Read mapping stringency and genetic relatedness to the reference genome significantly impact multispecies population genetic and phylogenetic analyses

Read mapping stringency and genetic relatedness to the reference genome significantly impact multispecies population genetic and phylogenetic analyses | 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 Search Search ADVANCED SEARCH SCROLL Molecular Ecology Resources This is a preprint and has not been peer reviewed. Data may be preliminary. 9 January 2025 V1 Latest version Share on Read mapping stringency and genetic relatedness to the reference genome significantly impact multispecies population genetic and phylogenetic analyses Authors : Rebekah Mohn 0000-0002-7489-8939 [email protected] , Mira Garner , Paul Manos , and Andrew Hipp 0000-0002-1241-9904 Authors Info & Affiliations https://doi.org/10.22541/au.173640379.95516989/v1 470 views 367 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract The increasing affordability of whole genome resequencing in the past five years and numbers of published reference genomes have enabled multispecies population genomic and phylogenomic studies on non-model organisms, but they raise new questions: what reference genomes should be used for read mapping in comparative studies, and what mapping methods provide the greatest and least bias in comparative genomics? Focusing on Eastern North American white oaks ( Quercus sect. Quercus ), which have an estimated 36 Ma divergence, we compared the effects of mapping resequencing data to four Quercus reference genomes, using three read-mapping methods: Bowtie2 –end-to-end, Bowtie2 –local, and BWA mapping methods. We analyzed the reference genomes and read-mapping methods in a fully factorial design to call variants and invariants for nine Quercus genome resequencing samples, then used the resulting datasets to test how different combinations of reference genome and method influence genotyping accuracy and bias. We found that both the genetic distance of the reference genome to the ingroup samples and mapping method together impacted sample heterozygosity, tree topology, and tree branch lengths. Specifically, the heterozygosity of closely-related sample/reference genome pairs using Bowtie2 –end-to-end alone was not significantly different from the average heterozygosity of samples that match the reference species. The outgroup reference genome resulted in low base pair recovery, low heterozygosity, and unbalanced phylogenies. We concluded that using a closely related, but not conspecific reference is ideal to minimize bias from the reference and Bowtie2 –end-to-end minimizes mismapping enabling the most accurate calls. Supplementary Material File (manuscript.pdf) Download 1.30 MB File (table1.xlsx) Download 10.19 KB File (table2.xlsx) Download 9.23 KB Information & Authors Information Version history V1 Version 1 09 January 2025 Copyright This work is licensed under a Non Exclusive No Reuse License. Collection Molecular Ecology Resources Keywords bowtie2 bwa quercus reference mapping snp-calling wgs Authors Affiliations Rebekah Mohn 0000-0002-7489-8939 [email protected] The Morton Arboretum View all articles by this author Mira Garner Field Museum of Natural History View all articles by this author Paul Manos Duke University View all articles by this author Andrew Hipp 0000-0002-1241-9904 The Morton Arboretum View all articles by this author Metrics & Citations Metrics Article Usage 470 views 367 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Rebekah Mohn, Mira Garner, Paul Manos, et al. Read mapping stringency and genetic relatedness to the reference genome significantly impact multispecies population genetic and phylogenetic analyses. Authorea . 09 January 2025. DOI: https://doi.org/10.22541/au.173640379.95516989/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. 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