The Plague

• A zoonoses of rodents and fleas in wild reservoirs.
• Spillover to mammalian hosts occasionally occurs.
• Humans are the most 'spectacular' victims.1

Research Questions

1. Where did plague originate?
2. How did pandemics spread across the continent?
3. How many pandemics have occurred?
4. What evolutionary mechanisms enhance virulence?

Problems: Big Data

• A large genomic dataset was assembled in 20191.
• This dataset was re-used by aDNA researchers.
• But this is only a fraction of the data available2!

Problems: Geospatial

• Spread maps aren't statistically constructed1.
• Leading to ambiguity and uncertainty.

Objectives

• What are all those extra Y. pestis genomes?
• When were they collected?
• Where were they collected?
• Do they add value to geospatial analysis?

Exploratory Analysis

Collection Location

Geocoding using OpenStreeMap and GeoPy.

Collection Date

Comparative Phylogeny

Maximum likelihood tree estimated with IQTREE.

Public Resource

Geospatial Analysis

Spread Maps

• How to visualize a phylogeny on a map over time?
• Inspired by the Ebola phylogeography paper1.
• Discrete mugration model in TreeTime.

The "Known"

• The Black Death: 14-18th Century Europe

The "Unknown"

• The Medievalis Clade.
• Emerges after the medieval "Big Bang".