A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10(-12)). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the 'intermediate phenotype' nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. DOI:http://dx.doi.org/10.7554/eLife.01123.001.

Molecular evidence of Pleistocene bidirectional faunal exchange between Europe and the Near East: the case of the bicoloured shrew (Crocidura leucodon, Soricidae).

We sequenced 1077 bp of the mitochondrial cytochrome b gene and 511 bp of the nuclear Apolipoprotein B gene in bicoloured shrew (Crocidura leucodon, Soricidae) populations ranging from France to Georgia. The aims of the study were to identify the main genetic clades within this species and the influence of Pleistocene climatic variations on the respective clades. The mitochondrial analyses revealed a European clade distributed from France eastwards to north-western Turkey and a Near East clade distributed from Georgia to Romania; the two clades separated during the Middle Pleistocene. We clearly identified a population expansion after a bottleneck for the European clade based on mitochondrial and nuclear sequencing data; this expansion was not observed for the eastern clade. We hypothesize that the western population was confined to a small Italo-Balkanic refugium, whereas the eastern population subsisted in several refugia along the southern coast of the Black Sea.

Vegetation succession and diversity on Teuravuoma experimental drainage area in northern Finland

Tiivistelmä: Kasvillisuuden sukkessio ja monimuotoisuus Teuravuoman koeojitusalueella Pohjois-Suomessa

High prevalence and lineage diversity of avian malaria in wild populations of great tits (Parus major) and mosquitoes (Culex pipiens).

Avian malaria studies have taken a prominent place in different aspects of evolutionary ecology. Despite a recent interest in the role of vectors within the complex interaction system of the malaria parasite, they have largely been ignored in most epidemiological studies. Epidemiology of the disease is however strongly related to the vector's ecology and behaviour, and there is a need for basic investigations to obtain a better picture of the natural associations between Plasmodium lineages, vector species and bird hosts. The aim of the present study was to identify the mosquito species involved in the transmission of the haemosporidian parasites Plasmodium spp. in two wild populations of breeding great tits (Parus major) in western Switzerland. Additionally, we compared Plasmodium lineages, based on mitochondrial DNA cytochrome b sequences, between the vertebrate and dipteran hosts, and evaluated the prevalence of the parasite in the mosquito populations. Plasmodium spp. were detected in Culex pipiens only, with an overall 6.6% prevalence. Among the six cytochrome b lineages of Plasmodium identified in the mosquitoes, three were also present in great tits. The results provide evidence for the first time that C. pipiens can act as a natural vector of avian malaria in Europe and yield baseline data for future research on the epidemiology of avian malaria in European countries.

Assessment of genetic diversity using RAPD analysis in a germplasm collection of sea buckthorn

Selostus: Tyrnin geneettisen monimuotoisuuden arviointi RAPD analyysillä

Experimentally increased group diversity improves disease resistance in an ant species.

A leading hypothesis linking parasites to social evolution is that more genetically diverse social groups better resist parasites. Moreover, group diversity can encompass factors other than genetic variation that may also influence disease resistance. Here, we tested whether group diversity improved disease resistance in an ant species with natural variation in colony queen number. We formed experimental groups of workers and challenged them with the fungal parasite Metarhizium anisopliae. Workers originating from monogynous colonies (headed by a single queen and with low genetic diversity) had higher survival than workers originating from polygynous ones, both in uninfected groups and in groups challenged with M. anisopliae. However, an experimental increase of group diversity by mixing workers originating from monogynous colonies strongly increased the survival of workers challenged with M. anisopliae, whereas it tended to decrease their survival in absence of infection. This experiment suggests that group diversity, be it genetic or environmental, improves the mean resistance of group members to the fungal infection, probably through the sharing of physiological or behavioural defences.

Atomic diversity, molecular diversity, and chemical diversity: the concept of chemodiversity.

This minireview is meant as an introduction to the following paper. To this end, it presents the general background against which the joint paper should be understood. The first objective of the present paper is thus to clarify some concepts and related terminology, drawing a clear distinction between i) atomic diversity (i.e., atomic-property space), ii) molecular or macromolecular diversity (i.e., molecular- or macromolecular-property spaces), and iii) chemical diversity (i.e., chemical-diversity space). The first refers to the various electronic states an atom can occupy. The second encompasses the conformational and property spaces of a given (macro)molecule. The third pertains to the diversity in structure and properties exhibited by a library or a supramolecular assembly of different chemical compounds. The ground is thus laid for the content of the joint paper, which pertains to case ii, to be placed in its broader chemodiversity context. The second objective of this paper is to point to the concepts of chemodiversity and biodiversity as forming a continuum. Chemodiversity is indeed the material substratum of organisms. In other words, chemodiversity is the material condition for life to emerge and exist. Increasing our knowledge of chemodiversity is thus a condition for a better understanding of life as a process.

The influence of environmental spatial structure on the life history traits and diversity of species in a metacommunity

Several models have been proposed to understand how so many species can coexist in ecosystems. Despite evidence showing that natural habitats are often patchy and fragmented, these models rarely take into account environmental spatial structure. In this study we investigated the influence of spatial structure in habitat and disturbance regime upon species' traits and species' coexistence in a metacommunity. We used a population-based model to simulate competing species in spatially explicit landscapes. The species traits we focused on were dispersal ability, competitiveness, reproductive investment and survival rate. Communities were characterized by their species richness and by the four life-history traits averaged over all the surviving species. Our results show that spatial structure and disturbance have a strong influence on the equilibrium life-history traits within a metacommunity. In the absence of disturbance, spatially structured landscapes favour species investing more in reproduction, but less in dispersal and survival. However, this influence is strongly dependent on the disturbance rate, pointing to an important interaction between spatial structure and disturbance. This interaction also plays a role in species coexistence. While spatial structure tends to reduce diversity in the absence of disturbance, the tendency is reversed when disturbance occurs. In conclusion, the spatial structure of communities is an important determinant of their diversity and characteristic traits. These traits are likely to influence important ecological properties such as resistance to invasion or response to climate change, which in turn will determine the fate of ecosystems facing the current global ecological crisis.

Some common indexes of group diversity: upper boundaries

Workgroup diversity can be conceptualized as variety, separation, or disparity. Thus, the proper operationalization of diversity depends on how a diversity dimension has been defined. Analytically, the minimal diversity must be obtained when there are no differences on an attribute among the members of a group, however maximal diversity has a different shape for each conceptualization of diversity. Previous work on diversity indexes indicated maximum values for variety (e.g., Blau"s index and Teachman"s index), separation (e.g., standard deviation and mean Euclidean distance), and disparity (e.g., coefficient of variation and the Gini coefficient of concentration), although these maximum values are not valid for all group characteristics (i.e., group size and group size parity) and attribute scales (i.e., number of categories). We demonstrate analytically appropriate upper boundaries for conditional diversity determined by some specific group characteristics, avoiding the bias related to absolute diversity. This will allow applied researchers to make better interpretations regarding the relationship between group diversity and group outcomes.