Some molecular evidence for human evolution

I don’t understand why? They contradict the (african apes)(gibbon+orangutan) as far as I can see. Though they just add to the number of hypotheses that contradict each other, still leaving the canonical relationship the most well supported one. For example I can see four rows that support the relationship (human+gorilla)(gibbon+orangutan+chimpanzee).

Those sites don’t actually contradict that tree, as they require one change on a tree that includes African apes as a clade as well as a tree that doesn’t. In other words, they’re only relevant to relationships within African apes. Picture a tree with one internal branch, separating African apes from gibbon and orangutan. Only sites that require two changes on that tree contradict the tree.

Out of curiosity, is incomplete lineage sorting a significant source of noise in these mitDNA comparisons? I would think that being a single copy genome along with a higher rate of sequence divergence would reduce ILS compared to genomic DNA, but I could be completely wrong here.

Wow. So the Designer has been coming by every few thousand years and creating new species de novo for the last 3.5 billion years?

When and how did you come up with that gem?

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No. It’s a source of exactly zero noise. Since the mitochondrial genome doesn’t recombine and is inherited at a unit, every site in the genome tracks the same phylogeny. Incomplete lineage sorting still might happen, but it would result in a single phylogeny that doesn’t match the organismal phylogeny. Further, there should be less a chance of this than for autosomal loci, since the probability of ILS depends on the effective population size, and mt genomes, to a first approximation, have a quarter of the effective population size of autosomes.

Ahh I get it now. It is possible to make trees with african ape-clades that still imply only one change. Like the top tree here. But I was thinking the first row only implied the second tree.

I also let myself be confused by knowledge of the canonical phylogeny with humans and chimps most closely related, which would imply two changes.

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Exactly.

Thanks, that makes a lot of sense. I suspected this was the case, but I wasn’t absolutely sure how intraspecies mitDNA variation played out without recombination.

because they share many traits in common.

You have the cart in front of the horse. They share traits because they share DNA. If you used completely different DNA then they could have completely different traits. Why would a designer need to share traits between separately created species?

We also have the flip side. You could have drastically different DNA and still have the same traits. For example, you could rewrite the anti-codons on tRNA’s which would allow you to have very different DNA sequences that produce the exact same proteins. Talkorigins has a great section on this concept:

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41 posts were split to a new topic: Design and Nested Hierarchies

A post was merged into an existing topic: Design and Nested Hierarchies

I have done this with the sequences from the L-GULO pseudogene and turned it into a classroom activity (that I just did with my students yesterday actually!). I picked the gene and the sequences pretty much at random. I used human, chimp, gorilla, orangutan, and macaque. It’s only a ~100bp stretch but it shows the human-chimp sister grouping very clearly, and the fact that macaca is the most divergent. It doesn’t resolve the gorilla and orang phylogeny, but that’s what exercise #2 is for (I switch to protein sequences for that).

The point here is that the evidence for common ancestry is very, very easy to find. I understand the concerns above that it doesn’t clarify things like selection, design, and so forth, but, at least in my mind, DNA sequences alone make common ancestry of all living things on earth about as scientifically certain as humanly possible. (And we have a lot more evidence than just DNA sequences.)

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Did you happen to try a chi-square test?

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I did not, because this is a course for non-SCI majors, so I keep it as math-free as possible, just counting basically. This way, they fully wrap their brains around what is happening and they do the analysis fully themselves, not even a calculator. Their eyes really open wide when they see how easy it is to see evidence for common ancestry. People always think that scientific data is just beyond them, totally inaccessible, and lots of it really isn’t!

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Hey Bill, are you going to explain and provide the supporting evidence for your latest assertion?

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Interesting.

One thing that strikes me is that this sequence of 76 nucleotides is very dense in mutations compared to all the other 694 positions. Why is that the case?
Moreover, this same sequence seems to display an abnormally high number of cases of homoplasy, doesn’t it?
IOW, I am wondering what is going on with this particular sequence?

Because this sequence is made up of all the sites in those genes that have relevant mutations, it’s not an actual 76bp sequence within the 694bp. Read the OP again.

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Thanks.

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Ok, we expect a certain amount of cases of homoplasy but do we expect such a high level of cases, in this case 22 out of 694 positions? This level seems extraordinary high to me, doesn’t it?