So, continuing on main vein of this thread, and going from post #277.
In this
material, we are still in section 2 of 7, titled "Patterns."
And in this post, I'm continuing with subsection titled, "Tree Building." This post will address the sub-page titled, "Using Parsimony (Parts 1 and 2)."
Using Parsimony (1 of 2)
After studying some major vertebrate lineages and
limiting the data to characters that are likely homologous, you might end up with the following evidence (note that there are many vertebrate lineages and many characters excluded from this example for the sake of simplicity):
Good to know that we would limit the data. You know to make things easier to fit our conclusion. Also, 'likely homologous' seems like a fairly accurate way to go. I'm likely being facetious here.
Anyway, the key here is a table is presented to help identify patterns between species. On the x axis is list of about a half dozen animal types, and on y axis is a half dozen characteristics with notations made whether animal has that characteristic (yes or no). This is how shared characteristics are identified.
From studying fossils and lineages closely related to the vertebrate clade, we hypothesize that the ancestor of vertebrates had none of these features:
Another table, 1 animal type (the pre-conceived ancestor) with determination that none of the characteristics are found in this hypothetical animal. Again, just setting up hypothetical pattern at this point to aid in understanding.
To build a phylogenetic tree from these data, we must base our clades on shared derived charactersnot shared ancestral characters. Since we have a good idea of what the ancestral characters are (see above), this is not so hard. We might start out by examining the egg character. We focus in on the group of lineages that share the derived form of this character (an amniotic egg) and hypothesize that they form a clade:
Thus a characteristic becomes a junction point for a clade. All those with yes (characteristic is shared) go to this clade (say on left), all those with no (not shared) go to other clade (say on right). Just trying to make sense of both our pre-conceived notions and observations that seem to be consistent from animal to animal, er, I mean species to species.
If we go through the whole table like this, grouping clades according to shared derived characters, we get the following hypothesis:
That the characteristics we identify form a family tree... of our own making.
Of course, this was just an example of the tree-building process. Phylogenetic trees are generally based on many more characters and often involve more lineages. For example, biologists reconstructing relationships between 499 lineages of seed plants began with more than 1400 molecular characters!
I'm sure the more details, the easier it is to overwhelm the reader with the sleight of hand understanding that is occurring here. Again, that understanding being that we are the determiner of what a) makes for a characteristic and b) what also makes for similar characteristic. The leap to derived shared characteristic is an interesting one especially when one attempts to remove both our intelligence and our designs from the hypothesis that is making up this process (model).
Using Parsimony (2 of 2)
What is parsimony?
The tree-building
process explained above is
based on the principle of parsimony. The parsimony principle is basic to all science and tells us to
choose the simplest scientific explanation that fits the evidence. In terms of tree-building, that means that the
best hypothesis is the one that requires the fewest evolutionary changes.
Sorry for using the concept of pre-conceived notion when parsimony is much more to the point. The fewer the (new) assumptions, the more right we are likely to be.
For example, we could compare the following hypotheses about vertebrate relationships using the parsimony principle:
Hypothesis 1 requires six evolutionary changes and Hypothesis 2 requires seven evolutionary changes, with a bony skeleton evolving independently, twice. Although both fit the available data, the parsimony principle says that Hypothesis 1 is bettersince it does not hypothesize unnecessarily complicated changes.
IOW, the more simple we can make the model, the less confusing it will be.
This principle was implicit in the tree-building process we went through earlier. However, in most cases, the data are more complex than those used in our example and may point to several different phylogenetic hypotheses. In those cases, the parsimony principle can help us choose between them.
Seems simplistic enough.
Again, in this portion that I covered, the word "observe" or "observation" does not appear. Though the word "examining" does appear once to help convey how particular characteristics may form a theoretical relationship.
Next up for this material is still in "Patterns" and is section titled, "Classification," which I'll get to in next post.
