Data from: A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees
Abstract
Retrophylogenomics makes use of genome-wide retrotransposon presence/absence insertion patterns to resolve questions in phylogeny and population genetics. In the genomics era, evaluating high-throughput data requires the associated development of appropriately powerful statistical tools. The currently used KKSC 3-lineage statistical test for estimating the significance of retrophylogenomic data is limited by the number of possible tree topologies it can assess in one step. To improve on this, we have extended the analysis to simultaneously compare 4-lineages, enabling us to evaluate ten distinct presence/absence insertion patterns for 26 possible tree topologies plus 129 trees with different incidences of hybridization or introgression. The new tool provides statistics for cases involving multiple ancestral hybridizations/introgressions, ancestral incomplete lineage sorting, bifurcation, and polytomy. The test is embedded in a user-friendly web R-application (http://retrogenomics.uni-muenster.de:3838/hammlet/) and is available for use by the scientific community.
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Sources of genomes used and RepeatMasker reports. Great ape phylogenetic project ............................................................................................................ 1 Dog lineage diversification project ........................................................................................................ 2 Mouse strains project. .......................................................................................................................... 3 Great ape phylogenetic project Homo sapiens Genome: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz RepeatMasker report: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.out.gz Pan troglodytes Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/880/755/GCA_002880755.3_Clint_PTRv2/GCA_002880755.3_Cli nt_PTRv2_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/880/755/GCA_002880755.3_Clint_PTRv2/GCA_002880755.3_Cli nt_PTRv2_rm.out.gz Pan paniscus Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/258/655/GCA_000258655.2_panpan1.1/GCA_000258655.2_pan pan1.1_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/258/655/GCA_000258655.2_panpan1.1/GCA_000258655.2_pan pan1.1_rm.out.gz Gorilla gorilla Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/151/905/GCA_000151905.3_gorGor4/GCA_000151905.3_gorGor 4_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/151/905/GCA_000151905.3_gorGor4/GCA_000151905.3_gorGor 4_rm.out.gz Pongo abelii Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/880/775/GCF_002880775.1_Susie_PABv2/GCF_002880775.1_Sus ie_PABv2_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/880/775/GCF_002880775.1_Susie_PABv2/GCF_002880775.1_Sus ie_PABv2_rm.out.gz
Dog lineage diversification project Boxer Genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/285/GCA_000002285.2_CanFam3.1/GCA_000002285.2_C anFam3.1_genomic.fna.gz RepeatMasker report: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/285/GCA_000002285.2_CanFam3.1/GCA_000002285.2_C anFam3.1_rm.out.gz Beagle Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/331/495/GCA_000331495.1_Beagle/GCA_000331495.1_Beagle_ genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/331/495/GCA_000331495.1_Beagle/GCA_000331495.1_Beagle_ rm.out.gz Gray Wolf Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/922/845/GCA_007922845.1_UniMelb_Wolf_Refassem _1/GCA_007922845.1_UniMelb_Wolf_Refassem_1_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/922/845/GCA_007922845.1_UniMelb_Wolf_Refassem_1/GCA_0 07922845.1_UniMelb_Wolf_Refassem_1.rm.out.gz German shepherd Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/641/055/GCA_008641055.1_ASM864105v1/GCA_008641055.1_ ASM864105v1_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/641/055/GCA_008641055.1_ASM864105v1/GCA_008641055.1_ ASM864105v1_rm.out.gz
Mouse strains project. CBA/J Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/624/475/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_ J_v1_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/624/475/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_ J_v1_rm.out.gz C57BL/6J Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/774/525/GCA_003774525.2_ASM377452v2/GCA_003774525.2_ ASM377452v2_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/774/525/GCA_003774525.2_ASM377452v2/GCA_003774525.2_ ASM377452v2_rm.out.gz BALB/cJ Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/632/525/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BA LB_cJ_v1_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/632/525/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BA LB_cJ_v1_rm.out.gz DBA/2J Genome: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/624/505/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DB A_2J_v1_genomic.fna.gz RepeatMasker report: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/624/505/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DB A_2J_v1_rm.out.gz