KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited Data
NCBI Sequence Read Archive: RNAseq data, ATACseq data, low coverage fastq files, ACUA time series fastq files	This paper	SUB8614498 (pending)
Dryad: qPCR data, local ancestry calls, phenotype data	This paper	doi:10.5061/dryad.c2fqz616p (pending)
Experimental Models: Organisms/Strains
Artificial crosses	Offspring generated from wild caught parental species	N/A
Hybrid population data	Wild caught samples	N/A
Oligonucleotides
Primer: sp8_for: ACACTTGAGGACGCACAGTT sp8_rev: CTGTTTTTCCGCCGGTCTCT	This paper	N/A
Primer: grn2_for: GGGAAGTGGGAACCTTGTG grn2_rev: CACAGCCACACAGTCATCCT	This paper	N/A
Software and Algorithms
Admix’em	69	https://github.com/melop/admixem
R/qtl	33	https://rqtl.org
ImageJ	66	https://imagej.nih.gov/ij/download.html
ancestryinfer	30	https://github.com/Schumerlab/ancestryinfer
mixnmatch	30	https://github.com/Schumerlab/mixnmatch
MUMmer	70	https://github.com/mummer4/mummer
TrimGalore!	76	https://github.com/FelixKrueger/TrimGalore
DESeq2	77	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
‘ashr’	78	https://github.com/stephens999/ashr
WASP	79	https://github.com/bmvdgeijn/WASP
bowtie	82	http://bowtie-bio.sourceforge.net/index.shtml
samtools	81	http://www.htslib.org/download/
HOMER	83	http://homer.ucsd.edu/homer/
DiffBind	84	https://bioconductor.org/packages/release/bioc/html/DiffBind.html
PAML	89	http://abacus.gene.ucl.ac.uk/software/paml.html
SIFT	42	https://sift.bii.a-star.edu.sg
bwa	94	http://bio-bwa.sourceforge.net
GATK	95	https://gatk.broadinstitute.org/hc/en-us
RAxML	96	https://github.com/stamatak/standard-RAxML
FIMO	92	http://meme-suite.org/doc/fimo.html
PhyloNet-HMM	48	https://bioinfocs.rice.edu/software/phmm
SLiM	97	https://messerlab.org/slim/