Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

peer-reviewedH.D.D., A.J.C., P.J.B. and B.J.H. would like to acknowledge the Dairy Futures Cooperative Research Centre for funding. H.P. and R.F. acknowledge funding from the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr ‘Synbreed—Synergistic Plant and Animal Breeding’ (grant 0315527B). H.P., R.F., R.E. and K.-U.G. acknowledge the Arbeitsgemeinschaft Süddeutscher Rinderzüchter, the Arbeitsgemeinschaft Österreichischer Fleckviehzüchter and ZuchtData EDV Dienstleistungen for providing genotype data. A. Bagnato acknowledges the European Union (EU) Collaborative Project LowInputBreeds (grant agreement 222623) for providing Brown Swiss genotypes. Braunvieh Schweiz is acknowledged for providing Brown Swiss phenotypes. H.P. and R.F. acknowledge the German Holstein Association (DHV) and the Confederación de Asociaciones de Frisona Española (CONCAFE) for sharing genotype data. H.P. was financially supported by a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft (DFG) (grant PA 2789/1-1). D.B. and D.C.P. acknowledge funding from the Research Stimulus Fund (11/S/112) and Science Foundation Ireland (14/IA/2576). M.S. and F.S.S. acknowledge the Canadian Dairy Network (CDN) for providing the Holstein genotypes. P.S. acknowledges funding from the Genome Canada project entitled ‘Whole Genome Selection through Genome Wide Imputation in Beef Cattle’ and acknowledges WestGrid and Compute/Calcul Canada for providing computing resources. J.F.T. was supported by the National Institute of Food and Agriculture, US Department of Agriculture, under awards 2013-68004-20364 and 2015-67015-23183. A. Bagnato, F.P., M.D. and J.W. acknowledge EU Collaborative Project Quantomics (grant 516 agreement 222664) for providing Brown Swiss and Finnish Ayrshire sequences and genotypes. A.C.B. and R.F.V. acknowledge funding from the public–private partnership ‘Breed4Food’ (code BO-22.04-011- 001-ASG-LR) and EU FP7 IRSES SEQSEL (grant 317697). A.C.B. and R.F.V. acknowledge CRV (Arnhem, the Netherlands) for providing data on Dutch and New Zealand Holstein and Jersey bulls.Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals

Holocene Cyclic Records of Ice-Rafted Debris and Sea Ice Variations on the East Greenland and Northwest Iceland Margins

The dynamics of the Greenland Ice Sheet and drift of sea ice from the Arctic Ocean reaching Denmark Strait are poorly constrained. We present data on the provenance of Fe oxide detrital grains from two cores in the Denmark Strait area and compare the Fe grain source data with other environmental proxies in order to document the variations and potential periodicities in ice-rafted debris delivery during the Holocene. Based on their Fe grain geochemistry, the sediments can be traced to East Greenland sources and to more distal sites around the Arctic Basin. On the Holocene time scales of the two cores, sea ice biomarker (IP25) data, and quartz weight percent reveal positive associations with T°C and inverse associations with biogenic carbonate wt%. Trends in the data were obtained from Singular Spectrum Analysis (SSA), and residuals were tested for cyclicity. Trends on the environmental proxies explained between 15 and 90% of the variance. At both sites the primary Fe grain sources were from Greenland, but significant contributions were also noted from Banks Island and Svalbard. There is a prominent cyclicity of 800 yrs as well as other less prominent cycles for both Greenland and arctic sources. The Fe grain sources from Greenland and the circum-Arctic Ocean are in synchronization, suggesting that the forcings for these cycles are regional and not local ice sheet instabilities

The geomorphology of UK estuaries: The role of geological controls, antecedent conditions and human activities

This paper provides an overview of the geomorphological characteristics of UK estuaries and the factors which control them. Many of the features included in previous classifications of UK estuaries are not true estuaries since they do not possess significant river influence. The features considered in this paper to be ‘true’ estuaries are divided into ‘restricted entrance’ and ‘unrestricted entrance’ types on the grounds that the size and geometry of the estuary mouth exerts a critical influence on water levels, tidal currents, wave action, sediment transport and morphological evolution. An estuary which has a wide mouth, narrows and becomes shallower towards the head is likely to be flood dominated, especially if it has a large tidal range, whereas an estuary which has a narrow mouth and widens and/or becomes deeper towards the head is more likely to display ebb dominance, especially if it has a relatively small tidal range. Wide-mouthed estuaries are influenced to a greater degree by wave processes than estuaries with a narrow mouth. Previous authors have hypothesised that estuaries may maintain a state of dynamic equilibrium through alternating periods of flood and ebb dominance, but it is concluded that there is presently no substantive evidence to support this hypothesis. UK estuaries have been affected to varying degrees by embanking, land claim, dredging, sea wall breaching and managed realignment. Some estuaries have adjusted quickly to such perturbations, but others continue to show progressive change, either sedimentary infilling or erosion and sediment loss. The quantification of estuary morphometry, identification of change over time, and testing of hypotheses regarding the morphodynamics and stability of estuaries requires adequate bathymetric/topographic, hydrodynamic and sediment data. At present, such data are available for relatively few UK estuaries

Optimal imaging with adaptive mesh refinement in electrical tomography

In non-linear electrical impedance tomography the goodness of fit of the trial images is assessed by the well-established statistical χ2 criterion applied to the measured and predicted datasets. Further selection from the range of images that fit the data is effected by imposing an explicit constraint on the form of the image, such as the minimization of the image gradients. In particular, the logarithm of the image gradients is chosen so that conductive and resistive deviations are treated in the same way. In this paper we introduce the idea of adaptive mesh refinement to the 2D problem so that the local scale of the mesh is always matched to the scale of the image structures. This improves the reconstruction resolution so that the image constraint adopted dominates and is not perturbed by the mesh discretization. The avoidance of unnecessary mesh elements optimizes the speed of reconstruction without degrading the resulting images. Starting with a mesh scale length of the order of the electrode separation it is shown that, for data obtained at presently achievable signal-to-noise ratios of 60 to 80 dB, one or two refinement stages are sufficient to generate high quality images

Geomorphological and ecological change in a coastal foreland dune system, Sandscale haws, Cumbria, UK: the management challenges posed by climate change

Many coastal sand dune systems in the UK and other parts of the world have experienced a decline in bare sand extent and dune mobility over the past 70 years, accompanied by increased coverage of coarse grass, scrub and woodland vegetation. This has raised concerns amongst nature conservationists about the survival of dune specialist species. Opinions are divided, however, regarding what management interventions should be made to counteract these trends. This paper reviews the factors which have contributed to progressive dune system stabilization at Sandscale Haws, located on the Irish Sea coast in Northwest England, considers the implications for the site of UKCP18 future climate change projections, and discusses the options and plans for future adaptive management. Analaysis of aerial photographs indicated a large reduction in bare sand area between 1946 and 1988 (from >34% to 9% of the dune system), since when there has been a further decline to 1.7%. Consideration of the evidence suggests that a trend towards a warmer, slightly wetter and less windy climate has been the main driver of stabilization, although atmospheric nitrogen deposition, increasing atmospheric CO2 concentrations, reduced grazing intensity, reduced human disturbance from the mid-1980s onwards and a tendency for shoreline progradation on the west-facing coast have played contributing roles. Some species characteristic of open habitats can still be found in good numbers in parts of the dune system, but without increased management it is likely they will decline further and some may become locally extinct. Since the site is of national and international importance for a number of nationally scarce plant and animal species it is considered that there is both a legal and an ethical duty to attempt to maintain suitable habitat for their survival. As a National Nature Reserve Sandscale Haws provides a suitable ‘natural laboratory’ within which to research the effectiveness of different intervention methods. A number of small-scale dune rejuvenation methods have been trialled since 2015, and options for larger scale interventions, including turf stripping and possible dune notching, are currently being evaluated as part of the nation-wide Dynamic Dunescapes project