The introduction of reindeer to Brøggerhalvøya, Svalbard: grazing preference and effect on vegetation

In 1978 after about 100 years of absence, 15 Svalbard reindeer, Rangifer tarandus platyrhynchus were reintroduced to Brøggerhalvøya, a peninsula on the north-western coast of Svalbard. This stock had increased to about 200 animals in 1989. Studies of reindeer grazing behaviour were carried out in 1979-1980 and 1988¬1989. Highly prefered lichen species such as Cetraria nivalis had almost completely disappeared by 1989, whereas a less prefered species, Cetraria delisei, was still abundant. Year round dietary intake of grasses, lichens and herbs e.g. Oxyria digyna, had decreased by 1989, whereas that of mosses had increased. Essentially reindeer showed a more opportunistic grazing behaviour with more balanced utilization of all types of plant associations in 1989. The grazing behaviour of the reindeer on Brøggerhalvøya is therefore similar to that observed for Svalbard reindeer in general

Epigenetics, heritability and longitudinal analysis

© 2018 The Author(s). Background: Longitudinal data and repeated measurements in epigenome-wide association studies (EWAS) provide a rich resource for understanding epigenetics. We summarize 7 analytical approaches to the GAW20 data sets that addressed challenges and potential applications of phenotypic and epigenetic data. All contributions used the GAW20 real data set and employed either linear mixed effect (LME) models or marginal models through generalized estimating equations (GEE). These contributions were subdivided into 3 categories: (a) quality control (QC) methods for DNA methylation data; (b) heritability estimates pretreatment and posttreatment with fenofibrate; and (c) impact of drug response pretreatment and posttreatment with fenofibrate on DNA methylation and blood lipids. Results: Two contributions addressed QC and identified large statistical differences with pretreatment and posttreatment DNA methylation, possibly a result of batch effects. Two contributions compared epigenome-wide heritability estimates pretreatment and posttreatment, with one employing a Bayesian LME and the other using a variance-component LME. Density curves comparing these studies indicated these heritability estimates were similar. Another contribution used a variance-component LME to depict the proportion of heritability resulting from a genetic and shared environment. By including environmental exposures as random effects, the authors found heritability estimates became more stable but not significantly different. Two contributions investigated treatment response. One estimated drug-associated methylation effects on triglyceride levels as the response, and identified 11 significant cytosine-phosphate-guanine (CpG) sites with or without adjusting for high-density lipoprotein. The second contribution performed weighted gene coexpression network analysis and identified 6 significant modules of at least 30 CpG sites, including 3 modules with topological differences pretreatment and posttreatment. Conclusions: Four conclusions from this GAW20 working group are: (a) QC measures are an important consideration for EWAS studies that are investigating multiple time points or repeated measurements; (b) application of heritability estimates between time points for individual CpG sites is a useful QC measure for DNA methylation studies; (c) drug intervention demonstrated strong epigenome-wide DNA methylation patterns across the 2 time points; and (d) new statistical methods are required to account for the environmental contributions of DNA methylation across time. These contributions demonstrate numerous opportunities exist for the analysis of longitudinal data in future epigenetic studies

Flexible modelling of spatial variation in agricultural field trials with the R package INLA

The objective of this paper was to fit different established spatial models for analysing agricultural field trials using the open-source R package INLA. Spatial variation is common in field trials, and accounting for it increases the accuracy of estimated genetic effects. However, this is still hindered by the lack of available software implementations. We compare some established spatial models and show possibilities for flexible modelling with respect to field trial design and joint modelling over multiple years and locations. We use a Bayesian framework and for statistical inference the integrated nested Laplace approximations (INLA) implemented in the R package INLA. The spatial models we use are the well-known independent row and column effects, separable first-order autoregressive ( AR1⊗AR1 ) models and a Gaussian random field (Matérn) model that is approximated via the stochastic partial differential equation approach. The Matérn model can accommodate flexible field trial designs and yields interpretable parameters. We test the models in a simulation study imitating a wheat breeding programme with different levels of spatial variation, with and without genome-wide markers and with combining data over two locations, modelling spatial and genetic effects jointly. The results show comparable predictive performance for both the AR1⊗AR1 and the Matérn models. We also present an example of fitting the models to a real wheat breeding data and simulated tree breeding data with the Nelder wheel design to show the flexibility of the Matérn model and the R package INLA

Microsatellite Support for Active Inbreeding in a Cichlid Fish

In wild animal populations, the degree of inbreeding differs between species and within species between populations. Because mating with kin often results in inbreeding depression, observed inbreeding is usually regarded to be caused by limited outbreeding opportunities due to demographic factors like small population size or population substructuring. However, theory predicts inclusive benefits from mating with kin, and thus part of the observed variation in inbreeding might be due to active inbreeding preferences. Although some recent studies indeed report kin mating preferences, the evidence is still highly ambiguous. Here, we investigate inbreeding in a natural population of the West African cichlid fish Pelvicachromis taeniatus which showed clear kin mating preferences in standardized laboratory experiments but no inbreeding depression. The presented microsatellite analysis reveals that the natural population has, in comparison to two reference populations, a reduced allelic diversity (A = 3) resulting in a low heterozygosity (Ho = 0.167) pointing to a highly inbred population. Furthermore, we found a significant heterozygote deficit not only at population (Fis = 0.116) but also at subpopulation level (Fis = 0.081) suggesting that inbreeding is not only a by-product of population substructuring but possibly a consequence of behavioral kin preferences

Differences in choice of diet between sheep breeds grazing mountain pastures in Norway

In the present study, the foraging behaviour of ewes from three common Norwegian sheep breeds; the long-tailed Dala sheep, and the two short-tailed breeds Spael sheep and Norwegian Fur sheep was studied. Based on difference in body size and digestive anatomy, we expected the lighter short-tailed ewes to browse more on woody plants than the Dala ewes. The experiments were conducted during two consecutive summers within the flocks' usual grazing areas, and we sampled the proportion of grazing time that ewes spent feeding on woody plant species. We tested the hypothesis by applying generalized linear mixed models to the feeding behaviour data. As predicted, the short-tailed ewes spent substantially more of their grazing time browsing on trees, bushes and heather compared to the Dala ewes. We discuss the results in the context of maintaining the, now threatened, pastoral landscapes of mountainous regions of Norway; short-tailed breeds should be more effective than the Dala breed in reducing tree and bush encroachment, but more detailed studies are needed to quantify the breed differences in this respect

The effects of a deferred grazing system on rangeland vegetation in a north-western, semi-arid region of Tanzania

The present study assessed the effects of deferred grazing management on rangeland condition using aboveground biomass, vegetation cover and species composition as indicators of range condition. The experiment was based on traditionally conserved exclosures (ngitili). Data were collected in Shinyanga rural and Meatu districts, Tanzania, from October to November 2011. Five grazing strategies were compared: old private ngitili, young private ngitili, old communal ngitili, young communal ngitili and continuously grazed land. Aboveground biomass was significantly higher in old private ngitili than continuously grazed land, but there was no significant difference in amount of biomass between communal ngitili and continuously grazed land. The mean percentage basal cover was significantly higher in ngitili than continuously grazed land. The duration of protection (old ngitili compared with young ngitili) was not found to have any significant influence on both aboveground herbaceous biomass production and basal cover. The Shannon–Wiener index and Simpson index of diversity revealed no significant differences in species diversity among the different strategies. Both the continuously grazed land and communal ngitili were generally in poor condition and a special rehabilitation programme for improvement of these fragile grazing lands should be investigated.Keywords: biomass, grazing management, ngitili, species diversity, vegetation coverAfrican Journal of Range & Forage Science 2013, 30(3): 141–14