DOI: 10.5061/dryad.2g1f4n5
title: Data from: A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error

description: Horseshoe crabs (Xiphosura) are traditionally regarded as sister to the
 clade of terrestrial chelicerates (Arachnida). This hypothesis has been
 challenged by recent phylogenomic analyses, but the non-monophyly of
 Arachnida has consistently been disregarded as artifactual. We reevaluated
 the placement of Xiphosura among chelicerates using the most complete
 phylogenetic dataset to date, expanding outgroup sampling and including
 data from whole genome sequencing projects. In spite of uncertainty in
 theplacement of some arachnid clades, all analyses show Xiphosura
 consistently nested within Arachnida as the sister group to Ricinulei
 (hooded tick spiders). It is apparent that the radiation of Arachnids is
 an old one and occurred over a brief period of time, resulting in several
 consecutive short internodes, and thus is a potential case for the
 confounding effects of incomplete lineage sorting (ILS). We simulated
 coalescent gene trees to explore the effects of increasing levels of ILS
 on the placement of horseshoe crabs. In addition, common sources of
 systematic error were evaluated, as well as the effects of fast evolving
 partitions and the dynamics of problematic long branch orders. Our results
 indicated that the placement of horseshoe crabs can not be explained by
 missing data, compositional biases, saturation, or incomplete lineage
 sorting. Interrogation of the phylogenetic signal showed that the majority
 of loci favor the derived placement of Xiphosura over a monophyletic
 Arachnida. Our analyses support the inference that horseshoe crabs
 represent a group of aquatic arachnids comparable to aquatic mites,
 breaking a long standing paradigm in chelicerate evolution and altering
 previous interpretations of the ancestral transition to the terrestrial
 habitat. Future studies testing chelicerate relationships should approach
 the task with a sampling strategy where the monophyly of Arachnida is not
 held as the premise.
description: Concateneated dataset
 3534 lociPrimary dataset composed
 of 3534 loci concateneated. This file in combination with the
 all_stats.xls and the corresponding partition file can be used to produce
 all data subsets described in the manuscript.Concat_3534_indep.fastaPartition file of the 3534 loci datasetPartition_3534.txt.best_scheme.nexMARE reduced dataset with 721 lociConcat_721_MARE.fastapartition file MAREMAREpart.nexfunctions for gene tree simulationssimulations.pympsiScript for calculating mean pair-wise sequences identity metricdroptipsScript to prune a reference tree (species tree) from leaves not present in a given alignment. The script is used as a preliminary for Dellta GLS calculations.splitDistScript and functions to list and count the bipartitions present in a collection of trees.matrices.xlxsSpreadsheet listing all partitions, general properties, amino acid substitution models and results of Delta GLS and TtreSpEx LB scores. This file can also be used to filter dataset and reproduce the matrices in the manuscript.matrices.xlsxSupplemental_Tables_and_FiguresSuplemental Tables and Figures including full annotated treesdatbacoca_pcaModified BaCoCa output used for PCA analyses.part_1499Nexus file defining partitions and amino acid substitution models for the decisive datasetNEWICKS 2Newick formatted trees.Pycnogonium_littorale_SAMN10093767Transcriptome assemblyLithobius_atkinsoni_SAMN10093766