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For hundreds of years, scientists could only look at things on a macro level: body plans and structures, modes of reproduction, and so on. Now, they have an incredibly powerful tool to help them understand evolutionary relationships and taxonomy. The power sander of taxonomy is genetics. Since most things at the macro level are determined by the expression of genes, studying those genes directly is the most exact way of comparing organisms.
Since all living things are made of cells and since all cells perform a few of the same basic functions, all living things contain at least a few of the same genes that govern these basic functions. Some of these genes are called housekeeping genes because, as vacuuming and dishwashing are necessary for any household, these genes are necessary for the smooth operation of any cell. If only we could get them to take out the trash.
The most widely studied housekeeping genes do not actually encode a protein, but instead they encode ribosomal RNA (rRNA). rRNA is used by all known living organisms to synthesize proteins from messenger RNA (mRNA). Even if the proteins being created are very different from one organism to the other, the process for making them is very similar. Once an evolved method works, it will probably remain that way in all future generations. If it ain't broke, don't fix it.
Since all organisms possess genes for rRNA, we can compare their rRNA sequences to look for differences caused by mutations. Assuming that mutations occur at a fairly steady rate within a given stretch of DNA, we can actually guess how much time has passed since two species diverged from a common ancestor. It's like the game of telephone. As a sentence gets whispered from one person to another, it changes slightly each time and ends up being different by the end.
When scientists compare the rRNA sequences from two different organisms, they are looking for how many "words in the sentence" have been changed. The more words have changed, the more times the sentence has been whispered. Or, the more nucleic acids are different between the two sequences, the more evolutionary changes have occurred. Scientists can then confirm this estimate with other data, such as fossils and carbon dating. This information allows systematists to create a chronological order of evolutionary events, each event represented as a new branch emerging from a node on a phylogenetic tree. This new scientific field is called molecular systematics.
Thanks to molecular systematics, scientists can go back through the phylogenies they created and test them for accuracy. The phylogeny in the figure below was based on patterns and structures of development. Do those relationships hold up when we look at the genetic data? Not entirely. The updated cladogram is shown in figure (B) below.
(A) A cladogram of the major animal phyla showing evolutionary relationships as we thought they were before we had the technology to compare their genetics.
(B) Updated cladogram of major animal phyla based on genetic analysis. Compare with Figure 11A. The colored labels on top of the diagram mark clades.
The first difference is that the clades based on the type of coelom are gone. That's because biologists had logically assumed that animals without a coelom came first, followed by the evolution of a pseudocoelom, and then a true coelom. However, when the genetic data were analyzed, systematists found that the acoelomate worms actually evolved from animals with more complex bodies, becoming simpler over time. This process is known as reversal. It occurs when a trait reverts to an earlier form, creating another kind of homoplasy.
The protostomes are now divided into two new clades, the Lophotrochozoa and the Ecdysozoa. The lophotrocozoa clade includes mollusks (Phylum Mollusca), segmented worms (Phylum Annelida), and several aquatic creatures with a ciliated ring of tentacles around their mouths. Ecdysozoa are all organisms that molt. ("Ecdysis" is the Greek word for molting.)
A Spirobranchus giganteus, or "white Christmas tree worm," part of the lophotrocozoa clade.
Based on this new phylogeny, we can make a few more observations. The clade Bilateria is itself now divided into three clades: Lophotrochozoa, Ecdysozoa, and Deuterostomia. This new phylogenetic tree predicts that segmentation arose independently not twice but thrice.
Okay. At this point, the only thing that has come out of molecular systematics is a few more terms for you to learn. How can it help in solving problems?
Is a bat a mouse that developed wings and lost its tail or a bird that lost its feathers? Should a bat be classified as a mammal or bird.
The easiest way to answer this question is to compare a gene that is a shared ancestral character for mammals and birds. Hemoglobin is a protein that red blood cells use to carry oxygen. It is found in all animals with blood. If we compare the hemoglobin sequence for bats to that of various birds and various mammals, we'll find that it is much more similar to that of mammals. This then leads us to the conclusion that mammals and birds diverged first and then bats diverged from a common mammalian ancestor. This conclusion can be confirmed when we note that bats also have mammary glands and all of the other characteristics common to mammals.