Gene flow values.

<p>The log₁₀ of the gene flow values are shown on a heatmap for both areas. The populations of origin are shown on the vertical axis.</p

Map of sampling sites.

<p>The top map shows the location of the two areas used in this study. The maps at the bottom show the location and name of each sampling site for both areas (B = Bjerringbro, K = Kalø) and management types of the field (C for conventional or O for organic) and ordinal number.</p

Pairwise <i>F</i>_st values.

<p>The pairwise <i>F</i>_st values for each pair of sampling sites are shown on a heatmap for both areas. Pairs that are significantly different, after sequential Bonferroni correction, are represented by a + sign on the heatmap.</p

Sampling details.

<p>Number of sampled individuals per sampling site, per year and in total (first to third column). Last column shows the type of management.</p

Genetic clusters recovered by GENELAND.

<p>The figure shows the genetic clusters for each area with each cluster being included in a solid line (black for Bjerringbro, white for Kalø).</p

Results of gene flow analyses (Bjerringbro).

<p>For each of the 9 runs performed with BIMr the most significant factor(s), their posterior probability and the alpha value for that factor(s) are reported. The results from the best run (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066208#s2" target="_blank">Materials and methods</a> for details) are shown in italics.</p

Supplementary 8 from Mice as stowaways? Colonization history of Danish striped field mice

Species from the steppe region of Eastern Europe likely colonized Northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse (<i>Apodemus agrarius</i> Pallas, 1783), is a steppe-derived species often found in human crops, that is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe because approximately10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the Northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland

Supplementary 2 from Mice as stowaways? Colonization history of Danish striped field mice

Species from the steppe region of Eastern Europe likely colonized Northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse (<i>Apodemus agrarius</i> Pallas, 1783), is a steppe-derived species often found in human crops, that is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe because approximately10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the Northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland