DOI: 10.5061/dryad.r8q72
title: Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

description: Premise of the study: Untapped information about allelic diversity within
 populations and individuals (i.e. heterozygosity) could improve
 phylogenetic resolution and accuracy. Many phylogenetic reconstructions
 ignore heterozygosity because it is difficult to assemble allele sequences
 and combine allelic data across unlinked loci and it is unclear how
 reconstruction methods accommodate variable sequences. We review the
 common methods of including heterozygosity in phylogenetic studies and
 present a novel method for assembling allele sequences from target
 enriched Illumina sequencing libraries. Methods: We perform supermatrix
 phylogeny reconstruction and species tree estimation of Artocarpus based
 on three methods of accounting for heterozygous sequences: a consensus
 method based on de novo sequence assembly, the use of ambiguity
 characters, and a novel method for phasing alleles. We characterize the
 extent to which highly heterozygous sequences impeded phylogeny
 reconstruction and determine whether the use of allele sequences improves
 resolution or decreases topological uncertainty. Key Results: We show that
 it is possible to infer phased alleles from target enriched Illumina
 libraries. We find that highly heterozygous sequences do not contribute
 disproportionately to poor phylogenetic resolution and that the use of
 allele sequences for phylogeny reconstruction does not have a clear effect
 on phylogenetic resolution or topological consistency. Conclusions: We
 provide a framework for inferring phased alleles from target enrichment
 data and for assessing the contribution of allelic diversity to
 phylogenetic reconstruction. In our dataset, the impact of allele phasing
 on phylogeny is minimal compared to the impact of using phylogenetic
 reconstruction methods that account for gene tree incongruence.
description: Gene
 alignmentsFASTA format alignments
 for 151 protein-coding using three assembly methods: consensus, ambiguity
 (iupac), and allele phasing. Alleles for each individual are annotated as
 _h1 or _h2; for SVDQuartets all SNPs are randomly assigned to _h1 or _h2.
 For the alleles dataset, alleles have been phased within the longest
 phaseable block. Outside this block, ambiguity codes are retained. Also
 contains partition files for RAxML, with each gene partitioned by codon
 position.artocarpus_alignments.zipPhyparts OutputOutput of Phyparts, a bipartition analysis method. Rooted gene trees were reconciled with the ASTRAL species tree produced for each of the assembly methods: consensus (default), ambiguity (IUPAC) and alleles.phyparts_output.zipSpecies TreesSpecies phylogenies for the three assembly methods: consensus (default), ambiguity (iupac), and alleles. For the coalescent-based methods, two types of gene trees were used as input: one with fully bifurcating gene trees, and one where branches were collapsed if they had less than 33% gene tree bootstrap support.Output_trees.zipscriptsBash shell and python scripts used to prepare alignments for gene tree inference, phase alleles, and extract introns and exons for multiple-sequence alignment.Gene_treesGene trees from three data assembly methods. The identity of each gene can be found in final_genelist.txttaxon_subst_artocarpusTable for translating accession IDs into taxon names.