‐genetic model is an original experimental evolution design referred to as on‐farm dynamic management of crop diversity. Investigating such model can help in understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro‐environments. We studied a French farmer‐led initiative where a mixture of four wheat landraces called ‘Mélange de Touselles’ (MDT) was created and circulated within a farmers' network. The 15 sampled MDT subpopulations were simultaneously submitted to diverse environments (e.g. altitude, rainfall) and diverse farmers' practices (e.g. field size, sowing and harvesting date). Twenty‐one space‐time samples of 80 individuals each were genotyped using 17 microsatellite markers and characterized for their heading date in a ‘common‐garden’ experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network‐based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. Rapid differentiation among populations within the mixture was detected, larger at the phenotypic and gene levels than at the neutral genetic level, indicating potential divergent selection. We identified two interacting selection processes: variation in the mixture component frequencies, and evolution of within‐variety diversity, that shaped the standing variability available within the mixture. These results confirmed that diversifying practices and environments maintain genetic diversity and allow for crop evolution in the context of global change. Including concrete measurements of farmers' practices is critical to disentangle crop evolution processes.     

Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers

The distribution of genetic variation and the phylogenetic relationships between 18 populations of the arctic-alpine plant Trollius europaeus were analysed in three main regions (Alps, Pyrenees and Fennoscandia) by using dominant AFLP markers. Analysis of molecular variance revealed that most of the genetic variability was found within populations (64%), although variation among regions (17%) and among populations within regions (19%) was highly significant (P < 0.001). Accordingly, the global fixation index FST averaged over loci was high (0.39). The among-population differentiation indicates restricted gene flow, congruent with limited dispersal of specific globeflower's pollinating flies (Chiastocheta spp.). Within-population diversity levels were significantly higher in the Alps (mean Nei's expected heterozygosity HE = 0.229) than in the Pyrenees (HE= 0.197) or in Fennoscandia (HE = 0.158). This finding is congruent with the species-richness of the associated flies, which is maximum in the Alps. We discuss the processes involved in shaping observed patterns of genetic diversity within and among T. europaeus populations. Genetic drift is the major factor acting on the small Pyrenean populations at the southern edge of T. europaeus distribution, while large Fennoscandian populations result probably from a founder effect followed by demographic expansion. The Alpine populations represent moderately fragmented relics of large southern ancestral populations. The patterns of genetic variability observed in the host plant support the hypothesis of sympatric speciation in associated flies, rather than recurrent allopatric speciations.     

Genetic diversity of the subterranean Gansu zokor in a semi-natural landscape

We studied the relationship between genetic diversity of the subterranean Gansu zokor Myospalax cansus and habitat variability in the Loess Plateau, Qinghai Province, China. We used a combination of geographic information systems and molecular techniques to assess the impact of habitat composition and human activities on the genetic diversity of zokor populations in this semi-natural landscape. Although they occurred relatively infrequently in the landscape, woodland and high-coverage grassland habitats were the main positive contributors to the genetic diversity of zokor populations. Rural residential land, plain agricultural land and low-coverage grassland had a negative effect on genetic diversity. Hilly agricultural land and middle-coverage grassland had little impact on zokor genetic diversity. There were also interactions between some habitat types, that is, habitat types with relatively better quality together promoted conservation of genetic diversity, while the interaction between (among) bad habitat types made situations worse. Finally, habitat diversity, measured as patch richness and Shannon's diversity index, was positively correlated with the genetic diversity. These results demonstrated that: (1) different habitat types had different effects on the genetic diversity of zokor populations and (2) habitat quality and habitat heterogeneity were important in maintaining genetic diversity. Habitat composition was closely related to land use thus emphasizing the importance of human activities on the genetic diversity of subterranean rodent populations in this semi-natural landscape. Although the Gansu zokor was considered to be a pest species in the Loess Plateau, our study provides insights for the management and conservation of other subterranean rodent species.     

Tropical maize germplasm: what can we say about its genetic diversity in the light of molecular markers?

Knowledge about genetic variability of a crop allows for more efficient and effective use of resources in plant improvement programs. The genetic variation within temperate maize has been studied extensively, but the levels and patterns of diversity in tropical maize are still not well understood. Brazilian maize germplasm represents a very important pool of genetic diversity due to many past introductions of exotic material. To improve our knowledge of the genetic diversity in tropical maize inbred lines, we fingerprinted 85 lines with 569 AFLP bands and 50 microsatellite loci. These markers revealed substantial variability among lines, with high rates of polymorphism. Cluster analysis was used to identify groups of related lines. Well-defined groups were not observed, indicating that the tropical maize studied is not as well organized as temperate maize. Three types of genetic distance measurements were applied (Jaccard’s coefficient, Modified Rogers’ distance and molecular coefficient of coancestry), and the values obtained with all of them indicated that the genetic similarities were small among the lines. The different coefficients did not substantially affect the results of cluster analysis, but marker types had a large effect on genetic similarity estimates. Regardless of genetic similarity coefficient used, estimates based on AFLPs were poorly correlated with those based on SSRs. Analyses using AFLP and SSR data together do not seem to be the most efficient manner of assessing variability in highly diverse materials because the result was similar to using AFLPs alone. It was seen that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.     

Apportionment of global human genetic diversity based on craniometrics and skin color

A number of analyses of classical genetic markers and DNA polymorphisms have shown that the majority of human genetic diversity exists within local populations (approximately 85%), with much less among local populations (approximately 5%) or between major geographic regions or "races" (approximately 10%). Previous analysis of craniometric variation (Relethford [1994] Am J Phys Anthropol 95:53-62) found that between 11-14% of global diversity exists among geographic regions, with the remaining diversity existing within regions. The methods used in this earlier paper are extended to a hierarchical partitioning of genetic diversity in quantitative traits, allowing for assessment of diversity among regions, among local populations within regions, and within local populations. These methods are applied to global data on craniometric variation (57 traits) and skin color. Multivariate analysis of craniometric variation shows results similar to those obtained from genetic markers and DNA polymorphisms: roughly 13% of the total diversity is among regions, 6% among local populations within regions, and 81% within local populations. This distribution is concordant with neutral genetic markers. Skin color shows the opposite pattern, with 88% of total variation among regions, 3% among local populations within regions, and 9% within local populations, a pattern shaped by natural selection. The apportionment of genetic diversity in skin color is atypical, and cannot be used for purposes of classification. If racial groups are based on skin color, it appears unlikely that other genetic and quantitative traits will show the same patterns of variation.     

Comparative Estimate of the sheep breed gene pools using ISSR-analysis

Using the ISSR-PCR technique, the genetic structure of nine sheep breeds (Ovis aries) bred on the territories of Russia and Mongolia was examined. Species-specific and breed-specific DNA fragments were identified. For the first time, data on the genetic diversity of Telengit and Buubey sheep breeds were obtained. The main parameters of the genetic diversity and the breed structure were assessed, and the phylogenetic relationships and genetic distances between the studied breeds were determined. Using the method of hierarchical frequency averaging, the prototypal sheep gene pool was reconstructed. The three-tiered analysis of diversity based on the ISSR fingerprinting data showed that 15.8% of variability was found between the breeds, 31.4% of variability was found between the populations within the breeds, and the diversity among the individuals within the populations constituted 52.8%.     

Genetic variation and spatial structure in sugar maple (Acer saccharum Marsh.) and implications for predicted global-scale environmental change

Current ecosystem model predictions concerning the effects of global temperature increase on forest responses do not account for factors influencing long‐term evolutionary dynamics of natural populations. Population structure and genetic variability may represent important factors in a species' ability to adapt to global‐scale environmental change without experiencing major alterations in current range limits. Genetic variation and structure in sugar maple (Acer saccharum Marsh.) were examined across three regions, between two stands within regions, and among four to five open‐pollinated families within stands (total N = 547 genotypes) using 58 randomly amplified polymorphic DNA (RAPD) markers. Differences within open‐pollinated families account for the largest portion of the total variation (29%), while differences among regions represent less than 2% of the total variation. Genetic diversity, as indicated by estimates of percent polymorphic loci, expected heterozygosity, fixation coefficients, and genetic distance, is greatest in the southern region, which consists of populations with the maximum potential risk due to climate change effects. The high level of genetic similarity (greater than 90%) among some genotypes suggests that gene flow is occurring among regions, stands, and families. High levels of genetic variation among families indicate that vegetational models designed to predict species' response to global‐scale environmental change may need to consider the degree and hierarchical structure of genetic variation when making large‐scale inferences.     

Gradual adaptation of HIV to human host populations: good or bad news?

The continuous evolution and adaptation of HIV to its host has produced extensive global viral diversity. Understanding the kinetics and directions of this continuing adaptation and its impact on viral fitness, immunogenicity and pathogenicity will be crucial to the successful design of effective HIV vaccines. Here we discuss some potential scenarios of viral and host coevolution.     

An experimental test of the role of environmental temperature variability on ectotherm molecular, physiological and life-history traits: implications for global warming

Global climate change is one of the greatest threats to biodiversity; one of the most important effects is the increase in the mean earth surface temperature. However, another but poorly studied main characteristic of global change appears to be an increase in temperature variability. Most of the current analyses of global change have focused on mean values, paying less attention to the role of the fluctuations of environmental variables. We experimentally tested the effects of environmental temperature variability on characteristics associated to the fitness (body mass balance, growth rate, and survival), metabolic rate (VCO(2)) and molecular traits (heat shock protein expression, Hsp70), in an ectotherm, the terrestrial woodlouse Porcellio laevis. Our general hypotheses are that higher values of thermal amplitude may directly affect life-history traits, increasing metabolic cost and stress responses. At first, results supported our hypotheses showing a diversity of responses among characters to the experimental thermal treatments. We emphasize that knowledge about the cellular and physiological mechanisms by which animals cope with environmental changes is essential to understand the impact of mean climatic change and variability. Also, we consider that the studies that only incorporate only mean temperatures to predict the life-history, ecological and evolutionary impact of global temperature changes present important problems to predict the diversity of responses of the organism. This is because the analysis ignores the complexity and details of the molecular and physiological processes by which animals cope with environmental variability, as well as the life-history and demographic consequences of such variability.