The phylogenomic framework and infrageneric classification of temperate Asian Caraganeae (Leguminosae, Papilionoideae)

The phylogenomic framework and infrageneric classification of temperate Asian Caraganeae (Leguminosae, Papilionoideae) | 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 Search Search ADVANCED SEARCH SCROLL Ecology and Evolution This is a preprint and has not been peer reviewed. Data may be preliminary. 16 September 2025 V1 Latest version Share on The phylogenomic framework and infrageneric classification of temperate Asian Caraganeae (Leguminosae, Papilionoideae) Authors : Na Wang , Pei-Liang Liu , Ling Zhang , Rui Ma , Liang Zhao , Hui WANG 0000-0003-4149-1144 [email protected] , and Zhao-Yang Chang Authors Info & Affiliations https://doi.org/10.22541/au.175805515.55178888/v1 Published Ecology and Evolution Version of record Peer review timeline 275 views 205 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract The legume tribe Caraganeae, consisting of the genus Caragana , Calophaca , and Halimodendron , is a mid-sized, shrubby clade mainly found in temperate Central and Eastern Asia. Within this tribe, Caragana is the largest genus comprising 63–74 species, and it is recognized for its taxonomic complexity. However, the phylogenetic framework of Caraganeae and the infrageneric delimitations in Caragana remain inadequately resolved. In this study, fifty-four species of Caraganeae were sampled, including 51 Caragana species representing all sections in previous taxonomical treatments. By using the genome skimming approach, we reconstructed the phylogenetic framework, inferred the infrageneric delimitations, and explored the historical diversification of the tribe. Our results demonstrated that Caraganeae is monophyletic, yet significant conflicts between the complete chloroplast genome and nuclear ribosomal DNA datasets were observed at both deep and shallow nodes. Within Caraganeae, the cp genome tree resolved nine highly supported lineages, with Calophaca and Halimodendron nested within Caragana . Molecular dating estimates suggest that Caraganeae originated during the Oligocene (stem age, 27.47 Ma, 95% HPD: 16.48–38.44 Ma), and diversified during the mid-Miocene (crown age, 16.79 Ma, 95% HPD: 7–30.13 Ma). These findings provide important insights for clarifying the phylogenetic relationships in Caraganeae. The observed cytonuclear discordance may result from hybridization and/or incomplete lineage sorting. Furthermore, climatic and geological changes since the Eocene-Oligocene Transition—including global cooling, progressive aridity, and the rapid uplift of the Qinghai-Tibetan Plateau—likely played essential roles in driving radiative diversification of Caraganeae. Supplementary Material File (250915main text.docx) Download 132.85 KB File (fig 6_na.tif) Download 8.42 MB File (fig. 2_250310 (2).tif) Download 5.62 MB File (fig. 3_250310 (1).tif) Download 1.78 MB File (fig. 4_250304 (2).tif) Download 2.19 MB File (fig. 5_wn.tif) Download 1.99 MB Information & Authors Information Version history V1 Version 1 16 September 2025 Peer review timeline Published Ecology and Evolution Version of Record 9 Dec 2025 Published Copyright This work is licensed under a Non Exclusive No Reuse License. Collection Ecology and Evolution Keywords none of the above plants sequencing terrestrial Authors Affiliations Na Wang Northwest A&F University College of Life Sciences View all articles by this author Pei-Liang Liu Northwest University View all articles by this author Ling Zhang Tarim University View all articles by this author Rui Ma Northwest A&F University College of Life Sciences View all articles by this author Liang Zhao Northwest A&F University College of Life Sciences View all articles by this author Hui WANG 0000-0003-4149-1144 [email protected] Northwest A&F University College of Life Sciences View all articles by this author Zhao-Yang Chang Northwest A&F University College of Life Sciences View all articles by this author Metrics & Citations Metrics Article Usage 275 views 205 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Na Wang, Pei-Liang Liu, Ling Zhang, et al. The phylogenomic framework and infrageneric classification of temperate Asian Caraganeae (Leguminosae, Papilionoideae). Authorea . 16 September 2025. DOI: https://doi.org/10.22541/au.175805515.55178888/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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