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.     

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.     

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.     

Increased DNA typing success for feces and feathers of capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix)

Noninvasive sampling, for example, of droppings or feathers, is a promising approach for molecular genetic studies on endangered and elusive animal species. Yet, such specimens are known for containing only minute amounts of DNA, resulting in lower typing success rates relative to analyses on fresh tissues such as muscle or blood. Furthermore, artefactual signals as well as contamination are more likely to occur when DNA is limited. To increase the reliability of DNA typing from noninvasive samples, optimized DNA extraction and polymerase chain reaction protocols were developed, taking advantage of developments in the forensic field aiming at successful molecular genetic analysis of DNA templates being low in quality and quantity. In the framework of an extensive monitoring project on population dynamics of capercaillie and black grouse in the Tyrolean Alps, feces samples and molted feathers from both species were collected. On a subset comprising about 200 specimens of either species, eight polymorphic short tandem repeat (STR) markers were analyzed to test these improved protocols. Besides optimizing DNA yields, both lowered sample consumption and reduced hands‐on time were achieved, and the rates of informative profiles amounted to 90.7% for capercaillie and 92.4% for black grouse. Similarly, high success rates had not been achieved in earlier studies and demonstrate the benefit of the improved methodology, which should be easily adaptable for use on animal species other than those studied here. The STR genotypes were not only powerful enough to discriminate among unrelated birds but also appeared fit for telling apart closely related animals, as indicated by Pi and Pi_sib values. The software package allelematch aided analysis of genotypes featuring possible dropout and drop‐in effects. Finally, a comparison between molecular genetic and morphology‐based species‐of‐origin determination revealed a high degree of concordance.     

Physiological costs enforce the honesty of lek display in the black grouse (Tetrao tetrix)

Females may use condition-dependent sexual traits as reliable cues of male “quality” if the costs of the expression of such traits vary with male “quality”, and if there is positive genetic correlation between male traits and condition. However, there are multiple ways of measuring the changes in body condition which reflect physiological costs meaning that the multifaceted nature of the physiological costs associated with the expression of sexual traits has rarely been thoroughly examined. In the lekking black grouse (Tetrao tetrix), mating success is highly skewed towards males defending central territories and having high survival rates to the following year, but the mechanisms underpinning such superior performance remain unclear. In this study, we quantified the changes in five measures of body condition before and after the mating season and related these changes to male lek performance (fighting rate, territory centrality and mating success) to understand the physiological costs of male reproductive effort. Between the two capture sessions, male body mass decreased significantly, blood parasite counts and plasma carotenoid concentration increased substantially while the total immunoglobulin concentration tended to increase. There was no overall impairment of individual body condition as the changes in the five measures of body condition were unrelated. Male fighting rate was unrelated to changes in the condition measures but males losing more body mass defended central territories and had high mating success. Therefore, females preferring central, dominant males may select males better able to afford the energetic costs of lek performance thereby effectively enforcing the honesty of male display.     

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.     

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.     

Forest fragmentation due to agriculture affects the reproductive success of the ground-nesting black grouse Tetrao tetrix

We used data from the Finnish wildlife triangle censuses (1989-92) to test the prediction that the reproductive success of ground-nesting bird species is lowered in forest landscapes fragmented by the occurrence of agricultural land, presumably as a consequence of increased densities of generalist predators Our study was based on 201 wildlife triangles located in central Finland (total length 2412 km) As expected, the proportion of black grouse hens with a brood in August decreased relative to the increasing proportion of agricultural land in a landscape (100 km²) However, on a smaller spatial scale (10 8 km²), the probability of an observed hen being with a brood was higher in the vicinity of fields This finding may be explained by differences in habitat selection between hens with a brood and those without a brood We did not find any negative effect of landscape composition on brood size We conclude that increased predation pressure in forest landscapes fragmented by agriculture affects nesting success, but not the survival of black grouse chicks after hatching Our results also emphasize the importance of spatial scale in studies of landscape ecology     

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.     

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.     

The Mhc class II of the Black grouse (Tetrao tetrix) consists of low numbers of B and Y genes with variable diversity and expression

We found that the Black grouse (Tetrao tetrix) possess low numbers of Mhc class II B (BLB) and Y (YLB) genes with variable diversity and expression. We have therefore shown, for the first time, that another bird species (in this case, a wild lek-breeding galliform) shares several features of the simple Mhc of the domestic chicken (Gallus gallus). The Black grouse BLB genes showed the same level of polymorphism that has been reported in chicken, and we also found indications of balancing selection in the peptide-binding regions. The YLB genes were less variable than the BLB genes, also in accordance with earlier studies in chicken, although their functional significance still remains obscure. We hypothesize that the YLB genes could have been under purifying selection, just as the mammal Mhc-E gene cluster.     

Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication

A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1.47 Gb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.     

Seasonality and causes of black grouse (Lyrurus tetrix,Galliformes, Tetraonidae) death in Western Russia according to count of remains

Black grouse (Lyrurus tetrix) death in north and middle zones of the Russian plain were studied in 1981–2013 according to counts of the remains of perished individuals. The average annual death of birds older than 1.5–2 months is estimated as 2.0–2.5 birds/km². Its maximum falls into spring or winter-spring season and minimum into summer. Predation is main cause of death; all other reasons (unusual weather, hunting, no established circumstances) determine only one-quarter of total loss. Raptors cause maximal death of black grouse in northern regions. No significant differences between death of males and females were detected, but seasonal patterns of their death is not the same, and factors that determine their act differently. The female losses as a result of activity of all predators are distributed relatively uniformly by seasons; male death is higher in spring than in other times of year. The dynamics of male and female removal by only raptors is similar: maximum in spring, decrease in summer, and drop to minimum in autumn and winter. Seasonal distribution of losses due to activity of carnivorous beasts is uneven; male death is higher in transitional seasons (as compared with winter and summer), and female losses are maximal in winter and minimal in spring-summer period.     

Whole genome sequencing and future breeding of rice

Contemporary crop improvement relies on the genetic analysis of progeny derived from a cross between different lines with contrasting phenotypes. Such analysis allowed positioning of genes for agronomically important traits, enabling development of DNA makers for marker-assisted selection (MAS). So far the identification of loci for desirable traits have been carried out by linkage analysis using DNA markers. This process required the development of DNA markers that are distributed over the genome as well as the genotyping of each progeny. Due to recent development in next generation sequencing (NGS) technology, whole genome sequencing (WGS) is becoming easier and cheaper. Using NGS, we developed a new method called MutMap that allows rapid isolation of useful alleles from rice mutant lines. An important feature of MutMap is that it does not require marker development. We foresee that the era of genetic markers will be eventually eclipsed by that of WGS applied to all the individuals in the breeding processes.     

Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan

Background

Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.

Results

We analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.

Conclusions

We present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1290-1) contains supplementary material, which is available to authorized users.     

Timing of breeding in Black Grouse Tetrao tetrix and Capercaillie Tetrao urogallus and distribution of insect food for the chicks

In Perthshire (Scotland), Black Grouse Tetrao tetrix broods less than 3 weeks old preferred herb-rich grassy flushes with Bog Myrtle Myrica gale , whereas in the northern Pennines (England), all broods were found on grass-dominated moorland or enclosed rough grazing habitats chiefly of grass and rushes. In both areas, broods used habitats with taller vegetation that had more invertebrates, particularly moth caterpillars and sawfly larvae (Sym-phyta, Hymenoptera). Within preferred habitats, broods were found in vegetation containing more flies (Diptera), plant bugs (Hemiptera) and ichneumon flies (Hymenoptera) than at randomly chosen sites. The main hatch of Black Grouse chicks in Perthshire coincided with the peak availability of moth caterpillars preferred by chicks. Broods in the Pennines hatched 1 week later than those in Scotland, and this later breeding in the south may be an adaptation to utilize the later peak biomass of sawfly larvae, the chief insect prey there. Data collected for Capercaillie Tetrao urogallus suggest a similar degree of synchronization between their peak hatch and the availability of moth caterpillars on Bilberry Vaccinium myrtillus.