# Characterizing Human-Pathogen Interactions and Natural Selection with Ancient DNA

> **NIH NIH R35** · CALIFORNIA STATE UNIVERSITY NORTHRIDGE · 2022 · $358,782

## Abstract

PROJECT SUMMARY
The possibility of recovering ancient DNA (aDNA) molecules from archeological samples has yielded
great opportunities for the study of human evolution and history. Compared to traditional datasets
composed of a single time point collected in the present, aDNA allows for the detection of lost genetic
lineages and enables the direct assessment of allele frequencies in different time transects.
Technologies for obtaining genomic data from archeological material have catapulted the development
of the field of paleogenomics, but statistical methods to leverage information from time-series genetic
datasets lag behind these technological advances. Over the next five years, the Amorim Lab will
develop and apply methods to study human host-pathogen coevolution and adaptation using aDNA.
We seek to advance the field of paleogenomics by generating aDNA datasets that comprise large
sample sizes per archeological site and developing new methods and approaches to leverage
information from time-series genetic data. We will use these novel resources to study host-pathogen
interactions during the outbreaks of the plague in Eurasia (e.g. the Black Death) and the period of
contact between Indigenous peoples from South America and European colonizers. Contrasting models
of population evolution, both analytical and computational, with observed allele frequencies and other
summary statistics in different time transects, we will identify the genetic signatures of host-pathogen
interactions, characterize the evolutionary processes involved in human response to pathogens, and
infer the strength and timing of selective sweeps. In addition, we will characterize the Distribution of
Fitness Effects (DFE) of new mutations in the human genome across different time transects and
analyze its evolution in light of the environmental shifts caused by disease outbreaks and other events.
This study represents an advance over the state-of-the-art knowledge in paleogenomics for its focus on
evolutionary process not yet characterized with aDNA (in particular, host-pathogen coevolution), the
characterization of the DFE using time-series data, and the development of new resources (datasets
and methods). The Amorim Lab is uniquely positioned to accomplish these goals because of our
experience in combining model-based approaches with genome data analysis from ancient and modern
DNA, as well as our previous experience with the study of medieval Europeans and Native American
populations.

## Key facts

- **NIH application ID:** 10465244
- **Project number:** 5R35GM142939-02
- **Recipient organization:** CALIFORNIA STATE UNIVERSITY NORTHRIDGE
- **Principal Investigator:** Carlos Eduardo Guerra Amorim
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $358,782
- **Award type:** 5
- **Project period:** 2021-08-09 → 2026-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10465244

## Citation

> US National Institutes of Health, RePORTER application 10465244, Characterizing Human-Pathogen Interactions and Natural Selection with Ancient DNA (5R35GM142939-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10465244. Licensed CC0.

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