DOI: 10.5061/dryad.4mw6m90gv
title: Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.)

description: The recognition and delineation of cryptic species remains a perplexing
 problem in systematics, evolution, and species delimitation. Once
 recognized as such, cryptic species complexes provide fertile ground for
 studying genetic divergence within the context of phenotypic and
 ecological divergence (or lack thereof). Herein we document the discovery
 of a new cryptic species of trapdoor spider, Promyrmekiaphila korematsui
 sp. nov. Using subgenomic data obtained via target enrichment, we document
 the phylogeography of the California endemic genus Promyrmekiaphila and
 its constituent species, which also includes P. clathrata and P. winnemem.
 Based on these data we show a pattern of strong geographic structuring
 among populations but cannot entirely discount recent gene flow among
 populations that are parapatric, particularly for deeply diverged lineages
 within P. clathrata. The genetic data, in addition to revealing a new
 undescribed species, also allude to a pattern of potential phenotypic
 differentiation where species likely come into contact. Alternatively,
 phenotypic cohesion among genetically divergent P. clathrata lineages
 suggests that some level of gene flow is ongoing or occurred in the recent
 past. Despite considerable field collection efforts over many years,
 additional sampling in potential zones of contact for both species and
 lineages is needed to completely resolve the dynamics of divergence in
 Promyrmekiaphila at the population-species interface.
description: # Microgeographic population structuring in a genus of California trapdoor
 spiders and discovery of an enigmatic new species (Euctenizidae:
 Promyrmekiaphila korematsui sp. nov.) Starrett J, Jochim E, Quayle I,
 Zahnle X, Bond J Folder: Supplementary_Figures
 Supplementary_Files_Information: figure legends for supplementary figures
 1-10 SuppFig1_clado_min95p_tree.tif SuppFig2_MSC_ASTRAL_95p_strict.tif
 SuppFig3_Promy_coi_v5_run_BSonly.treefile.tif SuppFig4_VAE_All.tif
 SuppFig5_VAE_clathrataOnly.tif SuppFig6_All_95p_AncCoef.tif
 SuppFig7_All_75p_AncCoef.tif SuppFig8_clathrata_95p_AncCoef.tif
 SuppFig9_clathrata_75p_AncCoef.tif
 SuppFig10_4_clades_jitterplots_supplementary_figure.tif Folder:
 Morphological_Measurements Tables_localities_measures_5Sept2023: Tables
 with Sheet locality data. n/a indicated for individuals not sequenced
 Sheet measurements for female specimens. n/a indicated for individuals not
 assigned to clade/lineage. Sheet measurements for male specimens. n/a
 indicated for individuals not assigned to clade/lineage. Folder:
 Sequencing_Stats Tables_Promy_sequencing_PUBstats: statistics for raw
 reads, cleaned reads, and probe matched contigs Folder:
 Promyrmekiaphila_plusoutgroups_spades_assemblies Scaffold files from de
 novo assemblies with Spades for all individuals (122). Folder:
 UCE_alignments mafft-nexus: locus alignments with mafft mafft-nexus-clean:
 locus alignments with UCE names removed mafft-nexus-clean-min-75p-taxa:
 loci with minimum locus occupancy 75%
 mafft-nexus-clean-min-75p-taxa-trimal-strict-raxml: data masked with
 trimal strict, concatenated loci mafft-nexus-clean-min-95p-taxa: loci with
 minimum locus occupancy 95%
 mafft-nexus-clean-min-95p-taxa-trimal-strict-raxml: data masked with
 trimal strict, concatenated loci Folder: SNP_data Datasets for generating
 SNPs All_Pro_species: data for all Promyrmekiaphila species
 PHASED-DATA-mafft-nexus-notrim-keepambiguous: alignments of phased loci
 PHASED-DATA-mafft-nexus-notrim-keepambiguous-clean: alignments of phased
 loci with UCE names removed
 PHASED-DATA-mafft-nexus-notrim-keepambiguous-min-75p-taxa: loci with
 minimum locus occupancy 75%
 PHASED-DATA-mafft-nexus-notrim-keepambiguous-min-75p-taxa-trimal-strict:
 data masked with trimal strict
 PHASED-DATA-mafft-nexus-notrim-keepambiguous-clean-min-75p-taxa-trimal-strict-randSNP1-5-concat: random SNP sets, concatenated PHASED-DATA-mafft-nexus-notrim-keepambiguous-min-95p-taxa: loci with minimum locus occupancy 95% PHASED-DATA-mafft-nexus-notrim-keepambiguous-min-95p-taxa-trimal-strict: data masked with trimal strict PHASED-DATA-mafft-nexus-notrim-keepambiguous-clean-min-95p-taxa-trimal-strict-randSNP1-5-concat: random SNP sets, concatenated Pclathrata_only: data for Promyrmekiaphila clathrata lineages PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous: alignments of phased loci PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous-clean: alignments of phased loci with UCE names removed PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous-clean-min-75p-taxa: loci with minimum locus occupancy 75% PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous-clean-min-75p-taxa-trimal-strict: data masked with trimal strict PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous-clean-min-75p-taxa-trimal-strict-randSNP1-5-concat: random SNP sets, concatenated PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous-clean-min-95p-taxa: loci with minimum locus occupancy 95% PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous-clean-min-95p-taxa-trimal-strict: data masked with trimal strict PHASED-DATA-clathrata-mafft-nexus-notrim-keepambiguous-clean-min-95p-taxa-trimal-strict-randSNP1-5-concat: random SNP sets, concatenated Folder: Trees Results of phylogenetic analyses COI_iqtree: dataset file, partition file, resulting maximum likelihood tree with bootstrap scores, iqtree info file Concatenated_iqtree: concatenated dataset files, partition files, resulting maximum likelihood tree with bootstrap scores, iqtree info file min75p: minimum 75% locus occupancy min95p: minimum 95% locus occupancy Gene_trees: individual locus gene trees from maximum likelihood analyses of minimum 75% and 95% locus occupancy datasets MSC_astral_bootstrap: bootstrap replicate trees from ASTRAL from minimum 75% and 95% locus occupancy datasets Folder: CLADES_data datasets for CLADES analysis: minimum locus occupancy 95%, phased Pclathrata: alpha and beta hypothesis test sequence alignments file: PromyclathClades3msc_seq species assignment: Promyclathrata_CLADES_pop_assign Pclathrata_alpha: alpha lineages hypothesis test sequence alignments file: PromyclathgroupcClades1msc_seq species assignment: Promyclathrata_CLADES_pop_assign Pclathrata_beta: beta lineages hypothesis test sequence alignments file: PromyclathgroupdClades1msc_seq species assignment: Promyclathrata_CLADES_pop_assign Folder: Gene flow datasets for D3 and 3s gene flow analyses PwiseDist_Pro_noOut_HKYdists_7Nov2023 (D3): Table with pairwise distances, based on neighbor joining tree with HKY model. Distances were calculated in Geneious Pro from the concatenated dataset. D3 statistic (Hahn and Hibbins, 2019) calculation based on average distances calculated. Empty cells are intentionally left blank and are null. 3s folder: Locus files: Promy_3sG1_AllLoci.phylip, Promy_3sG2_AllLoci.phylip Control files: Promy_Group1_3s.ctl, Promy_Group2_3s.ctl Outputs from 3s analyses: Promy_G1_Run6-8_k16.out, Promy_G2_Run4-6_k16.out