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The supplemental material contains additional Figures. Included figure files are provided below. Figure S1. Scatterplot matrix of the unmixed simulation data. Figure S2. Scatterplot matrix of the rotated simulation data. Figure S3. Visualization of genomic regions that have been used for the analysis. Figure S4. Scatterplot with cluster labels of the k-means clustering for t-SNE, Isomap and the LLE. Figure S5. Scatterplot with cluster labels of the k-means clustering for Diffusion Maps and kernel PCA. Figure S6. Scatterplot matrix for t-SNE output with k=7 applied to the real chicken data. Figure S7. Scatterplot matrix for t-SNE output with k=2 applied to the real chicken data. Figure S8. Scatterplot matrix of the first 7 components of the LLE output applied to the real chicken data. Figure S9. Scatterplot matrix of the first 7 components of the Isomap output applied to the real chicken data. Figure S10. Scatterplot matrix of the first 7 components of the kPCA output applid to the real chicken data. Figure S11. Scatterplot matrix of the first 7 components of the DM output applied to the real chicken data. Figure S12. The values of the level of agreement across the regions of interest. Figure S13. The individual genetic distances between main population to the mode of the subpopulation. (PDF 2130 kb)

The poultry breeding is world wide concentrated in few and large breeding companies and none of them are situated in Nordic countries. Regarding egg laying stock the hybrids offered by these companies are primarily developed in order to produce in cage systems and although they are high producing stock they has some short comings when kept in free range systems in terms of inadequate behaviour, mislaying of eggs and sometimes high mortality. The question of using cages for keeping hens has been a matter of much concern for many people and an animal welfare approaches has lead to regulations in individual countries as well as at the EEC level. In Sweden use of conventional cages was forbidden from 2002 and the EEC has given rules which declare that it will be forbidden to use conventional cages in any member state after 2012. The breeding companies operating world wide has the attitude that Northern Europe is a comparatively small part of their market share and they are therefore not willing to put a lot of effort into a breeding programme focussing particularly on free range productivity of laying hens. So far they have market hybrids they claim has a better adaptability to free range condition, but they have not been particularly bred for this purpose, but is the results of trying some cross combinations with lines they already had in their gene bank. In the light of this world wide developing in breeding with poultry it could be worth while to look if there should be gene materials hidden in the Nordic countries that has qualities in terms of being better genetic adapted to free range production. The description of what was found indicates that three two-way crosses found in respectively: Denmark, Sweden and Norway seems to fulfil the requirement that they are either genetically adapted to free range, produce on protein weak food and has a satisfying behaviour and finally has a reasonable productivity. It is not clear if all of the three crosses are good enough on all four criteria. In addition there are some breeds/strains under the gene conservation programme that might be of interest in crosses as they seems to have some production potential on top of being bred for adaptability for free range conditions. To get a better understanding of the potential of Nordic breeding material as back ground for laying hens in free range systems a higher level of knowledge it is needed in order to recommend this breeding material.