@anon68328710
John Mercer brings up some comments you write on your youtube video regarding the possibility that you might get incongruent phylogenetic trees derived from different genetic loci.
It’s true, you might, and there are plenty of examples in the literature. However what you’re not explaining in your comments is the degree of disagreement between the different trees. The trees can be strictly incongruent because they’re not exactly alike, and yet still be highly similar in degree.
I think it would be really helpful here to consider an analogy:
Imagine you have a large number of ultra-sensitive thermometers that can measure the temperature in a room to an accuracy of six significant figures. As in, it measures not just 21 degrees Celsius, but 21.0031 degrees Celsius.
Now suppose you have thirty different thermometers of that type, and you put them all in the same room on a line, and you measure literally thirty different values between 21.0031 and 21.0078 degrees Celsius.
So now you have this problem that no two thermometers match exactly, they all disagree on the exact temperature on the room. Should we now conclude we have no good evidence for the temperature in the room since all the thermometers disagree? Of course not.
The fact is they’re all extremely close to each other, which in a sense is to be expected since we can easily imagine that the temperature in the room isn’t actually so exactly uniform in all positions. So we can still say that the thermometers match each other to an extremely high degree, and for that reason we can be highly confident that the true temperature in the room lies somewhere in the measured range.
It is highly likely that the true temperature in the room is somewhere in the range between 21.0031 and 21.0078 degrees Celcius.
In the field called statistics, there are principles that describe how significant some particular matchs is. Unsurprisingly called Statistical significance - Wikipedia.
This same principle applies with phylogenetic trees derived from different sets of data.
Each phylogenetic tree thus is a kind of “measurement” of the relationships between the species(it gives us some information about what the true relationship is like, like how the thermometer also gives us some information about what the true temperature is like), given the “thermometers” used (which could be particular genes, or morphology).
To bring this back to phylogenetic trees, you can quickly determine the degree of similarity with phylogenetic trees when you see which species are grouped together. You will generally never find a phylogenetic tree that puts a bird among sharks, or a pig among plants, or a primate among insects, etc.
The trees might disagree on the scale of similar clades (is this species of mouse A more closely related to this other species of mouse B, or to mouse C? Some trees will disagree on this scale.)
Even if we don’t get completely exact matches every time (though often times we do get that), the fact that we get highly similar trees even if not always exact matches, is still a very significant result.
It is the result we expect given common descent, and we do not have any other good reasons for expecting the phylogenetic trees from different and independent data sets to give so similar (and often time exactly matching) results.
