Systematics and evolutionary history of raft and nursery-web spiders (Araneae: Dolomedidae and Pisauridae)
Data files
Feb 24, 2025 version files 324.21 MB
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Divergence_time_compare.zip
14.89 KB
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MCMCtree.zip
4.65 MB
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README.md
5.88 KB
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Supporting_information.zip
315 MB
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UCE_submatrix.zip
4.53 MB
Abstract
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.
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)
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 and our self-archived project paper: Yu, Cheng et al., 2024 (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), 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 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), 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 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). 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.
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.
