DOI: 10.5061/dryad.2v6wwpzz4
title: Data from: Phylogenomics of North American cybaeid spiders (Araneae, F. Cybaeidae), including the description of new taxa from the Klamath Mountains Geomorphic Province

description: The systematics of humble-in-appearance brown spiders (“marronoids”),
 within a larger group of spiders with a modified retrolateral tibial
 apophysis (the RTA Clade), has long vexed arachnologists. Although not yet
 fully settled, recent phylogenomics has allowed the delimitation and
 phylogenetic relationships of families within marronoids to come into
 focus. Understanding relationships within these families still awaits more
 comprehensive generic-level sampling, as the bulk of described marronoid
 genera remain unsampled for phylogenomic data. Here we conduct such an
 analysis in the family Cybaeidae Banks, 1892. We greatly increase
 generic-level sampling, assembling ultraconserved element (UCE) data for
 18 of 22 described cybaeid genera, including all North American genera,
 and rigorously test family monophyly using a comprehensive outgroup taxon
 sample. We also conduct analyses of traditional Sanger loci, allowing
 curation of some previously published data. Our UCE phylogenomic results
 support the monophyly of recognized cybaeids, with strongly supported
 internal relationships, and evidence for five primary molecular subclades.
 We hypothesize potential morphological synapomorphies for several of these
 subclades, bringing a robust phylogenomic underpinning to cybaeid
 classification. We discover and describe a new cybaeid genus (Siskiyu gen.
 nov.) and species (Siskiyu armilla sp. nov.) from far northern California
 and adjacent southern Oregon and describe a new species in the elusive
 genus Cybaeozyga (C. furtiva sp. nov.) from far northern California.
description: <strong><em>Input
 Matrices:</em></strong>
 <strong>50p_filtered and 80p_filtered
 matrices</strong> - UCE loci were aligned, trimmed, and filtering
 using FUSe. This included aligning with the MAFFT globapair option, and
 trimming using trimAl with the -automated1 option. We removed highly
 divergent sequences (60%) (--remove-div -d 0.6) and sequences shorter than
 70% of the total alignment length (--remove-short -s 0.7), retaining
 alignments with a minimum of 4 sequences and longer than 50bp. Subsequent
 50% and 80% completeness matrices were created (--get-completeness -e 0.8
 and -e 0.5). We manually curated the above alignments in Geneious Prime
 2023, removing any remaining obviously divergent individual sequences, and
 matrices with an average pairwise identity below 80%.
 <strong>50p_PhyIN and 80p_PhyIN</strong>
 <strong>matrices</strong> – Here we combined PhyIN and FUSe.
 This workflow consisted of aligning with MAFFT using the globalpair
 option, followed by removal of highly divergent sequences (70% divergence)
 (--remove-div -d 0.7), trimming of gaps using a Simple Gappiness Filter
 (sgp.py) with options -gS -gB -t -1 in combination with PhyIN using
 options -b 10 -d 2 -p 0.5 -e. After trimming, remaining short sequences
 were removed using FUSe (--remove-short -s 0.7) and 50 and 80%
 completeness matrices were created.
 <strong><em>Sanger
 </em></strong><strong>matrices</strong> - Sanger
 loci were harvested from UCEs, low-coverage genomes and transcriptome data
 using custom scripts (“loci_byCatch.sh”). A reference fasta file
 (“reference_cyb.fasta”) containing target loci was created from previously
 published ingroup data. Cleaned fastq files were mapped against this
 reference using BWA. Resulting BAM files were used for calling consensus
 sequences for each sample and locus using the consensus function of
 SAMTOOLS v1.16. For each mapped sample and locus we retained the longest
 sequence for downstream analysis. Consensus sequences were merged, aligned
 and trimmed with FUSe using the MAFFT globalpair option for aligning and
 trimAl -automated1 option for trimming, followed by alignment inspection
 in Geneious Prime 2023.
 <strong><em>Phylogenetic
 Analyses:</em></strong>
 <strong>IQ–TREE
 Analyses</strong><strong><em> -
 </em></strong>For all UCE concatenated, Sanger concat and
 individual Sanger loci matrices we conducted maximum likelihood analyses
 with IQ–TREE 2. Concatenated analyses included individual loci as separate
 partitions, with 1000 replicates of ultrafast bootstrapping and optimal
 model search using ModelFinder.
 <strong>Concordance Factor
 Analyses</strong><strong><em> -
 </em></strong>For 50p_filtered and 80p_filtered matrices, we
 estimated gene trees from individual UCE alignments and calculated gene
 (gCF) and site (sCF) concordance factors using IQTree; sCF values were
 estimated with the likelihood option --scfl.
 <strong>ASTRAL
 Analyses</strong><strong><em> -
 </em></strong>For 50p_filtered and 80p_filtered matrices,
 species trees were estimated under a multispecies coalescent model using
 weighted ASTRAL (wASTRAL). Input gene trees for wASTRAL were estimated
 using IQ–TREE 2 with 1000 replicates of ultrafast bootstrapping and
 treated as unrooted. We used the wASTRAL hybrid scheme to weight gene
 trees using both long terminal branches and weakly-supported nodes.
 Internal ASTRAL branch lengths were estimated in coalescent units, with
 branch support measured as local posterior probability values.
 References for all Methods used above can be found in the main
 manuscript text. <strong><em>Taxon
 Labels:</em></strong> Identification labels
 for two specimens found in input matrices, output files, and output .tre
 files have been changed, as follows:
 SDSU_G4110_Willisus_sp_nov =
 SDSU_G4110_Willisus_gertschi
 SDSU_G1150_Cryphoecine_nov_gen = SDSU_G1150_ Cybaeina
 dixoni
description: # Phylogenomics of North American cybaeid spiders (Araneae, F. Cybaeidae),
 including the description of new taxa from the Klamath Mountains
 Geomorphic Province
 [https://doi.org/10.5061/dryad.2v6wwpzz4](https://doi.org/10.5061/dryad.2v6wwpzz4) ## Description of the data and file structure ### Files and variables #### File: Cybaeidae80p\_PhyIN\_Archive.zip **Description:** individual locus alignments for 80p_PhyIn matrices #### File: concatenated\_partitions.txt **Description:**  partitions file for concatenated Sanger matrix ##### Variables * DNA: * 18s = 1-1554: #### File: Cybaeidae50p\_filtered\_Archive.zip **Description:**  individual locus alignments for 50p_Filtered matrices #### File: Cybaeidae50p\_PhyIN\_Archive.zip **Description:**  individual locus alignments for 50p_PhyIn matrices #### File: H3\_MH.nex **Description:** H3 Sanger data matrix #### File: Astral\_80pFiltered.log **Description:** phylogenetic output log files from Astral_80p analysis #### File: concatenated.nex **Description:** concatenated Sanger matrix #### File: Astral\_50pFiltered.log **Description:** phylogenetic output log files from Astral_80p analysis #### File: Cybaeidae80p\_filtered\_Archive.zip **Description:**  individual locus alignments for 80p_Filtered matrices #### File: IQTree\_Sanger18S.nex.log **Description:** phylogenetic output log files from Sanger 18S matrix analysis #### File: 28S\_MH.nex **Description:** 28S Sanger matrix #### File: 18S\_MH.nex **Description:** 18S Sanger matrix #### File: IQTree\_Sanger\_H3.nex.log **Description:** phylogenetic output log files from Sanger H3 matrix analysis #### File: IQTree\_80p\_PhyIN.log **Description:** phylogenetic output log files from 80p_PhyIn matrix analysis #### File: Cybaeidae\_jAstral-50pFiltered.tre **Description:** .tre file from Astral_50pFiltered analysis #### File: Cybaeidae\_Sanger\_H3.tre **Description:** .tre file from Sanger H3 matrix analysis #### File: Cybaeidae\_Sanger\_zConcat.tre **Description:** .tre file from Sanger Concatenated matrix analysis #### File: Cybaeidae\_Sanger\_18s.tre **Description:** .tre file from Sanger 18S matrix analysis #### File: Cybaeidae\_Sanger\_28s.tre **Description:** .tre file from Sanger 28S matrix analysis #### File: IQTree\_80pFiltered.log **Description:** phylogenetic output log files from 80p_Filtered matrix analysis #### File: IQTree\_Sanger28S.fasta.log **Description:** phylogenetic output log files from Sanger 28S matrix analysis #### File: Cybaeidae\_IQTREE\_80pFiltered.tre **Description:** .tre file from 80pFiltered analysis #### File: Cybaeidae\_IQTREE\_PhyIN50p.tre **Description:** .tre file from 50pPhyIn analysis #### File: Cybaeidae\_IQTREE\_PhyIN80p.tre **Description:** .tre file from 80pPhyIn analysis #### File: IQTree\_50p\_PhyIN.log **Description:** phylogenetic output log files from 50p_PhyIn matrix analysis #### File: Cybaeidae\_IQTREE\_50pFiltered.tre **Description:** .tre file from 50pFiltered analysis #### File: Cybaeidae\_IQTREE\_80pFiltered.scf.tree **Description:** .tre file from 80pFiltered site concordance factor analysis #### File: Cybaeidae\_IQTREE\_50pFiltered.scf.tree **Description:** .tre file from 50pFiltered site concordance factor analysis #### File: Cybaeidae\_IQTREE\_50pFiltered.gcf.tree **Description:** .tre file from 50pFiltered gene concordance factor analysis #### File: Cybaeidae\_IQTREE\_80pFiltered.gcf.tree **Description:** .tre file from 80pFiltered gene concordance factor analysis #### File: Cybaeidae\_jAstral-80pFiltered.tre **Description:** .tre file from Astral_80pFiltered analysis #### File: IQTree\_Sanger\_concat.log **Description:** phylogenetic output log files from Sanger loci concatenated matrix analysis #### File: IQTree\_50pFiltered.log **Description:** phylogenetic output log files from 50pFiltered matrix analysis ## Code/software Matrix and log files can be viewed using a basic text editor .tre files can be viewed with a text editor, or FigTree Sanger loci were harvested from UCEs, low-coverage genomes and transcriptome data using the “loci_byCatch.sh” custom script. This was also based on the reference fasta file (“reference_cyb.fasta”) containing target loci, created from previously published ingroup data.