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.