DOI: 10.5061/dryad.3n5tb2rsh
title: Data from: Phylogenomics, reticulation, and biogeographical history of Elaeagnaceae

description: The angiosperm family Elaeagnaceae comprises three genera and ca. 100
 species distributed mainly in Eurasia and North America. Little
 family-wide phylogenetic and biogeographic research on Elaeagnaceae has
 been conducted, limiting the application and preservation of natural
 genetic resources. Here, we reconstructed a strongly supported
 phylogenetic framework of Elaeagnaceae to better understand inter- and
 intrageneric relationships, as well as the origin and biogeographical
 history of the family. For this purpose, we used both nuclear and plastid
 sequences from Hyb-Seq and genome skimming approaches to reconstruct a
 well-supported phylogeny and, along with current distributional data,
 infer historical biogeographical processes. Our phylogenetic analyses of
 both nuclear and plastid data strongly support the monophyly of
 Elaeagnaceae and each of the three genera. Elaeagnus was resolved as
 sister to the well-supported clade of Hippophae and Shepherdia. The
 intrageneric relationships of Elaeagnus and Hippophae were also well
 resolved. High levels of nuclear gene tree conflict and cytonuclear
 discordance were detected within Elaeagnus, and our analyses suggest
 putative ancient and recent hybridization. We inferred that Elaeagnaceae
 originated ca. 90.48 Ma (95% CI = 89.91–91.05 Ma), and long-distance
 dispersal likely played a major role in shaping its intercontinentally
 disjunct distribution. This work presents the most comprehensive
 phylogenetic framework for Elaeagnaceae to date, offers new insights into
 previously unresolved relationships in Elaeagnus, and provides a
 foundation for further studies on classification, evolution, biogeography,
 and conservation of Elaeagnaceae.
description: <strong>Data Collection: </strong>
 Leaf material was gathered from multiple herbaria and the field.
 Total DNA extraction was performed via a modified CTAB method.
 <strong>Sequencing and Processing:
 </strong> Hybridization enrichment sequencing
 (Hyb-seq) was used to capture 100 low-copy nuclear genes. Raw sequenced
 reads underwent cleaning and filtering processes, which included trimming
 Illumina adapter sequence artifacts, discarding low-quality reads, and
 trimming low-quality read ends using TRIMMOMATIC v0.32. Assembly of
 processed nuclear reads was executed using HybPiper v1.2. As a result, 83
 loci were kept for further analysis. Genome skimming
 sequencing data were assembled into high-quality plastome sequence using
 GetOrganelle, then the plastomes were annotated with the software PGA,
 coding sequences of the plastome were extracted using the python script
 “get_annotated_regions_from_gb.py” from https://github.com/Kinggerm/PersonalUtilities. <strong>Sequence Alignment and Cleaning: </strong> The sequences of 83 nuclear genes were aligned using MAFFT, following which the original alignments were cleaned to reduce errors, removing gap-heavy and ambiguously aligned sites. To reduce errors in our alignments (i.e., gap-heavy and ambiguously aligned sites), the original alignment of each gene was cleaned using the pipeline of KewHybSeqWorkshop.
description: # Data from: Phylogenomics, reticulation, and biogeographical history of
 Elaeagnaceae This archive contains code and data used for the paper
 "Phylogenomics, reticulation, and biogeographical history of
 Elaeagnaceae" (Gu, Wei; Zhang, Ting; Liu, Shui-Yin; Tian, Qin1; Yang,
 Chen-Xuan; Lu, Qing; Fu, Xiao-Gang; Kates, Heather; Stull, Gregory;
 Soltis, Pamela; Soltis, Douglas; Folk, Ryan; Guralnick, Robert; Li,
 De-Zhu; Yi, Ting-Shuang), Plant Diversity, 2024. This work focuses on the
 phylogenetic relationships within Elaeagnaceae, hybridizations,
 origination and dispersals of the family, and presents the most
 comprehensive phylogenetic framework for Elaeagnaceae to date, offers new
 insights into previously unresolved relationships in Elaeagnus, and
 provides a foundation for further studies on classification, evolution,
 biogeography, and conservation of Elaeagnaceae. You can reuse these
 scripts and data under the license terms specified in the Dryad repository
 these files are hosted on. For further information, please contact Wei Gu
 ([guwei1@mail.kib.ac.cn](mailto:guwei1@mail.kib.ac.cn)). ## Folder
 structure This Assembled_data.7z contains several subfolders: \-
 "Nuclear capture": 83 nuclear genes from hyb-seq and one
 concatenated matrix \- "Off-target plastid CDS": Off-target
 plastid CDS assembled from Hyb-Seq raw data \- "Plastid":
 plastid data   -"All cds renamed": renamed cds alignments
 extracted from assembled plastid data   -"Complete plastome":
 assembled plastid genomes from genome skimming raw data ## Other files ```
 Config_file_for_treePL.txt is the config file used in treePL for dating
 analysis Phytools_cophylo20220516.R is the script used in comparing
 topologies between two phylogenetic trees Astral_tree_of_Elaeagnaceae.tre
 is the coalescent tree constructed using ASTRAL based on 83 nuclear genes
 RAxML_concatenated_tree_of_Rosales_based_on_nuclear_genes.tre is the ML
 tree based on the concatenated matrix of all species used in this study
 areas_in_biogeography_analyses.csv is the area setting file used in RASP
 BAYAREALIKE_J.txt is the result of biogeographical analysis
 Assembled_data.7z included the nuclear genes and all newly assembled
 chloroplast sequences used in this study
 RAxML_concatenated_tree_of_Elaeagnaceae_based_on_plastid_CDS.tre is the ML
 tree based on plastome DNA Dated_ML_tree_of_Elaeagnaceae.tre is the dated
 tree of Elaeagnaceae ``` \# Note ``` Bait for 100 nuclear genes will be
 uploaded with the agreements of all collaborators ``` ## Acknowledgements
 This research was supported by the National Natural Science Foundation of
 China, Key International (regional) Cooperative Research Project (no.
 31720103903), the Science and Technology Basic Resources Investigation
 Program of China (no. 2019FY100900), the Strategic Priority Research
 Program of Chinese Academy of Sciences (no. XDB31000000), the National
 Natural Science Foundation of China (no. 31270274), the Yunling
 International High-end Experts Program of Yunnan Province, China (no.
 YNQR-GDWG-2017-002 and no. YNQR-GDWG-2018-012), the China Scholarship
 Council (202004910775), the Chinese Academy of Sciences (CAS)
 President's International Fellowship Initiative (no. 2020PB0009), the
 China Postdoctoral Science Foundation (CPSF), and the United States
 Department of Energy (grant no. DE-SC0018247 to PSS, RPG, and DES). We are
 grateful to the following institutions for providing specimens or
 silica-dried materials: the herbarium of the California Academy of
 Sciences (CAS); the herbarium of Kunming Institute of Botany, Chinese
 Academy of Sciences (KUN); the Germplasm Bank of Wild Species and
 Molecular Biology Experiment Center, Kunming Institute of Botany, Chinese
 Academy of Sciences; the Missouri Botanical Garden Herbarium (MO); the New
 York Botanical Garden Herbarium (NY); the Ohio State University Herbarium
 (OS) and the University of Texas Herbarium (TEX). We are also grateful to
 Jiajin Wu for help with sampling and DNA extraction; to Germplasm Bank of
 Wild Species (Kunming institute of botany, Chinese Academy of Science) for
 providing genome skimming data of Elaeagnaceae; to Tiantian Xue (Institute
 of Botany, Chinese Academy of Sciences) for his suggestions on the
 project; and to the iFlora High Performance Computing Center of Germplasm
 Bank of Wild Species (iFlora HPC Center of GBOWS, KIB, CAS) for computing.