Overview

NeStage computes the variance effective population size (Ne) for stage-structured plant and animal populations, implementing the framework of Yonezawa et al. (2000). It is designed for conservation biologists and population geneticists who need to translate demographic transition matrices into genetic drift metrics.

In stage-structured populations, individuals move through distinct life-history stages — seedling → juvenile → reproductive adult — each with different survival and fecundity rates. Standard Ne formulas that assume simple age structure are not appropriate for these systems. NeStage derives Ne directly from the variance of allele-frequency change across stages.

Key biological insight: Ne is often only 10–30% of the census size N in stage-structured populations (Frankham 1995). A population of 40 Lepanthes orchids — already large for this endangered genus — typically achieves Ne of only 7–37, well below the short-term inbreeding threshold of Ne ≥ 50 (Franklin 1980).

The Yonezawa (2000) model

For a population with s stages, the generation-time effective size is: