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.
by Robin Waples, last updated 2/24/17, sharing set to public
LDNe is a program for estimating effective population size (Ne) from genotypic data on linkage disequilibrium.
The current Version is 1.31
Authors: Robin S. Waples and Chi Do
Note: The revised and updated NeEstimator V2 (Do et al. 2014; see below for link to the program) includes a new version of LDNe that incorporates the improved method for dealing with missing data proposed by Peel et al. (2013). The new results are identical to old LDNe results if there are no missing data. Check back in the future in this space for an updated version of LDNe that includes this and other new features.
LDNe is a compiled Fortran program with a Visual Basic interface that implements a bias correction for estimates of contemporary effective population size (Ne) based on linkage disequilibrium data. The program can accommodate large numbers of samples, individuals, loci, and alleles, as well as two mating systems: random and lifetime monogamy. LDNE calculates separate estimates using different criteria for excluding rare alleles, which facilitates evaluation of data for highly polymorphic markers such as microsatellites. The program uses the Burrows method, which does not require any assumptions about random mating or information or about haplotypic frequencies. LDNe also introduces a jackknife method for obtaining confidence intervals that appears to perform better than parametric methods currently in use.
Like other methods that estiamte effective size, the LD method makes some simplifying assumptions (markers are selectively neutral and independent; population has discrete generations and is closed to immigration; sampling is random. See below for references that have evaluated sensitivity to some of these assumptions.
LDNe reads genotypic data from input files in two standard formats; GenePop and FSTAT. LDNe was compiled for Windows and DOS operating systems, it was not designed for use on Mac, Linux or other OSs--but check back soon for a Linux version. For Windows Vista and Windows 7, please install LDNe by running setup.exe. After installation, run LDNeinterface.exe from the installation directory. For previous versions of Windows or or to run the DOS version without the graphical interface, no installation is necessary; just run from the command line. LDNe allows batch processing of multiple files through creating a .bat file to pass arguments to the LDNE.exe executable.
Please download the zipped file below (LDNe.zip) and consult the included users manual [LDNE Users Manual.doc] for more detailed documentation.
Do, C., R.S. Waples, D. Peel, G.M. Macbeth, B.J. Tillet, and J.R. Ovenden. 2014. NeEstimator V2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources14:209-214.
Waples, R.S. (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics 7:167-184. [link]
Waples, R. S. and C. Do. (2008) LDNe: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8:753–756. [link]
Waples, R. S., and C. Do. 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: A largely untapped resource for applied conservation and evolution. Evolutionary Applications 3:244-262. [link]
England, P.E., G. Luikart, and R.S. Waples. 2010. Early detection of population fragmentation using linkage disequilibrium estimation of effective population size. Conservation Genetics 11:2425–2430. [link]
Peel, D., R.S. Waples, G.M. Macbeth, C. Do, and J.R. Ovenden. 2013. Accounting for missing data in genetic effective population size (Ne) estimation. Molecular Ecology Resources 13:243-253 (doi: 10.1111/1755-0998.12049).
Tallmon, D.A, D. Gregovich, R.S. Waples, C. S. Baker, J. Jackson, B. Taylor, E. Archer, K. K. Martien, and M.K. Schwartz. 2010. When are genetic methods useful for estimating contemporary abundance and detecting population trends? Molecular Ecology Resources 10, 684–692. [link]
Waples, R. S., and P. R. England. 2011. Estimating contemporary effective population size based on linkage disequilibrium in the face of migration. Genetics 189:633–644. [link]
The revised and updated NeEstimator V2 [http://molecularfisherieslaboratory.com.au/neestimator-software/] includes a new version of LDNe that incorporates the improved method for dealing with missing data proposed by Peel et al. (2013)
OneSamp [link] An approximate Bayesian Computation program for computing single-sample estimates of Ne. based on LD and other genetic indices.
AgeNe [link] Computes Ne for species with overlapping generations based on age-specific survival and fecundity. Also will compute Ne for species that change sex.
SalmonNb [link] Implements modification to the standard temporal method for estimating Ne to account for life history of Pacific salmon (semelparous but variable age at maturity). Will provide separate estimates of Nb (effective number of breeders per year) for each year if at least 3 temporal samples are available.