Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.
J Hered. 2022 Oct 21;113(5):563-567. doi: 10.1093/jhered/esac039.
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/.
在分子生态学、保护生物学和进化生物学的研究中，经常根据从种群中抽取的两个或更多时间间隔的个体的标记基因型数据来估计种群的当前或近期有效大小（Ne）。尽管已经开发了许多贝叶斯、似然和矩估计量，但只有少数几个可以同时使用时间和空间间隔的个体样本来联合估计有效大小（Ne）和进入种群的迁移率（m）。在本说明中，我描述了在 MLNe 软件中实现这些 Ne 和 m 的联合估计器的新方法，该软件可在具有或没有图形用户界面（GUI）的多个平台（Windows、Mac、Linux）上运行，并且具有集成的模拟模块，可用于模拟基因型数据，以研究各种因素（如样本量和采样间隔）对估计精度和准确性的影响，利用消息传递接口（MPI）和 openMP 利用多个核和节点进行并行计算，以加快分析速度。该程序不需要数据预处理，并且接受原始基因型数据文件和参数文件的多种格式作为输入。GUI 方便了数据和参数的输入，并生成具有出版质量的输出图形，而软件的非 GUI 版本则方便了在模拟中对多个数据集的批量分析。MLNe 将有助于推进对时间遗传标记数据的分析，以估计种群之间的 Ne 和 m，这些都是重要的参数，将有助于生物学家对自然和管理种群进行保护管理。MLNe 可以从网站 http://www.zsl.org/science/research/software/ 免费下载。
