Molecular Systematics

Molecular Systematics
Molecular Systematics

Molecular systematics is the discipline of classifying organisms based on variations in protein and DNA in order to make fine taxonomic categorizations not solely dependent on morphology.

Taxonomy, sometimes called systematics, is the study of categorizing organisms into logically related groupings. Historically, the way to perform taxonomy was to examine physical characteristics of organisms and classify species according to the most commonly held traits. Unfortunately, this method of systematizing plants and animals assumed that because they have common physical traits, they have common ancestry.

A gross form of this miscategorization might take place, for example, if one suggested that since both mushrooms and ivy can grow on the sides of trees, they are closely related. The two species certainly have common physical traits but only vaguely resemble each other.

It is such a realization that motivated systematists to begin using molecular differences to compare species and populations. Molecular systematics uses variations in protein and deoxyribonucleic acid (DNA) molecules to determine how similar, or dissimilar, sets of organisms are. These molecular differences provide a much more accurate taxonomic picture.

Systematics and Evolution

Molecular Systematics of Plants
Molecular Systematics of Plants
Molecular Systematics, Second Edition
Molecular Systematics, Second Edition

The real power of molecular systematics is that it allows the examination of how species have changed over evolutionary time, as well as of the relationships between species that have no common physical characteristics. Molecular changes can be used to explore phylogenetics (how populations are related evolutionarily and genetically).

It has been suggested that the amount of change that takes place in DNA over time can act as a molecular clock, gauging how much evolutionary time has passed. The clock is set by first examining geological and historical records to determine how long two species have been physically separated.

By examination of the number of molecular changes that have occurred between those species over that known time, a time frame of change can be established. Genes are thought to evolve and mutate at a constant, predictable rate, giving rise to this evolutionary clock hypothesis.

There are three major domains of life: prokaryotes (modern bacteria), Archae bacteria (descendants of ancient bacteria), and eukaryotes (cellular organisms with nuclei and organelles).

All these organisms share a common ancestry of hundreds of millions of years. All species over time are connected to one another through a web of interlacing DNA as they reproduce, separate to become new species, and reproduce again.

All organisms carry their ancestors’ genetic information with them as a bundle in each cell, and the more closely related organisms are to one another, the more similar the contents of that bundlewill stay over time.

Humans share common genes, unchanged over millennia, with all other organisms—from the bacterium Escherichia coli to barley to gophers. The more important the job of a gene, the less it changes over time; this concept is called conservation. Conservation is the force that keeps a biological or genetic link between every species on earth.

Protein-Level Analysis

Pharmacy in vegetables
Pharmacy in vegetables
Proteins were the earliest biomolecules used to study phylogenetics. Initially, protein differences could be studied only at the grossest levels.

It was found that populations of organisms could be distinguished based on possessing different alleles (genetic sites) that made proteins possessing the same function but with different chemical structures. These enzymes were called isozymes. Isozymes can be separated and compared for size by employing a technique called gel electrophoresis.

Gel electrophoresis uses a slab of gelatin-like mediumand an electric field to separate molecules on the basis of size and electric charge. The genetic similarity of two different species can be determined based on common molecular weight of the isozymes.

Proteins are composed of strings of the twenty amino acids common to all life on earth. It is possible to ascertain the amino acid sequence of a protein.

If the amino acid sequence of the same protein is ascertained among several different species, that sequence should be more similar between closely related species than more distantly related species. These differences allow taxonomists to gauge similarity of populations.

Antibodies are biomolecules that are able to recognize and bind very specifically to other molecules. Biologists employ antibodies that specifically recognize molecules at the surface of cells to test relationships between species.

Antibodies that recognize cell-surface molecules on one species should recognize those same molecules in closely related species, but not from distantly related species, allowing a researcher to gauge similarity between species.

DNA-Level Analysis

The most common method used to establish taxonomic relationships is to compare DNA sequences between species. DNA is the double-stranded, polymeric molecule that encodes the proteins that direct the inner workings of all cells.

The DNA molecule is structure like a ladder, with rungs formed by pairings of of four molecules, the bases guanine (G), adenine (A), thymine (T), and and cytosine (C).

These bases, arranged in unique order, are read by special enzymes and encode messages that are translated into proteins. Sequences encoding for the same protein can change between species. In taxonomy, DNA sequences are obtained from several populations of organisms.

Analysis of these sequences allows one to obtain a picture of how different populations have changed over time. This DNA sequencing may be used to compare many different types of DNA: regions that encode for genes, do not encode for genes, reside in chloroplast DNA, or reside in mitochondrial DNA.

Another common method of DNA phylogenetic analysis is called restriction mapping. In this method, DNA from different species is subjected to enzymatic treatment from proteins called endonucleases. These endonucleases have the ability to cleave DNA into fragments.

Where the enzymes cleave the DNA is determined by the DNA sequence itself. The size and pattern of the fragments created by this treatment should be more similar in related species than in unrelated species.

A fairly new method of DNA analysis examines repetitive DNAs, called microsatellite sequences, that are found in all eukaryotic organisms. Microsatellite sequences are short arrangements of bases, such asGATC, repeated over and over. The number of repeats at a particular genetic location is usually more similar in related species than in unrelated ones.

The differences in these repeated sequences are called “simple sequence polymorphisms” and are detected by a special enzymatic reaction called the polymerase chain reaction. Once detected, the fragments are separated and compared for size by means of gel electrophoresis.

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