Phylogeny - Help me see what you see

Sometimes, people don’t know who their great grandparents are.

Therefore, we can’t say that all humans are related to one another.

You think?

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For those interested in more recent work making progress to resolve Squamate relationships:


We’ve been over all that. Fifty times by now. Nobody says the trees are always identical, and the trees don’t have to be identical. In fact we frequently expect them not to be identical for multiple, empirically well-founded reasons. Variations in rates of molecular vs morphological evolution, saturation, homoplasy, horizontal gene transfer, and incomplete lineage sorting are all things that demonstrably occur in observational reality, and which can force different pieces of the data to yield incongruencies when trees derived from these different data sets are compared. What matters then are the magnitudes of incongruence between different parts of the data, and how many parts of the data disagree.

Is some future possible where this elementary concept can find rest in your mind?


If we could not get him to abandon his flawed self-replicating robot argument against evolution, I doubt this could happen.

Per the article cited by @John_Harshman, the miRNA-based phylogenies now match “traditional” phylogenies. Any major debate left is only in your head.

You are fond of citing papers showing puzzles or problems existing at or close to the time of their publications. You don’t look for subsequent papers that show empirically-based solutions or attempts to solve those puzzles. This indicates you are not truly searching for what is evidence-based.


They say it’s not a fusion. I’ve listened to the explanation.

Did common ancestry predict it? Was there a prediction that there would be two more chromosomes before it was discovered among primates? That would be interesting to know.

Well, it is. There is centromere and telomere sequence in the arms of the chromosome which is smoking gun evidence for a fusion.

The prediction was that we would find evidence of a fusion.

Frankly, I don’t understand why creationists are trying to act as if fusions don’t happen. There are humans with different chromosome counts in the modern human population, and they are doing just fine.


@scd is the guy that keeps complaining that the mechanic hasn’t fixed his car, after taking it in for the 20th time because he filled it with diesel.

And yet it looks exactly like what you would expect a fusion of two chromosomes to look like. They share synteny to the closest relatives without fused chromosomes, the fused chromosome has double centromeres and end-to-end telomeres. What should a chromosome fusions look like if not this?

You might be able to convince yourself with some elaborate rationalization that it’s not a chromosome fusion, but you can’t seriously argue it doesn’t conform to what a chromosome fusion should look like.

Yes. Since humans have fewer chromosomes than our closest primate relatives, logically speaking if we are to share common ancestry there must be some mechanism by which humans could end up with fewer chromosomes. One of which would be a fusion event. Assuming here we can rule out loss of an entire chromosome that has numerous essential genes.

The hypothesis of a fusion event would in turn also lead to numerous other predictions. Think about it this way. If two human chromosomes which are highly similar to chimp chromosomes, fused, we would expect that the fused human chromosome should look like it was derived from two chimp chromosomes fused together end-to-end. This would entail for example double centromeres, with one part showing synteny to one chimp chromosome, and another part to another chimp chromosome. And so on and so forth. All of these predictions bear out. As I said, it looks exactly like a chromosomal fusion should.

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No I meant, did we know about the number of chromosomes of humans and said those two look like a fusion before we knew about the number in chimps? I’m assuming that maybe not - but mostly because chromosomes were known before specifics about them were known?

This maybe should be a different topic, but I wanted it to be a short question, not a discussion about this issue.

I have no idea whether they do or don’t. They just give reasons why this case is not solid; obviously they’d need to.

Provide the reference to that explanation. I suspect it has something to do with Jeffrey Tompkins.

‘They’ are wrong. It is unambiguously a fusion. If I was inclined to see the hand of God in anything, it would be that the fusion site is ‘too good’.

Yes. Or more accurately, common ancestry predicts that there be a transition between an ancestral karyotype and the derived karyotypes. A fusion in the human lineage would have been the most parsimonious, but not the only possibility. Then again, all of this was resolved extremely quickly after the initial karyotypes were produced. Order of events was basically: Human karyotype (several years) other ape karyotypes (basically immediately) probably a fusion (several years) better quality karyotypes for everything (same publication) probably a fusion of these specific chromosomes in the human lineage at approximately this location (~20 years) actual sequence data confirming the fusion.

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There was that paper by Matzke in Science on the phylogeny of anti-evolution litigation…


Thank you evograd. That does look helpful.
Unfortunately the link didn’t work for me. It mentions a session time-out.

Yeah, I know. Pretty sad and desperate, isn’t it?

No. When it was found that humans had one fewer chromosome pair than other great apes, the only reasonable explanation, if one believed that common descent is true, was that there was a fusion in our genome. And, when it eventually became possible to detect such a fusion, there it was.

Pretty amazing coincidence, isn’t it? Or do you have another explanation? Such as that common descent is true?

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4 posts were split to a new topic: Phylogeny and Incongruent Trees

Darn. I was hoping no one would ask me difficult questions. :slight_smile:

I suppose I would leave that to who ever has sufficient knowledge in this area.

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This thread’s title was actually the first words of the chorus of an early draft of a particularly lyrical Billy Joel song:

Phy-lo-ge-ny. Please help me see what you see.
Lots of nested hi-er-archies.
Taxon-o-my is such a useful word.
Life fits nice-ly into de-scrip-tive tree-eeeees.

(Joel eventually revised the song for a broader audience and the result was “Honesty”, a top 40 hit in 1978. This sidebar is for @Dan_Eastwood and the other dinosaurs among us.)

And perhaps a geek root.


Phylogenies have been inferred for many aspects of human culture: languages, legislation, computer viruses, medieval manuscripts. These often involve horizontal copying as well as vertical descent. (For example, we are communicating in a Teutonic language with many words from French).

But I was asking about genetics, not phylogenetics.

The prediction of a fusion came after we knew that chimps had one more pair of chromosomes than we did.

I’m not sure it is even anything creationists need to worry about. If humans were separately created there could have been a chromosomal fusion early in history that then spread to the rest of the population. A bottleneck at the flood may have fixed the chromosome count.

Personally, I’ve never seen the chromosomal fusion evidence as very strong evidence for human/chimp common ancestry.