Polymorphic microsatellite DNA markers in black grouse (Tetrao tetrix)

Ten GATA microsatellite DNA markers were isolated and characterized from black grouse (Tetrao tetrix) using an enrichment cloning procedure. High levels of heterozygosity (mean H_O = 0.74 ± 0.026), and a large number of alleles (range = 5–16) were resolved in 70 individuals, indicating these markers will be useful for examining parentage, inbreeding and population structure in black grouse. No evidence for linkage disequilibrium or the presence of null alleles was found.     

Combs and sexual selection in black grouse (Tetrao tetrix)

We studied supra-orbital combs in lekking black grouse (Tetrao tetrix) in relation to sexual selection at five leks in Finland1991-1998 and four leks in Sweden 1992-1995. Comb size wasestimated in two ways: by observing its natural size in thefield at different behaviors ("observed comb size"), and bymeasuring the comb size from captured birds ("measured combsize"). The size of combs is highly variable, and individualscan change it within seconds. Males express their larger combsduring display, as compared to other behaviors. Observed mean comb sizes were larger on leks with a higher number of malesand a higher number of copulations. Measured and observed combsizes and copulatory success did not significantly correlatewhen all males where analyzed, but a positive and significantrelationship between observed comb size and copulatory success was found within males that achieved copulations. Measured comblength correlated positively with the amount of testosterone.While females were present on the lek, displaying and successfulmales showed the largest observed comb size. When we comparedobserved comb size during fighting between successful and unsuccessfulmales and correlated comb size of pairs of fighting males withtheir fighting activity, no significant differences in combsize were found. The result that comb size correlated significantlywith an increase in testosterone level and that larger combsize, within successful males, predicted higher copulatorysuccess suggests that combs may be a cue for females to assessmale quality. The lack of a significant relationship betweenobserved comb size and fighting behavior suggests that combsize either has minor importance in male-male signaling onthe lek or that males may express similar-sized combs duringfighting to avoid serious fights and thus risk of comb injuries.     

Queuing for territory positions in the lekking black grouse (Tetrao tetrix)

The importance of a central territory position as a determinantof male mating success in lekking species has been debated.The process by which a male can obtain a central territory hasbeen especially lacking a quantitative analysis. We presenta stochastic queuing model describing territory succession towardthe lek center and apply it to a 8-year sequence of territorycentrality measures on a black grouse Tetrao tetrix lek. Thelek shows a value of intermediate queue discipline, which deviatessignificantly both from strict orderly queuing and from randomranking of males. Thus, high-ranking males are partly able tomaintain their superior position over years, but queue-jumpingis not excluded; especially because highly succesful males donot attempt to change their territory position toward the lekcenter. As a result of stochastic queuing, a central territoryindicates an older than average male, as well as a male witha history of high fighting rates. These results are consistentwith the hypotheses that territory position is an honest signalof male quality and that the long-term fighting effort and survivalrequired to acquire a central territory may increase the reliabilityof the signal over that of short-term display effort. The impartialqueue discipline, however, also leaves room for other male characteristicsto play a role in determining individual mating success.     

Reintroducing capercaillie (Tetrao urogallus) into southern Scotland: identification of minimum viable populations at potential release sites

Capercaillie (Tetrao urogallus) populations are declining in western parts of their range, including Scotland. It has been proposed that their numbers, and the extent of their range in Scotland be increased to reduce the risk of a second extinction in the UK. The feasibility of a reintroduction of capercaillie to coniferous plantations in southern Scotland was assessed by undertaking a population viability analysis. Following a review of capercaillie ecology and habitat requirements, VORTEX population simulation software was used to identify a minimum viable population (MVP). From this the minimum dynamic area of suitable habitat required in order to support such a MVP was then calculated. It was estimated that a minimum of 60 individuals would be required in approximately 5000ha of habitat in order for the population to have a >0.95 probability of surviving for 50 years. Supplementation of populations with two unrelated individuals every five years reduced the MVP to ten individuals. Further simulations were run in order to establish the sensitivity of the model to changes in three key parameters. Assessment of areas of suitable habitat identified two potential release sites, Wauchope and Newcastleton forests, in southern Scotland. Some practical considerations relating to management of a release population are outlined. It was concluded that an appropriately planned and resourced reintroduction was feasible.     

No genetic evidence of sex-biased dispersal in a lekking bird, the capercaillie (Tetrao urogallus)

Sex-biased dispersal is often connected to the mating behaviour of the species. Even if patterns of natal dispersal are reasonably well documented for monogamous birds, only a few data are available for polygynous and especially lekking species. We investigated the dispersal of the capercaillie (Tetrao urogallus) by examining sex-specific gene flow among the leks. Genetic information was extracted using nuclear and mitochondrial molecular markers for sexed faecal samples and analysed by novel Bayesian statistical methods. Contrary to the traditional view that the males are highly philopatric and female is the dispersing sex, we found roughly equivalent gross and effective dispersal of the sexes. The level of polygamy has a strong influence on the effective population size and on the effective dispersal. The results do not support the theories that dispersal evolves solely as a result of resource competition or other advantages to males obtained through kin selection in lekking species.     

Sex-specific population dynamics and demography of capercaillie (Tetrao urogallus L.) in a patchy environment

Modeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Here, we develop an open population spatial capture–recapture (SCR) model with sex-specific detection and population dynamics parameters to investigate population trend and sex-specific population dynamics of a capercaillie (Tetrao urogallus) population in Switzerland living in eight distinct forest patches totaling 22 km² within a region of 908 km² and sampled via scat collection. Our model accounts for the patchy distribution of habitat and the uncertainty introduced by collecting data only every third year, while producing sex by patch population trajectories. The estimated population trajectory was a decline of 2% per year; however, the sex specificity of the model revealed a decline in the male population only, with no evidence of decline in the female population. The decline observed in males was explained by the demography of just two of the eight patches. Our study highlights the flexibility of open population SCR models for assessing population trajectories through time and across space and emphasizes the desirability of estimating sex-stratified population trends especially in species of conservation concern.     

Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapes

We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as theta, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities.     

Optimizing the use of shed feathers for genetic analysis

Shed feathers obtained by noninvasive genetic sampling (NGS) are a valuable source of DNA for genetic studies of birds. They can be collected across a large geographical range and facilitate research on species that would otherwise be extremely difficult to study. A limitation of this approach is uncertainty concerning the quality of the extracted DNA. Here we investigate the relationship between feather type, feather condition and DNA quality (amplification success) in order to provide a simple, cost-effective method for screening samples prior to genetic analysis. We obtained 637 shed feathers of the powerful owl (Ninox strenua) from across its range in southeastern Australia. The extracted DNA was amplified using polymerase chain reaction for a range of markers including mitochondrial DNA, ND3 and nuclear DNA, a simple sequence repeat (Nst02) and a portion of the CHD-1 gene (P2/P8). We found that feather condition significantly influenced the amplification success of all three loci, with feathers characterized as 'good' having greater success. Feather type was found to be of lower importance, with good quality feathers of all types consistently producing high success for all three loci. We also found that the successful amplification of multilocus genotypes was dependant on the condition of the starting material and was highly correlated with successful amplification of the sex-linked CHD-1 locus. Samples with low DNA quality have a higher probability of amplification failure and are more likely to produce incorrect genotypes; therefore, identifying samples with high DNA quality can save substantial time and cost associated with the genetic analysis of NGS. As a result, we propose a method for screening shed feathers in order to provide a subset of samples which will have a greater probability of containing high quality DNA suitable for the amplification of multilocus genotypes.     

Effect of suboptimal environment and host age on helminth community of black grouse (Tetrao tetrix)

Helminths have often been considered responsible in driving partially wildlife population density fluctuations; therefore more information have to be achieved when target hosts are endangered or threatened species, such as black grouse (Tetrao tetrix). During 8 years (2003–2010), we collected and analyzed 431 intestinal contents of hunted black grouse from Central Alps (Verbania), recording age, body weights, biometric measures, and the culling site to investigate (1) their helminth community structure, (2) how much infection varies in relation to age class and to prealpine and alpine origin area, and (3) if parasites may act as population destabilizing factors. The helminth community is composed by two nematodes Ascaridia compar and Aonchotheca caudinflata. A. compar is the predominant species, and a significant higher intensity of both helminths is recorded in juveniles. A. caudinflata has a negative effect on weights of all the population subjects (p?<?0.001), independently of age and origin area. Prealpine population, characterized by significantly lower weights than those of the alpine ones (p?<?0.05), is found more infected by both helminths, with also a negative impact (p?<?0.001) of A. compar recorded on prealpine adults’ weights. The negative effect noticed for A. caudinflata emphasizes its pathogenicity and shows that this infection can be considered a further stressor for the studied population. Moreover, A. compar affects essentially adults in prealpine area and this fact, together with the major infection of the entire prealpine population, supports the hypothesis that habitat characteristics play a role in the infectious process.     

Female‐biased dispersal alone can reduce the occurrence of inbreeding in black grouse (Tetrao tetrix)

Although inbreeding depression and mechanisms for kin recognition have been described in natural bird populations, inbreeding avoidance through mate choice has rarely been reported suggesting that sex‐biased dispersal is the main mechanism reducing the risks of inbreeding. However, a full understanding of the effect of dispersal on the occurrence of inbred matings requires estimating the inbreeding risks prior to dispersal. Combining pairwise relatedness measures and kinship assignments, we investigated in black grouse whether the observed occurrence of inbred matings was explained by active kin discrimination or by female‐biased dispersal. In this large continuous population, copulations between close relatives were rare. As female mate choice was random for relatedness, females with more relatives in the local flock tended to mate with genetically more similar males. To quantify the initial risks of inbreeding, we measured the relatedness to the males of females captured in their parental flock and virtually translocated female hatchlings in their parental and to more distant flocks. These tests indicated that dispersal decreased the likelihood of mating with relatives and that philopatric females had higher inbreeding risks than the actual breeding females. As females do not discriminate against relatives, the few inbred matings were probably due to the variance in female dispersal propensity and dispersal distance. Our results support the view that kin discrimination mate choice is of little value if dispersal effectively reduces the risks of inbreeding.     

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution

Background

The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. The advent of the next generation sequencing technologies has made it possible to study which genomic regions are evolutionary liable to change and which are static, as well as enabling an increasing number of genome studies of non-model species. However, de novo sequencing of the whole genome of an organism remains non-trivial. In this study, we present the draft genome of the black grouse, which was developed using a reference-guided assembly strategy.

Results

We generated 133 Gbp of sequence data from one black grouse individual by the SOLiD platform and used a combination of de novo assembly and chicken reference genome mapping to assemble the reads into 4572 scaffolds with a total length of 1022 Mb. The draft genome well covers the main chicken chromosomes 1 ~ 28 and Z which have a total length of 1001 Mb. The draft genome is fragmented, but has a good coverage of the homologous chicken genes. Especially, 33.0% of the coding regions of the homologous genes have more than 90% proportion of their sequences covered. In addition, we identified ~1 M SNPs from the genome and identified 106 genomic regions which had a high nucleotide divergence between black grouse and chicken or between black grouse and turkey.

Conclusions

Our results support the hypothesis that the chromosome X (Z) evolves faster than the autosomes and our data are consistent with the MHC regions being more liable to change than the genome average. Our study demonstrates how a moderate sequencing effort can be combined with existing genome references to generate a draft genome for a non-model species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-180) contains supplementary material, which is available to authorized users.     

Small-scale habitat use of black grouse (Tetrao tetrix L.) and rock ptarmigan (Lagopus muta helvetica Thienemann) in the Austrian Alps

We investigated the small-scale habitat use of two grouse species, black grouse (Tetrao tetrix L.) and rock ptarmigan (Lagopus muta helvetica Thienemann) in a study area in the Austrian Central Alps in summer. To build habitat suitability models, we applied multiple logistic regression using presence–absence data from fieldwork as the response variable and a set of habitat characteristics as explanatory variables, respectively. To gain a better understanding of the mechanisms that drive habitat selection, we tested for two-way interaction terms before excluding any variables from the initial variable set. Four explanatory variables significantly contributed to the black grouse model: dwarf shrub cover, dwarf shrub height, patchiness and ant hills. The final model for rock ptarmigan contained three explanatory variables: dwarf shrub cover, rock cover and dwarf shrub height. Most notably, the interaction terms dwarf shrub cover × patchiness in the black grouse model and dwarf shrub cover × dwarf shrub height, rock cover × dwarf shrub height in the rock ptarmigan model point out trade-off mechanisms between food, cover and overview providing features. Thus, our models do not only identify the parameters that mainly drive habitat selection, but also deepen our understanding about the causal relationships between these factors. Therefore, the information gained in this study allows for a deduction of appropriate habitat management strategies and supports conservation efforts of local stakeholders.     

A new method for DNA extraction from feces and hair shafts of the South China tiger (Panthera tigris amoyensis)

It is commonly known that tigers (Panthera tigris) groom themselves by licking their coats, which leads to an abundance of hairs in their feces. These hairs are designated specially as “fecal hairs”. In our study, in order to explore fecal hairs potential as a DNA source for genetic analysis, 55 fecal hair samples were collected from 23 captive South China tigers (P. t. amoyensis). According to the amplification of mitochondrial primers loop F and loop R, DNA quality of noninvasive samples were grouped into three grades: grade I—the highest-quality DNA, grade II—high-quality DNA, and grade III—poor-quality DNA. No failed amplifications on microsatellite primers and only 0.27% genotyping errors occurred with grade I fecal hair DNA, as compared with 9.4% failed amplifications on microsatellite primers and 9.5% genotyping errors with grade II fecal hair DNA. It was found that 25.45% of fecal hair DNA was grade I and 65.45 and 10.00% of fecal hair DNA were grades II and III, respectively, as compared with 4.35% grade I fecal DNA and 34.78 and 60.87% grades II and III fecal DNA, respectively. Thus, higher-quality DNA can be extracted from fecal hairs than feces. In addition, DNA could be extracted from hair shafts of tigers and a minimum of 2000 hair shafts were required for visible DNA bands on a 1% agarose gel. These findings demonstrate that fecal hairs may serve as a convenient and reliable genomic DNA source for genotype analysis. Zoo Biol 28:49–58, 2009. © 2008 Wiley-Liss, Inc.     

Temporal and spatial analyses disclose consequences of habitat fragmentation on the genetic diversity in capercaillie (Tetrao urogallus)

As a result of habitat fragmentation, the capercaillie ( Tetrao urogallus ) population in the Black Forest mountain range in southwestern Germany has declined rapidly during the last decades and now persists in patchy isolated fragments. To study the effects of fragmentation, we quantified dispersal patterns by genotyping 213 individuals in four subpopulations. We used a landscape genetics approach to analyse individual genetic variation, and despite overall low genetic structure, we found strong indications for a major boundary separating the northern part of the Black Forest area from the other subpopulations. Males and females display different gene flow patterns across the landscape. Females tend to disperse across longer distances than do males. We additionally studied the effects of the population decline on genetic diversity during the last hundred years. Although the population has dramatically declined from over 4000 to 250 males over a few decades, genetic diversity was not affected in the same way. We found two haplotypes that were present only in historic samples but microsatellite markers revealed no significant reduction in genetic diversity. Among historic samples, genetic differentiation was very low, indicating that the current genetic structure is caused by recent habitat fragmentation. We argue that inferences about reduced genetic diversity are drawn cautiously and recommend sampling over different temporal scales.     

Genetic impoverishment of the last black grouse (Tetrao tetrix) population in the Netherlands: detectable only with a reference from the past

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 genetic diversity in the last extant Dutch population with Dutch museum samples and three other black grouse populations (from England, Austria and Norway, respectively) representing isolated and continuous populations. We found significantly lower allelic richness, observed and expected heterozygosities in the present Dutch population compared to the continuous populations (Austria and Norway) and also to the historical Dutch population. However, using a bottleneck test on each population, signs of heterozygosity excess were only found in the likewise isolated English population despite that strong genetic drift was evident in the present Dutch population in comparison to the reference populations, as assessed both in pairwise F(ST)and STRUCTURE analyses. Simulating the effect of a population reduction on the Dutch population from 1948 onwards, using census data and with the Dutch museum samples as a model for the genetic diversity in the initial population, revealed that the loss in number of alleles and observed heterozygosity was according to genetic drift expectations and within the standard error range of the present Dutch population. Thus, the effect of the strong decline in the number of grouse on genetic diversity was only detectable when using a reference from the past. The lack of evidence for a population reduction in the present Dutch population by using the program bottleneck was attributed to a rapidly found new equilibrium as a consequence of a very small effective population size.