Using nuclear genomic data to address intractable relationships and gene tree discordance in an ancient group of gymnosperms ( Ephedra , Gnetales)

Using nuclear genomic data to address intractable relationships and gene tree discordance in an ancient group of gymnosperms ( Ephedra , Gnetales) | 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 Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed.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. 22 January 2026 V1 Latest version Share on Using nuclear genomic data to address intractable relationships and gene tree discordance in an ancient group of gymnosperms ( Ephedra, Gnetales) Authors : Ruben Blokzijl 0000-0002-5963-3537 [email protected] and Catarina Rydin 0000-0002-3347-7820 Authors Info & Affiliations https://doi.org/10.22541/au.176909808.80545669/v1 141 views 100 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract The evolutionary history of Ephedra L. has over time proved to be a very difficult phylogenetic problem, something which is probably best reflected by the incongruent phylogenetic relationships demonstrated in and among previous studies. Low number of phylogenetically informative sites and different rooting strategies have been suggested as explanations, but the role of gene tree discordance and its underlying causes and influence on phylogenetic reconstruction in Ephedra has largely remained unexplored. In the present study we address the phylogeny of Ephedra using information from a large set of nuclear low-copy genes obtained with a specifically designed bait set. We explore the potential effect of putative paralogy, intra-locus recombination and chimeric sequences on phylogenic estimation in Ephedra , while striving at minimizing the risk for gene tree error. Our results indicate that recombination and putatively paralogous sequences have limited influence on phylogenetic results, although handling of putative paralogs and recombinants did improve overall species tree resolution and statistics. A robust Ephedra species phylogeny was obtained by analyzing gene trees in which orthologous clades were inferred from data composed of orthologous and putative paralogous sequences. The results support the division of Ephedra into three geographically defined clades, with the American clade as sister to the Mediterranean clade and the Asian clade. Relationships among species within these three clades were relatively consistent among our analytical approaches, but our results highlighted moderate to strong signals of gene tree discordance at many nodes. ILS is a possible explanation for this discord for many nodes, but hybridization/introgression are also commonly indicated. Supplementary Material File (blokzijl_2026_manuscript.docx) Download 540.19 KB Information & Authors Information Version history V1 Version 1 22 January 2026 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords molecular evolution plants sequencing terrestrial Authors Affiliations Ruben Blokzijl 0000-0002-5963-3537 [email protected] Stockholm University View all articles by this author Catarina Rydin 0000-0002-3347-7820 Stockholm University View all articles by this author Metrics & Citations Metrics Article Usage 141 views 100 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Ruben Blokzijl, Catarina Rydin. Using nuclear genomic data to address intractable relationships and gene tree discordance in an ancient group of gymnosperms ( Ephedra , Gnetales). Authorea . 22 January 2026. DOI: https://doi.org/10.22541/au.176909808.80545669/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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