Some molecular evidence for human evolution

@glipsnort (aka Stephen Schaffner) discusses the mechanisms that cause mutations and how the evidence supports the conclusion that the differences between the genomes of species is due to these mechanisms:

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Then, to answer @scd’s question, the two are nothing at all alike. They are independent sorts of evidence for common descent.

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@scd tried to argue that those results could be equally well explained by the species being created with identical sequences then diverging through neutral mutations. That’s the parallel. I’ll try to find the thread.

Edit: here it is, scd starts posting at #82:

But it isn’t a parallel. @scd is suggesting, in effect, a star phylogeny. The pattern @glipsnort shows could indeed be produced by a star phylogeny, as tree topology is irrelevant to it. Not so, however, with the data here.

He was replying to my comment #24, which basically explained exactly that.

I am not sure we would not expect the same data if special creation was staggered in time. If Apes and humans were designed in closer time proximity to each other we would get the same data as the neutral mutations would be more similar as the sequence starting point is sooner and has diverged less from the original sequence.

The design condition is the designs are staggered in time which agrees with the fossil record.

If they were separately created, why would they share any DNA sequences?

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Maybe you should work that up into an actual, testable model. What you have described there does not fit the data, as far as can be seen from your vague statement.

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