Local breed proportions and local breed heterozygosity in genomic predictions for crossbred dairy cows

For genomic prediction of crossbred animals, models that account for the breed origin of alleles (BOA) in marker genotypes can allow the effects of marker alleles to differ depending on their ancestral breed. Previous studies have shown that genomic estimated breeding values for crossbred cows can be calculated using the marker effects that are estimated in the contributing pure breeds and combined based on estimated BOA in the genotypes of the crossbred cows. In the presented study, we further exploit the BOA information for improving the prediction of genomic breeding values of crossbred dairy cows. We investigated 2 types of BOA-derived breed proportions: global breed proportions, defined as the proportion of marker alleles assigned to each breed across the whole genome; and local breed proportions (LBP), defined as the proportions of alleles on chromosome segments which were assigned to each breed. Further, we investigated 2 BOA-derived measures of heterozygosity for the prediction of total genetic value. First, global breed heterozygosity, defined as the proportion of marker loci that have alleles originating in 2 different breeds over the whole genome. Second, local breed heterozygosity (LBH), defined as proportions of marker loci on chromosome segments that had alleles originating in 2 different breeds. We estimated variance related to LBP and LBH on the remaining variation after accounting for prediction with solutions from the genomic evaluations of the pure breeds and validated alternative models for production traits in 5,214 Danish crossbred dairy cows. The estimated LBP variances were 0.9, 1.2, and 1.0% of phenotypic variance for milk, fat, and protein yield, respectively. We observed no clear LBH effect. Cross-validation showed that models with LBP effects had a numerically small but statistically significantly higher predictive ability than models only including global breed proportions. We observed similar improvement in accuracy by the model having an across crossbred residual additive genetic effect, accounting for the additive genetic variation that was not accounted for by the solutions from purebred. For genomic predictions of crossbred animals, estimated BOA can give useful information on breed proportions, both globally in the genome and locally in genome regions, and on breed heterozygosity

Methodological approaches to determining the marine radiocarbon reservoir effect

The marine radiocarbon reservoir effect is an offset in 14C age between contemporaneous organisms from the terrestrial environment and organisms that derive their carbon from the marine environment. Quantification of this effect is of crucial importance for correct calibration of the <sup>14</sup>C ages of marine-influenced samples to the calendrical timescale. This is fundamental to the construction of archaeological and palaeoenvironmental chronologies when such samples are employed in <sup>14</sup>C analysis. Quantitative measurements of temporal variations in regional marine reservoir ages also have the potential to be used as a measure of process changes within Earth surface systems, due to their link with climatic and oceanic changes. The various approaches to quantification of the marine radiocarbon reservoir effect are assessed, focusing particularly on the North Atlantic Ocean. Currently, the global average marine reservoir age of surface waters, R(t), is c. 400 radiocarbon years; however, regional values deviate from this as a function of climate and oceanic circulation systems. These local deviations from R(t) are expressed as +R values. Hence, polar waters exhibit greater reservoir ages (δR = c. +400 to +800 <sup>14</sup>C y) than equatorial waters (δR = c. 0 <sup>14</sup>C y). Observed temporal variations in δR appear to reflect climatic and oceanographic changes. We assess three approaches to quantification of marine reservoir effects using known age samples (from museum collections), tephra isochrones (present onshore/offshore) and paired marine/terrestrial samples (from the same context in, for example, archaeological sites). The strengths and limitations of these approaches are evaluated using examples from the North Atlantic region. It is proposed that, with a suitable protocol, accelerator mass spectrometry (AMS) measurements on paired, short-lived, single entity marine and terrestrial samples from archaeological deposits is the most promising approach to constraining changes over at least the last 5 ky BP

Evidence for rangewide panmixia despite multiple barriers to dispersal in a marine mussel

Oceanographic features shape the distributional and genetic patterns of marine species by interrupting or promoting connections among populations. Although general patterns commonly arise, distributional ranges and genetic structure are species-specific and do not always comply with the expected trends. By applying a multimarker genetic approach combined with Lagrangian particle simulations (LPS) we tested the hypothesis that oceanographic features along northeastern Atlantic and Mediterranean shores influence dispersal potential and genetic structure of the intertidal mussel Perna perna. Additionally, by performing environmental niche modelling we assessed the potential and realized niche of P. perna along its entire native distributional range and the environmental factors that best explain its realized distribution. Perna perna showed evidence of panmixia across > 4,000 km despite several oceanographic breaking points detected by LPS. This is probably the result of a combination of life history traits, continuous habitat availability and stepping-stone dynamics. Moreover, the niche modelling framework depicted minimum sea surface temperatures (SST) as the major factor shaping P. perna distributional range limits along its native areas. Forthcoming warming SST is expected to further change these limits and allow the species to expand its range polewards though this may be accompanied by retreat from warmer areas.Fundacao para a Ciencia e Tecnologia (FCT-MEC, Portugal) [UID/Multi/04326/2013, IF/01413/2014/CP1217/CT0004]; South African Research Chairs Initiative (SARChI) of the Department of Science and Technology; National Research Foundation; South African National Research Foundation (NRF); Portuguese Fundacao para a Ciencia e Tecnologia (FCT) [SFRH/BPD/85040/2012, SFRH/BPD/111003/2015]info:eu-repo/semantics/publishedVersio

Environmental changes off North Iceland during the deglaciation and the Holocene: foraminifera, diatoms and stable isotopes

A combined study of foraminifera, diatoms and stable isotopes in marine sediments off North Iceland records major changes in sea surface conditions since about 15800 cal years (yr) BP. Results are presented from two gravity cores obtained at about 400 m water depth from two separate sedimentary basins on each side of the submarine Kolbeinsey Ridge. The chronology of the sedimentary record is based partly on AMS 14C dates, partly on the Vedde and the Saksunarvatn tephra markers, as well as the historical Hekla AD 1104 tephra. During the regional deglaciation, the planktonic foraminiferal assemblages are characterised by consistently high percentages of sinistrally coiled Neogloboquadrina pachyderma. However, major environmental variability is reflected by changes in stable isotope values and diatom assemblages. Low ∂18O values indicate a strong freshwater peak as well as possible brine formation by sea-ice freezing during a pre-Bølling interval (Greenland Stadial 2), corresponding to the Heinrich 1 event. The foraminifera suggest a strong concurrent influence of relatively warm and saline Atlantic water, and both the foraminifera and the diatoms suggest mixing of cold and warm water masses. Similar but weaker environmental signals are observed during the Younger Dryas (Greenland Stadial 1) around the level of the Vedde Ash. Each freshwater peak is succeeded by an interval of severe cooling both at the beginning of the Bølling–Allerød Interstadial Complex (Greenland Interstadial 1) and during the Preboreal, presumably associated with the onset of intense deep water formatiom in the Nordic Seas. The Holocene thermal optimum, between 10200 and about 7000 cal years (yr) BP, is interrupted by a marked cooling of the surface waters around 8200 cal yr BP. This cold event is clearly expressed by a pronounced increase in the percentages of sinistrally coiled N. pachyderma, corresponding to a temperature decrease of about 3°C. A general cooling in the area is indicated after 7000–6000 cal yr BP, both by the diatom data and by the planktonic foraminiferal data. After a severe cooling around 6000 cal yr BP, the planktonic foraminiferal assemblages suggest a warmer interval between 5500 and 4500 cal yr BP. Minor temperature fluctuations are reflected both in the foraminiferal and in the diatom data in the upper part of the record, but the time resolution of the present data is not high enough to pick up details in environmental changes through the late Holocene

Segregation between breeds and local breed proportions in genetic and genomic models for crossbreds

Abstract Background The breeding value of a crossbred individual can be expressed as the sum of the contributions from each of the contributing pure breeds. In theory, the breeding value should account for segregation between breeds, which results from the difference in the mean contribution of loci between breeds, which in turn is caused by differences in allele frequencies between breeds. However, with multiple generations of crossbreeding, how to account for breed segregation in genomic models that split the breeding value of crossbreds based on breed origin of alleles (BOA) is not known. Furthermore, local breed proportions (LBP) have been modelled based on BOA and is a concept related to breed segregation. The objectives of this study were to explore the theoretical background of the effect of LBP and how it relates to breed segregation and to investigate how to incorporate breed segregation (co)variance in genomic BOA models. Results We showed that LBP effects result from the difference in the mean contribution of loci between breeds in an additive genetic model, i.e. breed segregation effects. We found that the (co)variance structure for BS effects in genomic BOA models does not lead to relationship matrices that are positive semi-definite in all cases. However, by setting one breed as a reference breed, a valid (co)variance structure can be constructed by including LBP effects for all other breeds and assuming them to be correlated. We successfully estimated variance components for a genomic BOA model with LBP effects in a simulated example. Conclusions Breed segregation effects and LBP effects are two alternative ways to account for the contribution of differences in the mean effects of loci between breeds. When the covariance between LBP effects across breeds is included in the model, a valid (co)variance structure for LBP effects can be constructed by setting one breed as reference breed and fitting an LBP effect for each of the other breeds

A quantitative X-ray diffraction inventory of the tephra and volcanic glass inputs into the Holocene marine sediment archives off Iceland: A contribution to V.A.S.T.

This paper re-evaluates how well quantitative x-ray diffraction (qXRD) can be used as an exploratory method of the weight percentage (wt%) of volcaniclastic sediment, and to identify tephra events in marine cores. In the widely used RockJock v6 software programme, qXRD tephra and glass standards include the rhyodacite White River tephra (Alaska), a rhyolitic tephra (Hekla-4) and the basaltic Saksunarvatn tephra. Experiments of adding known wt% of tephra to felsic bedrock samples indicated that additions ≥10 wt% are accurately detected, but reliable estimates of lesser amounts are masked by amorphous material produced by milling. Volcaniclastic inputs range between 20 and 50 wt%. Primary tephra events are identified as peaks in residual qXRD glass wt% from fourth-order polynomial fits. In cores where tephras have been identified by shard counts in the > 150 µm fraction, there is a positive correlation (validation) with peaks in the wt% glass estimated by qXRD. Geochemistry of tephra shards confirms the presence of several Hekla-sourced tephras in cores B997-317PC1 and -319PC2 on the northern Iceland shelf. In core B997-338 (north-west Iceland), there are two rhyolitic tephras separated by ca. 100 cm with uncorrected radiocarbon dates on articulated shells of around 13 000 yr B.P. These tephras may be correlatives of the Borrobol and Penifiler tephras found in Scotland. The number of Holocene tephra events per 1000 yr was estimated from qXRD on 16 cores and showed a bimodal distribution with an increased number of events in both the late and early Holocene.Keywords: X-ray diffraction; tephras; Iceland Holocene(Published: 26 February 2013)To access the supplementary material for this article, please see the supplementary files in the column to the right (under Readers Tools). Citation: Polar Research 2013, 32, 11130, http://dx.doi.org/10.3402/polar.v32i0.1113