Canine transmissible venereal tumor genome reveals ancient introgression from coyotes to pre-contact dogs in North America

摘要

a Bar plot showing the contributions of the signatures to genome sample mutation counts. b Heatmap showing exposures in each genome sample. Samples are grouped according to their levels of exposure to the signatures, as can be seen in the dendrogram on the left. Samples labeled by asterisks are exceptions in the group. c A flowchart of the pipeline from genotyping of each tumor to classification of loci. d Approximate maximum-likelihood tree. All samples are colored according to the geographical groups. Node labels indicate bootstrap values. e Principal component analysis of 102 individuals (excluding golden jackals). Different geographical groups are colored differently. f Heatmap of outgroup f3-statistics of the form f3(CTVT founder, Pop2; Coyote), where Pop2 represents 69 dogs in the reference panel. Higher f3 values (warm-toned points) indicate increased genetic drift shared between samples, and therefore higher genetic similarity between the CTVT founder and Pop2 sample. g CNV profiles of five CTVTs and coyote introgressed regions in genome of the CTVT founder. Starting from the outer circle and moving to inner circles, each circle shows copy number profiles for T.KM2, T.KM1, T.609, T.79, and T.24, a chromosome ideogram, loci sharing with coyote diagnostic alleles (orange), coyote diagnostic allele positions (blue), two haplotypes of RFMix results (gray, Arctic sled dogs’ ancestry; blue, New World wolves’ ancestry; red, coyotes’ ancestry), fdM-statistics in 500 kb windows by 250 kb step size for sliding window (blue, top 1% negative windows), fd- statistics in 500 kb windows by 250 kb step size for sliding window (red, top 1% negative windows), D-statistics in 500 kb windows by 250 kb step size for sliding window (green, negative value). The red reference axis in the 5 outer circles represents the status of diploidy. Data are plotted using circos.15h The maximum-likelihood graph based on TreeMix with m = 3. The scale bar shows ten times the average standard error of the entries in the sample covariance matrix. Weighted colorful arrows indicate relative migration ratio and direction. GDJ, golden jackals; CYT, coyotes; NWW, New World wolves; OWW, Old World wolves; TMR, Taimyr wolf; PCD, pre-contact dogs; ASD, Arctic sled dogs; EAD, East Asia dogs; NCD, Northern China dogs; IPD, India Peninsula dogs; MECAD, Middle East and Central Asia dogs; AFD, African dogs; MSD, mixed sled dogs; EUD, European dogs; NGD, Newgrange dog; HXH, Herxheim dog; CTC, Cherry Tree Cave dog; SIH, Siberian Husky; ALH, Alaskan Husky; ALM, Alaskan Malamute; GRD, Greenland dog; ESL, East Siberian Laika; SAM, Samoyed; CTVT_I, CTVT intersected with panel’s SNPs; CTVT_P, CTVT private alleles; CTVT_F, the CTVT founder