GONe

GONe estimates effective population size (N(e)) in populations with overlapping generations using the Jorde-Ryman modification of the temporal method that incorporates age structure.

Key Features:

• Age-Structured Estimation: Incorporates age-specific survival and birth rates to account for overlapping generations when estimating N(e).
• Genotypic Data Formats: Reads genotypic data formatted for GENEPOP or TEMPOFS.
• Temporal Sampling: Analyzes allele frequencies measured in two or more consecutive cohorts and provides N(e) estimates for each interval between consecutive cohorts.
• Per-Locus and Multilocus Estimates: Calculates N(e) at individual loci and aggregated over all loci.
• Genetic Drift Estimators: Supports three genetic drift estimators: F(s), F(c), and F(k).
• Confidence Intervals: Derives confidence intervals for N(e) using a chi-square distribution with degrees of freedom equal to the number of independent alleles.
• Validation Across Demographics: Validated across a wide range of N(e) values and demographic scenarios, including sex-specific survival and birth rates, unequal sex ratios, and varying reproductive variances.

Scientific Applications:

• Evolutionary Biology: Estimates N(e) to study genetic drift and evolutionary processes in populations with overlapping generations.
• Conservation Genetics: Informs assessments of genetic diversity and extinction risk to guide conservation strategies.
• Population Ecology: Quantifies effects of age structure and demography on genetic effective size to inform population viability analyses.

Methodology:

Analyzes allele-frequency changes measured in two or more consecutive cohorts using the Jorde-Ryman modification of the temporal method with age-specific survival and birth rates; reads GENEPOP or TEMPOFS genotypic files; computes per-locus and multilocus N(e) using F(s), F(c), and F(k); and derives chi-square-based confidence intervals with degrees of freedom equal to the number of independent alleles.