Population History Across Timescales in an Urban Archipelago

Area of Science:

• Evolutionary biology
• Population genetics
• Genomics

Background:

• Population genetic variation reflects demographic history, including splitting, migration, and size changes.
• Current methods for reconstructing demographic history often lack sufficient temporal resolution.
• Urbanized archipelagos present unique systems for studying dynamic population histories due to geological and contemporary changes.

Purpose of the Study:

• To infer the demographic history of white-footed mice (Peromyscus leucopus) in Boston Harbor using whole genome sequences.
• To assess the temporal resolution of different genomic variation summaries for demographic inference.
• To investigate the influence of geological and recent human factors on population genetic structure.

Main Methods:

• Whole genome sequencing of Peromyscus leucopus populations.
• Analysis of joint site frequency spectrum (jSFS) to model demographic history.
• Examination of linkage disequilibrium patterns.
• Investigation of rare variant clustering and simulations of recent migration.

Main Results:

• Demographic models based on jSFS align with the geological history of Boston Harbor.
• Linkage disequilibrium patterns indicate recent population size collapses not captured by jSFS models.
• Rare variant clustering suggests recent migration, a pattern absent in jSFS models but supported by simulations.

Conclusions:

• Urban archipelago populations are shaped by both ancient geological processes and recent human influence.
• Integrating multiple genomic variation patterns enhances the temporal resolution of demographic history reconstruction.
• Novel patterns of variation can reveal recent demographic events missed by traditional methods.