Why molecular phylogenetics matters

Before I discuss another piece of evidence for macroevolutionary patterns in whales, I’m going to discuss a new concept: molecular phylogenetics.

Phylogenetics is the study, primarily the inference, of the evolutionary relationships between different species and/or populations. If you have ever seen something described as an “evolutionary tree”, this is the layman’s term for a “phylogeny”.

phylogeny_tree_med

Above is an example of a phylogeny which includes six species of vertebrates. What you’ll notice is that it takes on the structure of a bifurcating tree, i.e., a branch will occasionally split into two branches. What each branch represents is a hypothetical species, assumed to have existed prior to the present, which may or may not terminate into an actual known species, such as the chimpanzee or bear illustrated above.

Since each branch represents a hypothetical species, then the bifurcations represent a single species splitting into two. The point where they split can be thought of as a hypothetical common ancestor.

So looking at the phylogeny above, the bear and the chimpanzee share a more recent common ancestor than the other species. This means that these two are more closely related to each other than they are to all other species in the phylogeny. Chimp+Bear are then more closely related to the lizard than they are to all other species in the phylogeny. Chimp+Bear+Lizard are most closely related to newt, and so on.

So how do scientists make these phylogenies? Rather than simply being constructed based on a priori assumptions, they are constructed using algorithms and/or statistical methods applied data. In other words, a phylogenetic estimation is something the data tells scientists rather than something that scientists invent for the sake of telling a story.

Historically, this was done using morphology, or physical features of the anatomy. What scientists would do first is pick a feature in the species being examined. Let’s say, for example, hair. If you looked at all of the animals in the above phylogeny, you’d notice that two have hair and four don’t. Another feature could be ossified (bony) vertebrae: five animals above have this, and one doesn’t. You can keep doing this for as many features as possible and compare the distributions of character states (e.g., present vs. absent) and you’d discover overall patterns of similarity. What the methods would do then is assume evolution and a bifurcating phylogeny, and you’d get a phylogeny such as that above.

SalticidCharacterMatrix

An example of a character matrix used in morphology based phylogenetics.

A revolution in many fields took place when scientists began sequencing DNA, but for our purposes, it impacted phylogenetics in a big way. Rather than having to rely on morphological characteristics, which are painstaking to gather and are extremely limited in the number of characters you can compare, scientists began comparing DNA among different species. The amount of characters that can be compared is now in the thousands to millions and beyond rather than the hundreds typical of anatomical data. This, coupled with more rigorous statistical methods that compare different phylogenies and incorporate models of molecular evolution (e.g., how easily do the different letters in DNA mutate from one to another?), has resulted in far more robust phylogenies that present extremely consistent and easily reproducible results.

Alignment

An example of a DNA alignment used in molecular phylogenetics.

So back to what this title proposed to address: why does molecular phylogenetics matter? I’ll start explaining why by re-hashing a point in a discussion that I once had with a creationist. The creationist pointed out that it didn’t matter that the DNA between, say, a chimpanzee and a gorilla were similar. If God created them to look similarly, why shouldn’t their underlying DNA, the blueprint for their bodies, also be similar? This point would certainly be an apt one, except for a very important problem: quite often, species that are similar in form (morphology) are not necessarily similar at the DNA levelThis is to be entirely expected in evolutionary biology, since we believe that two different lineages of organisms can adapt to have very similar anatomical features (convergent evolution), but their underlying DNA should reflect their divergent past. By comparison, this seems to be much more difficult to explain from a creationist perspective.

Questions for creationists

What would you expect to happen to genes if species evolved through time? Is this consistent with what we find in nature? If God created life in its present form, how similar would you predict genes to be in different species? Would you expect similar looking plants and animals to have all of their genes more similar to each other or only those genes that are associated with similar characteristics?

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