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MLNe: Simulating and estimating effective size and migration rate from temporal changes in allele frequencies

Wang, Jinliang; (2022) MLNe: Simulating and estimating effective size and migration rate from temporal changes in allele frequencies. Journal of Heredity , 113 (5) pp. 563-567. 10.1093/jhered/esac039. Green open access

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Abstract

In studies of molecular ecology, conservation biology, and evolutionary biology, the current or recent effective size (Ne) of a population is frequently estimated from the marker genotype data of two or more temporally spaced samples of individuals taken from the population. Despite the developments of numerous Bayesian, likelihood, and moment estimators, only a couple of them can use both temporally and spatially spaced samples of individuals to estimate jointly the effective size (Ne) of and the migration rate (m) into a population. In this note, I describe new implementations of these joint estimators of Ne and m in software MLNe which runs on multiple platforms (Windows, Mac, Linux) with or without a graphical user interface (GUI), and has an integrated simulation module to simulate genotype data for investigating the impacts of various factors (such as sample size and sampling interval) on estimation precision and accuracy, exploits both message passing interface (MPI) and openMP for parallel computations using multiple cores and nodes to speed up analysis. The program does not require data pre-processing and accepts multiple formats of a file of original genotype data and a file of parameters as input. The GUI facilitates data and parameter inputs and produces publication-quality output graphs, while the non-GUI version of software is convenient for batch analysis of multiple datasets as in simulations. MLNe will help advance the analysis of temporal genetic marker data for estimating Ne of and m between populations, which are important parameters that will help biologists for the conservation management of natural and managed populations. MLNe can be downloaded free from the website http://www.zsl.org/science/research/software/.

Type: Article
Title: MLNe: Simulating and estimating effective size and migration rate from temporal changes in allele frequencies
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/jhered/esac039
Publisher version: https://doi.org/10.1093/jhered/esac039
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Allele frequency, effective size, genetic drift, inbreeding, markers, migration rate, temporal samples
UCL classification: UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10155470
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