Do all deer share a common ancestor?

[colewd (Bill Cole)]

@T_aquaticus

Species can share common cellular components and not fall into a nested hierarchy. You still don’t seem to understand what a nested hierarchy is.

What cases do you think there are of animals built with with 80% or more common genes not fitting the phylogenetic tree better then the null hypothesis?

[T_aquaticus]

@colewd

What cases do you think there are of animals built with with 80% or more common genes not fitting the phylogenetic tree better then the null hypothesis.

That’s word salad. I have no idea how that is a response to what I said.

There is absolutely no reason why a designer could not mix and match genes from a wide assortment of species. Even humans do this when they genetically modify organisms. You could have an exact copy of a chicken, mouse, jellyfish, sponge, and protist gene in the same species. There is nothing that would preclude this. By exact copy, I mean the exact sequence. At most, you might have to adjust some of the promoters.

There is absolutely nothing about species sharing common features that would necessitate a nested hierarchy. There is absolutely nothing about design that would necessitate a nested hierarchy. Nothing. The fact that humans regularly design organisms that violate the nested hierarchy is yet more evidence of this conclusion.

[colewd (Bill Cole)]

@T_aquaticus

There is absolutely no reason why a designer could not mix and match genes from a wide assortment of species. Even humans do this when they genetically modify organisms. You could have an exact copy of a chicken, mouse, jellyfish, sponge, and protist gene in the same species. There is nothing that would preclude this. By exact copy, I mean the exact sequence. At most, you might have to adjust some of the promoters.

There is absolutely nothing about species sharing common features that would necessitate a nested hierarchy. There is absolutely nothing about design that would necessitate a nested hierarchy. Nothing. The fact that humans regularly design organisms that violate the nested hierarchy is yet more evidence of this conclusion.

The mix and matching of genes are generating unique animals. The genes can be inferred to be purposely arranged.

There is no reason separate designs with this strategy will not build animals that can fit a phylogenetic tree better then the null hypothesis.

Its time to find a new gene and chromosome modification and generating mechanism.

[John_Harshman]

@colewd

The mix and matching of genes are generating unique animals. The genes can be inferred to be purposely arranged.

There is no reason separate designs with this strategy will not build animals that can fit a phylogenetic tree better then the null hypothesis.

Its time to find a new gene and chromosome modification and generating mechanism.

You have been asked repeatedly to stop posting word salad and think a little bit, just a little bit, before you respond. Maybe read it over at least once before sending, too.

Mix and matching of genes is not something we commonly see in nature, and “purposely arranged” has no meaning. There is a reason why separate designs won’t fit a phylogenetic tree. Human designs don’t. No design principle says they should. Not sure what your null hypothesis is, and neither are you. And your final non sequitur seems out of place and irrelevant. Please try to do better, or people will stop trying to talk to you.

[colewd (Bill Cole)]

@John_Harshman

Mix and matching of genes is not something we commonly see in nature, and “purposely arranged” has no meaning.

The Venn diagrams show different groups of genes belong to different animals. This is what I mean by mixing and matching.

@John_Harshman

There is a reason why separate designs won’t fit a phylogenetic tree. Human designs don’t.

Have you tested this?

@John_Harshman

No design principle says they should.

How do you know this? What about Winston’s example.

http://dx.doi.org/10.5048/BIO-C.2018.3.f5

@John_Harshman

Not sure what your null hypothesis is, and neither are you. And your final non sequitur seems out of place and irrelevant. Please try to do better, or people will stop trying to talk to you.

The null comes from you which is most the nodes not fitting the tree better then chance.

[John_Harshman]

@colewd

The Venn diagrams show different groups of genes belong to different animals. This is what I mean by mixing and matching.

That’s not what mixing and matching means. It refers to departure from nested hierarchy. Notice that the various different genes fit a nested hierarchy.

@colewd

Have you tested this?

Many times. Have you?

@colewd

How do you know this? What about Winston’s example.

I’m not quite sure what the nodes in that tree actually represent. But isn’t that a single program? In that case it would correspond to a single genome, not a tree of species.

@colewd

The null comes from you which is most the nodes not fitting the tree better then chance.

I said no such thing. I don’t even know what “nodes not fitting the tree” would even mean.

Please stop with the thoughtless one-liners.

[colewd (Bill Cole)]

@John_Harshman

@colewd

How do we know if the test has failed?

If most branches had no better than chance support, that would tell us that either there was no common descent or the data were inadequate. As it happens, we don’t have that problem. Test passed. If you think of that as a test for separate origins, that hypothesis is decisively rejected

Did I miss what you mean by this?

[John_Harshman]

@colewd

Did I miss what you mean by this?

One must assume so, or maybe you are just incapable of communicating what you mean.

[John_Harshman]

@colewd

@John_Harshman

No design principle says they should.

How do you know this? What about Winston’s example.

http://dx.doi.org/10.5048/BIO-C.2018.3.f5

Just checked the paper. As I suspected, you have no idea what that figure actually shows. Hint: it does not show that the programs form a nested hierarchy. That tree was imposed on the data.

[Tim]

Yes, Ewert’s paper states:

Figure 5 shows the tree used for the common descent model of JavaScript applications. The process used to determine this tree is described in the Methods sections. It involves trying many possible trees to determine the tree which gives the best fit of the data to the tree model. Figure 6 shows a simplified version of the true dependency graph for these same applications. The colors correspond to frameworks. A framework is a module that provides the basic tools necessary to build an application. It is like a module that defines a body plan shared amongst several species. Each individual species builds on this basic plan to define the actual species. A framework will contain a large amount of code, consequently an application will share much code with other applications which use the same framework.

Upon inspection, we can see that the tree is actually reflecting the reality of the dependency graph. In the tree, applications using the same framework tend to cluster together, due to the shared code. However, applications which share non-framework modules are put closer together in an attempt to explain that reuse. The applications using the angular2 framework (tan) are oddly placed, branching out of the react based applications (pink). However, this is because hn-ng2 and react-news both use the large firebase module. Mamba, vim-awesome, and sound-redux are pulled closer to the root because they reuse the lodash and immutable modules which are also used by the angular applications (green). The tree is working to approximate the dependency graph.

It should be noted that Figure 6, which Ewert explicitly calls “a simplified version of the true dependency graph” looks nothing like a nest hierarchy.

[colewd (Bill Cole)]

@John_Harshman

That tree was imposed on the data.

How is this different than a phylogenetic or morphological tree? In Winston’s case all the nodes are filled from top to bottom unlike a typical phylogenetic tree where the ancestor nodes are left unnamed.

[John_Harshman]

@colewd

How is this different than a phylogenetic or morphological tree?

Because they aren’t imposed. More importantly, the branches of that tree have not been tested for support. The tree as a whole was tested against a star tree, but that’s not at all the same thing. Note that Ewert himself uses this as an example of a data set that does not fit a tree. The data are not arranged in a nested hierarchy.

@colewd

In Winston’s case all the nodes are filled from top to bottom unlike a typical phylogenetic tree where the ancestor nodes are left unnamed

You are confused about what the nodes are, perhaps because the tree in the figure is oddly drawn. But no, you’re wrong about all that.

[colewd (Bill Cole)]

Table 3: The log Bayes factors for the models in the synthetic datasets

On page 10 shows a better fit for the tree then the null.

The JavaScript applications fit the tree or the depen- dency graph better than the null model. However, the dependency graph is preferred to the tree. This again confirms one of the predictions, software can exhibit a hierarchical signal while being produced by a dependency graph. Nevertheless, it still fits the dependency graph better than the hierarchical pattern.

Is Winston wrong that the test detected a hierarchical signal?

[T_aquaticus]

@colewd

There is no reason separate designs with this strategy will not build animals that can fit a phylogenetic tree better then the null hypothesis.

We don’t see species with the mixture of genes I describe. Instead, we see a nested hierarchy.

There is absolutely no reason why separate design would produce a nested hierarchy. All you can seem to do is fumble around words and pretend not to understand the concepts we are talking about.

[T_aquaticus]

@colewd

Is Winston wrong that the test detected a hierarchical signal?

The dependency graph hypothesis predicts that there will be many modules which do not correspond to a taxonomic category, and a substantial portion of the genes should be attributed to these non-taxonomic modules rather than taxonomic modules. On the other hand, common descent predicts there would be few non-taxonomic modules, and most genes would remain attributed to the taxonomic modules. Therefore, if the inferred dependency graph is simply the tree of life with a few minor additions, that would suggest that the dependency graph hypothesis is incorrect.
–Winston Ewert

We observe the tree of life.

[John_Harshman]

@colewd

Table 3: The log Bayes factors for the models in the synthetic datasets

On page 10 shows a better fit for the tree then the null.

You are very, very confused about what that means.

@colewd

Is Winston wrong that the test detected a hierarchical signal?

Yes. The test he subjected the data to wasn’t a very rigorous one.

[T_aquaticus]

So the questions remain.

Why do we see this pattern of chromosomal fusions and common ancestry in the muntjac deer species:

This is exactly what we would expect from common ancestry, and completely inexplicable if these genomes were created separately. Each of the fusion events (C_5 through C_1) carries down each branch as we would expect from common ancestry, and there is no reason why separate creation should have this pattern.

More importantly, the leftover centromeres from those fusions are still there (as shown by the example of the fusion in human chromosome 2):

.

Our results confirmed that chromosome fusions are the dominant type of rearrangements that account for the drastic interspecific variations of muntjac chromosomal numbers (Fig. 1d). We further identified the putative orientation of centromeres’ positions in the acrocentric chromosome preserved in H. inermis and M. reevesi (Supplementary Fig. 8). A fusion event was defined as tandem fusion if it connected the apical centromeres of one ancestral chromosomes and the distal telomere of another ancestral chromosome, and a fusion event was defined as Robertsonian fusion if it connected the apical centromeres of two ancestral chromosomes. Based on the centromeres’ position and chromosomal synteny, in the female M. crinifrons we identified 28 tandem fusion events and 3 Robertsonian fusion events derived from the 2n = 70 ancestral karyotype (Fig. 1a and Supplementary Table 7).
Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer | Nature Communications

If those genomes are not the result of those fusion events, then what in the world are those cryptic centromeres doing in those chromosomes, right where they would be if a fusion event really occurred?

The evidence is OVERWHELMINGLY in favor of common ancestry:

1. Tree like pattern of shared fusion events.
2. Cryptic centromeres.

[colewd (Bill Cole)]

@T_aquaticus

The evidence is OVERWHELMINGLY in favor of common ancestry:

If you look at a narrow part of the evidence you might think common ancestry is a possibility. What was never looked at was the original question.

@colewd

Can we reconcile the common ancestry of deer based on population genetics for chromosome variation and gene family variation?

From the paper Rum cited:

While the molecular mechanism driving rapid karyotype change in muntjacs is not yet known, comparison of nearly 20,000 gene orthologs between the two species identified a number of genes with accelerated evolution in muntjacs, several of which are plausibly associated with chromosome maintenance and are therefore candidates for further study.

[John_Harshman]

@colewd

If you look at a narrow part of the evidence you might think common ancestry is a possibility. What was never looked at was the original question.

If you look at all the evidence, or any significant part of the evidence, you (a reasonable person, rather) would think common ancestry is the unavoidable conclusion. This is as true for the chromosome evidence as for anything else. You can see what changes are necessary, and you can observe the remnants of those changes in the genome.

@colewd

From the paper Rum cited:

Notice that it says nothing about population genetics. It’s talking about an increased rate of mutation, and it points to some possible explanations. How is this a problem? And note that separate origins has nothing even close to that: no positive evidence, no mechanism, no explanation for the data. And yet you prefer it. Why?

[T_aquaticus]

@colewd

If you look at a narrow part of the evidence you might think common ancestry is a possibility. What was never looked at was the original question.

The og question:

“Can we reconcile the common ancestry of deer based on population genetics for chromosome variation and gene family variation?”

That’s exactly what I looked at. The answer is yes. Fusion events in groups C_5 through C_1 exactly follow the pattern we would expect from common ancestry. They happen at those nodes and are passed down the branches in exactly the pattern common ancestry would produce.

We also find cryptic centromeres in the arms of the chromosomes along with the expected synteny (i.e. gene order). Again, this is EXACTLY what chromosomal fusion and common ancestry should produce.

So yes, it is reconciled.