Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution.

Over the last decade, the genomic revolution has offered the possibility to generate tremendous amounts of data that contain valuable information on the genetic basis of phenotypic traits, such as those linked to human diseases or those that allow for species to adapt to a changing environment. Most ecologically relevant traits are controlled by a large number of genes with small individual effects on trait variation, but that are connected with one another through complex developmental, metabolic and biochemical networks. As a result, it has recently been suggested that most adaptation events in natural populations are reached via correlated changes at multiple genes at a time, for which the name polygenic adaptation has been coined.

History and environment shape species pools and community diversity in European beech forests.

A central hypothesis of ecology states that regional diversity influences local diversity through species-pool effects. Species pools are supposedly shaped by large-scale factors and then filtered into ecological communities, but understanding these processes requires the analysis of large datasets across several regions. Here, we use a framework of community assembly at a continental scale to test the relative influence of historical and environmental drivers, in combination with regional or local species pools, on community species richness and community completeness.

Molecular evolution and invasion pattern of Cryphonectria hypovirus 1 in Europe: Mutation rate, and selection pressure differ between genome domains.

Understanding virus evolution is a fundamental goal of virology, evolutionary biology, and disease epidemiology. We provide a detailed analysis of evolution and origin of Cryphonectria hypovirus 1 (CHV1) populations in Europe, based on the complete genome sequence of all European subtypes. Phylogenetic analyses divided European strains into two closely related clades.

Genomic Quantitative Genetics to Study Evolution in the Wild.

Quantitative genetic theory provides a means of estimating the evolutionary potential of natural populations. However, this approach was previously only feasible in systems where the genetic relatedness between individuals could be inferred from pedigrees or experimental crosses. The genomic revolution opened up the possibility of obtaining the realized proportion of genome shared among individuals in natural populations of virtually any species, which could promise (more) accurate estimates of quantitative genetic parameters in virtually any species.

Enhanced land use datasets and future scenarios of land change for Slovakia.

The presented datasets relate to the research article entitled "Land changes in Slovakia: past processes and future directions" [8]. The datasets include the land use and cover (LUC) maps of Slovakia for the years 2006 and 2012 and maps of five future land use scenarios for 2040 developed along the axes of globalisation vs. regionalisation and low vs.

Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity.

Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data.

Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions.

Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested whether >3500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q.

Expert-based versus habitat-suitability models to develop resistance surfaces in landscape genetics.

Landscape genetics aims to investigate functional connectivity among wild populations by evaluating the impact of landscape features on gene flow. Genetic distances among populations or individuals are generally better explained by least-cost path (LCP) distances derived from resistance surfaces than by simple Euclidean distances. Resistance surfaces reflect the cost for an organism to move through particular landscape elements.

Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri.

Numerous landscape genomic studies have identified single-nucleotide polymorphisms (SNPs) and genes potentially involved in local adaptation. Rarely, it has been explicitly evaluated whether these environmental associations also hold true beyond the populations studied. We tested whether putatively adaptive SNPs in Arabidopsis halleri (Brassicaceae), characterized in a previous study investigating local adaptation to a highly heterogeneous environment, show the same environmental associations in an independent, geographically enlarged set of 18 populations.

Impact of alkaline dust pollution on genetic variation of Usnea subfloridana populations.

Very little is known whether and how air pollution impacts genetic diversity of lichenized fungi that are well-known indicators of environmental quality. We studied the genetic variation of eight Usnea subfloridana populations in Pinus sylvestris-dominated boreal forest stands in southern Estonia, Northern Europe; four of these populations were exposed to long-term dust pollution released from unpaved road. The mean bark pH of lichen phorophyte differed considerably between polluted and unpolluted forest stands.

Repetitive flanking sequences challenge microsatellite marker development: a case study in the lepidopteran Melanargia galathea.

Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.

Relative reproductive success of co-infecting parasite genotypes under intensified within-host competition.

In nature, host individuals are commonly simultaneously infected with more than one genotype of the same parasite species. These co-infecting parasites often interact, which can affect their fitness and shape host-parasite ecology and evolution. Many of such interactions take place through competition for limited host resources.

A practical guide to environmental association analysis in landscape genomics.

Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible.

Functional adjustments of xylem anatomy to climatic variability: insights from long-term Ilex aquifolium tree-ring series.

The present study assessed the effects of climatic conditions on radial growth and functional anatomical traits, including ring width, vessel size, vessel frequency and derived variables, i.e., potential hydraulic conductivity and xylem vulnerability to cavitation in Ilex aquifolium L.

Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing.

The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species.

Singing from the grave: DNA from a 180 year old type specimen confirms the identity of Chrysoperla carnea (Stephens).

Historically serving as repositories for morphologically-based taxonomic research, natural history collections are now increasingly being targeted in studies utilizing DNA data. The development of advanced molecular techniques has facilitated extraction of useable DNA from old specimens, including type material. Sequencing diagnostic molecular markers from type material enables accurate species designation, especially where modern taxonomic hypotheses confirm morphologically cryptic species complexes.

A new East-Asian species in the Chrysoperla carnea-group of cryptic lacewing species (Neuroptera: Chrysopidae) based on distinct larval morphology and a unique courtship song.

Larval morphology and substrate-borne vibrational courtship songs have been hypothesized to distinguish and isolate Chrysoperla 'nipponensis-B' from true 'Type A' Chrysoperla nipponensis (Okamoto), both of which occur sympatrically in eastern Asia. Here, we formally describe C. 'nipponensis-B' as Chrysoperla nigrocapitata sp.

Modelling the meteorological forest fire niche in heterogeneous pyrologic conditions.

Fire regimes are strongly related to weather conditions that directly and indirectly influence fire ignition and propagation. Identifying the most important meteorological fire drivers is thus fundamental for daily fire risk forecasting. In this context, several fire weather indices have been developed focussing mainly on fire-related local weather conditions and fuel characteristics.

Human-wildlife interactions and zoonotic transmission of Echinococcus multilocularis.

The life cycle of the zoonotic cestode Echinococcus multilocularis depends on canids (mainly red foxes) as definitive hosts and on their specific predation on rodent species (intermediate hosts). Host densities and predation rates are key drivers for infection with parasite eggs. We demonstrate that they strongly depend on multi-faceted human-wildlife interactions: vaccination against rabies, elimination of top predators, and changing attitude towards wildlife (feeding) contribute to high fox densities.

Validation of outlier loci through replication in independent data sets: a test on Arabis alpina.

Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets.

Isolation-by-distance in landscapes: considerations for landscape genetics.

In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern).

Multiple introductions and recombination in Cryphonectria hypovirus 1: perspective for a sustainable biological control of chestnut blight.

Cryphonectria hypovirus 1 (CHV1) is a mycovirus which decreases the virulence of its fungal host Cryphonectria parasitica, the causal agent of chestnut blight recently introduced in Europe. The understanding of the evolutionary processes which have shaped CHV1 populations in Europe is required to develop a sustainable biocontrol strategy targeting chestnut blight and effective in European chestnut forests. To retrace the evolutionary history of CHV1, we analyzed sequences from two genomic regions on a collection of 55 CHV1 strains from France and northern Spain, two countries where multiple introductions of C.