Ultraconserved element data for phylogenomic analysis of Ghatippus paschima jumping spider (Salticidae, Plexippini, Plexippina)
Data files
Feb 20, 2024 version files 39.05 MB
-
Ghatippus_paschima_ConcatMatrixWithTrees.nex.zip
12.40 MB
-
README.md
2.38 KB
-
UCE_matrices_from_SPAdes_preGblocks.zip
26.65 MB
Abstract
Based on UCE phylogenomic data, we propose a new genus and species of plexippine jumping spider, Ghatippus paschima, discovered in the Western Ghats of India. This study, which includes 18 taxa (15 ingroup taxa and 3 outgroup taxa), is also the first to resolve the broader relationships within Plexippina using UCE data.
README: Ultraconserved element data for phylogenomic analysis of Ghatippus paschima jumping spider (Salticidae, Plexippini, Plexippina)
https://doi.org/10.5061/dryad.zcrjdfnkw
The dataset includes (1) ultraconserved element (UCE) matrices and (2) concatenated matrices used in the phylogenomic analysis of a new plexippine jumping spider genus and species, Ghatippus paschima. The dataset (2) also comprises 10 maximum-likelihood trees and 1000 bootstrap trees generated using IQ-TREE.
Methods
We used target enrichment UCE sequencing, dual-indexed TruSeq-style libraries were prepared following methods used previously (e.g. Maddison et al. 2020b). Targeted enrichment using the RTA_v2 probeset (Zhang et al. 2023) was performed using the myBaits v. 4.01 protocol (Arbor Biosciences, https://arborbiosci.com/wp-content/uploads/2023/06/myBaits_Manual_v5.03.pdf). Libraries were sequenced on partial lanes of illumina NovaSeq 6000 S4 runs with 150-bp paired end reads.
Raw demultiplexed reads were processed with PHYLUCE v. 1.6 (Faircloth 2016), quality control and adapter removal were performed with Illumiprocessor wrapper (Faircloth 2013), and assemblies were created with SPAdes v. 3.14.1 (Nurk et al. 2013) using options at default settings. The UCE loci were recovered using RTA_v2 probeset (Zhang et al. 2023). The recovered loci were aligned with MAFFT using L-INS-i option (Katoh and Standley 2013). The aligned UCE loci were then trimmed with Gblocks (Castresana 2000; Talavera and Castresana 2007) using –b1 0.5, –b2 0.7, –b3 8, –b4 8, –b5 0.4 setting and re-aligned with MAFFT using L-INS-i option within Mesquite v. 3.61 (Maddison and Maddison 2019). As in the analysis of Maddison et al. (2020a), suspected paralogous loci were deleted based on branch lengths in RAxML (Stamatakis 2014) inferred gene trees. Loci represented in fewer than 10 taxa total were deleted.
Description of the data
(1) A compressed folder (UCE_matrices_from_SPAdes_preGblocks.zip) containing UCE matrices recovered from SPAdes assemblies. These matrices are aligned but are not trimmed using Gblocks Gblocks.
(2) A NEXUS file (Ghatippus_paschima_ConcatenatedMatricesWithTrees.nex.zip) of Gblocks trimmed, re-aligned, concatenated dataset of 3060 UCE matrices for 18 (15 ingroup and 3 outgroup) taxa used for maximum likelihood phylogenetic and bootstrap analysis.