Do you have a formal mathematical basis to decide at what point common descent becomes unviable as an explanation?
The reason I am asking is because of all the this talk of accuracy and statistics.
It could falsify the correlation between trees based on morphology and trees based on DNA sequence. You can also measure the phylogenetic signal in an individual tree:
I donât have much experience with the nuts and bolts of these methods, but perhaps others can dive in.
We would expect reticulation in entire domains of life in bacteria because there is horizontal genetic transfer between distant parts of the tree. I have used this feature myself on a few occasions, moving DNA from gram negative E. coli to distantly related gram positive bacteria. The same process also happened at the root of the eukaryote tree. Hybridization in complex eukaryotes occurs between closely related branches, and that is where we see the signal of reticulation in those trees, right where we would expect to see it.
Birds and mammals are distantly related, and those features evolved well into those branches. There is no way for those traits to meet each other through known evolutionary mechanisms, so we shouldnât see them in any one species.
Traditionally, 95% confidence is the gold standard, but there is a huge ongoing debate in the scientific community about this topic. From the larger reviews I have seen, the correlation between trees is much higher than 95%.
[note: 95% confidence is probably not the best term to use, but hopefully others will jump in to correct my mistakes]
This figure from TalkOrigins shows how the consistency index for phylogenies is well above the 95% confidence level:
Figure 1.2.1. A plot of the CI values of cladograms versus the number of taxa in the cladograms . CI values are on the y-axis; taxa number are on the x-axis. The 95% confidence limits are shown in light turquoise. All points above and to the right of the turquoise region are statistically significant high CI values. Similarly, all points below and to the left of the turquoise region are statistically significant low values of CI. (reproduced from Klassen et al . 1991, Figure 6).
If you remember , recently Winston ewert proposed an idea called based on âdependency graphsâ and presented a statistical argument for why it is closer than a tree to biological data.
Itâs similar to common descent in that it also does not deal with how the change happens.
If further research shows that something like the dependency graph explains the observed patteen better than common descent, would it falsify common descent?
Ewertâs paper is discussed in another thread:. The consensus is that it has a long way to go before it can show what Ewert wants it to show. However, we all give Ewert a lot of credit for tackling this data.
From what I can tell, the dependency graph requires violations of the nested hierarchy. For example, Ewert talks about zebras and zebrafish sharing a gene that other fish and mammals do not. That would be an obvious violation of the nested hierarchy. However, Ewertâs conclusions seem to depend on complete annotation of all genomes and wide coverage of species groups, which isnât the case.
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Didnât understand this part.
Annotation is the process of assigning a function to a stretch of DNA. If genomes are not completely annotated and if the databases are not complete then you may think a gene is absent from a species when it really isnât. Also, if you are only looking at one species out of a large group you could be seeing gene loss in just one small branch and missing the presence of that gene in the larger group.
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Still confused about the difference between the causes of mutation and common descent. And still confused about what common descent is; reticulate evolution is a subset of common descent.
And still confused about the difference between common descent and universal common descent.
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And now AiGâs Tory Lacey tells us about his interpretation of this fossil.
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