Phylogenomics of North American cybaeid spiders (Araneae, F. Cybaeidae), including the description of new taxa from the Klamath Mountains Geomorphic Province

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 s..., Input Matrices:
50p_filtered and 80p_filtered matrices - 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%.
50p_PhyIN and 80p_PhyIN matrices – 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 Simpl..., , # 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: con...