The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird.

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts.

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.

Introduced house sparrows (Passer domesticus) have greater variation in DNA methylation than native house sparrows.

As a highly successful introduced species, house sparrows (Passer domesticus) respond rapidly to their new habitats, generating phenotypic patterns across their introduced range that resemble variation in native regions. Epigenetic mechanisms likely facilitate the success of introduced house sparrows by aiding particular individuals to adjust their phenotypes plastically to novel conditions. Our objective here was to investigate patterns of DNA methylation among populations of house sparrows at a broad geographic scale that included different introduction histories: invading, established, and native. We defined the invading category as the locations with introductions less than 70 years ago and the established category as the locations with greater than 70 years since introduction. We screened DNA methylation among individuals (n = 45) by epiRADseq, expecting that variation in DNA methylation among individuals from invading populations would be higher when compared with individuals from established and native populations. Invading house sparrows had the highest variance in DNA methylation of all three groups, but established house sparrows also had higher variance than native ones. The highest number of differently methylated regions were detected between invading and native populations of house sparrow. Additionally, DNA methylation was negatively correlated to time-since introduction, which further suggests that DNA methylation had a role in the successful colonization's of house sparrows.

A review of constraints and solutions for collecting raptor samples and contextual data for a European Raptor Biomonitoring Facility.

The COST Action 'European Raptor Biomonitoring Facility' (ERBFacility) aims to develop pan-European raptor biomonitoring in support of better chemicals management in Europe, using raptors as sentinel species. This presents a significant challenge involving a range of constraints that must be identified and addressed. The aims of this study were to: (1) carry out a comprehensive review of the constraints that may limit the gathering in the field of raptor samples and contextual data, and assess their relative importance across Europe; and (2) identify and discuss possible solutions to the key constraints that were identified. We applied a participatory approach to identify constraints and to discuss feasible solutions. Thirty-one constraints were identified, which were divided into four categories: legal, methodological, spatial coverage, and skills constraints. To assess the importance of the constraints and their possible solutions, we collected information through scientific workshops and by distributing a questionnaire to stakeholders in all the countries involved in ERBFacility. We obtained 74 answers to the questionnaire, from 24 of the 39 COST participating countries. The most important constraints identified were related to the collection of complex contextual data about sources of contamination, and the low number of existing raptor population national/regional monitoring schemes and ecological studies that could provide raptor samples. Legal constraints, such as permits to allow the collection of invasive samples, and skills constraints, such as the lack of expertise to practice necropsies, were also highlighted. Here, we present solutions for all the constraints identified, thus suggesting the feasibility of establishing a long-term European Raptor Sampling Programme as a key element of the planned European Raptor Biomonitoring Facility.

Heavy metal effects on bird morphometry: A case study on the house sparrow Passer domesticus.

We examined some possible effects of heavy metal accumulations on bird morphometry. House sparrows Passer domesticus were caught in unpolluted and polluted areas having a thermal power plant, in Turkey. Fifteen different morphometric characters were compared with the heavy metal accumulations of Cu, Co, Zn, Mn, Ni, and Cr in samples from muscle, kidney, and liver. We found positive or negative correlations between some heavy metal accumulations in some tissues and the length of some morphometric characters of sparrows (p < 0.01). The most correlated heavy metal with as many characters was Zn in muscle and liver, followed by Cu in liver and Cu in muscle. We found mainly negative coefficient values of some heavy metal bioaccumulation for morphometry using stepwise linear regression analysis. Negative coefficient values of Zn accumulation in muscle and the liver for body mass and feathers were found (p < 0.01). Length of bill and claws were affected by the bioaccumulation; the positive coefficient values of Zn in the muscle and the liver and negative coefficient values of Cu in the kidney for the length of the bill, positive coefficient value of Cu in muscle and the negative coefficient value of Mn in the kidney for length of the claws were found respectively (p < 0.01). The heavy metal accumulations in the tissues were found to affect morphometric characters' length. The effects of heavy metal accumulations in tissues should be considered in further morphometrical studies of a bird species, especially in polluted areas.

Parasitologic and pathologic observations of the house sparrow (Passer domesticus).

This study describes the parasites and related pathologic observations in the house sparrow (Passer domesticus). In total, 48 birds were examined and 41 sparrows were found to be infected with one or more endoparasites (85.4%). The most common parasites were liver trematodes identified as Brachydistomum microscelis and Brachydistomum gracupicae. In addition, coccidia and a cestode (Infula spp.) were observed. In one bird, one female Tetrameres sp. and one female Microtetrameres sp. were found in the proventriculus. No blood parasite was found after examination of the blood smears. No gross pathologic lesion was seen in the organs except for the proventriculus, gut, and liver. At histologic examination small necrotic areas and inflammatory reactions were seen in the liver and the gastrointestinal system related to the parasites. Incidentally, anthracosis was diagnosed in 23 and mild pneumonia in 12 of the lungs.

Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus.

Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage-specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.

Diversity, loss, and gain of malaria parasites in a globally invasive bird.

Invasive species can displace natives, and thus identifying the traits that make aliens successful is crucial for predicting and preventing biodiversity loss. Pathogens may play an important role in the invasive process, facilitating colonization of their hosts in new continents and islands. According to the Novel Weapon Hypothesis, colonizers may out-compete local native species by bringing with them novel pathogens to which native species are not adapted. In contrast, the Enemy Release Hypothesis suggests that flourishing colonizers are successful because they have left their pathogens behind. To assess the role of avian malaria and related haemosporidian parasites in the global spread of a common invasive bird, we examined the prevalence and genetic diversity of haemosporidian parasites (order Haemosporida, genera Plasmodium and Haemoproteus) infecting house sparrows (Passer domesticus). We sampled house sparrows (N = 1820) from 58 locations on 6 continents. All the samples were tested using PCR-based methods; blood films from the PCR-positive birds were examined microscopically to identify parasite species. The results show that haemosporidian parasites in the house sparrows' native range are replaced by species from local host-generalist parasite fauna in the alien environments of North and South America. Furthermore, sparrows in colonized regions displayed a lower diversity and prevalence of parasite infections. Because the house sparrow lost its native parasites when colonizing the American continents, the release from these natural enemies may have facilitated its invasion in the last two centuries. Our findings therefore reject the Novel Weapon Hypothesis and are concordant with the Enemy Release Hypothesis.

Comparative tissue distribution of heavy metals in house sparrow (Passer domesticus, Aves) in polluted and reference sites in Turkey.

Bioindicators are useful for environmental monitoring in ecosystems with pollution loads. We compared concentrations of selected 10 metals in 42 samples of House Sparrow in a polluted by thermal power plant and reference sites. We found mean tissue concentrations of some metals to be significantly higher in sparrows from the polluted area when compared to tissues from the reference site. In liver mean concentrations of Cu (35.85 ± 17.22 mg kg(-1)) and Zn (101.76 ± 26.38 mg kg(-1)) were significantly higher and concentration of Ni (0.43 ± 0.49 mg kg(-1)) were significantly lower in sparrows from the polluted area (p<0.05). The concentration of Cu was significantly higher in muscle and liver at the polluted site. Gender did not seem to influence residue levels, of the elements studied, among sparrows with the exception of kidney cobalt concentrations; which were higher in female sparrows than in males (p<0.05, t=-2.409).