DOI: 10.5061/dryad.m63xsj4c6
title: Systematics and evolutionary history of raft and nursery-web spiders (Araneae: Dolomedidae and Pisauridae)

description: Pisauridae are a global and heterogeneous assemblage of spider genera with
 diverse morphologies and lifestyles. So far, the monophyly of Pisauridae
 and the inclusion of fishing spiders (Dolomedes) in this family have not
 been thoroughly tested. Here, we amend the systematics and classification
 of these lineages within a UCE phylogenomic framework and through a
 detailed morphological reappraisal. For estimations of their evolutionary
 age, we perform and compare outcomes from two divergence estimation
 approaches, an a posteriori likelihood, and an a priori Bayesian.
 Phylogenies reject the monophyly of both Pisauridae and Dolomedes: 1)
 Focal Clade I groups true Pisauridae genera including Pisaura; 2) Focal
 Clade II contains Blandinia and is sister to Trechaleidae and Lycosidae;
 3) Focal Clade III groups Dolomedes, Megadolomedes, and Ornodolomedes, and
 is sister to Blandinia, Trechaleidae, and Lycosidae. We therefore propose
 to delimit Pisauridae by removing Dolomedidae rank resurrected (including
 Dolomedes, Bradystichus, Megadolomedes, Caledomedes, Mangromedes,
 Ornodolomedes, and Tasmomedes) and Blandinia incertae sedis. Likelihood
 and Bayesian time calibration approaches yield comparable divergence
 estimations: Pisauridae origin is estimated at 29–40 Ma; Blandinia 21–34
 Ma; Dolomedidae 10–17 Ma; Dolomedes 9–16 Ma. Reconstructions suggest that
 the evolution of terrestrial and web-building lifestyles from semi-aquatic
 ancestors in Pisauridae coincided with cooling and drying climates during
 the mid-Miocene, but this was not the case in the few recent cases of
 terrestrialization in Dolomedes species. This historic reconstruction
 illustrates how climatic changes, or rapid radiation, can drive lifestyle
 diversification.
description: # Systematics and evolutionary history of raft and nursery-web spiders
 (Araneae: Dolomedidae and Pisauridae): Open Source Data --- We have
 submitted our raw UCE submatrix (**UCE_submatrix.zip**), configuration and
 input files for MCMCtree divergence time estimation (**MCMCtree.zip**),
 comparisons between MCMCtree and RelTime calibration methods
 (**Divergence_time_compare.zip**), and the publication's supporting
 information (**Supporting_information.zip**). ## Descriptions ###
 **UCE\_submatrix** The folder contains the UCE matrix, in nexus format,
 used to estimate the divergence time of the taxon in question. This matrix
 was aligned from 300 UCE loci randomly subsampled from the full UCE matrix
 in our self-archived project paper: Yu, Cheng *et al*., 2024
 ([https://doi.org/10.1101/2024.08.23.609317](https://doi.org/10.1101/2024.08.23.609317)) ### **MCMCtree** This folder contains two subfolders (listed below) containing an R script and configuration files to run MCMCtree divergence time estimation under PAML 4.10 (Yang, 2007). Please also read the program manuals at [https://gensoft.pasteur.fr/docs/paml/4.9j/MCMCtree.Tutorials.pdf](https://gensoft.pasteur.fr/docs/paml/4.9j/MCMCtree.Tutorials.pdf) and our self-archived project paper: Yu, Cheng *et al*., 2024 ([https://doi.org/10.1101/2024.08.23.609317](https://doi.org/10.1101/2024.08.23.609317)). Please note that here, a time unit equals 10 million years. * **baseml**: This subfolder contains three files, listed below, to estimate the parameters needed for the divergence time estimation. * *Pisauridae_300loci_20240706_baseml_input.phy*, the UCE submatrix, in phylip format, that was used for the parameters and the divergence time estimation.  * *Pisauridae_ML_topology.tre*, the maximum likelihood topology that was used for the parameter estimation. The tree was obtained from our self-archived project paper, Yu, Cheng *et al*., 2024 ([https://doi.org/10.1101/2024.08.23.609317](https://doi.org/10.1101/2024.08.23.609317)), with all branch lengths removed. An annotation of the approximated node age (@4.75) was added at one of the calibration points to make the program run properly. * *baseml.ctl*, the configuration file to derive the program. Please see the online manual  [https://gensoft.pasteur.fr/docs/paml/4.9j/MCMCtree.Tutorials.pdf](https://gensoft.pasteur.fr/docs/paml/4.9j/MCMCtree.Tutorials.pdf) for more details * **mcmctree**: This subfolder contains five files, listed below, to run MCMCtree divergence time estimation. * *Pisauridae_ML_topology_raw.tre*, the maximum likelihood topology that was used as the input to set the prior of each time calibration point. The tree was obtained from our self-archived project paper, Yu, Cheng *et al*., 2024 ([https://doi.org/10.1101/2024.08.23.609317](https://doi.org/10.1101/2024.08.23.609317)), with all branch lengths and annotations removed. * *MCMCTreeR.R*, the R script that was used to set the priors of the time calibration points to *Pisauridae_ML_topology_raw.tre*. * *Pisauridae_ML_topology_prior.tre*, the maximum likelihood topology with all the priors set. This file is the input for mcmctree analysis. * *in.BV*, required parameters estimated from baseml (above subfolder) * *mcmctree_all.ctl*, the configuration file to derive the program. Please see the online manual  [https://gensoft.pasteur.fr/docs/paml/4.9j/MCMCtree.Tutorials.pdf](https://gensoft.pasteur.fr/docs/paml/4.9j/MCMCtree.Tutorials.pdf) for more details ### **Divergence\_time\_compare** This folder contains two phylogenies (listed below) showing the output of the two different divergence time estimation methods. * *MCMCtree.tre*, the time calibration results of MCMCtree. Please note that here a time unit equals 10 million years. * *RelTime_Yu_et_al_2024.tre*, the time calibration results of RelTime, obtained from our self-archived project paper: Yu, Cheng *et al*., 2024 ([https://doi.org/10.1101/2024.08.23.609317](https://doi.org/10.1101/2024.08.23.609317)). Please note that here a time unit equals 1 million years. ### **Supporting\_information** This file contains the supporting information, consisting of a subfolder and two pdf files (listed below), of Systematics and evolutionary history of raft and nursery-web spiders (Araneae: Dolomedidae and Pisauridae). * *zsc12719-sup-0001-supinfo*, this file contains the supporting tables and figures of Systematics and evolutionary history of raft and nursery-web spiders (Araneae: Dolomedidae and Pisauridae). The same file can also be found at DOI: 10.1111/zsc.12719. * **Supporting_figure_full_size**: This subfolder contains the supplementary figures (S1-S7) in full resolutions, figure legends can be found in *zsc12719-sup-0001-supinfo*. * *zsc12719-sup-0002-supinfo*, this file contains the taxonomic history, proposed taxonomic acts, and the diagnoses of the taxa in question of Systematics and evolutionary history of raft and nursery-web spiders (Araneae: Dolomedidae and Pisauridae). The same file can also be found at DOI: 10.1111/zsc.12719. ## Key Information Sources The data used and analyzed in this study were acquired originally or from our self-archived project paper: Phylogenomics, Classification, and Lifestyle Evolution in Raft- and Nursery Web- Spiders (Araneae: Dolomedidae and Pisauridae). The archived paper can be found here: [https://doi.org/10.1101/2024.08.23.609317](https://doi.org/10.1101/2024.08.23.609317). ## Code/Software Phyluce v1.7.3 is required to transfer the UCE matrix into different formats; R 4.3.3 is required to run *MCMCTreeR.R*; PAML 4.10 is required to run MCMCtree, both baseml and mcmctree. All .BV, .ctl, and .tre files can be opened and edited in Windows Notepad or any other similar software while it is better to visualize .tre files in a phylogenetic related software, such as FigTree.