Figure 2. Phylogeny of the subfamily Caprinae in the mitochondrial and genomic level.
(a) Takin was closely related to goat clade, but far to muskox in the mitochondrial genomic level. The neighbor-joining (NJ) method with 1000 bootstrap replicates using MEGA (v11) (Tamura et al. 2021);(b) Takin was most closely related to muskox in the genomic level. 5862 single-copy homologous genes were used to construct the phylogenetic tree by RAxML (v8.2.12) with Maximum Likelihood (ML) method. The divergence time were calculated using PAML (v4.9j) with calibrated from divergence time of goat and sheep (3.9-8.1Mya) (Chen et al. 2019). The estimated divergence time (Mya) was marked on each node (95% confidence intervals).
Figure 3. Reconstruction of ancestral chromosomes of cattle, goat, sheep and takin.
(a) The distribution of ancestral chromosome segments in the genomes of cattle, goat, sheep and takin, including chromosome fission and fusion events. The asterisks represent chromosome fission events;(b) The collinear relationship of takin, sheep and cattle. Sperm whale as outgroup.