DOI: 10.5061/dryad.0zpc8673w
title: Dynamic evolution of locomotor performance independent of changes in extended phenotype use in spiders

description: Many animals utilise self-built structures (extended phenotypes) to
 enhance body functions, such as thermoregulation, prey capture or defence.
 Yet, it is unclear whether the evolution of animal constructions
 supplements or substitutes body functions – with disparate feedbacks on
 trait evolution. Here, using brown spiders (Araneae: marronoid clade), we
 explored if the evolutionary loss and gain of silken webs as extended prey
 capture devices correlates with alterations in traits known to play an
 important role in predatory strikes – locomotor performance (sprint speed)
 and leg spination (expression of capture spines on front legs). We found
 that in this group high locomotor performance, with running speeds of over
 100 body lengths per second, evolved repeatedly – both in web building and
 cursorial spiders. There was no correlation with running speed, and leg
 spination was only poorly correlated, relative to the use of extended
 phenotypes, indicating that web use does not reduce selective pressures on
 body functions involved in prey capture and defence per se.
 Consequently, extended prey capture devices serve as supplements rather
 than substitutions to body traits and may only be beneficial in
 conjunction with certain life history traits, explaining the rare
 evolution and repeated loss of trapping strategies in predatory animals.
description: Animal collection and material sourcing
 Spiders were collected in New South Wales, South Queensland,
 Tasmania, the South Island of New Zealand and Germany under scientific
 licenses SL101868, FA18285, PTU19-001938 and 71225-RES. Tissue samples and
 specimens for morphology for some species were sourced from museum and
 institutional collections. Species were identified with primary or (if
 available) secondary taxonomic literature. In addition, in some cases,
 specimens were compared with type specimens for taxonomic identification.
 Vouchers were preserved in ethanol and deposited at curated arachnological
 collections. The full list of specimens used in the phylogenomic study,
 including their collection data and voucher locations are found in
 supplemental material S1 and S2 of the associated article. 
 DNA extraction and UCE analysis Genomic DNA
 extraction of all samples was performed using either the leg(s) or the
 whole specimen (depending on the size of the spider), following the DNeasy
 Blood and Tissue Kit (Qiagen, Valencia, CA) manufacturer’s protocol, and
 quantified using a Qubit fluorometer (Life Technologies, Inc.). UCE
 library preparations were performed following the protocol of Starrett et
 al. [1] and Derkarabetian et al. [2] as well as the Hybridization Capture
 for Targeted NGS manual v4.01 protocol (https://arborbiosci.com/wp-content/uploads/2018/04/myBaits-Manual-v4.pdf). Library preparation for a subset of the samples (n = 23) was conducted using the MYbaits Arachnida 1.1Kv1 kit (Arbor Biosciences, Ann Arbor, MI, USA) [1] (see details in supplemental material S1) and sequenced on a NovaSeq 6000 at the Bauer Core Facility at Harvard University. For the remaining samples (n = 75), the extracted DNA was dried using an Eppendorf Concentrator plus speed-vac and transported to NGS Division, Arbor Biosciences (Ann Arbor, MI) for UCE library preparation using the Spider 2Kv1 kit [3]. Processing of the raw demultiplexed read data was performed using the PHYLUCE v1.6.8 pipeline [4]. Reads were cleaned with the Trimmomatic wrapper [5] and Illumiprocessor [6], using default settings, and then assembled using both Trinity v2.1.1 [7], with default settings, and ABySS v1.5.2 [8] (using 64-kmer value setting), and the results combined into a single assembly file. Probes were matched to contigs using the Spider 2Kv1 probeset file using minimum coverage and minimum identity values of 65. The UCE loci were aligned using MAFFT [9] and trimmed using GBLOCKS [10, 11] with custom gblocks settings (b1 = 0.5, b2 = 0.5, b3 = 6, b4 = 6) applied in the PHYLUCE pipeline. Aligned UCEs were then imported into Geneious 11.1.5 [12] and visually inspected for obvious alignment or sequencing errors. Method references [1] Starrett, J., Derkarabetian, S., Hedin, M., Bryson Jr, R.W., McCormack, J.E. & Faircloth, B.C. 2017 High phylogenetic utility of an ultraconserved element probe set designed for Arachnida. Molecular Ecology Resources 17, 812-823. [2] Derkarabetian, S., Benavides, L.R. & Giribet, G. 2019 Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault. Molecular Ecology Resources 19, 1531-1544. [3] Kulkarni, S., Wood, H., Lloyd, M. & Hormiga, G. 2020 Spider‐specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae). Molecular Ecology Resources 20, 185-203. [4] Faircloth, B.C. 2016 PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32, 786-788. [5] Bolger, A.M., Lohse, M. & Usadel, B. 2014 Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120. [6] Faircloth, B. 2013 Illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. (doi:https://doi.org/10.6079/J9ILL). [7] Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R. & Zeng, Q. 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29, 644-652. [8] Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J. & Birol, I. 2009 ABySS: a parallel assembler for short read sequence data. Genome Res 19, 1117-1123. [9] Katoh, K. & Standley, D.M. 2013 MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30, 772-780. [10] Castresana, J. 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540-552. [11] Talavera, G. & Castresana, J. 2007 Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56, 564-577. [12] Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S. & Duran, C. 2012 Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649.
description: # Dynamic evolution of locomotor performance independent of changes in
 extended phenotype use in spiders
 [https://doi.org/10.5061/dryad.0zpc8673w](https://doi.org/10.5061/dryad.0zpc8673w) This dataset contains the extracted and aligned UCE (ultraconserved elements) sequences for species of the marronoid clade of spiders (Araneae) used for phylogenomic analyses by Kelly et al. (2023). ## Description of the data and file structure The zip-archive contains sequence alignment files (Nexus) for each UCE loci. In addition, there is a single alignment file containing the 50 most informative loci in a concatenated alignment (see methods and associated article for details). The sequences can be included into future phylogenomic studies based on UCE traget enrichment sequencing, i.e. to supplement a taxon sample. ## Sharing/Access information For further information and associated phenotypic data, please read the associated research article, including electronic supplemental materials. A preprint of the article can be accessed from EcoEvoRxiv: [https://doi.org/10.32942/X2BP44](https://doi.org/10.32942/X2BP44) Supplemental data (metadata, scripts and phenotypic data) can, further, be found on the Zenodo archive: https://doi.org/10.32942/X2BP44