Historic <i>Treponema pallidum</i> genomes from Colonial Mexico retrieved from archaeological remains

<div><p><i>Treponema pallidum</i> infections occur worldwide causing, among other diseases, syphilis and yaws. In particular sexually transmitted syphilis is regarded as a re-emerging infectious disease with millions of new infections annually. Here we present three historic <i>T</i>. <i>pallidum</i> genomes (two from <i>T</i>. <i>pallidum</i> ssp. <i>pallidum</i> and one from <i>T</i>. <i>pallidum</i> ssp. <i>pertenue</i>) that have been reconstructed from skeletons recovered from the Convent of Santa Isabel in Mexico City, operational between the 17^th and 19^th century. Our analyses indicate that different <i>T</i>. <i>pallidum</i> subspecies caused similar diagnostic presentations that are normally associated with syphilis in infants, and potential evidence of a congenital infection of <i>T</i>. <i>pallidum</i> ssp. <i>pertenue</i>, the causative agent of yaws. This first reconstruction of <i>T</i>. <i>pallidum</i> genomes from archaeological material opens the possibility of studying its evolutionary history at a resolution previously assumed to be out of reach.</p></div

Examples for bone lesions for the three positive individuals.

<p>(A) The right tibia of individual 94A displays reactive periosteal bone on the anterior aspect of the diaphysis accompanied by progressive layering of the reactive bone. (B) The <i>pars basilaris</i> portion of the cranium of individual 94A showing pathological reactive bone in the endocranial surface, active at time of death. (C) An unidentified long bone from individual 94B displays fulminating periosteal reaction involving the whole of the diaphysis fragment. (D) The left femur of individual 133 presenting periosteal bone formation and expansion with cortical resorption characteristic of treponemal diseases. Source of the pictures: skeletal collection from Santa Isabel Convent, Mexico City, in custody of the Laboratory of Osteology, Post Graduate Studies Division, National School of Anthropology and History (ENAH), Mexico.</p

Phylogenetic trees and Circos plot [90] of the three ancient strains in comparison to modern strains.

<p>(A) Maximum Likelihood tree with bootstrap support for 39 modern strains and the three ancient strains. The strains 94A (magenta) and 94B (orange) branch with the syphilis SS14 clade while strain 133 (brown) branches with Fribourg-Blanc and other yaws strains. The scale represents the mean number of substitutions per site according to the GTR+GAMMA. Colored bars highlight the three subspecies <i>Treponema pallidum</i> ssp <i>pallidum</i> (TPA), <i>pertenue</i> (TPE) and <i>endemicum</i> (TEN). Strains of subspecies <i>pallidum</i> cause syphilis, subspecies <i>pertenue</i> cause yaws and subspecies <i>endemicum</i> causes bejel. (B) Bayesian trees visualized in Densitree overlaying phylogenetic trees based on the most probable topologies. Blue colored trees represent the most probable topology followed by red colored trees. For the ancient strains 94A and 94B two conflicting topologies are visible. The bars represent the 95% highest probability density intervals of the heights of the clades. The support value given at each clade is the fraction of trees in the tree-set that contain the clade. (C) Circos plot showing the shared SNP positions with specific clades and the coverage of the three ancient strains. From outer circle to the inner circle regions of possible recombination detected by ClonalFrameML are denoted on the outermost circle (purple). ‘ORI’ refers to the origin of replication. The genome coverages of the ancient strains 94B, 94A and 133 are represented in orange magenta and brown respectively from outward to inwards. Based on the SNPs that are specifically shared with different clades, colored bars are shown for strains 94B and 94A respectively in the innermost circles. Red bars highlight the SNP positions specifically shared with Fribourg-Blanc (supporting a phylogenetic position ancestral to the two syphilis clades). The green bars highlight the SNP positions shared with the SS14 clade while the blue bars highlight the SNP positions shared with the Nichols clade.</p

Summary statistics of the three positive historic samples.

<p>Summary statistics of the three positive historic samples.</p

Density of SNPs along all chromosomes and location of GWAS hits.

<p>Black line shows number of SNPs per 100 kb window. Centromere locations are indicated by grey shading. Vertical lines indicate SNPs associated with root phenotypes (red) and climatic variables (blue) (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007155#pgen.1007155.t001" target="_blank">Table 1</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007155#pgen.1007155.s007" target="_blank">S5 Table</a>).</p

Relationship among herbarium and modern samples.

<p><b>(A)</b> Neighbor joining tree with all 123 samples (dots) and rooted with the most distant sample. The black clade of almost-identical samples is the HPG1 lineage. Scale line shows the equivalent branch length of over 25,000 nucleotide changes. <b>(B)</b> Neighbor joining tree only with the HPG1 black clade from (A). Colors represent herbarium (blue) and modern individuals (green). Scale line shows the equivalent branch length of 80 nucleotide changes. Note that no outgroup was included. <b>(C, D)</b> Network of samples using the parsimony splits algorithm, before <b>(C)</b> and after <b>(D)</b> removing three intra-HPG1 recombinants (in red). Note that the network algorithm returns in (D) a network devoid of any reticulation, which indicates absence of intra-haplogroup recombination.</p

Genic SNPs associated with different traits.

<p>For nonsynonymous SNPs, the amino acid change and the Grantham score (ranging from 0 to 215), which measures the physico-chemical properties of the amino acids, are reported. All SNPs in the table were significant (p < 0.05) after raw p-values were corrected by an empirical p-value distribution from a permutation procedure. * highlights those that also passed a double Bonferroni threshold, correcting by number of SNPs and number of phenotypes (p < 0.0001). LD corresponds to how many other SNP hits are in high linkage (r²>0.5). <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007155#pgen.1007155.s007" target="_blank">S5 Table</a> contains information on all significant SNPs and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007155#pgen.1007155.s006" target="_blank">S4 Table</a> for details on phenotypes and climatic variables.</p

Substitution rates.

<p><b>(A)</b> Bayesian phylogenetic analyses employing tip-calibration. A total of 10,000 trees were superimposed as transparent lines, and the most common topology was plotted solidly. Tree branches were calibrated with their corresponding collection dates. <b>(B)</b> Maximum Clade Credibility (MCC) tree summarizing the trees in (A). Note the scale line shows the equivalent branch length of 50 nucleotide changes. The grey transparent bar indicates the 95% Highest Posterior Probability of the root date. <b>(C)</b> Regression between pairwise net genetic and time distances. The slope of the linear regression line corresponds to the genome substitution rate per year. <b>(D)</b> Substitution spectra in HPG1 samples, compared to greenhouse-grown mutation accumulation (MA) lines. <b>(E)</b> Comparison of genome-wide, intergenic, intronic, and genic substitution rates in HPG1 and mutation rates in greenhouse-grown MA lines. Substitution rates for HPG1 were re-scaled to a per generation basis assuming different generation times. Confidence intervals in HPG1 substitution rates were obtained from 95% confidence intervals of the slope from 1,000 bootstraps (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007155#pgen.1007155.s006" target="_blank">S4 Table</a> for actual values).</p

Geographic location and temporal distribution of HPG1 samples.

<p><b>(A)</b> Sampling locations of herbarium (blue) and modern individuals (green). <b>(B)</b> Temporal distribution of samples (random vertical jitter for visualization purposes). <b>(C)</b> Linear regression of latitude and longitude as a function of collection year (p-value of the slope and Pearson correlation coefficient are indicated).</p

Shotgun sequences for bird remains from Swahili coast archaeological sites

Shotgun sequences for bird remains from Swahili coast archaeological sites. Files that are labeled "JK" correspond to specific archaeological bone samples, each 4-digit number representing a single library: JK2992, JK3005, JK2999, JK2989, JK3002, JK2995, JK2993, JK3004, JK3003, JK2994, JK2988, JK3001, JK2990, JK3008, JK2998, JK3007, JK1996, JK3006, JK3000, JK2991, JK2997 . The other files represent extraction blanks (EBB1, EBB2) and library blanks (LBB2, LBB1). Please see supplementary data in the Prendergast et al. paper to link JK numbers to archaeological contexts