CoachGenes in two species descended from one gene in their common ancestor are orthologues; genes within a species descended from a duplication are paralogues. Blocks of chromosome in which gene order is conserved between species are syntenic; synteny lets a gene be located in one genome from its position in another and reveals the rearrangements that separate two karyotypes (about between human and mouse). Sequences conserved across distant species that code for no protein — conserved non-coding elements, some ultraconserved to the base over between human and fish — are mostly enhancers of developmental genes. Whole-genome duplications have marked the history of lineages: two rounds at the origin of vertebrates (the four Hox clusters of mammals against the one of invertebrates), one in the ancestor of salmonids, one in the yeast lineage, several in flowering plants; the duplicate genes are mostly lost over tens of millions of years, and the survivors diverge in function.
Examples
Example 4.10 (Human and chimpanzee)
Aligned single-copy sequence differs between human and chimpanzee by of bases — some million substitutions — and by insertions and deletions that together amount to another of each genome. Two humans differ at about one base in a thousand, some million sites, plus a few thousand structural variants; two chimpanzees, whose population has been larger for longer, at rather more. A child carries about new mutations absent from both parents, four fifths of them from the father, and the number rises by about two per year of paternal age — the arithmetic of Chapter 3 applied to the many divisions of spermatogenesis.