Phylogeography of willow grouse (Lagopus lagopus) in the Arctic: taxonomic discordance as inferred from molecular data

Using independently segregating nuclear single nucleotide polymorphisms (SNPs) and mitochondrial control region sequences, we found an east–west division among sampled willow grouse Lagopus lagopus subspecies. This division cut across the range of the subspecies with the largest distribution (lagopus) and thus contradicted existing taxonomic classifications. Russian Lagopus lagopus lagopus tended to cluster with North American willow grouse partly classified as other subspecies. Scandinavian willow grouse (L. l. lagopus) clustered with red grouse from Britain and Ireland (Lagopus lagopus scoticus and Lagopus lagopus hibernicus) but substructuring confirmed the monophyly of the latter. In North America, we could not detect any major genetic divisions apart from two birds described as alexandrae from the Heceta Island (Alaska) when using mitochondrial sequences. Other samples from North America were intermingled regardless of whether they were described as muriei, alexandrae or lagopus. A specimen described as alexandrae was to some extent distinct when analysing the SNP data. The genetic analyses indicated some concordance between genetics and taxonomy but not complete congruence. This is particularly evident for mitochondrial DNA network analyses. We suggest that the taxonomy of this species would benefit by a careful re‐examination of the available evidence for subspecies. It appears as if subspecies status is a poor proxy for assigning evolutionary significant units and management units in this species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 77–90.     

TEMPORAL ALLOZYME FREQUENCY CHANGES IN DENSITY FLUCTUATING POPULATIONS OF WILLOW GROUSE (LAGOPUS LAGOPUS L.)

The population density of willow grouse (Lagopus lagopus L.) in northern Scandinavia changes in synchrony with the cyclic density variations in populations of microtine rodents. To assess the genetic changes accompanying the variations in population number, allozyme variation was studied at 23 loci in 640 willow grouse, representing four mainland and one island locality sampled during high and low population density. The average heterozygosity (H = 8.3%) and proportion of polymorphic loci (P = 26%) is not lower in willow grouse than in avian species with a more stable demography; the recurrent population density changes do not appear to affect drastically the long term effective population size, presumably because of extensive migration. Significant allele frequency differences were found both between populations and between different density phases. The genetic distance (D; Nei, 1972) was, in about 50% of the cases, larger between two consecutive time periods than between two localities in a certain year. Spatial and temporal allele frequency variation each represented around 3% of the gene diversity. The temporal heterogeneity may be caused by nonrandom sampling of family groups, rather than drift of allele frequencies between generations due to small effective population size, as has been suggested for microtine species.     

Museum samples provide novel insights into the taxonomy and genetic diversity of Irish red grouse

The taxonomic status of red grouse in Ireland has been the subject of considerable debate over the past century. Irish red grouse are usually classified as Lagopus lagopus scoticus, which is the same subspecies as that found in Britain, but some ornithologists believe that native Irish red grouse constitute an endemic subspecies, namely L. lagopus hibernicus. The considerable decline of Irish red grouse over the past century, along with possible hybridization with introduced grouse from Britain, have highlighted the need to resolve their taxonomic status as part of a biodiversity management plan. However, genetic analysis of samples from a single point in time will provide limited insight into potentially confounding historical events such as hybridization and introgression. We therefore compared mtDNA sequences from both current and historical samples of the two putative subspecies, scoticus and hibernicus, to see if they are or were genetically distinct. Red grouse from Britain and Ireland shared mitochondrial haplotypes, and our historical data suggest that this is unlikely to be the result of recent hybridization and introgression. These findings, combined with a general lack of documented differences in behaviour and ecology, suggest that Irish red grouse should remain classified as L. lagopus scoticus. At the same time, we found evidence that a significant amount of genetic diversity has been lost from Irish red grouse over the past century, presumably as a result of diminishing population sizes and fragmentation of extant populations. A loss of habitat, combined with the declining numbers and genetic diversity of Irish red grouse, justify their designation as an All-Ireland Priority (Red List) species and a Northern Ireland Priority Species for conservation.     

Genetic variation among endangered Irish red grouse (<Emphasis Type="Italic">Lagopus lagopus hibernicus</Emphasis>) populations: implications for conservation and management

Extant populations of Irish red grouse (Lagopus lagopus hibernicus) are both small and fragmented, and as such may have an increased risk of extinction through the effects of inbreeding depression and compromised adaptive potential. Here we used 19 microsatellite markers to assay genetic diversity across 89 georeferenced samples from putatively semi-isolated areas throughout the Republic of Ireland and we also genotyped 27 red grouse from Scotland using the same markers. The genetic variation within Ireland was low in comparison to previously published data from Britain and the sample of Scottish red grouse, and comparable to threatened European grouse populations of related species. Irish and Scottish grouse were significantly genetically differentiated (F_ST = 0.07, 95% CI = 0.04–0.10). There was evidence for weak population structure within Ireland with indications of four distinct genetic clusters. These correspond approximately to grouse populations inhabiting suitable habitat patches in the North West, Wicklow Mountains, Munster and Cork, respectively, although some admixture was detected. Pair-wise F_ST values among these populations ranged from 0.02 to 0.04 and the overall mean allelic richness was 5.5. Effective population size in the Munster area was estimated to be 62 individuals (95% CI = 33.6–248.8). Wicklow was the most variable population with an AR value of 5.4 alleles/locus. Local (Munster) neighbourhood size was estimated to 31 individuals corresponding to an average dispersal distance of 31 km. In order to manage and preserve Irish grouse we recommend that further fragmentation and destruction of habitats need to be prevented in conjunction with population management, including protection of the integrity of the existing population by refraining from augmenting it with individuals from mainland Britain to maximise population size.     

Can acaricide‐impregnated leg bands fitted to female red grouse reduce sheep tick parasitization of chicks and increase chick survival?

In parts of northern England, North Wales and the Scottish Highlands, increasing numbers of sheep ticks Ixodes ricinus (Ixodida: Ixodidae), and the louping ill virus they can carry, are considered to be important factors that reduce red grouse Lagopus lagopus scotica productivity. The present study tested this hypothesis by fitting adult female grouse with leg bands impregnated with the acaricide cypermethrin to experimentally control ticks on their chicks on two managed grouse moors in northeast Scotland. The chicks of females fitted with acaricide leg bands showed reduced tick infestations and improved survival in one of the two study years, relative to chicks of control females. Acaricide leg bands constitute a potential management technique that may be adopted by grouse moor managers in circumstances of high tick infestations on grouse chicks.     

The influence of different aspects of grouse moorland management on nontarget bird assemblages

相似文献   

No Evidence for Resistance to Fenbendazole in Trichostrongylus tenuis,a Nematode Parasite of the Red Grouse

ABSTRACT The parasitic nematode Trichostrongylus tenuis has a detrimental effect on red grouse (Lagopus lagopus scoticus) at the individual and population levels. Treatment using grit coated with the anthelmintic fenbendazole hydrochloride reduces parasite infection and increases grouse density. However, a frequent and low dose of anthelmintic increases selection pressure for parasite resistance, a serious practical and economic problem. We used an egg hatch assay to test resistance of T. tenuis from 12 moors in northern England, which differed in grit treatment intensity. The anthelmintic concentration that prevented 50% and 95% of T. tenuis eggs from hatching (ED₅₀ and ED₉₅, respectively) did not differ among moors and were not related to treatment. We suggest annual monitoring and responsible anthelmintic use to prevent resistance so that medicated grit continues to enhance red grouse management.     

Local genetic structure in red grouse (Lagopus lagopus scoticus): evidence from microsatellite DNA markers

Allelic variation at seven hypervariable tri- and tetranucleotide microsatellite loci was used to determine levels of population differentiation between 14 populations of red grouse ( Lagopus lagopus scoticus ) in northeast Scotland, UK. Despite the potential for long-distance dispersal in grouse, and a semicontinuous habitat, significant population divergence was observed (mean R _ST = 0.153; P < 0.01) and an isolation-by-distance effect detected (Mantel test: P < 0.001). Examination of the spatial trend in principal component scores derived from allele frequencies among populations highlighted a barrier to gene flow that was confounding a simple isolation-by-distance effect. This barrier corresponded to an area of unsuitable habitat for grouse associated with a river system that bisected the study area. Mean genetic relatedness was higher for males than for females in all but one of the study populations, suggesting that the territorial behaviour and natal philopatry displayed by cocks have a manifold effect in generating the observed spatial genetic structure. Lower female relatedness values suggest a higher level of female-mediated gene flow, which is sufficient to prevent the loss of genetic variation from within populations and the onset of inbreeding effects. The potential consequences of local subdivision for red grouse populations are discussed.     

Adaptive and neutral genetic differentiation among Scottish and endangered Irish red grouse (<Emphasis Type="Italic">Lagopus lagopus scotica</Emphasis>)

Studying patterns of intra-specific genetic variation among populations allows for a better understanding of population structure and local adaptation. However, those patterns may differ according to the genetic markers applied, as neutral genetic markers reflect demographic processes and random genetic drift, whereas adaptive markers also carry the footprint of selection. In combination, neutral and adaptive genetic markers permit to assess the relative roles of drift and selection in shaping population structure. Among the best understood adaptive genetic loci are the genes of the major histocompatibility complex (MHC). We here study variation and differentiation at neutral SNP markers and MHC class II genes in red grouse (Lagopus lagopus scotica) from Ireland and Scotland. Irish red grouse populations are fragmented and drastically declining, but red grouse are abundant in Scotland. We find evidence for positive selection acting on the MHC genes and variation in MHC gene copy numbers among Irish individuals. Furthermore, there was significant population differentiation among red grouse from Ireland and Scotland at the neutral SNP markers (F_ST = 0.084) and the MHC-BLB genes (F_ST: BLB1 = 0.116, BLB2 = 0.090, BLB3 = 0.104). Differentiation at the MHC-BLB1 was significantly higher than at the neutral SNP markers, suggesting that selection plays an important role in shaping MHC variation, in addition to genetic drift. We speculate that the observed differentiation pattern might be due to local adaptation to different parasite regimes. These findings have strong conservation implications and we advise against the introduction of Scottish red grouse to supplement Irish populations.     

Reducing Tick Burdens on Chicks by Treating Breeding Female Grouse With Permethrin

ABSTRACT Ticks are important arthropod vectors of diseases of human, livestock, and wildlife hosts. In the United Kingdom, the sheep tick (Ixodes ricinus) is increasingly recognized as a main limiting factor of red grouse (Lagopus lagopus) populations, a game bird of high economic value. We evaluated the effectiveness of a new practical technique that could help managers reduce negative impacts of ticks on young grouse. In a replicated field experiment, we treated breeding females with leg bands impregnated with permethrin, a slow-releasing potent acaracide. We found that treatment reduced tick burdens on young chicks. Because this treatment is easily applied, it offers a new practical management tool to tackle problems caused by ticks in game bird populations.     

Digging for gold nuggets: uncovering novel candidate genes for variation in gastrointestinal nematode burden in a wild bird species

The extent to which genotypic variation at a priori identified candidate genes can explain variation in complex phenotypes is a major debate in evolutionary biology. Whereas some high‐profile genes such as the MHC or MC1R clearly do account for variation in ecologically relevant characters, many complex phenotypes such as response to parasite infection may well be underpinned by a large number of genes, each of small and effectively undetectable effect. Here, we characterize a suite of novel candidate genes for variation in gastrointestinal nematode (Trichostrongylus tenuis) burden among red grouse (Lagopus lagopus scotica) individuals across a network of moors in north‐east Scotland. We test for associations between parasite load and genotypic variation in twelve genes previously identified to be differentially expressed in experimentally infected red grouse or genetically differentiated among red grouse populations with overall different parasite loads. These genes are associated with a broad physiological response including immune system processes. Based on individual‐level generalized linear models, genotypic variants in nine genes were significantly associated with parasite load, with effect sizes accounting for differences of 514–666 worms per bird. All but one of these variants were synonymous or untranslated, suggesting that these may be linked to protein‐coding variants or affect regulatory processes. In contrast, population‐level analyses revealed few and inconsistent associations with parasite load, and little evidence of signatures of natural selection. We discuss the broader significance of these contrasting results in the context of the utility of population genomics and landscape genomics approaches in detecting adaptive genomic signatures.     

Past and potential future population dynamics of three grouse species using ecological and whole genome coalescent modeling

Studying demographic history of species provides insight into how the past has shaped the current levels of overall biodiversity and genetic composition of species, but also how these species may react to future perturbations. Here we investigated the demographic history of the willow grouse (Lagopus lagopus), rock ptarmigan (Lagopus muta), and black grouse (Tetrao tetrix) through the Late Pleistocene using two complementary methods and whole genome data. Species distribution modeling (SDM) allowed us to estimate the total range size during the Last Interglacial (LIG) and Last Glacial Maximum (LGM) as well as to indicate potential population subdivisions. Pairwise Sequentially Markovian Coalescent (PSMC) allowed us to assess fluctuations in effective population size across the same period. Additionally, we used SDM to forecast the effect of future climate change on the three species over the next 50 years. We found that SDM predicts the largest range size for the cold‐adapted willow grouse and rock ptarmigan during the LGM. PSMC captured intraspecific population dynamics within the last glacial period, such that the willow grouse and rock ptarmigan showed multiple bottlenecks signifying recolonization events following the termination of the LGM. We also see signals of population subdivision during the last glacial period in the black grouse, but more data are needed to strengthen this hypothesis. All three species are likely to experience range contractions under future warming, with the strongest effect on willow grouse and rock ptarmigan due to their limited potential for northward expansion. Overall, by combining these two modeling approaches, we have provided a multifaceted examination of the biogeography of these species and how they have responded to climate change in the past. These results help us understand how cold‐adapted species may respond to future climate changes.     

Testing the interactive effects of testosterone and parasites on carotenoid‐based ornamentation in a wild bird

Abstract Testosterone underlies the expression of most secondary sexual traits, playing a key role in sexual selection. However, high levels might be associated with physiological costs, such as immunosuppression. Immunostimulant carotenoids underpin the expression of many red‐yellow ornaments, but are regulated by testosterone and constrained by parasites. We manipulated testosterone and nematode burdens in red grouse (Lagopus lagopus scoticus) in two populations to tease apart their effects on carotenoid levels, ornament size and colouration in three time‐step periods. We found no evidence for interactive effects of testosterone and parasites on ornament size and colouration. We showed that ornament colouration was testosterone‐driven. However, parasites decreased comb size with a time delay and testosterone increased carotenoid levels in one of the populations. This suggests that environmental context plays a key role in determining how individuals resolve the trade‐off between allocating carotenoids for ornamental coloration or for self‐maintenance needs. Our study advocates that adequately testing the mechanisms behind the production or maintenance of secondary sexual characters has to take into account the dynamics of sexual trait expression and their environmental context.     

Variation in chicken populations may affect the enzymatic activity of lysozyme

The chicken lysozyme gene encodes a hydrolase that has a key role in defence, especially in ovo. This gene was resequenced in global chicken populations [red, grey, Ceylon and green jungle fowl (JF)] and related bird species. Networks, summary statistics and tests of neutrality indicate that although there is extensive variation at the gene, little is present at coding sites, with the exception of one non‐synonymous site. This segregating site and a further fixed non‐synonymous change between red JF and domestic chicken populations are spatially close to the catalytic sites of the enzyme and so might affect its activity.     

Successful adult willow grouse are exposed to increased harvest risk

Age and sex ratios in bag records are frequently used as indices of population composition for harvested populations. However, vulnerability to harvest may differ by age and sex thereby producing bias in population estimates. We assessed whether age and sex affected vulnerability to harvest for willow grouse (Lagopus lagopus) where adult density and brood size were known in the harvested populations. We collected bag records during 2 days of controlled hunting in 4 areas in 2 years (2007 and 2008) in Jämtland county, Sweden. We found that vulnerability to harvest was different for chicks and adults, but not between male and female adults. Hunters encountered broods at a higher rate than single birds compared to personnel conducting pre-harvest counts along line transects. Furthermore, the probability of shooting a grouse was higher in encounters of broods than individual grouse. Proportionally, we calculated about a 50% probability of a hunter shooting either a chick or an adult independent of encountering a single bird or broods of 2–10 grouse. Increasing adult density also increased the vulnerability to harvest for adults relative to chicks, independent of the chick to adult ratio in the pre-harvest population. The different vulnerability of adults and chicks to harvest observed in this study will dampen variation in age classes in bag records compared to the population, and we caution against extrapolation of age ratios in bag records to harvested populations. © 2012 The Wildlife Society.     

Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences

Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (psmc ) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (N_e) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid‐Brunhes event (~430 kya) and following climatic oscillations decreased the N_e of willow grouse and rock ptarmigan, but increased the N_e of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) – black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying psmc signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower N_e. Our results highlight the usefulness of the psmc approach in investigating species’ reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.     

Sequence Polymorphism in Candidate Genes for Differences in Winter Plumage between Scottish and Scandinavian Willow Grouse (Lagopus lagopus)

Background

Population variation in the degree of seasonal polymorphism is rare in birds, and the genetic basis of this phenomenon remains largely undescribed. Both sexes of Scandinavian and Scottish Willow grouse (Lagopus lagopus) display marked differences in their winter phenotypes, with Scottish grouse retaining a pigmented plumage year-round and Scandinavian Willow grouse molting to a white morph during winter. A widely studied pathway implicated in vertebrate pigmentation is the melanin system, for which functional variation has been characterised in many taxa.

Methodology/Principal Findings

We sequenced coding regions from four genes involved in melanin pigmentation (DCT, MC1R, TYR and TYRP1), and an additional control involved in the melanocortin pathway (AGRP), to investigate the genetic basis of winter plumage in Lagopus. Despite the well documented role of the melanin system in animal coloration, we found no plumage-associated polymorphism or evidence for selection in a total of ∼2.6 kb analysed sequence.

Conclusions/Significance

Our results indicate that the genetic basis of alternating between pigmented and unpigmented seasonal phenotypes is more likely explained by regulatory changes controlling the expression of these or other loci in the physiological pathway leading to pigmentation.     

Characterising functionally important and ecologically meaningful genetic diversity using a candidate gene approach

Over the past two decades the fields of molecular ecology and population genetics have been dominated by the use of putatively neutral DNA markers, primarily to resolve spatio-temporal patterns of genetic variation to inform our understanding of population structure, gene flow and pedigree. Recent emphasis in comparative functional genomics, however, has fuelled a resurgence of interest in functionally important genetic variation that underpins phenotypic traits of adaptive or ecological significance. It may prove a major challenge to transfer genomics information from classical model species to examine functional diversity in non-model species in natural populations, but already multiple gene-targeted candidate loci with major effect on phenotype and fitness have been identified. Here we briefly describe some of the research strategies used for isolating and characterising functional genetic diversity at candidate gene-targeted loci, and illustrate the efficacy of some of these approaches using our own studies on red grouse (Lagopus lagopus scoticus). We then review how candidate gene markers have been used to: (1) quantify genetic diversity among populations to identify those depauperate in genetic diversity and requiring specific management action; (2) identify the strength and mode of selection operating on individuals within natural populations; and (3) understand direct mechanistic links between allelic variation at single genes and variance in individual fitness.     

Rising burden of immature sheep ticks (Ixodes ricinus) on red grouse (Lagopus lagopus scoticus) chicks in the Scottish uplands

The sheep tick Ixodes ricinus (L.) (Acari: Ixodidae) is an ectoparasite of major economic and pathogenic importance in Scotland. Its distribution in the Scottish uplands is assumed to be governed by the abundance and distribution of its definitive hosts (deer and sheep) and climatic variables such as temperature and rainfall. As the numbers of its major host in Scotland, red deer, have increased dramatically and climatic conditions have become more favourable, the level of parasitism could have been expected to rise. We use data gathered from tick counts on over 4000 red grouse chicks Lagopus lagopus scoticus Latham (Galliformes: Tetraonidae) in various experiments over the past 19 years to ascertain whether the intensity and prevalence of parasitism has been increasing. From 1985 to 2003 the average tick burden of a parasitized red grouse chick has grown from 2.60 +/- 1.12 ticks per chick to 12.71 +/- 1.44. Over this period the percentage of chicks of a given brood parasitized has also increased from 4 +/- 2% to 92 +/- 3%. The possible implications of this increase in parasitism for red grouse production are discussed.     

Parasites and Scottish ptarmigan numbers

Summary Unlike red grouse (Lagopus lagopus scoticus), which have almost 100% prevalence of the parasitic threadworm Trichostrongylus tenuis and frequently high tapeworm numbers, 70% (n=71) of Scottish ptarmigan (Lagopus mutus) had no threadworms and only 4% had tapeworms. Other parasites and pathogenic bacteria were infrequent. Threadworms occurred in 12% (n=25) of birds on granite hills where mean ptarmigan densities were low, and in 43% (n=46) of birds over schists and limestones where mean densities were high. The notion that parasites cause the cyclic-type ptarmigan declines observed on the granite Cairngorms massif is unlikely (ptarmigan fluctuations over the richer rocks are irregular).