DOI: 10.5061/dryad.79cnp5j7g
title: Building a robust backbone for Astragalus (Fabaceae) using a clade-specific target enrichment bait set

description: With over 3100 species, Astragalus (Fabaceae) has long fascinated
 botanists as the largest genus of flowering plants. With an origin in the
 Middle Miocene, Astragalus has one of the highest diversification rates
 known in flowering plants. Comprehensive taxonomic treatments exist, and
 the genus is currently subdivided into 136 sections in the Eastern
 Hemisphere and 93 sections in the Western Hemisphere based on
 morphological characters. Despite considerable efforts, a comprehensive
 and well-resolved phylogeny of the genus is still lacking.  Here,
 we reconstruct the backbone phylogeny of Astragalus using a custom bait
 set capturing 819 loci specifically designed for a target enrichment
 approach in the Astragalean clade. We carefully selected a set of 107 taxa
 representing all major clades currently recognized in Astragalus. Of
 those, 80 newly sequenced taxa were obtained from herbarium specimens as
 old as 110 years.  We retrieved all the targeted loci and
 additional off-target plastome sequences for all samples, including the 80
 herbarium specimens. Our phylogenetic analysis reinforced the currently
 accepted backbone phylogeny of Astragalus with high support and novel
 details, additionally providing insights into cytonuclear phylogenetic
 conflicts in the genus. Evidence for potential reticulate evolution was
 found, providing a possible explanation for the conflicts
 observed.  This work represents an important milestone in
 obtaining a comprehensive, herbarium-based phylogeny of Astragalus, which
 will constitute the base to study a wealth of relevant biological
 questions, for example, the still unanswered question of what drove the
 rapid diversification of Astragalus, with important repercussions on our
 understanding of diversification in natural contexts.
description: # Building a robust backbone for Astragalus (Fabaceae) using a
 clade-specific target enrichment bait set Dataset DOI:
 [10.5061/dryad.79cnp5j7g](10.5061/dryad.79cnp5j7g) ## Description of the
 data and file structure This repository contains data and codes necessary
 to replicate the results in Buono et al. (under Review). The study aims to
 reconstruct the backbone phylogeny of Astragalus (Fabaceae) using target
 enrichment data obtained from herbarium material. The data covers 80
 species of which 77 Astragalus and 3 outgroups obtained from herbarium
 material, plus additional sequences obtained from previous studies. The
 data includes 819 exons from 686 genes. Phylogenetic analysis recovered a
 well supported phylogeny using both concatenated maximum likelihood
 (IQtree2) and coalescent-based method (Astral and Astral-pro). Gene
 discordance (PhyPart and QuartetSampling) analysis highlighted existence
 of gene discordance especially in shallow nodes in the phylogeny. Evidence
 of reticulate evolution was found using phylonet analysis. ### Files and
 variables #### File:
 IQtree2_Astragalus_concatenated_tree_publication_AJB.newik
 **Description:** ML plastome tree produced using IQtree2 #### File:
 bait_sequences_astra819.tar.gz **Description:** bait sequences for
 Astragalean819 bait set #### File: astragalean_bait_reference_file.zip
 **Description:** reference file for Astragalean819 bait set #### File:
 astral_MO_ortho_publication_AJB.newik **Description:** ASTRAL
 coalescent-based species tree produced with ortholog sequences using
 ASTRAL III #### File: astral-pro_homologs_publication_AJB.tre
 **Description:** ASTRAL-pro coalescent-based species tree produced with
 homolog sequences using ASTRAL-pro #### File:
 IQtree2_Astragalus_concatenated_tree_publication_AJB.newik
 **Description:** ML concatenated species tree produced with homolog
 sequences using IQtree2 **File:**
 IQtree2_Astragalus_plastome_tree_publication_AJB.figtree **Description:**
 ML plastome tree produced with plastome sequences using IQtree2 ## Access
 information Other publicly accessible locations of the data: * Target
 enrichment data generated for this study can be found in the NCBI
 BioProject PRJNA1242075