Lineage-specific conservation of regulatory regions (Table S4 ) was determined for primates, rodents, ungulates, and carnivores using a similar strategy as that for highly conserved elements (Figure 6 ). ChIP-seq enriched regions were compared between a reference species (human, mouse, cow, and dog) and other species in the clade using either the EPO multiple alignment when possible or pairwise Lastz alignments otherwise. Elements functionally conserved across the high-quality genomes in each lineage, but not in any other species, were identified for each histone mark (i.e., in human, macaque, and marmoset for primates; mouse, rat, and rabbit for rodents; cow and pig for ungulates; and dog and cat for carnivores). These were then categorised into lineage-specific promoters and enhancers based on their dominant histone mark enrichment across species within the clade, as described above.
Recently evolved promoters and enhancers were determined for a reference species in each lineage (human, mouse, cow, and dog). Enriched regions in the reference species that showed functional conservation in any alignable species were discarded. The number of species that were used for comparison with each reference species was 18 (human), 12 (mouse), 12 (cow) and 10 (dog). These include: (1) nine species in the 13 eutherian mammals EPO multiple alignment, (2) other species within the clade, evaluated with ad hoc LastZ pairwise alignments with the reference species (e.g., mouse-guinea pig, mouse-naked mole rat and mouse-tree shrew) and (3) all other species but naked mole rat for human, using pairwise LastZ alignments. Recently evolved elements were then categorised into promoters and enhancers by overlapping the two histone marks in each reference species.
Recently evolved elements were similarly identified for two non-reference species (naked mole rat and dolphin). When the number of genomic alignments available for a species was small (e.g., for dolphin, only alignments with human and cow were available), we additionally mapped the promoters and enhancers of the species of interest to their orthologous locations in the reference species of its clade (in this case, cow) and tested whether they correspond to marked regions in any other species in the EPO alignment.
Recently evolved promoters and enhancers were determined for a reference species in each lineage (human, mouse, cow, and dog). Enriched regions in the reference species that showed functional conservation in any alignable species were discarded. The number of species that were used for comparison with each reference species was 18 (human), 12 (mouse), 12 (cow) and 10 (dog). These include: (1) nine species in the 13 eutherian mammals EPO multiple alignment, (2) other species within the clade, evaluated with ad hoc LastZ pairwise alignments with the reference species (e.g., mouse-guinea pig, mouse-naked mole rat and mouse-tree shrew) and (3) all other species but naked mole rat for human, using pairwise LastZ alignments. Recently evolved elements were then categorised into promoters and enhancers by overlapping the two histone marks in each reference species.
Recently evolved elements were similarly identified for two non-reference species (naked mole rat and dolphin). When the number of genomic alignments available for a species was small (e.g., for dolphin, only alignments with human and cow were available), we additionally mapped the promoters and enhancers of the species of interest to their orthologous locations in the reference species of its clade (in this case, cow) and tested whether they correspond to marked regions in any other species in the EPO alignment.
Free full text: Click here
