Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.)
Data files
Jan 17, 2024 version files 1.41 GB
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Dryad_Data_Promyrmekiaphila_Starrettetal2023.zip
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README.md
Abstract
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.
README: 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