DOI: 10.5061/dryad.v9s4mw72k
title: Artifactual orthologs and the need for diligent data exploration in complex phylogenomic datasets: A museomic case study from the Andean flora

description: The Andes mountains of western South America are a globally important
 biodiversity hotspot, yet there is a paucity of resolved phylogenies for
 plant clades from this region. Filling an important gap to our
 understanding of the World’s richest flora, we present the first phylogeny
 of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest
 radiation. Our dataset was obtained via hybrid-enriched target sequence
 capture of Angiosperms353 universal loci for 50 of the ca. 75 spp.,
 obtained almost entirely from herbarium specimens. We identify high
 phylogenomic complexity in Freziera, including a significant proportion of
 paralogous loci and a high degree of gene tree discordance. Via gene tree
 filtering, by-eye observation of gene trees, and detailed examination of
 warnings from recently improved assembly pipelines, we identified that
 cryptic paralogs (i.e., the presence of only one copy of a multi-copy gene
 due to assembly errors) were a major source of gene tree heterogeneity
 that had a negative impact on phylogenetic inference and support. These
 cryptic paralogs likely result from limitations in data collection that
 are common in museomics, combined with a history of genome duplication;
 they may be common in plant phylogenomic datasets. After accounting for
 cryptic paralogs as source of gene tree error, we identified a
 significant, but non-specific signal of introgression using Patterson’s D
 and f4 statistics. Despite phylogenomic complexity, we were able to
 resolve Freziera into nine well-supported subclades whose histories have
 been shaped by myriad evolutionary processes, including incomplete lineage
 sorting, historical gene flow, and gene duplication. Our results highlight
 the complexities of plant phylogenomics, and point to the need to test for
 multiple sources of gene tree discordance via careful examination of
 empirical datasets.
description: # Strong phylogenetic signal despite high phylogenomic complexity in an
 Andean plant radiation (Freziera, Pentaphylacaceae)
 ## Description of the data
 and file structure Data files are organized into three main directories:
 alignments, gene trees and species trees. Below is a summary of the file
 structure in which each folder is noted by a bullet. Names of folders are
 bolded; descriptions of the folders are provided after the folder name. *
 **alignments**: .nexus files, DNA sequence data * **Hybpiper_v1.3.1**:
 alignments of supercontigs assembled by HybPiper v1.3.1 for loci without
 paralog warnings (318 loci). Sequences identified by TreeShrink as
 producing abnormally long branch lengths have been removed from alignments
 ("treeshrunk"). * **paralogs**: alignments of supercontigs
 assembled by HybPiper v1.3.1 for loci with paralog warnings (31 loci). *
 **Hybpiper_v2.0.1**: alignments of supercontigs assembled by HybPiper
 v2.0.1 for loci without long paralog warnings (269 loci). Sequences
 identified by TreeShrink as producing abnormally long branch lengths have
 been removed from alignments ("treeshrunk"). * **paralogs**:
 alignments of supercontigs assembled by HybPiper v2.0.1 for loci with long
 paralog warnings (84 loci). * **gene trees**: .tre files, newick format *
 **datasets**: multiphylo files with filtered HybPiper v1.3.1 gene trees
 for each of the 11 datasets used; input files for ASTRAL species tree
 analyses. * **datasets_with_HybPiper2_gene_trees**: multiphylo files with
 filtered HybPiper v2.0.1 gene trees for the 2 datasets that used
 thresholds based on HybPiper v2.0.1 assembly. * **Hybpiper_v1.3.1**: gene
 trees inferred using IQTree from alignments of supercontigs assembled by
 HybPiper v1.3.1 for loci without paralog warnings. Gene trees with &lt;25
 ingroup samples have been removed, leaving 313 gene trees. *
 **Hybpiper_v2.0.1**: gene trees inferred using IQTree from alignments of
 supercontigs assembled by HybPiper v2.0.1 for loci without paralog
 warnings. Gene trees with &lt;25 ingroup samples have been removed,
 leaving 267 gene trees. * **species trees**: .tre files, newick format;
 output files from ASTRAL analyses of the 11 datasets used. *
 **datasets_with_HybPiper2_gene_trees**: output files from ASTRAL analyses
 of the 2 datasets that used HybPiper v2.0.1 gene trees.