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Effective management of both endangered native and invasive alien crayfishes requires knowledge about distribution, monitoring of existing and early detection of newly established populations. Complementary to traditional survey methods, eDNA sampling has recently emerged as a highly sensitive non-invasive detection method to monitor crayfish populations. To advance the use of eDNA as detection tool for crayfish we used a twofold approach: 1) we designed a novel set of specific eDNA-assays for all native (Austropotamobius torrentium, Austropotamobius pallipes, Astacus astacus) and the most relevant invasive crayfish species (Pacifastacus leniusculus, Faxonius limosus, Faxonius immunis) in Central Europe. To ensure specificity each primer pair was tested in silico, in vitro, and in situ; 2) we assessed the influence of spatio-temporal variables (distance to upstream population, season, stream size) on eDNA detection in seven streams using two different detection methods (qualitative endpoint PCR and quantitative droplet digital PCR, ddPCR). The newly developed eDNA assays successfully detected all crayfish species across different lotic and lentic habitats. eDNA detection rate (endpoint PCR) and eDNA-concentration (ddPCR) were significantly influenced by distance and season. eDNA detection was successful up to 7 km downstream of the source population and across all seasons, although detectability was lowest in winter. eDNA detection rate further decreased with increasing stream size. Finally, eDNA-concentration correlated positively with estimated upstream population size. Overall, we provide near operational eDNA assays for six crayfish species, enabling year-round detection, which represents a clear benefit over conventional methods. Due to its high sensitivity, eDNA detection is also suitable for the targeted search of as-yet unrecorded or newly emerging populations. Using quantitative ddPCR might further allow for a rough estimation of population size, provided that the identified spatio-temporal factors are accounted for. We therefore recommend implementing eDNA-detection as a complementary survey tool, particularly for a large-scale screening of data-deficient catchments or a year-round monitoring.

This special issue of Evolutionary Applications consists of 10 publications investigating\ud the use of next-generation\ud tools and techniques in population genetic analyses and\ud biodiversity assessment. The special issue stems from a 2016 Next Generation\ud Genetic Monitoring Workshop, hosted by the National Institute for Mathematical\ud and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of\ud next-generation\ud sequencing platforms has allowed molecular ecologists to rapidly\ud produce large amounts of data. However, with the increased availability of new\ud genomic markers and mathematical techniques, care is needed in selecting appropriate\ud study designs, interpreting results in light of conservation concerns, and determining\ud appropriate management actions. This special issue identifies key attributes\ud of successful genetic data analyses in biodiversity evaluation and suggests ways to\ud improve analyses and their application in current population and conservation genetics\ud research.

Time and financial constraints often force conservationists to make ad hoc management decisions without sufficient knowledge to predict their effects. In particular, the effects of management on reproduction and survival are rarely evaluated and habitat dynamics are rarely taken into account. We evaluated the effects of three different forms of habitat alteration on the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador during the phases of population increase and stabilization. More specifically, we monitored the effect of a natural experiment with three approaches (clearing, grazing and burning) to preserve the semi-open habitat of this species on the reproductive success of 220 breeding events over seven years and on the survival of 73 adults over three consecutive years. Habitat alteration had contrasting effects on reproduction and survival. All approaches increased the number of fledged chicks per breeding event while the population stabilized, but not while it increased. However, vegetation burning reduced survival probability of adult individuals. In addition, survival was strongly correlated to the presence of water in the territories. Overall, we revealed that the negative effects of vegetation burning on survival overrode the positive effects on reproduction, and could—if implemented at a larger scale—destroy the conservation aim of increasing the population size. Importantly, we show that the effectiveness of management differs depending on the actual population trend. Our study therefore shows that the a posteriori evaluation of ad hoc vegetation control can constitute an integral part of adaptive management and thereby also of long-term conservation planning of endangered species.

The Golden eagle (Aquila chrysaetos) is among the most widespread of the birds of prey, covering basically the whole Palaearctic from Europe and North Africa through Asia and Japan, to the North American continent. Only few studies have addressed the species’ genetic structure and the consequences of its demographic history so far, and none of them has covered larger areas of the distribution range. Our present study aims at closing this gap. Based on 283 samples (mostly feathers collected in the field or from museum collections) across the species’ distribution, but with a focus on Europe, we uncover the phylogeography of the Golden eagle. Results imply a phylogeographic split between mainly Northern Europe, Continental Asia, Japan and North America on the one hand and Central–Southern Europe on the other. The observed pattern is likely to be caused by the Last Ice Age, when the population survived in two reproductively isolated glacial refugia. Repopulation of Northern Europe occurred from a presumed Asian refugium, whereas the Alpine range was probably repopulated from a refugium in the Mediterranean region. In Eastern Europe, the Mediterranean and Alpine region we find a co-occurrence of both lineages that heavily influences the local genetic diversity. This pattern is unlike that in most other large raptors in which usually a western and an eastern Eurasian lineage have been recovered.

Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes. Landscape genomics has tremendous potential for addressing fundamental and applied research questions in various research fields, including ecology, evolution, and conservation biology. However, the unique combination of different scientific disciplines and analytical approaches also constitute a challenge to most researchers wishing to apply landscape genomics. Here, we present an introductory overview of important concepts and methods used in current landscape genomics. For this, we first define the field and explain basic concepts and methods to capture different hypotheses of landscape influences on neutral genetic variation. Next, we highlight established and emerging genomic tools for quantifying adaptive genetic variation in landscape genomic studies. To illustrate the covered topics and to demonstrate the potential of landscape genomics, we provide empirical examples addressing a variety of research question, i.e., the investigation of evolutionary processes driving population differentiation, the landscape genomics of range expanding species, and landscape genomic patterns in organisms of special interest, including species inhabiting aquatic and terrestrial environments. We conclude by outlining remaining challenges and future research avenues in landscape genomics.

The genetic diversity and population structure of a population of African lions in Hwange National Park, Zimbabwe, was studied using 17 microsatellite loci. Spatial genetic analysis using Bayesian methods suggested a weak genetic structure within the population and high levels of gene flow across the study area. We were able to identify a few individuals with aberrant or admixed ancestry, which we interpreted as either immigrants or as descendants thereof. This, together with relatively high genetic diversity, suggests that immigrants from beyond the study area have influenced the genetic structure within the park. We suggest that the levels of genetic diversity and the observed weak structure are indicative of the large and viable Okavango-Hwange population of which our study population is a part. Genetic patterns can also be attributed to still existing high levels of habitat connectivity between protected areas. Given expected increases in human populations and anthropogenic impacts, efforts to identify and maintain existing movement corridors between regional lion populations will be important in retaining the high genetic diversity status of this population. Our results show that understanding existing levels of genetic diversity and genetic connectivity has implications, not only for this lion population, but also for managing large wild populations of carnivores.

In migratory birds, traits such as orientation and distance are known to have a strong genetic background, and they often exhibit considerable within-population variation. How this variation relates to evolutionary responses to ongoing selection is unknown because the underlying mechanisms that translate environmental changes into population genetic changes are unclear. We show that within-population genetic structure in southern German blackcaps (Sylvia atricapilla) is related to individual differences in migratory behavior. Our 3-year study revealed a positive correlation between individual migratory origins, denoted via isotope (δ (2)H) values, and genetic distances. Genetic diversity and admixture differed not only across a recently established migratory polymorphism with NW- and SW-migrating birds but also across δ (2)H clusters within the same migratory route. Our results suggest assortment based on individual migratory origins which would facilitate evolutionary responses. We scrutinized arrival times and microhabitat choice as potential mechanisms mediating between individual variation in migratory behavior and assortment. We found significant support that microhabitat choice, rather than timing of arrival, is associated with individual variation in migratory origins. Moreover, examining genetic diversity across the migratory divide, we found migrants following the NW route to be genetically more distinct from each other compared with migrants following the traditional SW route. Our study suggests that migratory behavior shapes population genetic structure in blackcaps not only across the migratory divide but also on an individual level independent of the divide. Thus, within-population variation in migratory behavior might play an important role in translating environmental change into genetic change.

Parasites can exert strong selection on hosts. Th roughout the year migrants are exposed to diff erent sets of parasites, which may aff ect life history traits such as migratory schedules. Here, we studied the relationship between parasite infection and arrival date of blackcaps Sylvia atricapilla to their breeding grounds in Germany throughout a period of six years (2007 – 2012). We used two data sets, one that included all blackcaps and one that included only recaptured birds. We assesed whether parasites infl uence spring arrival to breeding grounds, and for the recaptured data set, we analysed temporal variation in parasitism (i.e. infection status and parasitaemia) throughout the breeding season. We used both microscopy and PCR (a fragment of ∼ 479 bp of the mtDNA cyt b) to determine haemosporidian infection. Blackcaps were mostly infected with Haemoproteus parabelopolskyi (lineages SYAT01 and SYAT02). Infection status, but not parasitaemia, was constant through time for individual birds; meaning that once a bird is infected, it most likely will retain the infection for life. We found that infection by haemosporidian parasites has no relationship to arrival date in this blackcap population; however, infection by H. parabelopolskyi has a marginally signifi cant eff ect on arrival date of recaptured blackcaps, somewhat delaying their arrival to breeding grounds. Birds captured later in the season were more likely to be infected than those from early spring, and parasitaemia was frequently lower in birds captured earlier in the season compared to those captured later (summer).

The Rufous Hummingbird (Selasphorus rufus) population is declining in some areas of North America, but not in others. The reasons for the decline are, as yet, unknown. Understanding the genetic population structure of this species could be useful in understanding its dispersal behaviour and whether particular geographical areas should be treated as separate conservation units. We tested 16 microsatellite markers designed for other hummingbird species for amplification in Rufous Hummingbirds. Using six polymorphic markers, we found that the Rufous Hummingbird population was weakly structured such that birds breeding in central British Columbia could be distinguished from those breeding on Vancouver Island and those in Alberta, each several hundred kilometres away. Whether landscape features such as the Rocky Mountains and Fraser River Valley significantly affect dispersal patterns requires further investigation.

In cooperative species, helping behaviour and reproductive success can be correlated, but understanding this correlation is often impaired by the difficulty to correctly infer causation. While helpers can incur costs by participating in brood care, it is yet unclear if their help depends on their individual quality. We address these questions in the previously unknown cooperative breeding system of the endangered El Oro parakeet (Pyrrhura orcesi). Specifically, we ask (i) whether breeders benefit directly from helpers by an enhanced reproductive success and if so, (ii) whether the amount of this potential benefit is regulated by the quality of contributing group members. Groups consist of a dominant breeding pair accompanied by helpers, but cooperation is not obligate. Microsatellite heterozygosity was used to assess individual quality; its suitability as indicator of quality was reflected in the positive relationship between offspring heterozygosity and recruitment into the population. The reproductive success of breeding pairs depended on helper (genetic) quality and the number of helpers. This relationship occurred on two different levels: clutch size and fledging success, indicating (i) that females profit from high-quality helpers and probably adjust clutch size accordingly and (ii) that the helpers increase fledging success. Congruently, we found that offspring body condition is positively affected by helper quality, which is most probably explained by the increased feeding rates when helpers are present. We suggest a causal link between cooperation and reproductive success in this frugivorous, endangered parakeet. Further, helper (genetic) quality can be a relevant factor for determining reproductive fitness in cooperative species, particularly in small and bottlenecked populations.

Density-dependent processes are fundamental mechanisms for the regulation of populations. Ecological theories differ in their predictions on whether increasing population density leads to individual adjustments of survival and reproductive output or to dominance and monopolization of resources. Here, we use a natural experiment to examine which factors limit population growth in the only remaining population of the endangered pale-headed brush finch (Atlapetes pallidiceps). For three distinct phases (a phase of population suppression, 2001–2002; expansion due to conservation management, 2003–2008; and equilibrium phase, 2009–2014), we estimated demographic parameters with an integrated population model using population size, the proportion of successfully breeding pairs and their productivity, territory size, and mark-recapture data of adult birds. A low proportion of successful breeders due to brood parasitism (0.42, 95% credible interval 0.26–0.59) limited population growth before 2003; subsequent culling of the brood parasite resulted in a two-fold increase of the proportion of successful breeders during the ‘expansion phase’. When the population approached the carrying capacity of its habitat, territory size declined by more than 50% and fecundity declined from 1.9 (1.54–2.27) to 1.3 (1.12–1.53) chicks per breeding pair, but the proportion of successful breeders remained constant (expansion phase: 0.85; 0.76–0.93; equilibrium phase: 0.86; 0.79–0.92). This study demonstrates that limiting resources can lead to individual adjustments instead of despotic behavior, and the individual reduction of reproductive output at high population densities is consistent with the slow life-history of many tropical species.

The red-billed chough (Pyrrhocorax pyrrhocorax) is of conservation concern in the British Isles and continental Europe, with historically declining populations and a highly fragmented distribution. We quantified the distribution of genetic variation within and among European populations to identify isolated populations that may need to be managed as demographically independent units, and assess whether individual populations are denuded of genetic diversity and so may show reduced viability. We genotyped 326 choughs from ten wild populations and 22 from one captive population at 16 nuclear microsatellite loci, and sequenced 34 individuals across three mitochondrial regions to quantify genetic structure, diversity and phylogeography. Microsatellite diversity was low (often 0.1), with a signature of isolation-by-distance. Bayesian-inferred a posteriori genetic clusters coincided with a priori populations, supporting strong genetic structure. Microsatellites also allowed us to identify the probable origin of the captive choughs and one recently founded wild population. Mitochondrial DNA sequence diversity was low (π = 0.00103). Phylogeographic structure was consequently poorly resolved, but indicated that sampled continental-European populations are ancestral to British Isles populations, which comprised a single clade. Our data suggest that British Isles chough populations are relatively isolated with infrequent gene flow and relatively genetically depauperate, potentially requiring genetic management. These findings should be integrated into conservation management policy to ensure long-term viability of chough populations.

Effective DNA extraction methods from bird feathers have facilitated non‐invasive sampling, leading to the suggestion that feathers are a great source for genetic studies. However, few studies have assessed whether all feathers can be used or provide equal numbers of useful templates. In this study, feathers collected in various ways from Red Grouse Lagopus lagopus were examined to establish the quality of DNA extracted. Individual samples were classified into two categories according to whether they were collected from shot birds or found in the field. DNA was extracted from all samples and genotyped at 19 microsatellite loci. PCR products were analysed on a MegaBACE 1000. A total of 93% of the ‘shot’ category produced a genotype that was considered successful (i.e. 15 of 18 loci) and 23% of the ‘collected’ category produced successful genotypes under the same criteria. There was a significant difference between shot and collected samples in genotyping success and the observed number of missing loci. Recommendations and best practices are discussed along with the utility of bird feathers as a source of DNA for population and conservation biology.

We isolated 13 polymorphic microsatellite DNA loci from Rock Bunting (Emberiza cia) to investigate population fragmentation in a species adapted to different environments. The loci were screened for polymorphism using 30 individuals from a population in Germany and primers amplified loci with high numbers of alleles ranging from 5 to 9 alleles per locus.

Functional connectivity between spatially disjoint habitat patches is a key factor for the persistence of species in fragmented landscapes. Modelling landscape connectivity to identify potential dispersal corridors requires information about those landscape features affecting dispersal. Here we present a new approach using spatial and genetic data of a highly fragmented population of capercaillie (Tetrao urogallus) in the Black Forest, Germany, to investigate effects of landscape structure on gene flow and to parameterize a spatially explicit corridor model for conservation purposes. Mantel tests and multiple regressions on distance matrices were employed to detect and quantify the effect of different landscape features on relatedness among individuals, while controlling for the effect of geographic distance. We extrapolated the results to an area-wide landscape permeability map and developed a new corridor model that incorporates stochasticity in simulating animal movement. The model was evaluated using both a partition of the data previously set apart and independent observation data of dispersing birds. Most land cover variables (such as coniferous forest, forest edges, agricultural land, roads, settlements) and one topographic variable (topographic exposure) were significantly correlated with gene flow. Although inter-individual relatedness inherently varies greatly and the variance explained by geographic distance and landscape structure was low, the permeability map and the corridor model significantly explained relatedness in the validation data and the spatial distribution of dispersing birds. Thus, landscape structure measurably affected within-population gene flow in the study area. By converting these effects into spatially explicit information our model enables localizing priority areas for the preservation or restoration of metapopulation connectivity.

Landscape genetics plays an increasingly important role in the management and conservation of species. Here, we highlight some of the opportunities and challenges in using landscape genetic approaches in conservation biology. We first discuss challenges related to sampling design and introduce several recent methodological developments in landscape genetics (analyses based on pairwise relatedness, the application of Bayesian methods, inference from landscape resistance and a shift from population-based to individual-based analyses). We then show how simulations can foster the field of landscape genetics and, finally, elaborate on technical developments in sequencing techniques that will dramatically improve our ability to study genetic variation in wild species, opening up new and unprecedented avenues for genetic analysis in conservation biology.

We demonstrate the potential of a set of novel microsatellite markers to investigate kin structure and population genetics in the Northern Wheatear (Oenanthe oenanthe). In this study, based on 242 individuals from a population in Rhineland-Palatinate (Germany), we found that 26% of the offspring in 46% of the broods were sired by other males than the social fathers. We tested different hypotheses why males engage in extrapair copulations and found that almost all identified genetic fathers originated from directly neighbouring territories. Additionally, we detected 2 out of 134 offspring in two broods that could not be assigned to their putative mother and thus were probably the result of intraspecific brood parasitism.

The ancestors of rock ptarmigan Lagopus muta originated in the Beringia area well before the disruption of the Beringian land bridge. They spread westwards to Siberia and eastwards to the North American arctic and Greenland. The distribution of rock ptarmigan has been affected by glaciations restricting it to geographically limited refugia. Today the species has a circumpolar distribution in arctic tundra and alpine habitats, with up to 30 subspecies recognised based on morphological characters. We sequenced the mitochondrial control region for 72 individuals and genotyped 69 individuals for 12 microsatellite loci to investigate neutral genetic variation within and among five rock ptarmigan populations, Greenland, Iceland, Scandinavia, Svalbard and Taimyr. Genetic structure among the studied samples was high, overall F-ST estimated from microsatellite loci was 0.18 and only one out of 16 mtDNA haplotypes was found in more than one population. Genetic variation (h, pi, H-e, allelic richness) was slightly lower in the Svalbard population than in other populations, suggesting a low effective population size, possibly due to isolation following colonisation. An unrooted network and a phylogenetic tree showed that the Scandinavian population has diverged from the other populations by at least ten mutational steps, probably due to independent colonisation of Europe and subsequent long-term isolation, and rules out Scandinavia as a source for colonisation of Svalbard. Alignment with partial control region sequences from other studies showed that the haplotype that was central in our network and found on Svalbard and in Taimyr, most likely corresponds to a haplotype found in Siberia, Alaska and the Canadian Arctic, but not in Greenland, Scandinavia and Iceland. This suggests an eastern origin of rock ptarmigan in Svalbard, although this question cannot be settled conclusively.

Microsatellites are DNA-fragments containing short repetitive motifs with 2-10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during the replication phase, termed slippage, although recombination is also observed. The aim of this study is to demonstrate evidence that non-reciprocal recombination processes changing the total genomic structure are common in microsatellites and flanking regions. We sequenced DNA fragments from birds in which microsatellites are located, and analyzed the structure of the microsatellites and their flanking regions. Additionally, other data and those from literature of three microsatellite regions of primates coding for the Ataxin-2, the Huntingtin and the TATA-box binding protein were analyzed. The structures of seven avian and three primate microsatellites support the hypothesis that non-reciprocal recombination is a common process that may also contribute considerably to the variation at microsatellite loci. We conclude that results of population genetic studies that are analyzed statistically with methods based on stepwise mutation models should be interpreted with caution if no detailed information on the allelic variation of microsatellites is available.

We have studied a small isolated population of black grouse (Tetrao tetrix) in the Netherlands to examine the impact of isolation and reduction in numbers on genetic diversity. We compared the ge ...

The zebra finch ( Taeniopygia guttata ) is a small Australian grassland songbird that has been domesticated over the past two centuries. Because it is easy to breed in captivity, it has become a widely used study organism, especially in behavioural research. Most work has been conducted on domesticated populations maintained at numerous laboratories in Europe and North America. However, little is known about the extent to which, during the process of domestication, captive populations have gone through bottlenecks in population size, leading to inbred and potentially genetically differentiated study populations. This is an important issue, because (i) behavioural studies on captive populations might suffer from artefacts arising from high levels of inbreeding or lack of genetic variation in such populations, and (ii) it may hamper the comparability of research findings. To address this issue, we genotyped 1000 zebra finches from 18 captive and two wild populations at 10 highly variable microsatellite loci. We found that all captive populations have lost some of the genetic variability present in the wild, but there is no evidence that they have gone through a severe bottleneck, as the average captive population still showed a mean of 11.7 alleles per locus, compared to a mean of 19.3 alleles/locus for wild zebra finches. We found significant differentiation between the captive populations ( F ST = 0.062). Patterns of genetic similarity closely match geographical relationships, so the most pronounced differences occur between the three continents: Australia, North America, and Europe. By providing a tree of the genetic similarity of the different captive populations, we hope to contribute to a better understanding of variation in research findings obtained by different laboratories.

The phylogeographic pattern of mitochondrial DNA variation in capercaillie (Tetrao urogallus) from 14 populations across the European range was examined using sequence variation in the central portion of the control region and the cytochrome B gene. Twenty-nine different haplotypes were resolved, which formed two distinct phylogenetic clades. The major division separated haplotypes found in the Pyrenees from those found in the rest of Europe. However, two Pyrenean birds were found within the central European clade. The Pyrenean population is likely to be derived from an Iberian glacial refugium, whereas the other European populations have been recolonized from a refugium in the East. Birds from the Eastern refugium spread west until they reached the Pyrenees, where they mixed with birds from the Iberian refugium. Connectivity between populations from central, eastern, and northern Europe and the Pyrenees was interrupted by the extinction of interconnecting populations, leading to the formation of a different subspecies (Tetrao urogallus aquitanicus). We argue that the Pyrenean birds should be therefore regarded as a separate evolutionary significant unit, and we discuss the status of the other capercaillie populations in a conservation context.

The low-latitude limits of species ranges are thought to be particularly important as long-term stores of genetic diversity and hot spots for speciation. The Iberian Peninsula, one of the main glacial refugia in Europe, houses the southern distribution limits of a number of boreal species. The capercaillie is one such species with a range extending northwards to cover most of Europe from Iberia to Scandinavia and East to Siberia. The Cantabrian Range, in North Spain, constitutes the contemporary south-western distribution limit of the species. In contrast to all other populations, which live in pure or mixed coniferous forests, the Cantabrian population is unique in inhabiting pure deciduous forests. We have assessed the existence of genetic differentiation between this and other European populations using microsatellite and mitochondrial DNA (mtDNA) extracted from capercaillie feathers. Samples were collected between 2001 and 2004 across most of the current distribution of the Cantabrian population. Mitochondrial DNA analysis showed that the Cantabrian birds form a distinct clade with respect to all the other European populations analysed, including the Alps, Black Forest, Scandinavia and Russia, which are all members of a discrete clade. Microsatellite DNA from Cantabrian birds reveals the lowest genetic variation within the species in Europe. The existence of birds from both mtDNA clades in the Pyrenees and evidence from microsatellite frequencies for two different groups, points to the existence of a Pyrenean contact zone between European and Cantabrian type birds. The ecological and genetic differences of the Cantabrian capercaillies qualify them as an Evolutionarily Significant Unit and support the idea of the importance of the rear edge for speciation. Implications for capercaillie taxonomy and conservation are discussed.

Genetic variation in a Chinese grouse Bonasa sewerzowi population was assessed using five microsatellite markers. The mean number of alleles and allelic richness were comparable with what has been observed in other grouse, e.g. black grouse Tetrao tetrix and capercaillie T. urogallus, populations studied with the same markers regardless of whether these populations were isolated or from within the continuous range of the respective species. However, the proportion of heterozygotes and FIS observed in Chinese grouse were more similar to isolated than to continuous grouse populations suggesting that the Chinese grouse population may show genetic signs of habitat fragmentation and relative isolation. Furthermore, demographic analyses indicated that the studied Chinese grouse population would not persist without immigration. We suggest that excess heterozygosity is a sign of a sink deme within a metapopulation system.

Genetic diversity and population structure were studied in eight populations of the kestrel Falco tinnunculus to identify the genetic consequences of spatial distribution and to infer the colonization patterns of the Cape Verde archipelago. We studied genetic differentiation and gene flow among seven island populations and one mainland population using nine microsatellite loci. Within the archipelago, differentiation was strong and genetic diversity and heterozygosity were low but variable among populations. Two subspecies F. tinnunculus neglectus on the northwestern islands and F. tinnunculus alexandri on all the other islands were identified as genetically distinct units. F. t. alexandri could be further separated into two groups on eastern and southern islands. Populations are probably founded by birds originating from the mainland. Immigration is more likely to the eastern and southern populations, whereas the northwestern islands with the lowest genetic diversity and highest differentiation are likely to exhibit fewer founding events by immigrants. The number of founding events on each island may depend not only on geographical distance to neighbouring populations, but also on directional immigration due to the northeastern trade winds. This may explain differences in genetic differentiation and diversity between populations and subspecies and may enable allopatric speciation.

The capercaillie inhabits a continuous range in large parts of the Palearctic boreal forest, but is patchily distributed in temperate Europe. An ongoing population decline, largely related to human land use changes, has been most pronounced in central and western Europe, where some local populations have become extinct. In this study, we document the genetic differentiation of capercaillie populations at different stages along a gradient of spatial structuring from high connectivity (continuous range in the boreal forest) to a metapopulation systems (Alps) and recent (central Europe) and historic (Pyrenees) isolation. Four hundred and sixty individuals from 14 sample sites were genotyped at 10 polymorphic microsatellite loci to assess genetic structure and variation of capercaillie populations across its European range. As expected, differentiation was least pronounced within the continuous range in the boreal forest. Within the metapopulation system of the Alps, differentiation was less than among the isolated populations of central Europe (Black Forest, Fichtelgebirge, Thuringia, Vosges). In the long-isolated population of the Pyrenees, and the recently isolated populations of central Europe, genetic diversity was significantly reduced compared with the Alps and boreal forest. Our results agree with the concept of a gradual increase in genetic differentiation from connectivity to isolation, and from recent to historic isolation. Anthropogenic habitat deterioration and fragmentation thus not only leads to range contractions and extinctions, but may also have significant genetic and evolutionary consequences for surviving populations. To maintain high levels of genetic variation in species in fragmented habitats, conservation should aim at securing connectivity between spatially distinct populations.

© 2014 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll-like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale-headed Brushfinch with two co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species.

Black grouse (Tetrao tetrix) in Central Europe have undergone a severe contraction of their range in recent decades with only a few small isolated remaining populations. Here we compare genetic diversity of two contemporary isolated populations (Sallandse Heuvelrug, Netherlands and Luneburger Heide, Germany) with historical samples from the same region collected within the last one hundred years. We use markers with both putatively neutral and functional variation to test whether the present small and highly fragmented populations hold lower genetic diversity compared to the former larger population. For this we applied three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs), both sets which have been found to be neutral, and two functional major histocompatibility complex (MHC) genes for which there is evidence they are under selection. The contemporary small isolated populations displayed lower neutral genetic diversity compared to the corresponding historical samples. Furthermore, samples from Denmark showed that this now extinct population displayed lower genetic variation in the period immediately prior to the local extinction. Population structure was more pronounced among contemporary populations compared to historical populations for microsatellites and SNPs. This effect was not as distinct for MHC which is consistent with the possibility that MHC has been subjected to balancing selection in the past, a process which maintains genetic variation and may minimize population structure for such markers. Genetic differentiation among the present populations highlights the strong effects of population decline on the genetic structure of natural populations, which can be ultimately attributed to habitat loss following anthropogenic land use changes.

Capercaillie Tetrao urogallus and black grouse T. tetrix are threatened species in central Europe. Their habitats are fragmented both at a continental and a regional scale, and spatial connectivity may play an important role for their (meta-)population dynamics and persistence. In order to identify conservation priorities, it is important to know if and to what extent exchange between local populations occurs. In this paper, we present the rationale and techniques of an ongoing project into the spatial structure of capercaillie and black grouse populations in central Europe using non-invasive genetic methods. In this project, we assess the genetic differentiation of spatially distinct populations using microsatellite analysis based on DNA extracted from feathers. This approach will allow us to identify critical geographic distances beyond which demographic connectivity between populations is not assured. We expect to find a correlation between geographic and genetic distance.

Although the European blackbird, Turdus merula, is one of the most abundant and conspicuous songbirds of the Western Palaearctic and, as such, has been subject of numerous behavioural and ecological studies, there is to date no specific, PCR-based marker system for this species, and information on the applicability of genetic markers from other species or genera is scant. Here, we report the successful amplification of eight microsatellite loci in the European blackbird. We compared levels of polymorphism between groups of individuals sampled during the breeding season at different geographic localities (Heligoland Island, North Sea and Radolfzell, south-western Germany). We found high levels of polymorphisms, which enabled us to ascertain population membership of individuals. The properties of the tested microsatellite markers make them suitable for population genetic studies as well as for kinship analyses.

Migratory divides are thought to facilitate behavioral, ecological, and genetic divergence among populations with different migratory routes. However, it is currently contentious how much genetic divergence is needed to maintain distinct migratory behavior across migratory divides. Here we investigate patterns of neutral genetic differentiation among Blackcap (Sylvia atricapilla) populations with different migratory strategies across Europe. We compare the level of genetic divergence of populations migrating to southwestern (SW) or southeastern (SE) wintering areas with birds wintering in the British Isles following a recently established northwesterly (NW) migration route. The migratory divide between SW and SE wintering areas can be interpreted as a result of a re-colonization process after the last glaciation. Thus we predicted greater levels of genetic differentiation among the SW/SE populations. However, a lack of genetic differentiation was found between SW and SE populations, suggesting that interbreeding likely occurs among Blackcaps with different migratory orientations across a large area; therefore the SW/SE migratory divide can be seen as diffuse, broad band and is, at best, a weak isolating barrier. Conversely, weak, albeit significant genetic differentiation was evident between NW and SW migrants breeding sympatrically in southern Germany, suggesting a stronger isolating mechanism may be acting in this population. Populations located within/near the SW/SE contact zone were the least genetically divergent from NW migrants, confirming NW migrants likely originated from within the contact zone. Significant isolation-by-distance was found among eastern Blackcap populations (i.e. SE migrants), but not among western populations (i.e. NW and SW migrants), revealing different patterns of genetic divergence among Blackcap populations in Europe. We discuss possible explanations for the genetic structure of European Blackcaps and how gene flow influences the persistence of divergent migratory behaviors

Policy makers and managers are increasingly called upon to assess the state of biodiversity, and make decisions regarding potential interventions. Genetic tools are well-recognised in the research community as a powerful approach to evaluate species and population status, reveal ecological and demographic processes, and inform nature conservation decisions. The wealth of genetic data and power of genetic methods are rapidly growing, but the consideration of genetic information and concerns in policy and management is limited by the currently low capacity of decision-makers to access and apply genetic resources. Here we describe a freely available, user-friendly online resource for decision-makers at local and national levels (http://congressgenetics.eu), which increases access to current knowledge, facilitates implementation of studies and interpretation of available data, and fosters collaboration between researchers and practitioners. This resource was created in partnership with conservation practitioners across the European Union, and includes a spectrum of taxa, ecosystems and conservation issues. Our goals here are to (1) introduce the rationale and context, (2) describe the specific tools (knowledge summaries, publications database, decision making tool, project planning tool, forum, community directory), and the challenges they help solve, and (3) summarise lessons learned. This article provides an outlook and model for similar efforts to build policy and management capacity

Tropical montane ecosystems are biodiversity hotspots harbouring many endemics that are confined to specific habitat types within narrow altitudinal ranges. While deforestation put these ecosystems under threat, we still lack knowledge about how heterogeneous environments like the montane tropics promote population connectivity and persistence. We investigated the fine-scale genetic structure of the two largest subpopulations of the endangered El Oro parakeet (Pyrrhura orcesi) endemic to the Ecuadorian Andes. Specifically, we assessed the genetic divergence between three sites separated by small geographic distances but characterized by a heterogeneous habitat structure. Although geographical distances between sites are small (3-17 km), we found genetic differentiation between all sites. Even though dispersal capacity is generally high in parrots, our findings indicate that dispersal is limited even on this small geographic scale. Individual genotype assignment revealed similar genetic divergence across a valley (~ 3 km distance) compared to a continuous mountain range (~ 13 km distance). Our findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species. These results may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.

In the original publication, Tables 3 and 6 were published with incorrect estimates of population heterozygosities. All other diversity statistics were correct as originally presented. Updated versions of Tables 3 and 6 with corrected heterozygosity estimates confirmed using Arlequin 3.5 (Excoffier and Lischer 2010) as in Davila et al. (2014) are provided in this erratum. Discrepancies were minor for populations on the British Isles. The correct estimates for Spain are slightly larger than those reported for La Palma by Davila et al. (2014), but this does not necessarily affect their interpretation that choughs on La Palma may have originated from multiple migration events. The original conclusion that chough populations on the British Isles have low genetic diversity compared to continental European populations remains and is now, in fact, strengthened.

We isolated 10 polymorphic microsatellite DNA loci from the blackcap (Sylvia atricapilla) and optimized them for future studies of population differentiation in populations with different migration strategies in southwestern Germany. The loci were screened for polymorphism using 178 individuals from two populations in Germany and Spain. The primers amplified highly variable loci characterized by two to 19 alleles per locus and their observed and expected heterozygosities range from 0.47 to 0.81 and from 0.50 to 0.91, respectively. © 2008 The Authors.

In the Alps, the capercaillie is distributed in a metapopulation pattern with local populations on mountain ranges separated by farmland valleys. Habitat deterioration, primarily related to human land use, resulted in population declines and range contractions became obvious. At the edge of a species' range, lower connectivity and less gene flow may render populations more susceptible to decline and extinction than in the core of the range. If this were true for the capercaillie in the Alps, edge populations should be subject to limited gene flow and should show genetic signs of a more severe population decline than core populations. To test this hypothesis, we used microsatellite DNA typing techniques. We assessed genetic variation within and among 18 local capercaillie populations across the Alps in relation to geographical distribution within the metapopulation system. All populations showed high levels of genetic variation in terms of average number of alleles, allelic richness and heterozygosity. Excess heterozygosity suggested a recent population decline, that was more pronounced in edge than core populations. We found high gene flow, but also significant differentiation among populations. Differentiation among edge populations was related to geographical distance, and appeared to be a recent process, most probably caused by reduced gene flow after population decline. In the core group, the high mountains of the central Alps seem to limit dispersal, and genetic drift was the most likely explanation for the observed differentiation among populations. We conclude that maintaining connectivity within the metapopulation system is vital for capercaillie conservation in the Alps.

We isolated 10 polymorphic microsatellite DNA loci from the Northern Wheatear (Oenanthe oenanthe) and optimized these for future studies in population genetics and behavioural ecology. The loci were screened for polymorphism using 107 individuals from one population in Germany. The primers amplified loci with high numbers of alleles ranging from two to 20 alleles per locus.

We isolated seven novel polymorphic microsatellite DNA loci from the burrowing parrot (Cyanoliseus patagonus) and optimised them for future studies of population differentiation and genetic variation. The loci were screened for polymorphism using 38 samples from wild individuals from three neighbouring colonies in Argentina. The primers amplified highly variable loci characterised by 3–10 alleles per locus and their observed and expected heterozygosities ranged from 0.15 to 0.78 and 0.15 to 0.81, respectively. When we analysed 52 samples across Argentina and Chile, we found strong genetic differentiation between the Chilean and the Argentinean subspecies as well as significant differentiation between two geographically separated subspecies within Argentina. Our results indicate the suitability of these microsatellites for investigating further questions regarding the population genetics in this species.