A Divergence-Calibrated Framework for Robust Cross-Species Comparison of Effective Population Size Ratios

A Divergence-Calibrated Framework for Robust Cross-Species Comparison of Effective Population Size Ratios | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 13 January 2026 V1 Latest version Share on A Divergence-Calibrated Framework for Robust Cross-Species Comparison of Effective Population Size Ratios Authors : Liangyu Lu 0009-0005-2685-4842 , wennan dai , Yuhao Pan 0000-0001-6060-1084 , and zheng yan [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.176830951.16997718/v1 128 views 71 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract 1. Comparing effective population size (Nₑ) ratios among autosomes, the X, Y, and mitochondrial genomes is a powerful approach for inferring sex-specific demography and selection; however, chromosome- and lineage-specific mutation-rate differences have prevented reliable cross-species comparisons. 2. We introduce a phylogenetically informed framework that uses interspecific divergence to calibrate chromosome-specific mutation rates, yielding unbiased Nₑ ratios that are free of external priors and directly comparable across diverse taxa. 3. For each genomic compartment, we combine genome-wide nucleotide diversity (π) with divergence (D) from a high-quality outgroup. Because neutral mutation rate (μ) and divergence time cancel in the π/D ratio, this approach produces internally calibrated, chromosome-specific Nₑ ratios and is implemented as an open-source, automated pipeline. 4. Applying this framework to hominids and three ant species with a Y-like chromosome reveals Nₑ-ratio patterns that are consistent with known biology, demonstrating the method’s ability to recover species-specific signals of reproductive strategy and population history. We provide a fully implemented and well-documented computational tool to facilitate broad adoption. Together, this work establishes a generalizable and robust basis for inferring reproductive strategies and demographic history through comparative analyses of Nₑ ratios. Supplementary Material File (ne_12.20_.docx) Download 13.84 MB File (table1_ne_simple.xls) Download 31.00 KB Information & Authors Information Version history V1 Version 1 13 January 2026 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords genetics method development multiple theoretical Authors Affiliations Liangyu Lu 0009-0005-2685-4842 Lanzhou University View all articles by this author wennan dai Lanzhou University View all articles by this author Yuhao Pan 0000-0001-6060-1084 Lanzhou University View all articles by this author zheng yan [email protected] Lanzhou University View all articles by this author Metrics & Citations Metrics Article Usage 128 views 71 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Liangyu Lu, wennan dai, Yuhao Pan, et al. A Divergence-Calibrated Framework for Robust Cross-Species Comparison of Effective Population Size Ratios. Authorea . 13 January 2026. DOI: https://doi.org/10.22541/au.176830951.16997718/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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