Whole Genome based Insights into the Phylogeny and Evolution of the Juglandaceae Huijuan Zhou Northwest A&F University: Northwest Agriculture and Forestry University Yiheng Hu Northwestern University Aziz Ebrahimi Purdue University Peiliang Liu Northwestern University Keith Woeste Purdue University Shuoxin Zhang Northwest A&F University: Northwest Agriculture and Forestry University Peng Zhao (
[email protected] ) Northwest University https://orcid.org/0000-0003-3033-6982 Research article Keywords: Diversication, Divergence time, Genome, Juglandaceae, Phylogenomics, Plastome Posted Date: May 24th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-495294/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/23 Abstract Background: The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships in the Juglandaceae are problematic, and their historical diversication has not been claried, in part because of low phylogenetic resolution and/or insucient marker variability. Results: We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversied in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversication events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J.