Britain.

<p>a) Non-metric multi-dimensional scaling of burial similarities. Note the association of grave furnishing (grave goods and coffins) with prone burials and burials with the cephalic extremity displaced. b) Cluster analysis of burial features.</p

Geographical distribution of the prone burials and burials with the cephalic extremity displaced.

<p>Each dot represents a site. Grey and black dots indicate, respectively, prone burials and burials with the cephalic extremity displaced. Note the wide distribution of prone burials in both Continental Europe and Britain, and the cluster of burials with the cephalic extremity displaced in the latter.</p

Continental Europe.

<p>a) Non-metric multi-dimensional scaling of burial similarities. Note the separation (lack of co-occurrence) between cephalic extremity displacement and prone burials, and the association between the latter and grave goods and grave furniture (coffins). b) Cluster analysis of burial features.</p

Frequency of each variable and combined variables in Britain and Continental Europe.

<p>Significant differences between the two areas are reported in bold. CD = Cephalic extremity displaced; CM = Cephalic extremity missing; PM = Postcranial bones missing.</p><p>Frequency of each variable and combined variables in Britain and Continental Europe.</p

Definition of the variables used in this study.

<p>* Due to misuse and inconsistent use of terms in the literature it is not always possible to assess whether both cranium and mandible were involved or solely the cranium, as well as the possible presence of uppermost cervical vertebrae.</p><p>Definition of the variables used in this study.</p

Time to the most recent common ancestor (tMRCAs) for the entire <i>M</i>. <i>leprae</i> tree and individual branches (HPD = Highest Posterior Density).

<p>Time to the most recent common ancestor (tMRCAs) for the entire <i>M</i>. <i>leprae</i> tree and individual branches (HPD = Highest Posterior Density).</p

Results of the genome-wide analysis for the samples with sufficient coverage.

<p>Results of the genome-wide analysis for the samples with sufficient coverage.</p

Worldwide distribution of the ancient and modern <i>M</i>. <i>leprae</i> strains analyzed in this study.

<p>Skulls represent strains from osteological specimens dated to the Medieval Period. Human silhouettes represent modern strains, sized to scale according to the number of samples, ranging from 1 (e.g. India) to 36 (South America) Animal silhouettes represent strains from the red squirrel, the nine-banded armadillo, and naturally infected nonhuman primates (a chimpanzee from Sierra Leone, a sooty mangabey from West Africa, and a cynomolgus macaque from The Philippines). Skulls outlined in black are the new <i>M</i>. <i>leprae</i> genomes reconstructed in this study, while skulls outlined in blue represent previously sequenced ancient genomes. Grey skulls are leprosy samples from this study that did not yield sufficient sequence for whole-genome analysis. The main <i>M</i>. <i>leprae</i> lineages, represented by branches (see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006997#ppat.1006997.g002" target="_blank">Fig 2</a>) are color-coded.</p

Phylogenetic analysis of ancient and modern <i>M</i>. <i>leprae</i> strains.

<p>(<b>A</b>) Maximum parsimony tree reconstructed from 3124 informative SNP positions. The tree is drawn to scale, with branch lengths representing number of substitutions. <i>M</i>. <i>lepromatosis</i> was used as outgroup. The novel strains from this study are labelled in red, and the previously published ancient strains are labelled in blue. Animal symbols indicate strains isolated from red squirrels, armadillos and non-human primates. The main branches are color-coded, and the SNP subtypes are marked with dotted vertical bars. Bootstrap values (500 replicates) are shown next to each node. (<b>B</b>) Bayesian phylogenetic tree based on 2371 SNP positions calculated with BEAST 1.8.1. Median divergence times in years B.C.E. and C.E. are shown on the main nodes (the 95% Highest Posterior Density ranges are given in square brackets). Tip labels for each sample show the name, the country of origin and the isolation date, or the radiocarbon dates. The novel strains from this study are labelled in red, and the previously published ancient strains are labelled in blue. Posterior probabilities for each node are shown in grey. The main branches are color-coded. The hypermutator strains 85054, Amami, S15, Br14-3, Br2016-15, Zensho-4, Zensho-5 and Zensho-9 (as described in [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006997#ppat.1006997.ref014" target="_blank">14</a>]) were excluded from this analysis.</p