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Livestock productivity and profitability are threatened by livestock diseases. In this study, we examine farmers' revealed preferences for testing and treating gastrointestinal parasites in sheep in Sweden, taking into account the sequential structure of these decisions. We control for preventive measures, as well as the potential impact of wildlife–livestock disease transmission on farmers' decisions. A zero-inflated ordered probit model is used to estimate the determinants of farmers' decisions, and we cross-validate the robustness of the results to alternative model assumptions. Results from the regressions are used to calculate the consequences of these choices for farmers' profits. The results show that treatment decisions are informed by faecal testing, while both testing and treatment are influenced by the grazing practices, the size of the operation and access to information. Contrary to expectations from the conceptual framework, preventive management practices are positively correlated with treatment. Farmers take multiple risk factors into account when deciding on testing, but we do not find that the same factors affect the outcome of treatment. The economic impacts are small and suggest that treatment without prior testing is more profitable for the farmer than informed treatment. If widespread treatment increases drug resistance, this could motivate policies that encourage testing.

We report a European wide assessment of the economic burden of gastrointestinal nematodes, Fasciola hepatica (common liver fluke) and Dictyocaulus viviparus (bovine lungworm) infections to the ruminant livestock industry. The economic impact of these parasitic helminth infections was estimated by a deterministic spreadsheet model as a function of the proportion of the ruminant population exposed to grazing, the infection frequency and intensity, the effect of the infection on animal productivity and mortality and anthelmintic treatment costs. In addition, we estimated the costs of anthelmintic resistant nematode infections and collected information on public research budgets addressing helminth infections in ruminant livestock. The epidemiologic and economic input data were collected from international databases and via expert opinion of the Working Group members of the European Co-operation in Science and Technology (COST) action COMbatting Anthelmintic Resistance in ruminants (COMBAR). In order to reflect the effects of uncertainty in the input data, low and high cost estimates were obtained by varying uncertain input data arbitrarily in both directions by 20 %. The combined annual cost [low estimate-high estimate] of the three helminth infections in 18 participating countries was estimated at € 1.8 billion [€ 1.0–2.7 billion]. Eighty-one percent of this cost was due to lost production and 19 % was attributed to treatment costs. The cost of gastrointestinal nematode infections with resistance against macrocyclic lactones was estimated to be € 38 million [€ 11–87 million] annually. The annual estimated costs of helminth infections per sector were € 941 million [€ 488 – 1442 million] in dairy cattle, € 423 million [€ 205–663 million] in beef cattle, € 151million [€ 90–213 million] in dairy sheep, € 206 million [€ 132–248 million] in meat sheep and € 86 million [€ 67–107 million] in dairy goats. Important data gaps were present in all phases of the calculations which

Ectotherm development rates often show adaptive divergence along climatic gradients, but the genetic basis for this variation is rarely studied. Here, we investigated the genetic basis for phenotypic variation in larval development in the moor frog Rana arvalis from five regions along a latitudinal gradient from Germany to northern Sweden. We focused on the C/EBP‐1 gene, a transcription factor associated with larval development time. Allele frequencies at C/EBP‐1 varied strongly among geographical regions. Overall, the distribution of alleles along the gradient was in concordance with the dual post‐glacial colonization routes into Scandinavia, with a large number of alleles exclusively present along the southern colonization route. Only three of 38 alleles were shared between the routes. Analysis of contemporary selection on C/EBP‐1 showed divergent selection among the regions, probably reflecting adaptation to the local environmental conditions, although this was especially strong between southern and northern regions coinciding also with lineages from different colonization routes. Overall, the C/EBP‐1 gene has historically been under purifying selection, but two specific amino acid positions showed significant signals of positive selection. These positions showed divergence between southern and northern regions, and we suggest that they are functionally involved in the climatic adaptation of larval development. Using phenotypic data from a common garden experiment, we found evidence for specific C/EBP‐1 alleles being correlated with larval development time, suggesting a functional role in adaptation of larval development to large‐scale climatic variation.

Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.

Gastrointestinal (GI) nematode control has an important role to play in increasing livestock production from a limited natural resource base and to improve animal health and welfare. In this synthetic review, we identify key research priorities for GI nematode control in farmed ruminants and pigs, to support the development of roadmaps and strategic research agendas by governments, industry and policymakers. These priorities were derived from the DISCONTOOLS gap analysis for nematodes and follow-up discussions within the recently formed Livestock Helminth Research Alliance (LiHRA). In the face of ongoing spread of anthelmintic resistance (AR), we are increasingly faced with a failure of existing control methods against GI nematodes. Effective vaccines against GI nematodes are generally not available, and anthelmintic treatment will therefore remain a cornerstone for their effective control. At the same time, consumers and producers are increasingly concerned with environmental issues associated with chemical parasite control. To address current challenges in GI nematode control, it is crucial to deepen our insights into diverse aspects of epidemiology, AR, host immune mechanisms and the socio-psychological aspects of nematode control. This will enhance the development, and subsequent uptake, of the new diagnostics, vaccines, pharma-/nutraceuticals, control methods and decision support tools required to respond to the spread of AR and the shifting epidemiology of GI nematodes in response to climatic, land-use and farm husbandry changes. More emphasis needs to be placed on the upfront evaluation of the economic value of these innovations as well as the socio-psychological aspects to prioritize research and facilitate uptake of innovations in practice. Finally, targeted regulatory guidance is needed to create an innovation-supportive environment for industries and to accelerate the access to market of new control tools.

Background: The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. Results: The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450. Conclusion: We used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular path

Background: The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. Results: The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450. Conclusion: We used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular path

The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences

As many seaduck populations around the world have been reported to be in decline, there is an increasing demand for knowledge about intrinsic and extrinsic factors determining population dynamics of these species. In this study, we analyzed long-term dynamics of the summer population of Velvet Scoters (Melanitta fusca) breeding in the Åland archipelago in the Baltic Sea; in particular, we examined the influence of winter weather and density dependence on population change. The studied population exhibited substantial fluctuations but only a weak negative trend during the total period of 58 years (1949–2007), and no significant trend at all during the latter three decades of the study (1977–2007). We tested for density dependence and incorporated the winter North Atlantic Oscillation index into the model to test for effects of winter conditions. Our final model explained 56.3 % of the variance of population growth of the studied population. Delayed density dependence explained 29.7 %, pre-breeding climate 8.3 %, and post-breeding climate 18.3 % of the variance. That breeding success is density dependent in a delayed manner is in accordance with the apprehension that Velvet Scoters breed at the age of 2 years. We conclude that density dependence and winter conditions must be taken into consideration when discussing population changes in seaducks in general and the Velvet Scoter in particular., As many seaduck populations around the world have been reported to be in decline, there is an increasing demand for knowledge about intrinsic and extrinsic factors determining population dynamics of these species. In this study, we analyzed long-term dynamics of the summer population of Velvet Scoters (Melanitta fusca) breeding in the Åland archipelago in the Baltic Sea; in particular, we examined the influence of winter weather and density dependence on population change. The studied population exhibited substantial fluctuations but only a weak negative trend during the total period of 58 years (1949–2007), and no significant trend at all during the latter three decades of the study (1977–2007). We tested for density dependence and incorporated the winter North Atlantic Oscillation index into the model to test for effects of winter conditions. Our final model explained 56.3 % of the variance of population growth of the studied population. Delayed density dependence explained 29.7 %, pre-breeding climate 8.3 %, and post-breeding climate 18.3 % of the variance. That breeding success is density dependent in a delayed manner is in accordance with the apprehension that Velvet Scoters breed at the age of 2 years. We conclude that density dependence and winter conditions must be taken into consideration when discussing population changes in seaducks in general and the Velvet Scoter in particular.

As many seaduck populations around the world have been reported to be in decline, there is an increasing demand for knowledge about intrinsic and extrinsic factors determining population dynamics of these species. In this study, we analyzed long-term dynamics of the summer population of Velvet Scoters (Melanitta fusca) breeding in the Åland archipelago in the Baltic Sea; in particular, we examined the influence of winter weather and density dependence on population change. The studied population exhibited substantial fluctuations but only a weak negative trend during the total period of 58 years (1949–2007), and no significant trend at all during the latter three decades of the study (1977–2007). We tested for density dependence and incorporated the winter North Atlantic Oscillation index into the model to test for effects of winter conditions. Our final model explained 56.3 % of the variance of population growth of the studied population. Delayed density dependence explained 29.7 %, pre-breeding climate 8.3 %, and post-breeding climate 18.3 % of the variance. That breeding success is density dependent in a delayed manner is in accordance with the apprehension that Velvet Scoters breed at the age of 2 years. We conclude that density dependence and winter conditions must be taken into consideration when discussing population changes in seaducks in general and the Velvet Scoter in particular., As many seaduck populations around the world have been reported to be in decline, there is an increasing demand for knowledge about intrinsic and extrinsic factors determining population dynamics of these species. In this study, we analyzed long-term dynamics of the summer population of Velvet Scoters (Melanitta fusca) breeding in the Åland archipelago in the Baltic Sea; in particular, we examined the influence of winter weather and density dependence on population change. The studied population exhibited substantial fluctuations but only a weak negative trend during the total period of 58 years (1949–2007), and no significant trend at all during the latter three decades of the study (1977–2007). We tested for density dependence and incorporated the winter North Atlantic Oscillation index into the model to test for effects of winter conditions. Our final model explained 56.3 % of the variance of population growth of the studied population. Delayed density dependence explained 29.7 %, pre-breeding climate 8.3 %, and post-breeding climate 18.3 % of the variance. That breeding success is density dependent in a delayed manner is in accordance with the apprehension that Velvet Scoters breed at the age of 2 years. We conclude that density dependence and winter conditions must be taken into consideration when discussing population changes in seaducks in general and the Velvet Scoter in particular.

Infections with parasitic helminths (nematodes and trematodes) represent a significant economic and welfare burden to the global ruminant livestock industry. The increasing prevalence of anthelmintic resistance means that current control programmes are costly and unsustainable in the long term. Recent changes in the epidemiology, seasonality and geographic distribution of helminth infections have been attributed to climate change. However, other changes in environment (e.g., land use) and in livestock farming, such as intensification and altered management practices, will also have an impact on helminth infections. Sustainable control of helminth infections in a changing world requires detailed knowledge of these interactions. In particular, there is a need to devise new, sustainable strategies for the effective control of ruminant helminthoses in the face of global change. In this paper, we consider the impact of helminth infections in grazing ruminants, taking a European perspective, and identify scientific and applied priorities to mitigate these impacts. These include the development and deployment of efficient, high-throughput diagnostic tests to support targeted intervention, modelling of geographic and seasonal trends in infection, more thorough economic data and analysis of the impact of helminth infections and greater translation and involvement of end-users in devising and disseminating best practices. Complex changes in helminth epidemiology will require innovative solutions. By developing and using new technologies and models, the use of anthelmintics can be optimised to limit the development and spread of drug resistance and to reduce the overall economic impact of helminth infections. This will be essential to the continued productivity and profitability of livestock farming in Europe and its contribution to regional and global food security.

Background: Dictyocaulus species are strongylid nematodes of major veterinary significance in ruminants, such as cattle and cervids, and cause serious bronchitis or pneumonia (dictyocaulosis or “husk”). There has been ongoing controversy surrounding the validity of some Dictyocaulus species and their host specificity. Here, we sequenced and characterized the mitochondrial (mt) genomes of Dictyocaulus viviparus (from Bos taurus) with Dictyocaulus sp. cf. eckerti from red deer (Cervus elaphus), used mt datasets to assess the genetic relationship between these and related parasites, and predicted markers for future population genetic or molecular epidemiological studies. Methods: The mt genomes were amplified from single adult males of D. viviparus and Dictyocaulus sp. cf. eckerti (from red deer) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), also employing data for other strongylids for comparative purposes. Results: The circular mt genomes were 13,310 bp (D. viviparus) and 13,296 bp (Dictyocaulus sp. cf. eckerti) in size, and each contained 12 protein-encoding, 22 transfer RNA and 2 ribosomal RNA genes, consistent with other strongylid nematodes sequenced to date. Sliding window analysis identified genes with high or low levels of nucleotide diversity between the mt genomes. At the predicted mt proteomic level, there was an overall sequence difference of 34.5% between D. viviparus and Dictyocaulus sp. cf. eckerti, and amino acid sequence variation within each species was usually much lower than differences between species. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 mt proteins showed that both D. viviparus and Dictyocaulus sp. cf. eckerti were closely related, and grouped to the exclusion of selected members of the sup

Black-tailed (Limosa limosa) and Hudsonian Godwits (L. haemastica) are sometimes described as a superspecies. The Black-tailed Godwit is further split into three subspecies on the basis of morphological differences (L. l. limosa, L. l. islandica and L. l. melanuroides). We studied variation in partial mtDNA control region sequences among Black-tailed and Hudsonian Godwits which showed 5% divergence. Black-tailed and Hudsonian Godwits were thus clearly differentiated and the separate species status for the two taxa is validated. All three subspecies described for the Black-tailed Godwit had unique haplotypes but the genetic distances were small (0.3–0.6%). Despite small genetic differences we could not detect any substantial gene flow between any of the subspecies as haplotypes were private to each subspecies. Thus, genetic variation within Black-tailed Godwits showed a clear geographic structure. We found a high proportion of rare private haplotypes in three fringe populations of the nominate subspecies of the Black-tailed Godwit (L. l. limosa) where godwits breed in low numbers, but no genetic variation at all in a sample from the Netherlands where godwits are abundant. This suggests that Dutch Godwits may have been affected by a founder effect., Black-tailed (Limosa limosa) and Hudsonian Godwits (L. haemastica) are sometimes described as a superspecies. The Black-tailed Godwit is further split into three subspecies on the basis of morphological differences (L. l. limosa, L. l. islandica and L. l. melanuroides). We studied variation in partial mtDNA control region sequences among Black-tailed and Hudsonian Godwits which showed 5% divergence. Black-tailed and Hudsonian Godwits were thus clearly differentiated and the separate species status for the two taxa is validated. All three subspecies described for the Black-tailed Godwit had unique haplotypes but the genetic distances were small (0.3–0.6%). Despite small genetic differences we could not detect any substantial gene flow between any of the subspecies as haplotypes were private to each subspecies. Thus, genetic variation within Black-tailed Godwits showed a clear geographic structure. We found a high proportion of rare private haplotypes in three fringe populations of the nominate subspecies of the Black-tailed Godwit (L. l. limosa) where godwits breed in low numbers, but no genetic variation at all in a sample from the Netherlands where godwits are abundant. This suggests that Dutch Godwits may have been affected by a founder effect.

Black-tailed (Limosa limosa) and Hudsonian Godwits (L. haemastica) are sometimes described as a superspecies. The Black-tailed Godwit is further split into three subspecies on the basis of morphological differences (L. l. limosa, L. l. islandica and L. l. melanuroides). We studied variation in partial mtDNA control region sequences among Black-tailed and Hudsonian Godwits which showed 5% divergence. Black-tailed and Hudsonian Godwits were thus clearly differentiated and the separate species status for the two taxa is validated. All three subspecies described for the Black-tailed Godwit had unique haplotypes but the genetic distances were small (0.3–0.6%). Despite small genetic differences we could not detect any substantial gene flow between any of the subspecies as haplotypes were private to each subspecies. Thus, genetic variation within Black-tailed Godwits showed a clear geographic structure. We found a high proportion of rare private haplotypes in three fringe populations of the nominate subspecies of the Black-tailed Godwit (L. l. limosa) where godwits breed in low numbers, but no genetic variation at all in a sample from the Netherlands where godwits are abundant. This suggests that Dutch Godwits may have been affected by a founder effect., Black-tailed (Limosa limosa) and Hudsonian Godwits (L. haemastica) are sometimes described as a superspecies. The Black-tailed Godwit is further split into three subspecies on the basis of morphological differences (L. l. limosa, L. l. islandica and L. l. melanuroides). We studied variation in partial mtDNA control region sequences among Black-tailed and Hudsonian Godwits which showed 5% divergence. Black-tailed and Hudsonian Godwits were thus clearly differentiated and the separate species status for the two taxa is validated. All three subspecies described for the Black-tailed Godwit had unique haplotypes but the genetic distances were small (0.3–0.6%). Despite small genetic differences we could not detect any substantial gene flow between any of the subspecies as haplotypes were private to each subspecies. Thus, genetic variation within Black-tailed Godwits showed a clear geographic structure. We found a high proportion of rare private haplotypes in three fringe populations of the nominate subspecies of the Black-tailed Godwit (L. l. limosa) where godwits breed in low numbers, but no genetic variation at all in a sample from the Netherlands where godwits are abundant. This suggests that Dutch Godwits may have been affected by a founder effect.

We found significant population structure and isolation by distance among samples of flounder (Platichthys flesus) in the Baltic, Kattegat and Skagerrak seas using microsatellite genetic markers. This pattern was almost entirely due to a difference between flounder that have demersal spawning in the northern Baltic, as compared to pelagic spawners in the southern Baltic and on the west coast of Sweden. Among demersal spawners we found neither genetic differentiation nor any isolation by distance among sampling sites. We speculate that demersal flounder are descendants of a population that colonized the Baltic previous to pelagic spawners. The demersal flounder may thus have had longer time to adapt to the low salinity in the Baltic, and accordingly display egg characteristics that make it possible to reproduce at the low salinity levels in the northern Baltic. Among pelagic spawners significant isolation by distance was detected. Pelagic spawners have previously been shown to display clinal variation in egg size, which allows them to float also at the moderate salinity levels up to the region north of the island Bornholm. Management units for harvesting should ideally be based on true biological populations, and for the commercially important flounder up to 15 different management stocks in the Baltic have been suggested. We could not find a population genetic foundation for such a high number of management units, and our data suggest three management units: the northern Baltic (demersal populations), southern Baltic with the Oresund straits and the most northwestern sampling sites (Skagerrak, Kattegat and North Sea).

1. During the last centuries, the breeding range of the great snipe Gallinago media has declined dramatically in the western part of its distribution. To examine present population dynamics in the Scandinavian mountains, we collected and analysed a 19-year time series of counts of great snipe males at leks in central Norway, 1987–2005. 2. The population showed large annual fluctuations in the number of males displaying at lek sites (range 45–90 males at the peak of the mating season), but no overall trend. 3. We detected presence of direct density-dependent mechanisms regulating this population. Inclusion of the density-dependent term in a Ricker-type model significantly improved the fit with observed data (evaluated with Parametric Bootstrap Likelihood Ratio tests and Akaike's Information Criterion for small sample size). 4. An analysis of (a number of a priori likely) environmental covariates suggests that the population dynamics were affected by conditions influencing reproduction and survival of offspring during the summer, but not by conditions influencing survival at the wintering grounds in Africa. This is in contrast to many altricial birds breeding in the northern hemisphere, and supports the idea that population dynamics of migratory nidifugous birds are more influenced by conditions during reproduction 5. Inclusion of these external factors into our model improved the detectability of density dependence. This illustrates that allowing for external effects may increase statistical power of density dependence tests and thus be of particular importance in relatively short time series. 6. In our best model of the population dynamics, two likely density-independent offspring survival covariates explained 47·3% of the variance in great snipe numbers (predation pressure estimated by willow grouse reproductive success and food availability estimated by the amount of precipitation in June), whereas density dependence explained 35·5%. Demographic stochasticity and, 1. During the last centuries, the breeding range of the great snipe Gallinago media has declined dramatically in the western part of its distribution. To examine present population dynamics in the Scandinavian mountains, we collected and analysed a 19-year time series of counts of great snipe males at leks in central Norway, 1987–2005. 2. The population showed large annual fluctuations in the number of males displaying at lek sites (range 45–90 males at the peak of the mating season), but no overall trend. 3. We detected presence of direct density-dependent mechanisms regulating this population. Inclusion of the density-dependent term in a Ricker-type model significantly improved the fit with observed data (evaluated with Parametric Bootstrap Likelihood Ratio tests and Akaike's Information Criterion for small sample size). 4. An analysis of (a number of a priori likely) environmental covariates suggests that the population dynamics were affected by conditions influencing reproduction and survival of offspring during the summer, but not by conditions influencing survival at the wintering grounds in Africa. This is in contrast to many altricial birds breeding in the northern hemisphere, and supports the idea that population dynamics of migratory nidifugous birds are more influenced by conditions during reproduction 5. Inclusion of these external factors into our model improved the detectability of density dependence. This illustrates that allowing for external effects may increase statistical power of density dependence tests and thus be of particular importance in relatively short time series. 6. In our best model of the population dynamics, two likely density-independent offspring survival covariates explained 47·3% of the variance in great snipe numbers (predation pressure estimated by willow grouse reproductive success and food availability estimated by the amount of precipitation in June), whereas density dependence explained 35·5%. Demographic stochasticity and

The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism., The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism.

We applied a phenotypic QST (PST) vs. FST approach to study spatial variation in selection among great snipe (Gallinago media) populations in two regions of northern Europe. Morphological divergence between regions was high despite low differentiation in selectively neutral genetic markers, whereas populations within regions showed very little neutral divergence and trait differentiation. QST > FST was robust against altering assumptions about the additive genetic proportions of variance components. The homogenizing effect of gene flow (or a short time available for neutral divergence) has apparently been effectively counterbalanced by differential natural selection, although one trait showed some evidence of being under uniform stabilizing selection. Neutral markers can hence be misleading for identifying evolutionary significant units, and adopting the PST–FST approach might therefore be valuable when common garden experiments is not an option. We discuss the statistical difficulties of documenting uniform selection as opposed to divergent selection, and the need for estimating measurement error. Instead of only comparing overall QST and FST values, we advocate the use of partial matrix permutation tests to analyse pairwise QST differences among populations, while statistically controlling for neutral differentiation., We applied a phenotypic QST (PST) vs. FST approach to study spatial variation in selection among great snipe (Gallinago media) populations in two regions of northern Europe. Morphological divergence between regions was high despite low differentiation in selectively neutral genetic markers, whereas populations within regions showed very little neutral divergence and trait differentiation. QST > FST was robust against altering assumptions about the additive genetic proportions of variance components. The homogenizing effect of gene flow (or a short time available for neutral divergence) has apparently been effectively counterbalanced by differential natural selection, although one trait showed some evidence of being under uniform stabilizing selection. Neutral markers can hence be misleading for identifying evolutionary significant units, and adopting the PST–FST approach might therefore be valuable when common garden experiments is not an option. We discuss the statistical difficulties of documenting uniform selection as opposed to divergent selection, and the need for estimating measurement error. Instead of only comparing overall QST and FST values, we advocate the use of partial matrix permutation tests to analyse pairwise QST differences among populations, while statistically controlling for neutral differentiation.

1. During the last centuries, the breeding range of the great snipe Gallinago media has declined dramatically in the western part of its distribution. To examine present population dynamics in the Scandinavian mountains, we collected and analysed a 19-year time series of counts of great snipe males at leks in central Norway, 1987–2005. 2. The population showed large annual fluctuations in the number of males displaying at lek sites (range 45–90 males at the peak of the mating season), but no overall trend. 3. We detected presence of direct density-dependent mechanisms regulating this population. Inclusion of the density-dependent term in a Ricker-type model significantly improved the fit with observed data (evaluated with Parametric Bootstrap Likelihood Ratio tests and Akaike's Information Criterion for small sample size). 4. An analysis of (a number of a priori likely) environmental covariates suggests that the population dynamics were affected by conditions influencing reproduction and survival of offspring during the summer, but not by conditions influencing survival at the wintering grounds in Africa. This is in contrast to many altricial birds breeding in the northern hemisphere, and supports the idea that population dynamics of migratory nidifugous birds are more influenced by conditions during reproduction 5. Inclusion of these external factors into our model improved the detectability of density dependence. This illustrates that allowing for external effects may increase statistical power of density dependence tests and thus be of particular importance in relatively short time series. 6. In our best model of the population dynamics, two likely density-independent offspring survival covariates explained 47·3% of the variance in great snipe numbers (predation pressure estimated by willow grouse reproductive success and food availability estimated by the amount of precipitation in June), whereas density dependence explained 35·5%. Demographic stochasticity and, 1. During the last centuries, the breeding range of the great snipe Gallinago media has declined dramatically in the western part of its distribution. To examine present population dynamics in the Scandinavian mountains, we collected and analysed a 19-year time series of counts of great snipe males at leks in central Norway, 1987–2005. 2. The population showed large annual fluctuations in the number of males displaying at lek sites (range 45–90 males at the peak of the mating season), but no overall trend. 3. We detected presence of direct density-dependent mechanisms regulating this population. Inclusion of the density-dependent term in a Ricker-type model significantly improved the fit with observed data (evaluated with Parametric Bootstrap Likelihood Ratio tests and Akaike's Information Criterion for small sample size). 4. An analysis of (a number of a priori likely) environmental covariates suggests that the population dynamics were affected by conditions influencing reproduction and survival of offspring during the summer, but not by conditions influencing survival at the wintering grounds in Africa. This is in contrast to many altricial birds breeding in the northern hemisphere, and supports the idea that population dynamics of migratory nidifugous birds are more influenced by conditions during reproduction 5. Inclusion of these external factors into our model improved the detectability of density dependence. This illustrates that allowing for external effects may increase statistical power of density dependence tests and thus be of particular importance in relatively short time series. 6. In our best model of the population dynamics, two likely density-independent offspring survival covariates explained 47·3% of the variance in great snipe numbers (predation pressure estimated by willow grouse reproductive success and food availability estimated by the amount of precipitation in June), whereas density dependence explained 35·5%. Demographic stochasticity and

The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism., The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism.

We applied a phenotypic QST (PST) vs. FST approach to study spatial variation in selection among great snipe (Gallinago media) populations in two regions of northern Europe. Morphological divergence between regions was high despite low differentiation in selectively neutral genetic markers, whereas populations within regions showed very little neutral divergence and trait differentiation. QST > FST was robust against altering assumptions about the additive genetic proportions of variance components. The homogenizing effect of gene flow (or a short time available for neutral divergence) has apparently been effectively counterbalanced by differential natural selection, although one trait showed some evidence of being under uniform stabilizing selection. Neutral markers can hence be misleading for identifying evolutionary significant units, and adopting the PST–FST approach might therefore be valuable when common garden experiments is not an option. We discuss the statistical difficulties of documenting uniform selection as opposed to divergent selection, and the need for estimating measurement error. Instead of only comparing overall QST and FST values, we advocate the use of partial matrix permutation tests to analyse pairwise QST differences among populations, while statistically controlling for neutral differentiation., We applied a phenotypic QST (PST) vs. FST approach to study spatial variation in selection among great snipe (Gallinago media) populations in two regions of northern Europe. Morphological divergence between regions was high despite low differentiation in selectively neutral genetic markers, whereas populations within regions showed very little neutral divergence and trait differentiation. QST > FST was robust against altering assumptions about the additive genetic proportions of variance components. The homogenizing effect of gene flow (or a short time available for neutral divergence) has apparently been effectively counterbalanced by differential natural selection, although one trait showed some evidence of being under uniform stabilizing selection. Neutral markers can hence be misleading for identifying evolutionary significant units, and adopting the PST–FST approach might therefore be valuable when common garden experiments is not an option. We discuss the statistical difficulties of documenting uniform selection as opposed to divergent selection, and the need for estimating measurement error. Instead of only comparing overall QST and FST values, we advocate the use of partial matrix permutation tests to analyse pairwise QST differences among populations, while statistically controlling for neutral differentiation.

We studied microsatellite genetic variation in different geographic populations of black grouse (Tetrao tetrix) across the European range. We applied a clustering algorithm based finding genetic clusters in linkage and Hardy-Weinberg and identified 5 independent clusters. These clusters were consisting of: Fenno-Scandian; British, Alpine, Dutch and lowland populations from Austria and Germany, respectively. Based on previous knowledge, populations were grouped in to three different categories: isolated, contiguous and continuous, respectively. Genetic diversity, measured as observed (HO) and expected heterozygosity (HE), respectively, were lower in isolated populations as compared to the other two categories that did not differ amongst one another. We found a higher number of alleles in contiguous populations as compared to isolated ones and yet more in continuous populations. Observed heterozygosity and average number of alleles showed positive relationships with estimates of census population size. These results imply that lowered genetic variability in black grouse populations is affected by both population size and isolation but the independent effects of each of these are hard to disentangle. Bottleneck analyses suggested that British populations and one isolated population in central Germany (Rhön) have been recently bottlenecked. It is possible that isolated populations may recover in numbers from population bottlenecks. However, to restore genetic variability requires longer time and connectivity. Our results imply that the connectivity of small and isolated populations in Western Europe should be improved or else these face the risk of extinction due to genetic and demographic stochasticity