DOI: 10.5061/dryad.cc2fqz660
title: Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

description: Target enrichment is becoming increasingly popular for phylogenomic
 studies. Although baits for enrichment are typically designed to target
 single-copy genes, paralogs are often recovered with increased sequencing
 depth, sometimes from a significant proportion of loci, especially in
 groups experiencing whole-genome duplication (WGD) events. Common
 approaches for processing paralogs in target enrichment data sets include
 random selection, manual pruning, and mainly, the removal of entire genes
 that show any evidence of paralogy. These approaches are prone to errors
 in orthology inference or removing large numbers of genes. By removing
 entire genes, valuable information that could be used to detect and place
 WGD events is discarded. Here we used an automated approach for orthology
 inference in a target enrichment data set of 68 species of Alchemilla s.l.
 (Rosaceae), a widely distributed clade of plants primarily from temperate
 climate regions. Previous molecular phylogenetic studies and chromosome
 numbers both suggested ancient WGDs in the group. However, both the
 phylogenetic location and putative parental lineages of these WGD events
 remain unknown. By taking paralogs into consideration and inferring
 orthologs from target enrichment data, we identified four nodes in the
 backbone of Alchemilla s.l. with an elevated proportion of gene
 duplication. Furthermore, using a gene-tree reconciliation approach we
 established the autopolyploid origin of the entire Alchemilla s.l. and the
 nested allopolyploid origin of four major clades within the group. Here we
 showed the utility of automated tree-based orthology inference methods,
 previously designed for genomic or transcriptomic data sets, to study
 complex scenarios of polyploidy and reticulate evolution from target
 enrichment data sets. 
description: This package contains the supplemental figures and tables
 referenced in the main text - Supplemental_material.zip
 Supplemental_material.zip 
 Supplemental figures S1-S12 Supplemental
 tables S1-S6 It also contains the data and
 software outputs (i.e. fasta filtes, alignments, trees, logs, etc) -
 Analyses_data.tar.gz Analyses_data.tar.gz
 1_original_fasta_files: Unaligned fasta files
 (*.fa) 2_raw_homologs: raw homolog trees. Cleaned
 alignments with Phyx (*.aln-cln) and RAxML bipartition labeled trees
 (*.tre) 3_final_homologs: filtered homologs
 (monophyletic clades and paraphyletic grades of same species masked,
 spurious tips removed with TreeShrink) 4_orthologs
  1_MO (monophyletic outgroups): 
 1_fasta_to_trees: fasta files, alignments, ortholog
 trees 2_analyses: ASTRAL, WGD mapping, Phyparts,
 QuartetSampling, RAxML   
  2_RT (rooted ingroups): 1_fasta_to_trees: fasta
 files, alignments, ortholog trees 2_analyses: ASTRAL,
 WGD mapping, Phyparts, QuartetSampling, RAxML 
 5_analyses_with_homologs
 1_ASTRAL-pro: : multilabeled homologs tres,
 ASTRAL-pro, Phyparts 2_grampa: GRAMPA analyses with
 complete and reduced trees
 3_Phyparts_Informative_trees: MO and RT with all homologs and
 only with longest homologs 
 6_cpDNA: fasta files, alignment, QuartetSampling
 7_Ks_plots: CDS and PEP files, Ks values (within-species and
 between-species) 8_other_files: HybPiper references,
 gene list, list of longest exons, gene annotations 
 If you have any question, please do not hesitate to contact me
 dfmoralesb@gmail.com Diego F. Morales-Briones