REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Tango Buffer (10X)	ThermoFisher Scientific	Cat#BY5
ATP (100mM)	ThermoFisher Scientific	Cat#R0441
T4 Polynucleotide Kinase (10U/ul)	ThermoFisher Scientific	Cat#EK0032
T4 DNA Polymerase 5U/ul	ThermoFisher Scientific	Cat#EP0062
USER Enzyme	NEB	Cat#M5505L
T4 DNA Ligase (5U/ul)	ThermoFisher Scientific	Cat#EL0011
Bst Polymerase, Large Fragments	NEB	Cat#M0275S
AccuPrime Pfx	ThermoFisher Scientific	Cat#12344024
T4 DNA ligase (400U/ul)	NEB	Cat#M0202S
T4 DNA polymerase (3U/ul)	NEB	Cat#M0203S
PEG-4000	Sigma-Aldrich	Cat#95904-250G-F
Critical commercial assays
High Sensitivity DNA kit	Agilent	Cat#5067-4626
DNeasy Blood & Tissue Kit	QIAGEN, Hilden, Germany	Cat#69504
Deposited data
Raw fastq reads	This study	Historical resequencing data: ENA:PRJEB35522; modern resequencing data: https://repo.data.nesi.org.nz/TAONGA-KAKAPO
de-novo assembly for Strigops habroptilus	This study	GenBank: GCF_004027225.2 and GCA_004011185.1; https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/027/225/GCF_004027225.2_bStrHab1.2.pri/GCF_004027225.2_bStrHab1.2.pri_genomic.fna.gz
Oligonucleotides
IS1 adaptor P5: 5′- A∗C∗A∗C∗TCTTTCCCTACACG ACGCTCTTCCG∗A∗T∗C∗T-3′	Meyer and Kircher34; Sigma-Aldrich	N/A
IS2 adaptor P7: 5′- G∗T∗G∗A∗CTGGAGTTCAGAC GTGTGCTCTTCCG∗A∗T∗C∗T-3′	Meyer and Kircher37; Sigma-Aldrich	N/A
IS3 adaptor P5+P7: 5′- A∗G∗A∗T∗CGGAA∗G∗A∗G∗C-3′	Meyer and Kircher37; Sigma-Aldrich	N/A
Illumina AmplifyingPrimer IS4: 5′- AATGATACGGCG ACCACCGAGATCTACACTCTTTCCCTACACGACG CTCTT-3′	Meyer and Kircher37; Sigma-Aldrich	N/A
Illumina Indexing Primer: 5′- CAAGCAGAAGACGGC ATACGAGATNNNNNNNGTGACTGGAGTTCAGAC GTGT-3′	Meyer and Kircher37; Sigma-Aldrich	N/A
Ns represent indexes		N/A
Software and algorithms
VGP pipeline	Rhie et al.18	https://vertebrategenomesproject.org/
BLAST+ 2.5.0	Camacho et al.35	NCBI
Qualimap v2.2.1	Okonechnikov et al.36	http://qualimap.bioinfo.cipf.es/
CpG site masking script	von Seth et al.14; Lord et al.37	https://github.com/tvdvalk/find_CpG
RepeatMasker v4.0.7	Smit et al.38	http://repeatmasker.org
MESPA pipeline	Neethiraj et al.39	https://sourceforge.net/projects/mespa/
BRAKER v2.1.1	Hoff et al.40; Stanke et al.41,42	https://github.com/Gaius-Augustus/BRAKER
SPALN2	Iwata and Gotoh43	https://github.com/ogotoh/spaln
cufflinks v 2.2.1	Trapnell et al.44; Roberts et al.45	http://cole-trapnell-lab.github.io/cufflinks/
eggNOG-mapper v4.5.1	Huerta-Cepas et al.46	http://eggnog-mapper.embl.de/
bcl2Fastq v1.17.1	Illumina	https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
SeqPrep	John47	https://github.com/jstjohn/SeqPrep
BWA v0.7.13	Li and Durbin48	http://bio-bwa.sourceforge.net/
SAMtools v1.3	Li et al.49	https://sourceforge.net/projects/samtools/files/samtools/1.3/
Picard v1.141	Broad Institute	http://broadinstitute.github.io/picard
Mapdamage v2.0	Jónsson et al.50	https://ginolhac.github.io/mapDamage/
Trimmomatic v0.32	Bolger et al.51	http://www.usadellab.org/cms/?page=trimmomatic
GATK v3.4.0	McKenna et al.52	https://gatk.broadinstitute.org/hc/en-us
bcftools v1.3	Li53	http://www.htslib.org/
BEDtools v2.29.2	Quinlan and Hall54	https://bedtools.readthedocs.io/en/latest/
PLINK v1.9	Purcell et al.55	https://www.cog-genomics.org/plink2/
SNPRelate	Zheng et al.56	https://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html
ADMIXTURE v1.3.0	Alexander et al.57	http://dalexander.github.io/admixture/publications.html
RapidNJ v2.3.2	Simonsen et al.58	https://anaconda.org/bioconda/rapidnj
Timetree	Kumar et al.68	http://timetree.org/
PSMC v0.6.5	Li and Durbin21	https://github.com/lh3/psmc
Fastsimcoal v2.6	Excoffier and Foll 59; Excoffier et al.60	http://cmpg.unibe.ch/software/fastsimcoal2/
PGDspider	Lischer and Excoffier61	http://www.cmpg.unibe.ch/software/PGDSpider/
Arlequin v3.5	Excoffier and Lischer62	http://cmpg.unibe.ch/software/arlequin35/
MSMC2	Schiffels and Wang 63	https://github.com/stschiff/msmc2
Beagle v5.1	Browning and Browning64	https://faculty.washington.edu/browning/beagle/beagle.html
vcftools	Danecek65	http://vcftools.sourceforge.net/
mlRho v2.7	Haubold et al.66	http://guanine.evolbio.mpg.de/mlRho/
R	R Development Core Team84	https://www.r-project.org/
GERP++	Davydov et al.67	http://mendel.stanford.edu/sidowlab/downloads/gerp/index.html
htsbox v1.0	N/A	https://github.com/lh3/htsbox
SNPeff v4.3	Cingolani et al.68	http://snpeff.sourceforge.net/index.html
Pilon v1.22	Walker et al.69	https://github.com/broadinstitute/pilon/releases/tag/v1.22
Panther v16.0	Mi et al.70	http://www.pantherdb.org/
SLiM 3	Haller and Messer71; Kim et al.72	https://messerlab.org/slim/
Other
Proteinase K	VWR	Cat#1.24568.0100
dNTPs	VWR	Cat#733-1854
Min Elute PCR purification Kit	QIAGEN	Cat#28006
Agencourt AmPure XP 5mL Kit	Beckman Coulter	Cat#63880