Ancient DNA × Climate Signal Explorer

A heuristic note for comparing time-binned ancient DNA allele-frequency estimates with paleoclimate proxy records.

Analytical purpose

The tool is designed for early-stage research design. It asks whether a time-stratified genetic signal and a paleoclimate proxy should be investigated together more formally. It should be used to organize questions, not to resolve causation.

Data preparation

Genetic rows require sample identifier, region, date in years before present, locus, and derived-allele dosage. Climate rows require years before present, proxy name, and proxy value. Before interpretation, users should verify sample provenance, cultural/archaeological context, sequencing/capture strategy, genotype-calling assumptions, and proxy chronology.

Binning procedure

Samples are grouped into user-selected temporal bins. Within each bin, derived-allele dosages are summed and divided by observed chromosomes. The resulting trajectory is plotted against the nearest climate-proxy observation. Alternative bin widths should be tested because sparse ancient DNA sampling can produce unstable trajectories.

Limits

The visualizer does not estimate selection coefficients. It does not model demographic replacement, drift, admixture, temporal uncertainty, kinship, population continuity, genotype likelihoods, capture bias, or spatially varying selective environments. The confidence band is only a binomial display aid.

Interpretive standard

A plausible visual association should be described as a candidate relationship. Publication-quality claims require formal inference and corroboration from archaeological, ecological, dietary, pathogen, mobility, and demographic evidence.

Selected references

1. Mathieson, Iain, et al. 2015. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528:499–503.
2. Stern, Aaron J., et al. 2019. An approximate full-likelihood method for inferring selection and allele-frequency trajectories from DNA sequence data. PLOS Genetics 15(9):e1008384.
3. Schraiber, Joshua G., Steven N. Evans, and Montgomery Slatkin. 2016. Bayesian inference of natural selection from allele frequency time series. Genetics 203(1):493–511.
4. NOAA National Centers for Environmental Information. World Data Service for Paleoclimatology.
5. Skoglund, Pontus, and Iain Mathieson. 2018. Ancient genomics of modern humans: the first decade. Annual Review of Genomics and Human Genetics 19:381–404.