Evolution: DNA Sequence Data

This section explores how DNA sequence data provides powerful evidence for evolutionary relationships between species. By comparing the DNA sequences of different organisms, scientists can infer their evolutionary history and construct phylogenetic trees.

Principles of DNA Sequencing and Variation

DNA as a Universal Genetic Code

All living organisms use DNA as their genetic material. The sequence of nucleotides (Adenine, Guanine, Cytosine, Thymine) within DNA encodes the instructions for building and maintaining an organism. The universality of DNA provides a common basis for comparing genetic information across species.

Mutations and Sequence Variation

Over time, mutations occur in DNA. These are changes in the nucleotide sequence. Mutations can be:

• Point mutations: Changes to a single nucleotide (e.g., substitution, insertion, deletion).
• Insertions and Deletions (Indels): Addition or removal of nucleotides.
• Larger-scale mutations: Duplication, inversion, or translocation of DNA segments.

These mutations accumulate over generations, leading to differences in DNA sequences between species. The rate of mutation can vary between different regions of the genome.

Neutral Mutations

Many mutations have no significant effect on an organism's phenotype. These are called neutral mutations. Because neutral mutations accumulate randomly, they are particularly useful for inferring evolutionary relationships. The more neutral mutations two species share, the more closely related they are likely to be.

Using DNA Sequence Data to Construct Phylogenetic Trees

Sequence Alignment

To compare DNA sequences, they must first be aligned. This involves arranging the sequences so that homologous (similar) regions are in the same columns. Alignment algorithms are used to maximize the similarity between sequences.

Phylogenetic Analysis

Once sequences are aligned, phylogenetic analysis is used to determine the evolutionary relationships between species. This involves comparing the number of differences (mutations) between sequences and using these differences to build a tree-like diagram (a phylogenetic tree) that represents the evolutionary history of the species.

Different Methods of Phylogenetic Analysis

1. Distance-based methods: Calculate the overall genetic distance between species based on the number of differences in their DNA sequences.
2. Maximum Parsimony: Identifies the phylogenetic tree that requires the fewest evolutionary changes to explain the observed sequence data.
3. Maximum Likelihood: Evaluates the probability of different phylogenetic trees given the DNA sequence data and a model of molecular evolution. The tree with the highest probability is considered the most likely.

Molecular Clock

The molecular clock hypothesis suggests that mutations accumulate at a relatively constant rate over time. This allows scientists to estimate the time of divergence between species by calibrating the mutation rate using fossil evidence or known events in the geological record.

Examples of DNA Sequence Data in Evolutionary Biology

Human Evolution

Comparing the DNA sequences of humans and other primates has revealed their close evolutionary relationship. DNA evidence supports the theory that humans evolved from a common ancestor with chimpanzees.

Evolution of Viruses

The rapid mutation rate of viruses, such as HIV and influenza, makes DNA sequence data particularly useful for tracking their evolution and understanding their adaptation to new hosts and environments. This information is crucial for developing effective antiviral drugs and vaccines.

Evolution of Bacteria

Analyzing the DNA sequences of bacteria can reveal their evolutionary history, track the spread of antibiotic resistance genes, and understand the evolution of bacterial virulence factors.

Limitations of DNA Sequence Data

While DNA sequence data is a powerful tool for studying evolution, it has some limitations:

• Horizontal Gene Transfer: Genetic material can be transferred between unrelated organisms, which can complicate phylogenetic analysis.
• Incomplete Lineage Sorting: Not all genes in an organism's genome are inherited from the same ancestor.
• Rate Variation: The rate of mutation can vary between different regions of the genome and between different species.

Summary Table

Feature	Description
DNA Sequence	The sequence of nucleotides (A, T, C, G) in a DNA molecule.
Mutations	Changes in the DNA sequence, including point mutations, insertions, and deletions.
Sequence Alignment	Arranging DNA sequences to identify homologous regions.
Phylogenetic Trees	Diagrams that represent the evolutionary relationships between species.
Molecular Clock	The concept that mutations accumulate at a constant rate over time.