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Social Isolation Model: A Noninvasive Rodent Model of Stress and Anxiety

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Isolation-by-distance-and-time in a stepping-stone model.

Nicolas Duforet-Frebourg¹, Montgomery Slatkin¹

¹Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, United States.

Theoretical Population Biology

|November 24, 2015

Summary

Genetic studies now include ancient DNA, but the combined effects of space and time on population genetics are unclear. This research introduces "Isolation by Distance and Time," showing ancient samples shift toward the center in principal component analysis (PCA) plots.

Keywords:

Ancient DNA Coalescence times Isolation-by-distance Principal component analysis

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Area of Science:

Population genetics
Ancient DNA analysis
Computational biology

Background:

Advances in ancient DNA extraction allow genetic analysis of past and present populations.
Existing population genetics theory insufficiently addresses the combined influence of geographic distance and time.
The classical stepping-stone model provides a foundation for exploring spatial-temporal population dynamics.

Purpose of the Study:

To develop a theoretical framework for "Isolation by Distance and Time" incorporating ancient DNA data.
To investigate the impact of temporal sampling on population structure analyses.
To evaluate the influence of ancient samples on Principal Component Analysis (PCA) plots.

Main Methods:

Developed theoretical models for allele frequency correlations based on the stepping-stone model.
Incorporated ancient samples into spatial-temporal population genetics theory.
Utilized forward-in-time simulations to study edge effects.
Analyzed coalescent times in circular and toroidal population models.
Evaluated the impact of the new theory on PCA visualizations.

Main Results:

Derived correlations of allele frequencies considering both space and time.
Demonstrated that the time separating samples is a significant factor in population structure analysis.
Forward-in-time simulations revealed the impact of edge effects in spatial-temporal models.
Coalescent time analyses provided insights into population dynamics in different spatial structures.
Ancient DNA samples were observed to cluster towards the center of PCA plots.

Conclusions:

The developed "Isolation by Distance and Time" theory offers a novel perspective on population genetics.
Temporal information from ancient DNA significantly influences interpretations of population structure.
PCA plots require careful interpretation when ancient samples are included, as they tend to centralize.