Phylogenetics and Molecular Phylogenetics

paraphyletic clade. This type of clade is truncated so that some of the descendants have been removed because of differences in their characteristics. Polyphyletic clades have at least one homoplasy in the clade members that hasn t been inherited by a common ancestor.

PHYLOGENETICS AND MOLECULAR PHYLOGENETICS

As mentioned earlier, phylogenetics is a way to study the evolutionary relationships between different species. Observable traits, DNA sequences, and protein sequencing are used to define most of the different relationships. Computers are commonly used to increase the likelihood of finding the most accurate relationships between descendants.

In the late 1800s, the idea of recapitulation was established when it comes to phylogeny. The common expression was ontogeny recapitulates phylogeny”, which indicated that the embryonic growth of an organism closely mirrored its evolutionary pathway. This theory is not longer considered valid.

Molecular phylogenetics is related to molecular evolution. In molecular phylogenetics, hereditary molecular differences and genetics are used to understand an organism s relationship to other organisms. It helps to understand what s behind the diversity of the different species. Molecular evolution suggests that mutations in certain genes, leading to protein changes, have affected the structure or morphology of the different descendant organisms. Phylogenetic trees can be developed from these biochemical data.

Orginally, things like carbohydrates, enzymes, and proteins were used to identify differences in the descendant organisms. Much later, DNA sequencing was instead used to get at the source of these differences. This process is long and expensive if it makes use of the entire genome of the organism. Instead, certain chromosomes and DNA sequences are looked at instead of the whole genome.

The idea is that, over time, there have been mutations in key DNA segments that have resulted in diversity among the different organisms. There will be DNA segments preserved over time that have come from the ancestor and segments that have changed. The percent divergence or percent of substitutions of base pairs in a DNA sequence will be used to define the disparity between the organisms. Multiple key sequences are used in the comparison. Clades are defined by their similarities in DNA sequences.

DNA sequences provide a better determination of the molecular clock or the time that the divergences happened because genetic mutations tend to happen over a relatively steady period

of time and at a constant rate. In some cases, the proteins are used to identify divergences rather than the DNA sequences.

In determining and identifying phylogenetic trees of different organisms, first the sequence is gotten through biochemical techniques. The sequences are then aligned to make comparisons and substitutions are uncovered. From this, the phylogenetic tree is built and evaluated.

The main limitations of using molecular methods to determine a phylogenetic tree is that it cannot always identify when portions of the tree have later come together rather than always diverging. It is also limited by horizontal gene transfer, which mainly occurs in microorganisms. It also assumes a single common ancestor or a rooted tree” and assumes a constant molecular clock, which may not be the case.