Genetic differentiation of common shrew Sorex araneus populations among different alpine valleys revealed by microsatellites

Geographical barriers may affect the genetic structure of populations by reducing gene exchanges among them. In Switzerland, the common shrew Sorer araneus Linnaeus, 1758 is mostly confined to mountainous areas because of a competing sister species, Millet's shrew S. coronatus Millet, 1828, which occupies most of the Swiss lowlands. The structure of common shrew populations found in different alpine valleys may therefore be affected by the topography. Using microsatellites, genetic structuring of seven shrew populations is investigated among four different valleys of, the Swiss Alps. Using the exact G-test, significant genetic structuring is detected between several valleys. Isolation by distance does not fully explain our results. It appears that high mountain ridges (> 2400 m) can significantly reduce gene flow. F- and R-statistics are estimated and compared to the exact G-tests results. Mantel tests show that F-ST, unlike R-ST, is significantly correlated with differentiation. F-ST remains however low even at high differentiation levels, while R-ST has a high variance. We discuss how these results may have wider implications with regards the interpretation of microsatellite data. Finally, a new microsatellite locus, L99, appears to discriminate S. araneus of the Vaud and Cordon races from both S. araneus Valais and S. coronatus.

Genetic variability of the Brazilian hair sheep breeds

The objectives of this work were to investigate the genetic structure of the Brazilian hair sheep breeds and to determine the origin of the Santa Inês breed. Molecular similarity was determined using Randomly Amplified Polymorphic DNA - Polymerase Chain Reaction markers in 238 individuals from five naturalized sheep breeds: Santa Inês (48 animals), Rabo Largo (48), Somali (48), Morada Nova (48) and Bergamasca (46), collected in Goiás, Sergipe, Bahia, and Ceará States as well as in the Federal District. Fifty-four loci were selected from 19 primers, after a pilot test using 140 primers. Qualitative analyses indicate diagnostic markers for all breeds. All breeds were significantly different from each other. Interbreed differences were explained by 14.92% of the total variation. Santa Inês clustered with Bergamasca (97% bootstrap) and with Rabo Largo, composing the third member of the group (81% bootstrap) while Morada Nova and Somali breeds clustered separately. Each breed should be considered as a separate management and conservation unit, and special care should be taken with Rabo Largo, Morada Nova and Somali breeds, represented by small herds in Brazil.

Genetic characterization of ninety elite soybean cultivars using coefficient of parentage

The objective of this work was to estimate the coefficient of parentage and to understand the genetic structure of 90 elite soybean cultivars, which are adapted to different Brazilian environments. A total of 4,005 coefficients of parentage (f) were obtained and used to group the cultivars by UPGMA method. The constructed dendrogram showed several related cultivar groups which shared similar ancestors and clearly showed the genetic structure of the main Brazilian cultivars. Effective population sizes (Ne) were also estimated for cultivars in different generations. The average f = 0.2124 value, obtained from cultivars classified into four decades according to the release year, suggested effective soybean population sizes of 11 and 13 calculated using arithmetic and weighted means, respectively. The relatively small Ne and the high parentage coefficient support the conclusion that there is a high similarity degree among the main soybean cultivars in Brazil.

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants.

A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv amplified fragment length polymorphisms data set from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonization of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.

Genetic diversity in caribou linked to past and future climate change

Climate-driven range fluctuations during the Pleistocene have continuously reshaped species distribution leading to populations of contrasting genetic diversity. Contemporary climate change is similarly influencing species distribution and population structure, with important consequences for patterns of genetic diversity and species' evolutionary potential1. Yet few studies assess the impacts of global climatic changes on intraspecific genetic variation2, 3, 4, 5. Here, combining analyses of molecular data with time series of predicted species distributions and a model of diffusion through time over the past 21 kyr, we unravel caribou response to past and future climate changes across its entire Holarctic distribution. We found that genetic diversity is geographically structured with two main caribou lineages, one originating from and confined to Northeastern America, the other originating from Euro-Beringia but also currently distributed in western North America. Regions that remained climatically stable over the past 21 kyr maintained a high genetic diversity and are also predicted to experience higher climatic stability under future climate change scenarios. Our interdisciplinary approach, combining genetic data and spatial analyses of climatic stability (applicable to virtually any taxon), represents a significant advance in inferring how climate shapes genetic diversity and impacts genetic structure.

Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps.

Abstract The giant hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as well as parts of North America. It has become a problematic species due to its ability to displace native flora and to cause public health hazards. Applying population genetics to species invasion can help reconstruct invasion history and may promote more efficient management practice. We thus analysed levels of genetic variation and population genetic structure of H. mantegazzianum in an invaded area of the western Swiss Alps as well as in its native range (the Caucasus), using eight nuclear microsatellite loci together with plastid DNA markers and sequences. On both nuclear and plastid genomes, native populations exhibited significantly higher levels of genetic diversity compared to invasive populations, confirming an important founder event during the invasion process. Invasive populations were also significantly more differentiated than native populations. Bayesian clustering analysis identified five clusters in the native range that corresponded to geographically and ecologically separated groups. In the invaded range, 10 clusters occurred. Unlike native populations, invasive clusters were characterized by a mosaic pattern in the landscape, possibly caused by anthropogenic dispersal of the species via roads and direct collection for ornamental purposes. Lastly, our analyses revealed four main divergent groups in the western Swiss Alps, likely as a consequence of multiple independent establishments of H. mantegazzianum.

Structure and function of RecA-DNA complexes.

While the E. coli RecA protein has been the most intensively studied enzyme of homologous recombination, the unusual RecA-DNA filament has stood alone until very recently. It now appears that this protein is part of a universal family that spans all of biology, and the filament that is formed by the protein on DNA is a universal structure. With RecA's role in recombination given new and greatly increased significance, we focus in this review on the energetics of the RecA-mediated strand exchange and the relation between the energetics and recombination spanning heterologous inserts.

Variable queen number in ant colonies: no impact on queen turnover, inbreeding, and population genetic differentiation in the ant Formica selysi.

Variation in queen number alters the genetic structure of social insect colonies, which in turn affects patterns of kin-selected conflict and cooperation. Theory suggests that shifts from single- to multiple-queen colonies are often associated with other changes in the breeding system, such as higher queen turnover, more local mating, and restricted dispersal. These changes may restrict gene flow between the two types of colonies and it has been suggested that this might ultimately lead to sympatric speciation. We performed a detailed microsatellite analysis of a large population of the ant Formica selysi, which revealed extensive variation in social structure, with 71 colonies headed by a single queen and 41 by multiple queens. This polymorphism in social structure appeared stable over time, since little change in the number of queens per colony was detected over a five-year period. Apart from queen number, single- and multiple-queen colonies had very similar breeding systems. Queen turnover was absent or very low in both types of colonies. Single- and multiple-queen colonies exhibited very small but significant levels of inbreeding, which indicates a slight deviation from random mating at a local scale and suggests that a small proportion of queens mate with related males. For both types of colonies, there was very little genetic structuring above the level of the nest, with no sign of isolation by distance. These similarities in the breeding systems were associated with a complete lack of genetic differentiation between single- and multiple-queen colonies, which provides no support for the hypothesis that change in queen number leads to restricted gene flow between social forms. Overall, this study suggests that the higher rates of queen turnover, local mating, and population structuring that are often associated with multiple-queen colonies do not appear when single- and multiple-queen colonies still coexist within the same population, but build up over time in populations consisting mostly of multiple-queen colonies.

Unicoloniality, recognition and genetic differentiation in a native Formica ant.

Some ants have an extraordinary form of social organization, called unicoloniality, whereby individuals mix freely among physically separated nests. This mode of social organization has been primarily studied in introduced and invasive ant species, so that the recognition ability and genetic structure of ants forming unicolonial populations in their native range remain poorly known. We investigated the pattern of aggression and the genetic structure of six unicolonial populations of the ant Formica paralugubris at four hierarchical levels: within nests, among nests within the same population, among nests of populations within the Alps or Jura Mountains and among nests of the two mountain ranges. Ants within populations showed no aggressive behaviour, but recognized nonnestmates as shown by longer antennation bouts. Overall, the level of aggression increased with geographic and genetic distance but was always considerably lower than between species. No distinct behavioural supercolony boundaries were found. Our study provides evidence that unicoloniality can be maintained in noninvasive ants despite significant genetic differentiation and the ability to discriminate between nestmates and nonnestmates.

Genetic diversity of cultivated accessions and wild species of rubber tree using EST‑SSR markers

The objective of this work was to evaluate the efficiency of EST‑SSR markers in the assessment of the genetic diversity of rubber tree genotypes (Hevea brasiliensis) and to verify the transferability of these markers for wild species of Hevea. Forty‑five rubber tree accessions from the Instituto Agronômico (Campinas, SP, Brazil) and six wild species were used. Information provided by modified Roger's genetic distance were used to analyze EST‑SSR data. UPGMA clustering divided the samples into two major groups with high genetic differentiation, while the software Structure distributed the 51 clones into eight groups. A parallel could be established between both clustering analyses. The 30 polymorphic EST‑SSRs showed from two to ten alleles and were efficient in amplifying the six wild species. Functional EST‑SSR microsatellites are efficient in evaluating the genetic diversity among rubber tree clones and can be used to translate the genetic differences among cultivars and to fingerprint closely related materials. The accessions from the Instituto Agronômico show high genetic diversity. The EST‑SSR markers, developed from Hevea brasiliensis, show transferability and are able to amplify other species of Hevea.

Multiple introductions boosted genetic diversity in the invasive range of black cherry (Prunus serotina; Rosaceae).

BACKGROUND AND AIMS: Black cherry (Prunus serotina) is a North American tree that is rapidly invading European forests. This species was introduced first as an ornamental plant, then it was massively planted by foresters in many countries, but its origins and the process of invasion remain poorly documented. Based on a genetic survey of both native and invasive ranges, the invasion history of black cherry was investigated by identifying putative source populations and then assessing the importance of multiple introductions on the maintenance of gene diversity. METHODS: Genetic variability and structure of 23 populations from the invasive range and 22 populations from the native range were analysed using eight nuclear microsatellite loci and five chloroplast DNA regions. KEY RESULTS: Chloroplast DNA diversity suggests there were multiple introductions from a single geographic region (the north-eastern United States). A low reduction of genetic diversity was observed in the invasive range for both nuclear and plastid genomes. High propagule pressure including both the size and number of introductions shaped the genetic structure in Europe and boosted genetic diversity. Populations from Denmark, The Netherlands, Belgium and Germany showed high genetic diversity and low differentiation among populations, supporting the hypothesis that numerous introduction events, including multiple individuals and exchanges between sites, have taken place during two centuries of plantation. CONCLUSIONS: This study postulates that the invasive black cherry has originated from east of the Appalachian Mountains (mainly the Allegheny plateau) and its invasiveness in north-western Europe is mainly due to multiple introductions containing high numbers of individuals.

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.

Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.

Linking genetic and species diversities in a community of freshwater gastropods

Summary Biodiversity is usually studied through species or genetic diversities. To date, these two levels of diversity have remained the independent .fields of investigations of community ecologists and population geneticists. However, recent joint analyses of species and genetic diversities have suggested that common processes may underlie the two levels. Positive correlations between species diversity and genetic diversity may arise when the effects of drift and migration overwhelm selective effects. The first goal of this thesis was to make a joint investigation of the patterns of species and genetic diversity in a community of freshwater gastropods living in a floodplain habitat. The second goal was to determine, as far as possible, the relative influences of the processes underlying the patterns observed at each level. In chapter 2 we investigate the relative influences of different evolutionary forces in shaping the genetic structure of Radix balthica populations. Results revealed that the structure inferred using quantitative traits was lower or equal to the one inferred using neutral molecular markers. Consequently, the pattern of structure observed could be only due to random drift, possibly to uniform selection, but definitely not to selection for local optima. In chapter 3, we analyze the temporal variation of species and genetic diversities in five localities. An extended period of drought occurred at the end of the study period leading to decay of both species and genetic diversities. This parallel loss of diversity following a natural perturbation highlighted the role sometimes predominant of random drift over selection on patterns of biodiversity in a floodplain habitat. In chapter 4, we compare the spatial genetic structures of two sympatric species: Radix balthica and Planorbis carinatus. We found that R. balthica populations are weakly structured and have moderate to high values of gene diversity. In contrast, P. carinatus populations are highly structured and poorly diverse. Then we measured correlations between various indices of species and genetic diversity using genetic data .from the two species. We found only one significant correlation: between species richness and gene diversity of P. carinatus. This result highlights the .need to use genetic date from more than one species to infer correlations between species and genetic diversities. Overall, this thesis provided new insights into the common processes underlying patterns of species and genetic diversity. Résumé La biodiversité est généralement étudiée au niveau de la diversité génétique ou spécifique. Ces deux niveaux sont restés jusqu'à maintenant les domaines d'investigation séparés des généticiens des populations et des écologistes des communautés. Cependant, des analyses conjointes des diversités génétique et spécifique ont récemment suggéré que des processus similaires pouvaient influencer ces deux niveaux. Des corrélations positives entre les diversités génétique et spécifique pourraient être dues aux effets de migration et de dérive qui dominent les effets sélectifs. Le premier but de cette thèse était de faire une étude conjointe des diversités génétique et spécifique dans une communauté de gastéropodes d'eau douce. Le second objectif était de déterminer les influences relatives des différents processus liés à chaque niveau de diversité. Dans le chapitre 2 nous cherchons à déterminer quelles forces évolutives influencent la structure génétique de quatre populations de Radix balthica. La structure mesurée sur des traits quantitatifs s'est révélée être plus faible ou égale à celle mesurée avec des marqueurs moléculaires neutres. La structure observée pourrait ainsi être due uniquement à la dérive génétique, potentiellement à la sélection uniforme, mais en aucun cas à la sélection locale pour différents optima. Dans le chapitre 3 nous analysons la variation temporelle des diversités génétique et spécifique dans cinq localités. Une récente période de sécheresse a causé une diminution parallèle des deux niveaux de diversité. Cette perturbation à mis en évidence le rôle parfois prépondérant de la dérive par rapport à celui de la sélection dans le déterminisme de la biodiversité dans un écosytème alluvial. Dans le chapitre 4, nous comparons la structure génétique spatiale de deux espèces vivant en sympatrie : Radix balthica et Planorbis carinatus. Les populations de R. balthica sont peu structurées et présentent un niveau de diversité relativement élevé alors que celles de P. carinatus sont fortement structurées et peu diversifiées. Nous avons ensuite mesuré différentes corrélations entre les diversités génétique et spécifique, mais la seule relation significative a été trouvée entre la richesse spécifique et la diversité génétique de P. carinatus. Ainsi, cette thèse a permis de découvrir de nouveaux aspects des processus qui influencent en parallèle la diversité aux niveaux génétique et spécifique.

Diversity and genetic struture in cajá tree (spondias mombin l.) populations in northeastern Brazil

Spondias mombin L. is a fruit tree from the American continent from the Anacardiaceae family. In Brazil it is common in different vegetation types but is more frequent in the Atlantic and Amazonian rainforests. It is economically important because of its fruits, which are widely consumed raw or processed as fruit jellies, juices and ice creams. The leaves have great importance in the pharmaceutical industry because of their antibacterial properties. In the state of Pernambuco, cajá tree is widely distributed in the Zona da Mata region and less frequently in the Agreste and Sertão areas. In this work diversity and genetic structure were studied in four populations of cajá tree from Pernambuco's Zona da Mata, Northeast Brazil, using isozymes polymorphism analyses from electrophoreses. The result showed 100% of polymorphism (P) for nine alleles and the average of alleles per locus s was 2.4. The expected heterozygosity ranged from 0.530 to 0.574 and the observed heterozygosity , from 0.572 to 0.735. It was not observed inbreeding and the average F IT was -0.175, whereas within population inbreeding (f) varied from -0.08 to- 0.37. The genetic divergence among the populations (F ST) ranged from 0.006 to 0.028 and the average was 0.026. The average of estimated gene flow (Nm) was high (5.27). The CG-IPA population, corresponding to the germplasm collection of IPA, showed more than 96% of genetic similarity with other populations; therefore, it is a good representative of the existent genetic diversity in the Zona da Mata region.

The interplay of spatial and climatic landscapes in the genetic distribution of a South American parrot

AimOur aim was to understand the interplay of heterogeneous climatic and spatial landscapes in shaping the distribution of nuclear microsatellite variation in burrowing parrots, Cyanoliseus patagonus. Given the marked phenotypic differences between populations of burrowing parrots we hypothesized an important role of geographical as well climatic heterogeneity in the population structure of this species. LocationSouthern South America. MethodsWe applied a landscape genetics approach to investigate the explicit patterns of genetic spatial autocorrelation based on both geography and climate using spatial principal component analysis (sPCA). This necessitated a novel statistical estimation of the species climatic landscape, considering temperature- and precipitation-based variables separately to evaluate their weight in shaping the distribution of genetic variation in our model system. ResultsGeographical and climatic heterogeneity successfully explained molecular variance in burrowing parrots. sPCA divided the species distribution into two main areas, Patagonia and the pre-Andes, which were connected by an area of geographical and climatic transition. Moreover, sPCA revealed cryptic and conservation-relevant genetic structure: the pre-Andean populations and the transition localities were each divided into two groups, each management units for conservation. Main conclusionssPCA, a method originally developed for spatial genetics, allowed us to unravel the genetic structure related to spatial and climatic landscapes and to visualize these patterns in landscape space. These novel climatic inferences underscore the importance of our modified sPCA approach in revealing how climatic variables can drive cryptic patterns of genetic structure, making the approach potentially useful in the study of any species distributed over a climatically heterogeneous landscape.