The phylogenetic tree is based on DNA sequence data.
So why do you ignore or dismiss it? (I will say that the analysis in that paper isn’t very good. It uses a questionable method, poorly described, with no measure of fit, on a data set that’s strangely pruned and has only 5 taxa, only two of them “deer”.) Note also that the musk deer is found to be closer to bovids than to cervids, which may explain some of your problems with the Venn diagram. And then you switch back to karyotypes, which the paper doesn’t mention. Are you incapable of following a topic?
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I did include karyotypes to look at all three issues we have been discussing on this post. If we try to only look at two of the three data types the analysis is incomplete.
The Venn diagram also shows white-tail deer are closer to primates than musk deer. Which is very different from where the phylogenetic tree places them.
Why do you think there is inconsistency between the chromosome, gene and sequence data?
But you use that to change the subject. When challenged on one point, you retreat to another.
All that shows is that you don’t know what the Venn diagram shows or what “closer” means.
No, why do you think that, in the sense of what could lead you to believe a falsehood of that sort?
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Chromosome numbers are not karyotypes.
The subject of “Do all deer share a common ancestor” has not changed. Chromosome counts, gene differences and phylogenetic arrangements are all part of the analysis.
The different relationships depending on comparing chromosomes, genes and sequences.
Deer…Tree Venn Chrosome count.pdf (22.2 KB)
@Tim admires this gloriously muddled table with awe.
We have truly reached Peak Bill Cole!
“Cattle Cattle 0 Cattle 60” – truly a message for the ages. 
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But when I try to talk about one, you change to another, without ever actually looking at anything. Is that not deliberate?
You fail to understand how data can be used to estimate relationships. Your little table is unreadable, and it’s impossible to determine what you think it means. Still, I’m willing to bet that you have no clue.
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I am trying to look at all the data together and not cherry pick. When you suggested phylogenetic analysis I included it in the discussion.
It is an excel document converted to PDF. I just re centered it so I hope you can look at it now.
I’m afraid you are not trying hard enough. So far you have actually looked at nothing.
The formatting is better, but the sense isn’t. I ask again: what do you think any of that means?
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Chromosome counts are not karyotypes.
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It means that the relationships can change when you look the different sequence, gene and chromosome data.
This is not what you would expect from a group of patterns that were the result of branching decent.
Its what you would expect if the chromosomes, genes and sequences were purposely arranged.
So far you haven’t shown or mentioned anything about relationships except for one tree based on fourfold degenerate sites. Your table shows nothing whatsoever about relationships and makes no claims about relationships, as far as I can tell. But most of it is simply uninterpretable. What, for example, does this mean?: “White tail deer/25M/Human/-661”? What is “Human” doing in all that?
What exactly isn’t what you would expect? Please be very specific.
What would you expect, and why? Please be very specific.
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“Genes missing from Cow”
What have we done to deserve such blessings?
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Note that the “Genes missing from Cow” is zero for cattle. A science triumph!
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And there, I think, was your mistake. You would have done far better to have simply (i) taken a screenshot of your excel spreadsheet, (ii) cropped that screenshot down to just what you wanted to show, and (iii) posted the resulting jpg. That way, you would not have had to worry about the conversion distorting the formatting.
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You’re assuming his meaning was distorted and that the PDF isn’t an accurate depiction of how Bill thinks.
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My suggestion would help with the jumbled formatting – I will leave helping the jumbled thinking to far braver souls than myself. 
I’ll just comment that I appreciate this thread.
That’s partly for the entertainment value. But it has also help fill in some gaps in my knowledge. It’s a pity that Bill hasn’t allowed it to fill in gaps for him.
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25M years for white tail deer is the time between the split of musk deer, cattle, sheep goats and white-tail deer.
Human -661 are the genes that exist in cattle and do not exist in humans.
I would not expect the order of gene similarity to change from the phylogenetic order of sequence similarity.
If the gene sequences, genes and chromosomes were the product of separate designs I would expect each to be optimized designs based on function. A mind can create purposeful order where random change cannot.