A network path for four informative substitutions shows that New World subsp. pertenue, or yaws-causing strains, are the closest relatives of modern subsp. pallidum strains.
Syphilis, caused by a spirochete bacteria, was first reported in Europe in 1495 and there have been a number of hypothese to explain its relatively recent appearance. I briefly mentioned the possibility that the Black Death may have played a role in its emergence.
For a long time the emergence of syphilis was associated with the discovery of the New World and is sometimes cited as being the only new disease to make the journey from New World to Old World (lots of diseases made the journey the other way, and diseases like smallpox and measles decimated the New World populations). But other diseases such as Yaws, caused by the same species of bacteria, have a widespread distribution in both the New and Old World.
A paper this week in PLoS Neglected Tropical Diseases provides evidence from a phylogenetic study that suggests that while other forms of the Treponema pallidum bacterium have plagued humans since early in our evolution, it emerged as venereal syphilis only when carried back to Europe by Columbus and his crew.