So, picking up on main vein of this thread, and going back to post #150.
In this
material, we are still in section 2 of 7, titled "Patterns."
And in this post, I'm going with subsection titled, "Understanding Phylogenies (1 of 2)."
Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendents of that ancestor. As you move from the root to the tips, you are moving forward in time.
I get this. How I understand it is, "here is a model for understanding relationships within taxonomy of evolutionary theory." Plus idea that the latest descendants (most recent) are on one of the tree, let's call that furthest branches, and earliest descendant(s) are on another end of tree, let's call that the root(s).
I put earliest descendants and roots in plural because that makes sense to me. Parallel evolution or another term that I can't think of off hand, but mentioned in this thread earlier, do suggest that there could be multiple common ancestors. So, to assume only one seems implausible to me at this time.
I also just want to be clear that my understanding the model, and following along with it in an intelligent way, doesn't mean a) that I explicitly agree with the model, nor b) that I think it is most intelligent way of understanding things. And to all the debaters out there, this admission I'm making now doesn't mean I have a much better way of understanding these things that I need to stop and convey that to you before anything else occurs.
When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.
To be clear and I do seek clarification here (from anyone reading this): speciation equals splits / divergence in lineage, yes?
For sake of following the model and just describing the pattern I don't need to know why that occurs, but I am curious about that far more than I am about the model being presented, and I'm sure for those reading this that wish I'd just get to the meat, my curiosity is something they already feel well aware of and can't wait for me to get there. All in good time my pretties, all in good time.
Not sure I understand specification of "two or more daughter lineages." i would guess it is because daughters / females carry reproductive means, and so for the split to have consequence beyond life of one organism, the female / reproductive organisms need to happen, otherwise speciation may not occur. If I am somehow misunderstanding this, feel free to chime in and clarify.
Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.
Hmm, this is where things get a tad tricky for me. I'll say this, for the model to make sense in how I understand the model, this is pretty much obvious. But for the model to represent the 'observed data' in an accurate way, I am simply left with more questions than looking at this as an answer. My questions don't, right now, amount to "I disagree with all of it, and doubt that it is at all possible." Not even close to that, but more in vein of, "how do we know something has shared ancestry, and how do we know that history is unique (or distinct) to the organism and also has unique traits that are shared lineage? Again, I'm guessing the material will get to this (eventually), but I am asking this to let anyone know that just because the model says it is so, doesn't mean I agree that this must be so apart from the model.
Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineagescommon ancestors.
And similar to previous point, I get this with the (simplistic) model, and question it with the observable data.
Already done with this page (part 1 of 2) and moving to next.
Understanding Phylogenies (2 of 2)
A clade is a grouping that includes a common ancestor and all the descendents (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogenyall of the organisms on that pruned branch make up a clade.
I do think I get clade and would say the pictorial representations make it easier to understand (I think) than trying to explain it and cover more than 1 variation of clade. For me, this just means within the model, we wish to distinguish certain branches from others in a sensible way. If there is a common ancestor for all branches at a root, then reality is all clades are related at a particular point.
Clades are nested within one anotherthey form a nested hierarchy. A clade may include many thousands of species or just a few. Some examples of clades at different levels are marked on the phylogenies below. Notice how clades are nested within larger clades.
I have noticed this. Understanding this pattern does feel helpful, but also feels like I'm asked to 'believe' something that may not translate real well to other portions, down the road. Since that remains to be seen, let me just leave it as, I think I understand clade sufficiently, given the model.
So far, weve said that the tips of a phylogeny represent descendent lineages. Depending on how many branches of the tree you are including however, the descendents at the tips might be different populations of a species, different species, or different clades, each composed of many species.
My translation, the simpler the model, the less accurate it may be (likely is) given awareness of entire data set. Furthermore, a simpler model will likely increase understanding for novice, while advanced model may confuse even an advanced learner.
It would seem though if phylogeny is important (and from some I'm guessing it is paramount) that the most accurate model is the best model, even if it is ridiculously large in scope.
Next up (in next post) is subsection titled "Tree Building" in the Patterns section.
