So we've discussed phylogenetic trees in a few different topics throughout this course, but I want to delve a little more into how to actually read them, and what all the lines and dots represent. Phylogenetic trees are evolutionary representations of what's called phylogeny. So, what is phylogeny? Phylogeny is the evolutionary relationship of a group of organisms. Phylogenetic trees illustrate the evolutionary relationships of a group of organisms, consisting of multiple structures. Firstly, we have a node, and each node represents a different organism being compared. There are two types of nodes: a terminal node, where the line ends and usually represents present-day organisms for which we have data, and internal nodes, representing common ancestors that existed before divergence. The branches represent evolutionary connections between organisms, and their lengths usually represent the amount of time between divergences.
I’m going to show you a tree in just a second, but first, let's explain a rooted tree. A rooted tree has an internal node that is a common ancestor to all other nodes on the tree. When we observe this phylogenetic tree of life, it consists of every organism on earth. Here are the terminal nodes representing current organisms. You will notice internal nodes where branches meet, each representing a different ancestor that evolved and became two different organisms. Terminal nodes extend out for each classification, while the internal nodes and large branches showcase the relationships. The length of the branches determines the time between divergences; longer branches represent a longer time since divergence. Lastly, we would say that this tree is rooted because all these organisms can be traced back to a single common ancestor represented by the internal node.
How are phylogenetic trees constructed? They are often constructed using homology, which refers to similarities shared between various species due to a common ancestor. This can relate to DNA sequences or phenotypic traits. A monophyletic group, or clade, includes all species descended from the group's most common ancestor. The cladistics approach to constructing a phylogenetic tree analyzes all possible evolutionary paths, represented by combinations (n factorial, where n is the number of organisms). This approach applies the Principle of Parsimony, selecting the simplest tree as the correct one.
Here are examples of homology in a phenotypic trait: different organisms might have similar bone structures that evolved differently. For instance, a fin and an arm may share the same basic bone colors and structures, indicating a common ancestral origin even though they evolved into different functions. These homologous structures usually resemble each other in formation, suggesting they originated from a common ancestor. By examining these homologies, both in phenotypic traits and DNA sequences, scientists can deduce which organisms came from a common ancestor and estimate the time since divergence.
With this understanding, we can now move on.
