First global phylogeny of whip spiders (Amblypygi)
Data files
May 09, 2024 version files 54.75 MB
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Data-availability.zip
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README.md
Abstract
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).
README: First global phylogeny of whip spiders (Amblypygi)
- Alignment files, input files, and parameters for quartet and dating analyses.
- 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.