Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus

How epistatic interactions between mutations determine the genetic architecture of fitness is of central importance in evolution. The study of epistasis is particularly interesting for RNA viruses because of their genomic compactness, lack of genetic redundancy, and apparent low complexity. Moreover, interactions between mutations in viral genomes determine traits such as resistance to antiviral drugs, virulence and host range. In this study we generated 53 Tobacco etch potyvirus genotypes carrying pairs of single-nucleotide substitutions and measured their separated and combined deleterious fitness effects. We found that up to 38% of pairs had significant epistasis for fitness, including both positive and negative deviations from the null hypothesis of multiplicative effects. Interestingly, the sign of epistasis was correlated with viral protein-protein interactions in a model network, being predominantly positive between linked pairs of proteins and negative between unlinked ones. Furthermore, 55% of significant interactions were cases of reciprocal sign epistasis (RSE), indicating that adaptive landscapes for RNA viruses maybe highly rugged. Finally, we found that the magnitude of epistasis correlated negatively with the average effect of mutations. Overall, our results are in good agreement to those previously reported for other viruses and further consolidate the view that positive epistasis is the norm for small and compact genomes that lack genetic robustness.     

The evolutionary history of a mammal species with a highly fragmented range: the phylogeography of the European snow vole

The European snow vole Chionomys nivalis has a patchy distribution restricted to rocky habitats across southern Europe and the Near and Middle East. We carried out a phylogeographic study to provide a biogeographic scenario, based on molecular data, outlining the major processes that determined the current distribution of the species. The samples include 26 snow voles from 14 different populations across the entire species range from Spain to Anatolia and Israel. Nearly complete sequences (1037 bp) of the mitochondrial gene for cytochrome b were sequenced. Relationships among haplotypes were inferred with neighbour-joining, maximum likelihood, maximum parsimony analyses and minimum spanning network. An analysis of mismatch distribution was used to cast light on past demographic expansion. We found 22 different haplotypes that fall into six distinct lineages, all but one is supported by high bootstrap values with all methods. Four lineages are allopatric (Tatra Mts., Iberia, Balkans and Middle East) while divergent haplotypes from two lineages show sympatry in the Alps and the Apennines. The basal relationships of these lineages could not be established by any tree. The mean pairwise genetic distance between lineages ranges from 2.4 to 4.2%. The shape of the mismatch distribution indicated a past expansion event dating back to between 158 000 and 84 000 years ago. These data can be interpreted with the existence of southern glacial refugia (Iberia, Balkans, Middle East and Italy) and one additional northern glacial refugium. The lack of phylogenetic resolution among lineages and the shape of mismatch distribution are indicative of a simultaneous and rapid splitting due to a relatively fast initial expansion of populations. Moreover, the analysis supports the hypothesis of the European origin of C. nivalis and its subsequent eastward dispersion during the Middle Pleistocene.     

Genetic variability in the endemic <Emphasis Type="Italic">Leucojum valentinum</Emphasis>

The genetic variability of Leucojum valentinum Pau (Amaryllidaceae), a vulnerable endemic species restricted to a small area in the region of Valencia (Eastern Spain), has been studied using random amplified polymorphic DNA (RAPD) markers. A total of 197 individuals from eleven populations were studied using 13 RAPD primers. Our results show high variability for the species, low differentiation among populations and uncorrelated levels of genetic variability and population size. Four groups in which three populations (SAG, PUG and COL) are separated from all the others were found, but without connection to geographical location.     

Habitat selection by Ortolan Buntings Emberiza hortulana in post-fire succession in Catalonia: implications for the conservation of farmland populations

The Ortolan Bunting Emberiza hortulana is a long-distance migrant that has suffered major population declines across much of its European breeding range. While northern populations are bound largely to farmland, Mediterranean populations are largely confined to habitats subject to recurrent wildfires. Habitat selection of the Ortolan Bunting was assessed in a recently burnt area in Catalonia at landscape and habitat scales. A Zero-inflated Poisson procedure was used to model the abundance of birds in relation to landscape and habitat variables. The most parsimonious landscape model predicted the highest abundance on south-facing slopes, with a gradient above 10°. The most parsimonious habitat model showed a positive quadratic effect of bare ground and regenerating oak Quercus spp., with predicted optima for abundance around 20–30% and 20% cover, respectively. There was a clear relationship between predicted abundance of the Ortolan Bunting and post-fire regenerating oak shrubs. South-facing, moderately sloping areas were favoured and bare ground was a key feature of the species' habitat. A matrix combining patches of sparse oak shrubs and patches of bare ground appears to be the optimal breeding habitat in the Mediterranean. The maintenance or provision of similar habitat features, especially patches of bare ground, may prove crucial for the conservation of rapidly declining Ortolan Bunting populations on farmland across temperate Europe.     

Adaptive Patch Searching Strategies in Fragmented Landscapes

The search strategies dispersers employ to search for new habitat patches affect individuals’ search success and subsequently landscape connectivity and metapopulation viability. Some evidence indicates that individuals within the same species may display a variety of behavioural patch searching strategies rather than one species-specific strategy. This may result from landscape heterogeneity. We modelled the evolution of individual patch searching strategies in different landscapes. Specifically, we analysed whether evolution can favour different, co-existing, behavioural search strategies within one population and to what extent this coexistence of multiple strategies was dependent on landscape configuration. Using an individual-based simulation model, we studied the evolution of patch searching strategies in three different landscape configurations: uniform, random and clumped. We found that landscape configuration strongly influenced the evolved search strategy. In uniform landscapes, one fixed search strategy evolved for the entire spatially structured population, while in random and clumped landscapes, a set of different search strategies emerged. The coexistence of several search strategies also strongly depended on the dispersal mortality. We show that our result can affect landscape connectivity and metapopulation dynamics. Co-ordinating editor: N. Yamamura     

Anthropogenic transformation of the biomes, 1700 to 2000

Aim To map and characterize anthropogenic transformation of the terrestrial biosphere before and during the Industrial Revolution, from 1700 to 2000. Location Global. Methods Anthropogenic biomes (anthromes) were mapped for 1700, 1800, 1900 and 2000 using a rule‐based anthrome classification model applied to gridded global data for human population density and land use. Anthropogenic transformation of terrestrial biomes was then characterized by map comparisons at century intervals. Results In 1700, nearly half of the terrestrial biosphere was wild, without human settlements or substantial land use. Most of the remainder was in a seminatural state (45%) having only minor use for agriculture and settlements. By 2000, the opposite was true, with the majority of the biosphere in agricultural and settled anthromes, less than 20% seminatural and only a quarter left wild. Anthropogenic transformation of the biosphere during the Industrial Revolution resulted about equally from land‐use expansion into wildlands and intensification of land use within seminatural anthromes. Transformation pathways differed strongly between biomes and regions, with some remaining mostly wild but with the majority almost completely transformed into rangelands, croplands and villages. In the process of transforming almost 39% of earth's total ice‐free surface into agricultural land and settlements, an additional 37% of global land without such use has become embedded within agricultural and settled anthromes. Main conclusions Between 1700 and 2000, the terrestrial biosphere made the critical transition from mostly wild to mostly anthropogenic, passing the 50% mark early in the 20th century. At present, and ever more in the future, the form and process of terrestrial ecosystems in most biomes will be predominantly anthropogenic, the product of land use and other direct human interactions with ecosystems. Ecological research and conservation efforts in all but a few biomes would benefit from a primary focus on the novel remnant, recovering and managed ecosystems embedded within used lands.     

Effect of double-stranded DNA on maturation of dendritic cells in vitro

A preparation of human genomic fragmented double-stranded DNA (dsDNA) was used as maturation stimulus in cultures of human dendritic cells (DCs) generated in compliance with the interferon protocol. Culturing of the DCs in medium with 5 μg/ml of the DNA preparation was associated with a decrease in the relative proportion of CD14 + cells and an increase in that of CD83 + cells. These changes are markers of DC maturation. The efficiency with which the DNA preparation was able to elicit DC maturation was commensurate with that of lypopolysaccharide from bacterial cell, the standard inducer of DC maturation. Generated ex vivo, matured in the presence of the human DNA preparation, pulsed with tumor antigens mouse DCs were used as a vaccine in biological tests for its antitumor activity. The experimental results demonstrate that reinfusion of mature pulsed with tumor antigens DCs cause a statistically significant suppression of tumor graft growth.     

Importance of Interhabitat Gaps and Stepping-Stones for Lesser Woodcreepers (Xiphorhynchus fuscus) in the Atlantic Forest, Brazil

Translocation experiments showed that a woodcreeper bird species is able to move between isolated forest fragments, but this ability is limited by increasing interpatch distances. Larger distances (> 100 m) were overcome by using small stepping‐stones (isolated trees), which enhance connectivity and are useful for the species conservation in fragmented landscapes.     

How fast and far might tree species migrate in the eastern United States due to climate change?

Aim We describe and use a model, SHIFT, to estimate potential migration due to climate change over the next 100 years. Location Eastern United States. Methods Five species, currently confined to the eastern half of the United States and not extending into Canada, were used to assess migration potential: Diospyros virginiana (persimmon), Liquidambar styraciflua (sweetgum), Oxydendrum arboreum (sourwood), Pinus taeda (loblolly pine), and Quercus falcata var. falcata (southern red oak). SHIFT is a matrix simulation model using simple inverse power functions to provide a distance decay of seed dispersal and is driven primarily by the abundance of the species near the boundary, the forest density within and beyond the boundary, and the distance between cells. For each cell outside the current boundary, the model creates an estimate of the probability that each unoccupied cell will become colonized over a period of 100 years. SHIFT is a ‘fat‐tailed’ migration model that allows rare very long distance dispersal events and colonization could occur up to 500 km beyond the current distribution boundary. Model outputs were analysed using transects through sections showing relatively low and high colonization probabilities as a result of low and high densities of target trees (high source strength) as well as high densities of forest (high sink strength). We also assess migration potential for species by concentric rings around the current boundary. Results Model outputs show the generally limited nature of migration for all five species over 100 years. There is a relatively high probability of colonization within a zone of 10–20 km (depending on habitat quality and species abundance) from the current boundary, but a small probability of colonization where the distance from the current boundary exceeds about 20 km. Whether biologically plausible or not, rare very long distance migration events are not sufficient to rescue migration. Species abundance (the source strength of migration) near the range boundary carried relatively more influence than percentage forest cover (sink strength) in determining migration rates. Main conclusion The transect evaluation revealed the importance of abundance of the species near the boundary, indicating that rare species may have much more difficulty in unassisted northward migration due to climate change. The concentric rings analysis of the model outputs showed that only the first 10–20 km of area would have a reasonably high probability of colonization. Rare, long‐distance events permit colonization of remote outliers, but much more needs to be understood about the likelihood of these rare events to predict the frequency of outlier establishment.     

Isolation of 10 polymorphic microsatellite loci from Antirhea borbonica (Rubiaceae)

We report here the characteristics of 10 microsatellite markers isolated from a microsatellite‐enriched DNA library from Antirhea borbonica, Gmel (Rubiaceae). Antirhea borbonica is an endemic tree on the islands of La Réunion and Mauritius (Indian Ocean) where it occurs on young lava flows (fragmented and perturbed habitat) and in old primary forest. Ten polymorphic loci were characterized, with two to 15 alleles per locus, based on samples from six populations. These loci will be useful for analysing population structure in a metapopulation context where populations frequently go extinct.