DOI: 10.5061/dryad.mw6m9064s
title: Comparative population genomic diversity and differentiation in trapdoor spiders and relatives (Araneae, Mygalomorphae)

description: Although patterns of population genomic variation are well-studied in
 animals, there remains room for studies that focus on non-model taxa with
 unique biologies. Here we characterize and attempt to explain such
 patterns in mygalomorph spiders, which are generally sedentary, often
 occur as spatially clustered demes, and show remarkable longevity.
 Genome-wide SNP data was collected for 500 individuals across a
 phylogenetically representative sample of taxa. We inferred genetic
 populations within focal taxa using a phylogenetically-informed clustering
 approach, and characterized patterns of diversity and differentiation,
 within- and among these genetic populations, respectively. Using
 phylogenetic comparative methods we asked whether geographic range sizes
 and ecomorphological variables (behavioral niche and body size)
 significantly explain patterns of diversity and differentiation.
 Specifically, we predicted higher genetic diversity in genetic populations
 with larger geographic ranges, and in small-bodied taxa. We also predicted
 greater genetic differentiation in small-bodied taxa, and in burrowing
 taxa. We recovered several significant predictors of genetic diversity,
 but not genetic differentiation. However, we found generally high
 differentiation across genetic populations for all focal taxa, and a
 consistent signal for isolation by distance irrespective of behavioral
 niche or body size. We hypothesize that high population genetic
 structuring, likely reflecting combined dispersal limitation and
 microhabitat specificity, is a shared trait for all mygalomorphs. Few
 studies have found ubiquitous genetic structuring for an entire ancient
 and species-rich animal clade.
description: # Comparative population genomic diversity and differentiation in trapdoor
 spiders and relatives (Araneae, Mygalomorphae) --- **Article Citation:**
 Monjaraz-Ruedas, R., Starret, J., Newton, L., Bond, J., Hedin, M. (YEAR).
 Comparative population genomic diversity and differentiation in trapdoor
 spiders and relatives (Araneae, Mygalomorphae). *Molecular Ecology*
 **Authors:** Rodrigo Monjaraz-Ruedas, James Starrett, Lacie Newton, Jason
 Bond, Marshal Hedin **Overview:** Here we characterize and explain
 patterns of population genomic variation in mygalomorph spiders. Using
 phylogenetic comparative methods we asked whether geographic range sizes
 and ecomorphological variables (behavioral niche and body size)
 significantly explain patterns of diversity and differentiation. This
 repository contains input data, output files, SNP data, and scripts used
 for analyses described in detail in the Methods section of the manuscript.
 **Contact:** For questions or issues related to the code, data, and
 analysis: Rodrigo Monjaraz-Ruedas -
 [monroderik@gmail.com](mailto:monroderik@gmail.com) --- ## Folder
 structure ``` . ├── PGLS ├── Pop_Files ├── Scripts ├── Trees │ ├──
 Astral_Tree │ ├── Iqtree_Trees │ └── Time-Calibrated │ └── Mygals-80p ├──
 VCFs │ ├── Apomastus │ ├── Apto │ ├── Athompi │ ├── Atypo │ ├── Bothrio │
 ├── Casoga │ ├── Hapachea │ ├── Megahex │ └── Microhex └── Pixy_Output ```
 --- ## Description #### Data Raw UCE data is deposited under BioProject
 PRJNA1157860 on the GenBank SRA repository. #### PGLS Input files needed
 for running PGLS analyses. * Range Size is provided in squared Kilometers
 * Abbreviations: * PGLS, Phylogenetic generalised least squares * Ave,
 Average * Pop, Population * pi, Genetic diversity #### Pop\_Files Input
 files containing Metadata information associated with VCF files, including
 Sample name, Population name, Latitude, and Longitude. * Abbreviations *
 Lat, Latitude * Lon, Longitude * Pop, population #### Scripts Script used
 for multiple analyses. #### Trees Tree files and log files obtained across
 multiple phylogenetic analyses. * ASTRAL -&gt; Log output file, newick
 file with gene trees and, newick file with ASTRAL tree. * IQ-TREE -&gt;
 Newick tree files for every focal taxon. * Time-Calibrated -&gt; Input
 files, configuration files and alignments (Mygals-80p) needed to replicate
 LSD2 analysis. #### VCFs VCF files per focal taxa, including All_Sites,
 Filtered, and Biallelic SNPs and their respective Reference fasta file.
 #### Pixy\_Output Folder containing the output file of the pixi runs, used
 for getting summary statistics with the script `Summarize_pixy_stats.R`