DOI: 10.5061/dryad.8sf7m0ctp
title: First global phylogeny of whip spiders (Amblypygi)

description: Asymmetrical rates of cladogenesis and extinction abound in the Tree of
 Life, resulting in numerous minute clades that are dwarfed by larger
 sister groups. Such taxa are commonly regarded as phylogenetic relicts or
 “living fossils” when they exhibit an ancient first appearance in the
 fossil record and prolonged external morphological stasis, particularly in
 comparison to their more diversified sister groups. Due to their special
 status, various phylogenetic relicts tend to be well-studied and
 prioritized for conservation. A notable exception to this trend is found
 within Amblypygi (“whip spiders”), a visually striking order of
 functionally hexapodous arachnids that are notable for their antenniform
 first walking leg pair (the eponymous “whips”). Paleoamblypygi, the
 putative sister group to the remaining Amblypygi, is known from Late
 Carboniferous and Eocene deposits but is survived by a single living
 species, Paracharon caecus Hansen, 1921, that was last collected in 1899.
 Due to the absence of genomic sequence-grade tissue for this vital taxon,
 there is no global molecular phylogeny for Amblypygi to date, nor a
 fossil-calibrated estimation of divergences within the group. Here, we
 report several individuals of a previously unknown species of
 Paleoamblypygi from a cave site in Colombia. Capitalizing upon this
 discovery, we generated the first molecular phylogeny of Amblypygi,
 integrating ultraconserved element sequencing with legacy Sanger datasets
 and including described extant genera. To quantify the impact of sampling
 Paleoamblypygi on divergence time estimation, we performed in silico
 experiments with pruning of Paracharon. We demonstrate that the omission
 of relicts has a significant impact on the accuracy of node dating
 approaches that outweighs the impact of excluding ingroup fossils. Our
 results underscore the imperative for biodiversity discovery efforts in
 elucidating the phylogenetic relationships of “dark taxa”, and especially
 phylogenetic relicts in tropical and subtropical habitats. The lack of
 reciprocal monophyly for Charontidae and Charinidae leads us to subsume
 them into one family, Charontidae (new synonymy).
description: # First global phylogeny of whip spiders (Amblypygi) ######
 **Supplementary Material for "The rediscovery of a relict unlocks the
 first global phylogeny of whip spiders (Amblypygi)**" 1. Alignment
 files, input files, and parameters for quartet and dating analyses. 2.
 Input files and importable results of the main biogeographic analysis,
 importable in RASP ## Supplementary Methods. ### Supplementary Tables
 S1-S7 ##### Supplementary Table S1 Extant diversity of phylogenetic
 relicts within Chelicerata that constitute sister groups to extant orders.
 ##### Supplementary Table S2 Locality and accession data for terminals
 that were included in the study. Nuclear histone 3, H3; mitochondrial
 cytochrome c oxydase subunit I, COI; nuclear 28S rDNA, 28S; nuclear 18S
 rDNA, 18S; mitochondrial 16S rDNA, 16S; mitochondrial 12S rDNA, 12S. #####
 Supplementary Table S3 Fossil calibrations and references for divergence
 time estimation. ##### Supplementary Table S4 Concatenation of UCE and
 six-marker data set. ##### Supplementary Table S5 Area coding scheme used
 for biogeographic analysis. ##### Supplementary Table S6 Statistics of
 model comparison inferred from the RASP analysis. ##### Supplementary
 Table S7 Likelihood percentages of inferred ancestral areas using RASP.
 Area coding is as follows: Nearctic-A; Oriental-B; Neotropical-C;
 Africa-D; Australasia-E; Mediterranean-F; Sundaland-G. ### Supplementary
 Figures S1-S6 ##### Supplementary Figure S1 Maximum likelihood phylogenies
 reconstructed using ultraconserved elements using Blended probe set (a-d)
 and Spider2Kv1 probe set (e-h) at occupancies 1% (a, e), 10% (b, f), 25%
 (c, g) and 40% (d, h). ##### Supplementary Figure S2 Sensitivity of age
 estimates of Amblypygi with *Paracharon* fossil. Median node ages inferred
 by MCMCTree (top) and LSD2 (bottom), upon retention or exclusion of
 Paracharontidae. ##### Supplementary Figure S3 Biogeographic analysis of
 Amblypygi with *Paracharon* coded as Neotropical+Africa. Pie charts at
 nodes indicate the probability of an individual or a combination of
 ancestral areas. Area coding is as follows: Nearctic-A; Oriental-B;
 Neotropical-C; Africa-D; Australasia-E; Mediterranean-F; Sundaland-G.
 ##### Supplementary Figure S4 Biogeographic analysis of Amblypygi using
 DEC model. Pie charts at nodes indicate the probability of an individual
 or a combination of ancestral areas. Nearctic-A; Oriental-B;
 Neotropical-C; Africa-D; Australasia-E; Mediterranean-F; Sundaland-G.
 ##### Supplementary Figure S5 Divergence time estimates optimized by
 MCMCTree and LSD2 using fossil-based node calibrations. Conventions of HPD
 intervals follow the bottom legend. ##### Supplementary Figure S6
 Biogeographic analysis of Amblypygi using DEC+j model with the exclusion
 of *Paracharon*. Pie charts at nodes indicate the probability of an
 individual or a combination of ancestral areas. Nearctic-A; Oriental-B;
 Neotropical-C; Africa-D; Australasia-E; Mediterranean-F; Sundaland-G.