<scp>NeEstimator</scp> v2: re‐implementation of software for the estimation of contemporary effective population size (<i>N</i>_<i>e</i>) from genetic data

TLDR

NeEstimator v2 is a fully revised software that estimates contemporary effective population size from a single input file using multiple methods. It implements updated linkage disequilibrium, heterozygote‑excess, and molecular coancestry single‑sample estimators, a two‑sample temporal method, and offers improved missing‑data handling, rare‑allele filtering, confidence intervals, large‑marker support, batch processing, and Plan I sampling correction, with flexible input and output control. The software, freely available with a new Java interface, runs on macOS, Linux, and Windows.

Abstract

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.