DNA sequencing is a fundamental tool in modern biology for understanding evolutionary relationships. Traditional classification, or taxonomy, relied heavily on observable physical traits (morphology). However, physical similarity can be deceiving due to convergent evolution, where unrelated species evolve similar traits in response to similar environments. DNA provides a molecular record of evolutionary history, allowing scientists to classify life based on shared ancestry rather than superficial appearance. By comparing the genetic code of different organisms, researchers can determine how closely related they are and when they last shared a common ancestor. This shift has transformed classification from a system based primarily on observation to one rooted in quantifiable genetic data.
Selecting Molecular Markers for Analysis
Scientists rarely sequence the entire genome of an organism for classification because the process is time-consuming and expensive. Instead, they focus on specific, manageable sections of DNA called molecular markers. The choice of marker depends on the evolutionary scale being investigated, ranging from deep history to recent speciation events.
For examining relationships across vast evolutionary time, such as between kingdoms or phyla, researchers often use genes for ribosomal RNA (rRNA). These genes are highly conserved, meaning they mutate very slowly, providing a stable point of comparison for distantly related organisms. Conversely, for classifying closely related species or populations, scientists select markers with faster mutation rates.
These more variable markers include specific genes within the mitochondrial DNA (mtDNA) or chloroplast DNA, as well as nuclear ribosomal DNA internal transcribed spacers (ITS). Organelle genomes, like those in mitochondria and chloroplasts, are easier to isolate and amplify for sequencing. For plants, genes like rbcL or matK found in the chloroplast are frequently used for species identification and classification.
Processing and Comparing DNA Sequences
The raw DNA sequences obtained from molecular markers require extensive computational processing before comparison. The first step is performing a multiple sequence alignment (MSA), which involves lining up the sequences from all the organisms being studied. This process ensures that each position in the alignment corresponds to a homologous site across all species.
Once the sequences are aligned, researchers calculate the genetic distance between every possible pair of sequences. This distance is a numerical measure of evolutionary divergence, quantified by counting the number of base pair differences or mismatches. The greater the number of differences, the larger the genetic distance, indicating that the two organisms diverged longer ago.
The resulting data is compiled into a genetic distance matrix, a table containing the distance value for every pairwise comparison. This matrix serves as the direct input for computer programs that transform the raw genetic differences into a visual model of evolutionary relationships.
Constructing Evolutionary Relationships (Phylogenetic Trees)
The processed genetic comparison data is used to construct a phylogenetic tree, a branching diagram that visually represents the inferred evolutionary history of the organisms. These trees are built using computational approaches that analyze sequence differences to find the most probable pattern of shared ancestry. One category of methods, like Neighbor-Joining, uses the calculated genetic distances to sequentially group the most similar sequences together.
Other methods, known as character-based approaches, analyze individual nucleotide changes across the alignment rather than the total distance. Maximum Parsimony seeks the tree that requires the fewest total evolutionary changes (mutations) to explain the observed sequence data. Maximum Likelihood evaluates different tree structures and chooses the one that makes the observed DNA sequences most probable, given a specific mathematical model of DNA evolution.
The resulting phylogenetic tree is interpreted by examining its components. The tips represent the studied species and the internal nodes signify common ancestors. The grouping of tips into nested sets is called a clade, representing a common ancestor and all its descendants. The length of the branches often represents the amount of genetic change that has occurred, with longer branches indicating greater evolutionary divergence.
Redefining the Classification of Life
The application of DNA sequencing has led to revisions across the established Linnaean classification system, demonstrating that many groups classified by appearance were not true evolutionary clades. Molecular evidence has exposed convergent evolution, where similar environmental pressures caused unrelated organisms to evolve similar physical forms. Classification is now based on the principle of monophyly, meaning all members of a taxonomic group must share a single common ancestor.
Molecular data has clarified relationships at both high and low taxonomic levels. For instance, DNA analysis revealed that fungi are more closely related to animals than they are to plants, a relationship that morphology completely obscured. Hippopotamuses share a more recent common ancestor with whales and dolphins (cetaceans) than they do with other hoofed mammals.
The use of specific ribosomal RNA sequences transformed the classification of bacteria and Archaea, establishing new domains of life unrecognizable by traditional methods. These molecular studies continue to refine the evolutionary tree, providing a stable, verifiable framework for understanding biodiversity on Earth. The ongoing process involves moving species into new genera, families, and even phyla to better reflect their genetic and evolutionary history.