Systematics, Molecular

Molecular systematics is the use of molecules to determine classification systems and relationships. For hundreds of years botanists used morphology , or overall appearance, to identify and classify plants. Morphological systematics has been important for the basic understanding of plant evolution and relationships; however, it has limitations. One limitation to morphology in plants is homology. Homology assumes that two similar structures have the same evolutionary origin. In other words, the trait arose in an ancestor and was passed down to its descendants. Homology in plant morphology is frequently very difficult to resolve since plant structures can become modified into other forms (e.g., spines of cacti are modified leaves).

Just as a botanist may compare the shape of a leaf between two different plants, molecular systematists compare molecules. Molecules have an advantage over morphology in two aspects. First, homology is usually much easier to determine in molecules than in morphology. Second, molecules tend to provide many more pieces of information than can be gained from morphology. A scientist studying morphology may compare one hundred traits, but a scientist using molecules will compare several hundred to several thousand traits depending on the technique.

Early molecular systematics began with micromolecules. The earliest of these studies can be traced as far back as the 1880s, but much of the work was conducted between the 1950s and 1970s. Micromolecules are small molecules mostly responsible for colors, scents, and chemical defenses of plants. Chemicals found in different plants are identified and compared across species for similarities. Species sharing compounds are presumed to be more closely related. Later botanists used macromolecules, which are proteins and nucleic acids. Much of the work on proteins was conducted in the 1970s and consisted of determining the order of amino acids in specific proteins (protein sequencing) or determining whether different populations or species of plants had different forms of specific enzymes (isozyme variability). Other protein-based studies utilized principles of serology and created antibodies for protein extracts that were compared to extracts from a different species. The degree to which the antibodies of one plant matched the proteins of a another plant provides an estimate of how closely the two plants are related.

Studies began to use deoxyribonucleic acid (DNA) in the late 1960s and 1970s with DNA-DNA hybridization. This method uses the principle that DNA is a double-stranded molecule and that high temperatures (greater than 80°C) can cause all of the DNA to become single-stranded. When cooled, the DNA resumes its double-stranded nature (re-annealling) and the temperature at which it becomes completely double-stranded is an indication of how similar the strands of DNA are. In this method, DNA from two plants is combined and heated. If all of the DNA is from closely related plants, the re-annealling temperature is high. If the DNA is from two distantly related plants it is lower. The re-annealling temperature is an estimate of how similar the plants are. The closer the temperatures are to the re-annealling temperature of a single plant, the more closely the plants are assumed to be related.

During the 1980s botanists made comparisons of DNA between plants using restriction site analysis. Scientists used restriction enzymes that cut DNA into fragments of various lengths. These enzymes cut the DNA at specific combinations of nucleotides every time this combination of sequences is encountered. The fragments are separated by size using gel electrophoresis and visualized by a probe that matches specific regions of the DNA. Comparing fragment sizes, it is possible to determine whether a specific restriction site is present or absent in any given species. The presence of a restriction site in two or more plants implies that the plants with the site have a more recent common ancestor. Restriction site data are capable of producing hundreds of sites depending on the numbers of enzymes that are used. Most botanists use the DNA from the chloroplast since it is smaller in comparison to other regions of the genome and a number of probes are available.

During the late 1980s and the 1990s molecular systematists made a shift to comparing DNA sequences. A specific gene or DNA region is selected and the order of nucleotides of that gene are determined (sequencing). DNA sequencing was made easier by the polymerase chain reaction (PCR), which allows millions of copies of a gene to be made (amplification) from a single copy. Once a gene is amplified, it is relatively easy to sequence. Nucleotide sequences generated from the same gene of different plants can be compared, or aligned. The traits that are compared are the nucleotides that occur at each aligned position in the gene. As with restriction sites, the shared presence of a specific nucleotide at a specific site in two or more plants is assumed to mean that these plants share a more recent common ancestor.

Many botanists utilize a gene called ribulose bis-phosphate carboxylastoxygenase, large subunit, abbreviated rubisco, found in the chloroplast DNA. This gene is functionally important for plants as it encodes the enzyme that allows plants to make CO₂ into complex molecules. Because it is so important, changes in the gene sequence are infrequent, allowing botanists to use these changes to answer questions about relationships and origins of flowering plants. Recently, botanists have expanded the number of genes studied. Many genes are now used depending on the taxonomic level of interest. Genes with lesser, or no, function evolve quickly and are useful to compare species or populations. Genes with functional constraints are more useful to compare genera or families.

It is common for scientists to use several genes for a study. As more genes are added, it strengthens the results by adding more data, and from genes that may evolve differently. One important example of this is the comparison of nuclear genes to chloroplast genes. Chloroplasts usually are inherited through a single parent (the mother), whereas nuclear genes are inherited from both parents. If a botanist studies only chloroplast genes, it is possible that only the maternal lineage will be resolved. This is especially critical in plant groups that are known to hybridize. To counter this potential error, many botanists look at chloroplast genes in conjunction with nuclear genes. Common nuclear genes that are used are the ribosomal ribonucleic acid (RNA) genes.

see also Phylogeny; Plant Identification; Systematics, Plant; Taxonomy.

James F. Smith

Bibliography

Donoghue, Michael J. "Progress and Prospects in Reconstructing Plant Phylogeny." Annals of the Missouri Botanical Garden 81 (1994): 405-18.

Judd, Walter S., Christopher S. Campbell, Elizabeth A. Kellogg, and Peter F. Stevens. Plant Systematics: A Phylogenetic Approach. Sunderland, MA: Sinauer Associates, Inc., 1999.

Soltis, Pamela S., Douglas E. Soltis, and Jeff J. Doyle, eds. Molecular Systematics of Plants. New York: Chapman & Hall, 1992.

——, eds. Molecular Systematics of Plants II: DNA Sequencing. Boston: Kluwer, 1998.

Stuessy, Tod F. Plant Taxonomy. New York: Columbia University Press, 1990.

Molecular Systematics

Molecular systematics is the use of molecular genetics to study the evolution of relationships among individuals and species. The goal of systematic studies is to provide insight into the history of groups of organisms and the evolutionary processes that create diversity among species.

For thousands of years, naturalists have looked at the world and attempted to describe and explain biological diversity. This attempt to examine and classify is called systematics—a system for imposing order on the seeming chaos of nature. In 1758 Swedish naturalist Carolus Linnaeus devised a hierarchical classification system using two-part Latin names to categorize plants and animals. This system is still used today. Linnaeus was opposed to the theory of evolution, and his system was originally based on morphological features of structure and form. However, evolutionists rapidly adopted the Linnaean system and developed it into a classification based on phylogenetics, the evolutionary development of species. By 1866, German zoologist Ernst Haeckel had published a collection of detailed phylogenetic "trees" depicting what was then known about the evolutionary history of life.

Interest in phylogeny waned over much of the nineteenth century, replaced by an emphasis on genetics, physiology , and geographic variances. That began to change with the work of botanist Walter Zimmerman in the 1940s, and German zoologist Willi Hennig, in the 1950s and 1960s. These scientists pioneered the definition of objective criteria for determining the shared genetic attributes of living and fossil organisms. A revolution in molecular biology took place in the 1960s. Methods for determining the molecular structure of proteins and amino acids allowed biologists to begin to estimate phylogenetic relationships. The exponential growth of molecular systematics in the late twentieth century is due to a combination of increased sophistication in molecular biology techniques, and computer advances in hardware and software that allow scientists to model large and complex data sets.

Molecular systematists use a variety of techniques to derive phylogenetic trees. Polymerase chain reaction (PCR) is used to investigate variations of DNA on a large scale. Gene amplification is also fundamental to new approaches to DNA fingerprinting. Scientists can use " molecular clocks " to predict both past and future molecular divergences in genes . This theory claims that molecular change is sufficiently constant to determine how current genetic lineages branch off from a common ancestor and to determine when the branching occurred. Genetic markers are used to make inferences about relationships between environment and morphology, as well as physiology and behavior.

The importance of phylogenetic trees, or estimates of evolutionary history, are that they allow biology to be predictive. Much as a chemist can use the periodic table of elements to predict chemical reactions, biologists can use phylogenetic trees to analyze biological variation and make predictions about behavior, morphology, and physiology, as well as biomolecular structure and other biological attributes.

The applications of molecular systematics in medicine are particularly important. The ability to predict the course of evolution allows scientists to track epidemic pathogens , research zootonic viruses (animal viruses that are transmissible to humans), understand the evolution of pharmaceuticals and drug resistance, and make predictions about emerging diseases. For example, phylogenetic studies of a form of influenza called influenza A have revealed reliable evolutionary behavior that can be used to predict how the viruses that cause influenza will evolve. This allows scientists to prepare vaccines for future strains in advance. Research into when simian immunodeficiency virus began to be transmitted to humans is vital to understanding how the transmission occurred and perhaps to prevent future zootonic transmissions.

Phylogeny is also an integral part of interpreting any coevolutionary relationships such as host and parasite. In the example of the coevolution of insects and their host plants, the plants evolve chemical defenses against the insects, who then evolve resistances to the chemicals. Because there are a limited number of chemical defenses available to the plants, researchers looked at whether insects are more likely to stay with the same plant as it evolves, or to switch to plants that contain chemicals to which they are already adapted. Studies of beetle phylogeny shows a closer match to plant chemistry than to plant phylogeny, indicating that the beetles have learned to switch plants as the host evolves new defenses.

Behavioral ecologists use phylogeny to reconstruct the evolution of behaviors. Molecular data can clarify the connections between animals previously thought to be unrelated. For example, flying foxes (Pteropus, also known as fruit bats), in contrast to other bats, have been shown to share significant features of brain organization with primates. These shared features lead scientists to believe that wings and flying evolved independently in these two lineages.

Evolution is not something that just happened in the past. It can be observed in the present and used to predict the future, by employing molecular systematics to compare data across genes, individuals, populations, and species.

Nancy Weaver

Bibliography

Hillis, David M. Molecular Systematics. Sunderland, MA: Sinauer Associates, Inc., 1996.

Johnson, George B. Biology: Visualizing Life. New York: Holt, Rinehart and Winston, Inc. 1998.

molecular systematics (biochemical taxonomy) The use of amino-acid or nucleotide-sequence data in determining the evolutionary relationships of different organisms. Essentially it involves comparing the sequences of functionally homologous molecules from each organism being studied, and determining the number of differences between them. The greater the number of differences, the more distantly related the organisms are likely to be. Moreover, since the number of nucleotide substitutions, and hence substitutions of corresponding amino acids, is generally proportional to time, some indication of the time scale involved can be obtained (see molecular clock). This information has proved particularly useful where there are gaps in the fossil record and can be combined with other evidence from morphology, physiology, and embryology to produce more accurate phylogenetic trees. In microbiology molecular systematics has transformed bacterial phylogeny, in particular prompting the view that there are two quite distinct lineages of bacteria, the archaebacteria and eubacteria.