by Robin Waples, last updated 9/30/13, sharing set to public
AgeNe calculates effective population size (Ne), effective number of breeders per year (Nb), and Ne/N and Nb/N in populations with overlapping generations
Chi Do and Robin Waples
Note: Version2.0 (September 2013) replaces V1.1 (March 2011) and fixes a bug in calculation of Nb when the user specifies overdispersed variance of same-age, same-sex individuals.
AgeNe is a stand-alone Fortran95 program for PCs that uses demographic data (age-specific vital rates, as are found in a Leslie matrix) to calculate Ne in age-structured populations. AgeNe combines the best features of Felsenstein's (1971) and Hill's (1972, 1979) methods. Like Felsenstein’s, the new method is based on age-specific survival and fertility rates and therefore can be directly applied to any species for which life-table data are available. Like Hill, we relax the restrictive assumptions in Felsenstein’s model regarding variance in reproductive success, which allows more general application. The basic principle underlying the new method is that age structure stratifies a population into winners and losers in the game of life: individuals that live longer have more opportunities to reproduce and therefore have a higher mean lifetime reproductive success. Grouping individuals by age at death provides a simple means of calculating lifetime variance in reproductive success of a newborn cohort.
Some features of AgeNe:
- - It uses demographic information of the type found in a life table or Leslie matrix.
- - It can accommodate two sexes with unequal primary sex ratio and/or different vital rates.
- - It can accommodate sex-specific and/or age-specific departures from Poisson variance in reproductive success.
- - It can calculate Ne and Ne/N based on various ways of defining N.
- - It can calculate the effective number of breeders each year (Nb), which represent the effective number of parents that produce a single cohort.
- - It can accommodate a haploid life history.
- - It can calculate Ne in species that change sex during their lifetime.
Please familiarize yourself with AgeNe's model and assumptions. For more information please consult the AgeNe ReadMe document and Waples et al. (2011); see details below.
AgeNe reads user-generated text input files and allows batch processing.
AgeNe runs in a DOS window and has a simple command-line interface. It is not necessary to install AgeNe; simply double-click AgeNe.exe and you will be prompted for the names of an input file and output file.
AgeNe is compiled for use on Windows and DOS operating systems; at present it is not designed for use on Mac, Linux or other operating systems.
Version 2.0 released September 2013, replaces Version 1.1 (March 2011)
For more information:
Waples, R.S., C. Do, and J. Chopelet. 2011. Calculating Ne and Ne/N in age-structured populations: a hybrid Felsenstein-Hill approach. Ecology 92:1513-1522.
Waples, R. S. 2010. Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Molecular Ecology Resources 10: 785–796.
Felsenstein, J. 1971. Inbreeding and variance effective numbers in populations with overlapping generations. Genetics 68:581–597.
Hill, W.G. 1972. Effective size of population with overlapping generations. Theoretical Population Biology 3:278–289.
Hill, W. G. 1979 A note on effective population size with overlapping generations. Genetics 92:317–322.
For an application, see:
Waples, R. S., G. Luikart, J. R. Faulkner, D. A. Tallmon. 2013. Simple life history traits explain key effective population size ratios across diverse taxa. Proc. Royal Society London, Ser. B. 280: 20131339, published 7 August 2013.