Extended Data Fig. 2: Mammalian genome evolution.

a, Phylogenetic tree constructed using fourfold degenerate sites from 7,946 one-to-one orthologues among seven representative species (human, mouse, opossum, platypus, echidna, chicken and green lizard). The fossil time calibration of the nodes marked by circles were obtained from a previously published study⁶⁷. The numbers of gene families that have undergone significant (Viterbi P < 0.05) lineage-specific expansions (green) and contractions (red) are marked on each branch. Exact P values are available in Supplementary Table 29. No multiple-testing correction was applied. b, Examples of some imprinting gene clusters improved in mOrnAna1 compared to OANA5. The first line of each synteny plot represents mOrnAna1 and the second line represents OANA5. Names of genes that have been found to be imprinted in human and mouse are highlighted in black, and non-imprinting genes in red. Fragmented genes with alignment rate lower than 70% are marked by triangles. The double slash represents the intermediate region longer than 100 kb. c, Distribution of MSHCEs on genomic elements. d, Enriched GO terms in the top-300 MSHCE-associated genes. P values of enrichment are calculated using a χ² test, and FDRs are computed to adjust for multiple testing. GO terms are clustered based on semantic similarity. GO terms related to nervous system development are highlighted in bold. e, A case of one MSHCE in BCL11A that overlaps with the enhancer signals inferred from H3K27ac ChIP-seq experiments at 8.5 and 12 weeks after conception (p.c.w.). f, Evolution highway comparative chromosome browser visualization of reconstructed MACs at a 500-kb resolution. Blocks overlaid on each MAC represent human syntenic fragments. Numbers within blocks indicate the homologous human chromosome. g, Evolution highway comparative chromosome browser visualization of the human genome at a 500-kb resolution, with each block overlaid on each human chromosome representing putative chromosome fragments of the ancestral mammalian genome. Numbers within blocks depict the ancestral mammal chromosome numbers. Silhouettes of the human and opossum are from https://www.flaticon.com/. The silhouette of the platypus is created by S. Werning and is reproduced under a Creative Commons Attribution 3.0 Unported licence (http://creativecommons.org/licenses/by/3.0/).