A word on “junk DNA” and other such things (from a geneticist in training.)
The majority of padding DNA (intergenic stretches) in mammals is defunct retroviral repeats. In mice, there are LINEs and SINEs, in humans there are huge stretches of Alu repeats. This low complexity DNA cannot even be sequenced through given our current technology. Another part of padding DNA consists of other even lower complexity DNA – simple repeat sequences that form a structural component, especially around the centers and ends of chromosomes. Collectively, repetitive sequence is called heterochromatin.
Large scale sequencing depends on recognizing overlaps to construct a long “contig” out of many short (1 kilobase) DNA sequencing reactions. If you have 30,000 base pairs of Alu, there just ain’t any way to get through it. It would be like assembling a jigsaw puzzle which is completely blue, made of identical pieces. There is a strict definition of when you are finished sequencing a genome, a this does not require sequencing heterochromatin. So we are left with large contigs of relevant DNA that are separated by unsequencable regions. I’m pretty sure that the vast majority of Alu repeat does nothing except act as genetic silencers between genes, and structural DNA is important to preserve chromatin integrity, but it can take huge hits before that function is compromised.
Evolutionary pressures on a nucleotide level are on totally different levels between these sequences and genic regions. It is probable that a few million years of evolution could produce all kinds of neutral changes in heterochromatin while leaving the genic regions mostly intact. In fact, 95% conservation for all DNA (including presumably heterochromatin) is a startlingly high number, given what I see in the fruit fly between two sister species that diverged within the past 20 million years (and still have limited interfertility). We include things in the Drosophila genus with over 60 million years of evolution between them – the time scale between humans and mice.
But, there is no molecular evolutionary definition of genus. As a molecular geneticist, I’m a little unclear on what it means even on a phylogenic/taxonomic level. I’m sure at some level, some taxonomist used the human/chimp division to actually define the word genus. So at some level, we will always be in a different genus because the word was probably invented to describe the human/chimp division (at least by someone).
I wish we had someone hear that understood the term “99.6 genetic similarity.” What is the difference between me and a cat? If chimps are 99.6%, what is the next closest animal? My guess is that the difference is probably far enough away (maybe 90%…). Does anyone really know?
And junk DNA is really important in that it allows the genes to remain intact during the cross-over that occurs during miosis.
You may be surprised to learn that Linnaeus originally placed chimpanzees in Homo and named them Homo troglodytes in 1758. The chimpanzee’s genus was then changed to Simia in 1775, and to Pan around 1816.
I gave this link earlier in this thread for those interested in the X% genetically similar question, but here it is again. Go there and I think you’ll get a good answer.
As for cats, I’d guess it’s about 90%, or about the same as a mouse.
To your other question, “what’s the next closest animal”, the answer is the gorilla. Shouldn’t be a big surprise, is it? I don’t remember the exact number and it really doesn’t matter as these numbers seem to change all the time.
The interesting thing is that not only are chimps our closest relatives, we are their closest relatives, also. In other words, chimps are more genetically similar to humans than they are to gorillas. That was a BIG surprise when geneticists first made the measurements some 25 odd yrs ago.
Yeah, I seem to recall that the general consensus of Linnaeus’ time was that chimps were possibly a race of humans that had degenerated into primitivism (hence the species name troglodytes). If memory serves, Linnaeus recieved his information about chimpanzees secondhand, and most of the stories coming out of Africa at the time were of the “shaggy man who lives in the woods and walks with the aid of a stick” variety, so the confusion is understandable. Obviously Linnaeus was justifiably impressed by the similarity of chimps to humans, but since the idea of common primate ancestry was not on the table yet, the “bestial human” idea must have seemed like the only sensible place for them in his taxonomic system.