Every cell has all the genes necessary to become any cell. How each cell "knows" which genes to actually use (to be expressed, is the usual expression,) was generally labeled cellular differentiation. Hox (short for homeobox) genes were discovered to play a role in development of the organism from the zygote. And it was discovered that the hox genes were found in numerous very different species, in a highly conserved form. Embryological evidence was always a major source of evidence for evolution. This discovery added the power of modern genetics to the study of evolution and the use of evolutionary theory to explain embryological development. Sean B. Carroll's Endless Forms Most Beautiful aims to bring these developments (nicknamed Evo Devo) to the general
There is a plate with photos of homo sapiens sapiens and homo sapiens neanderthalensis skulls.
The text takes the now prevalent view that they were different species. There is a table whose caption includes the word "homonin." The orthodox spelling, used in the text, of course is hominin. There is a diagrams of the developmental tool kit with terms that are unidentified in the text. The distinctions between Hox genes, the homeodomains, genetic switches and so forth I think are clear in Dr. Carroll's mind but not clear in the text, at least not for me. Copy number variants are not discussed. As I recall, the number of chromosomes in chimpanzees is different from the number of chromosomes in human beings. But this goes unmentioned in the chapter on human evolution. There is no discussion of chromosome structure at all. That was odd enough in Molecular Biology of the Gene which I read thirty years ago. It is entirely inappropriate in this context. As I don't recall, the word "intron" is not used at all, while it too should have a clear explication in this context.
I'm usually fairly good at following explanations. At the worst, usually, I can spot the sentences and paragraphs where I get lost. But I can't follow this. Given the gross errors in editing, I believe the problem is that Dr. Carroll got no editorial assistance worthy of the name. I must suggest avoiding this book unless you already know a fair amount on the subject. Then perhaps you can fill in the blanks and appreciate the new material. It is a real shame because it is clear that Carrol had original research insights to share.