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Pig mortality is a big welfare and economic challenge. This study investigated the feasibility of reducing mortality of pigs from day 5 to slaughter and from birth to slaughter by breeding. Data of 163,782 female pigs were from DanBred Yorkshire breeding herds. Variances and breeding values were estimated using a linear, a logit and a probit model based on mortality record (0, 1) at individual level. Estimates of direct heritabilities ranged from 0.013 to 0.017 and maternalheritabilities from 0.005 to 0.017. Estimated breeding values (EBVs) from the three models were highly consistent. Although low heritabilities, validation accuracies of EBVs ranged from 0.415 to 0.420 for direct EBVs, from 0.192 to 0.392 for maternal EBVs, and from 0.357 to 396 for total EBVs. The results indicate that reducing pig mortality by breeding is feasible, and linear model is efficient for genetic evaluation of pig mortality.

This study compared four genotyping scenarios of genomic prediction for survival in a simulated pig population with survival rate of 80%. Breeding values were predicted using a linear mixed model and a logit model, based on individual records. The scenarios in order of prediction accuracy were: genotyping all individuals, randomly genotyping 80% individuals, genotyping alive individuals, and no genotyping. Using variance components estimated from pedigree-based model, genomic predictions with genotypes only from alive animals were unbiased. Given the same number of genotyped individuals, random genotyping 80% individuals led to higher prediction accuracy than only genotyping alive individuals, indicating the importance of genotype information of dead pigs. Moreover, the linear and the logit models achieved similar accuracy. We concludethat genotyping dead individuals should be considered, and a linear model can be used for predicting breeding values of survival in pigs.

Grise er sociale dyr, som interagerer med de dyr, som de går sammen med. Derfindes grise, som gør noget godt for de andre grise, og der findes grise, som haren negativ indflydelse på andre grise. I arbejdet med at øge dyrevelfærden igriseproduktionen og forbedre produktiviteten har forskere fra danske SEGESSvineproduktion, Aarhus Universitet og SRUC (Scotland's Rural College)undersøgt, om de sociale egenskaber hos grise kan forbedres gennem avl.Resultaterne tyder på, at det faktisk er muligt. Forskningen er gennemført medstøtte fra GUDP (Grønt Udviklings- og Demonstrationsprogram) underLandbrugs- og Fiskeristyrelsen. Målet har været at udvikle en metode til atberegne en social avlsværdi til avlsgrise og dermed udvælge de grise med debedste sociale gener som forældre til fremtidens grise for avlsselskabetDanBred.

The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this “Great Divide”, including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.Competing Interest StatementThe authors have declared no competing interest.

Records on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure on single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy of genetic evaluation of quantitative traits with individual records. Here, we investigated the value of genomic information for traits with group records. Besides, we investigated the improvement in accuracy of genetic evaluation for group-recorded traits when including information on a correlated trait with individual records. The study was based on a simulated pig population, including three scenarios of group structure and size. The results showed that both the genomic information and a correlated trait increased the accuracy of estimated breeding values (EBVs) for traits with group records. The accuracies of EBV obtained from group records with a size 24 were much lower than those with a size 12. Random assignment of animals to pens led to lower accuracy due to the weaker relationship between individuals within each group. It suggests that group records are valuable for genetic evaluation of a trait that is difficult to record on individuals, and the accuracy of genetic evaluation can be considerably increased using genomic information. Moreover, the genetic evaluation for a trait with group records can be greatly improved using a bivariate model, including correlated traits that are recorded individually. For efficient use of group records in genetic evaluation, relatively small group size and close relationships between individuals within one group are recommended.

Additional file 1: Figure S1. Scatter plot of Pearson’s correlations of (genomic) estimated breeding value ((G)EBV) based on full and reduced datasets ( $$\rho_{f,r}$$ ρ f , r ) versus the absolute difference in (G)EBV between the full and reduced datasets ( $$d_{f,r}$$ d f , r ) for all 323 groups for univariate PBLUP (panel A), bivariate PBLUP (panel B), univariate ssGBLUP (panel C), and bivariate ssGBLUP (panel D).

Changes in funerary practices are key to the understanding of social transformations of past societies. Over the course of the Nordic Bronze Age, funerary practices changed from inhumation to cremation. The aim of this study is to shed light on this fundamental change through a cross-examination of archaeometric provenance data and archaeological discussions of the context and layouts of early cremation graves. To this end, we conducted 19 new provenance analyses of strontium isotopes from Early Nordic Bronze age contexts in Thisted County and Zealand and Late Bronze Age contexts from Thisted County and Vesthimmerland (Denmark). These data are subsequently compared with data from other extant relevant studies, including those from Late Bronze Age Fraugde on the Danish island of Fyn.Overall, the variations within our provenience data suggest that the integration and establishment of cremation may not have had a one-to-one relationship with in-migration to Nordic Bronze Age Denmark. Moreover, there seems to be no single blanket scenario which dictated the uptake of cremation as a practice within this part of Southern Scandinavia. By addressing habitus in relation to the deposition of cremations as juxtaposed with these provenance data¸ we hypothesize several potential pathways for the uptake of cremation as a new cultural practice within the Danish Nordic Bronze Age and suggest that this may have been a highly individual process, whose tempo may have been dictated by the specificities of the region(s) concerned.

Om afsnittet Kirker og Bosætninger: I begyndelse af 1800-årene tog det Kongelige Nordiske Oldskriftselskab initiativet til systematiske registreringer og kortlægning af de mange ruiner i henholdsvis Sydvestgrønland og i området omkring Nuuk. Kirkebygningerne fik særlig opmærksomhed. De var letgenkendelige i landskabet, og forskningen var især rettet mod arkitekturen og kirkernes dateringer. De sidste skete ved sammenligninger med kirkearkitekturen på de Britiske Øer og i Skandinavien. Mange nye kirker er registreret siden Oldskrifselskabet udgav det monumentale tre-bind-værk Grønlands Historiske Mindesmærker (1838 – 1845). Med brugen af 14C dateringsmetoden er det i dag muligt at komme tættere på dateringerne af brugen af de enkelte kirker, og bygningerne kan nu også vurderes i et bredere socioøkonomisk perspektiv. Her vurderes bebyggelsesdynamikken i nordbobygderne med udgangspunkt i kirkebyggeriet.

Additional file 1. Investigation of predictive performance.

The aim of this study was to examine (i) the genetic variation in macro-environmental sensitivity (macro-ES) for ADG in Danish Duroc pigs, (ii) the genetic heterogeneity among sexes, and (iii) residual variance heterogeneity among herds. Record of ADG for 32,297 boars (19 herds) and 42,724 gilts (16 herds) was used for analysis. The data were provided by the National Danish Pig Research Centre. The analysis was performed by fitting univariate reaction norm models with the herd-year-month on test (HYM) effect as environmental covariates and herd-specific residual variance for boars and gilts separately under a Bayesian setting. The environmental covariate was inferred simultaneously with other parameters of the model. Gibbs sampling was used to sample model dispersion and location parameters. The posterior means and highest posterior density intervals of the additive genetic variance, genetic correlations for ADG, and heritability were calculated over the continuous environmental range of −3σh to +3σh (SD of the HYM effect). The coheritability of ADG at the average environmental level and ADG in the environments along the −3σh to +3σh environmental gradient were also calculated. The analysis showed significant variation in macro-ES, revealing genotype by environment interactions (G × E) for ADG. The presence of G × E resulted in changes in additive genetic variance and heritability across the −3σh to +3σh range. The genetic correlations were high and positive between ADG in environments differing by 1σh units or less and decreased to moderately positive between ADG in the extreme environments in both sexes. The coheritability of ADG in the environment at the average level and the −3σh environment for boars were greater than the heritability in the environment at the average level, while it was less for gilts. The coheritability of ADG in the environment at the average level and the +3σh environment for boars was less than heritability in the environment at the average level, while it was either the same or greater for gilts, depending on the residual variance. Boars had larger additive genetic and residual variances than gilts. Heterogeneity of residual variances across herds was shown for both sexes. In conclusion, this study shows the presence of macro-ES, genetic variance heterogeneity among sexes for ADG in pigs, and residual variance heterogeneity across herds. The aim of this study was to examine (i) the genetic variation in macro-environmental sensitivity (macro-ES) for ADG in Danish Duroc pigs, (ii) the genetic heterogeneity among sexes, and (iii) residual variance heterogeneity among herds. Record of ADG for 32,297 boars (19 herds) and 42,724 gilts (16 herds) was used for analysis. The data were provided by the National Danish Pig Research Centre. The analysis was performed by fitting univariate reaction norm models with the herd-year-month on test (HYM) effect as environmental covariates and herd-specific residual variance for boars and gilts separately under a Bayesian setting. The environmental covariate was inferred simultaneously with other parameters of the model. Gibbs sampling was used to sample model dispersion and location parameters. The posterior means and highest posterior density intervals of the additive genetic variance, genetic correlations for ADG, and heritability were calculated over the continuous environmental range of -3σh to +3σh (SD of the HYM effect). The coheritability of ADG at the average environmental level and ADG in the environments along the -3σh to +3σh environmental gradient were also calculated. The analysis showed significant variation in macro-ES, revealing genotype by environment interactions (G × E) for ADG. The presence of G × E resulted in changes in additive genetic variance and heritability across the -3σh to +3σh range. The genetic correlations were high and positive between ADG in environments differing by 1σh units or less and decreased to moderately positive between ADG in the extreme environments in both sexes. The coheritability of ADG in the environment at the average level and the -3σh environment for boars were greater than the heritability in the environment at the average level, while it was less for gilts. The coheritability of ADG in the environment at the average level and the +3σh environment for boars was less than heritability in the environment at the average level, while it was either the same or greater for gilts, depending on the residual variance. Boars had larger additive genetic and residual variances than gilts. Heterogeneity of residual variances across herds was shown for both sexes. In conclusion, this study shows the presence of macro-ES, genetic variance heterogeneity among sexes for ADG in pigs, and residual variance heterogeneity across herds.