DOI: 10.5068/d1z404
title: Ancient introgression between distantly related white oaks (Quercus sect Quercus) shows evidence of climate-associated asymmetric gene exchange

description: Ancient introgression can be an important source of
 genetic variation that shapes the evolution and diversification of many
 taxa. Here, we estimate the timing, direction and extent of gene flow
 between two distantly related oak species in the same section
 (Quercus sect. Quercus). We estimated these demographic
 events using genotyping by sequencing data (GBS), which generated 25,702
 single nucleotide polymorphisms (SNPs) for 24 individuals of California
 scrub oak (Quercus berberidifolia) and 23 individuals of Engelmann oak (Q.
 engelmannii). We tested several scenarios involving gene flow between
 these species using the diffusion approximation-based population genetic
 inference framework and model-testing approach of the Python
 package DaDi. We found that the most likely demographic scenario
 includes a bottleneck in Q. engelmannii that coincides
 with asymmetric gene flow from Q.
 berberidifolia into Q. engelmannii. Given that the
 timing of this gene flow coincides with the advent of a Mediterranean-type
 climate in the California Floristic Province, we propose that changing
 precipitation patterns and seasonality may have favored the introgression
 of climate-associated genes from the endemic into the non-endemic
 California oak. 
description: Leaf tissue was collected from mature individuals of
 both <em>Quercus engelmannii </em>and <em>Q.
 berberidifolia</em> during the summer of 2017. Tissue was collected
 from two individuals per site at 12 unique sites per species (24 total
 sites, 48 total individuals). Leaf tissue was flash frozen in liquid
 nitrogen in lab and ground with a mortar and pestle into a fine powder.
 DNA was extracted following a modified Qiagen DNEasy plant kit
 protocol. DNA was prepared using GBS sequencing
 protocols (Elshire<i>, et al.</i>, 2011) including a bead
 clean up step to ensure proper sized fragments. Libraries were sequenced
 at the Technology Center for Genomics and Bioinformatics at the University
 of California, Los Angeles on an Illumina Hiseq3000 (Illumina Inc. 5200
 Illumina Way San Diego, CA) in August of 2017. To equalize coverage
 between species, samples were re-sequenced in July 2018. Samples were
 sequenced using two lanes (48 samples per lane) and the combined sequence
 data for each individual was used for this project. Each individual
 library was sequenced 2-3 times. Sequences were filtered for quality and
 sequencing depth and aligned to the <i>Quercus lobata
 v.3.0 </i>reference genome. SNPs were called from the aligned reads
 using GATK.
description: Raw sequence reads are included in the folders GBS1_2017 for the
 initial sequencing run and in GBS2_2018 for any subsequent resequencing
 performed on the same libraries. Each individual has up to 3 raw sequence
 files that were mapped to the Quercus lobata v.3.0 reference genome
 then combined in order to call SNPs for the final analysis.
 Called variants for each individual are compiled in
 GBS_Variants.vcf  Final variants used in analysis after
 filtering for linkage disequilibrium are compiled in
 PW_Filter_2018.vcf