Fig. 3

Organization of ancestral Amniota CARs in tetrads (a) Circos plot [45] showing the pairs of ohnologs involving each of the four chromosomes (Homo sapiens) or CARs (Amniota) of the tetrad carrying the Hox genes (Tetrad 1 in D). The pairs of ohnologs in the human genome were the descendants of those of Amniota (6121 pairs of human ohnologs vs. 7441 pairs of amniote ohnologs). The human Hox cluster tetrad is mainly composed of human chromosomes 2, 7, 12, and 17. The Amniota Hox cluster tetrad is composed of CARs 108, 24, 99, and 6_39_140. An ohnolog pair is represented (green lines) between two Amniota CARs or two human chromosomes if at least one of the two genes of the pair falls on a chromosome/CAR of the tetrad. The Amniota Hox CARs are involved in 634 pairs, while the human Hox chromosomes are involved in 2171 pairs of ohnologs. This figure shows that the reconstruction of Amniota ancestor displays a clearer picture of the 1R-2R than the human genome. (b) Ohnolog partners per CAR/chromosome in the Amniota (left) and human (right) genomes. Each boxplot shows the distribution of the number of CARs (Amniota) or chromosomes (Human) found to be ohnologous to a given CAR/chromosome by the proportionality test. The x-axis shows the Bonferroni adjusted p value thresholds used to select ohnologous chromosome/CARs. Triangles indicate the average number of partners. The Amniota genome shows a clear and stable distribution of three partners per CAR across a wide range of p values, as expected after two WGDs where chromosomes are grouped in tetrads. In contrast, the distribution in Homo sapiens shows that extremely low p value thresholds must be used to reach the expected average of three partners, justifying the fragmentation of the human genome as described in [6]. (c) Example of how a group of significantly ohnologous CARs was analyzed to form tetrad 3. Black double-headed arrows (p value < 5.10⁻² after Bonferroni adjustment) represent the raw output of the proportion test, showing CARs with significant ohnology relationships. CARs 73, 117, and 250 form a triad of mutually ohnologous CARs. Dotted lines are additional ohnologous relationships that are supported without the Bonferroni adjustment. Numbers in black indicate CARs of at least 50 genes, while smaller CARs (< 50 genes) are in grey. Additional evidence (see text) was used to complete the tetrad. (d) Seventeen tetrads composed of 51 CARs. CARs are numbered arbitrarily and are joined by underscores in an arbitrary order when assembled. The letters “a” or “b” indicate that the CAR has been split in two segments (CARs 5 and 118) as part of the conversion to a post-2R karyotype (see text) and one CAR is present twice in two different tetrads (CAR 10_240_2) to facilitate the representation (pale yellow shapes)