Phylogenetic inference is the scientific process of determining the evolutionary relationships among organisms like species, genes, or even viruses. It functions much like creating a detailed family tree, reconstructing the historical connections that link organisms together over vast stretches of time. This process uses observable evidence available today to piece together the events of the evolutionary past, providing a framework for understanding how the diversity of life on Earth arose from common ancestors.
Data for Phylogenetic Analysis
The foundation of any phylogenetic study is the data collected from the organisms of interest. One of the original sources is morphology, which involves the study of physical characteristics. Scientists code features such as bone structure, the shape of teeth, or the arrangement of petals on a flower. For paleontologists, morphological data is indispensable, as it is often the only information that can be gleaned from the fossilized remains of extinct species.
A more recent source of evidence is molecular data, derived from the genetic material of organisms like DNA, RNA, and proteins. The principle is that as organisms evolve and diverge, their genetic sequences accumulate changes. By comparing these sequences, scientists can quantify their relatedness, as more similar sequences indicate a closer evolutionary relationship. Before comparison, sequences must undergo alignment, which arranges them to identify regions of similarity from shared ancestry. Some analyses combine both morphological and molecular data for a more robust picture of evolutionary relationships.
Methods of Tree Construction
Once data is collected and prepared, scientists use computational methods to build the phylogenetic tree. Different methods operate on different principles and can produce slightly different results from the same dataset. The choice of method depends on the nature of the data and the specific research question being addressed.
One method is parsimony, guided by a principle similar to Occam’s razor: the simplest explanation is often the best. In phylogenetics, parsimony seeks the tree that requires the fewest evolutionary changes—such as mutations in a DNA sequence—to explain the observed relationships. The method evaluates possible tree structures, and the one with the lowest score is considered the most parsimonious and the preferred hypothesis.
A more statistically complex approach is maximum likelihood. This method evaluates how probable the observed data is, given a specific phylogenetic tree and a mathematical model of evolution. The model of evolution accounts for factors like the probability of one nucleotide base changing into another over time. The method calculates a likelihood score for each possible tree, and the tree with the highest probability of having produced the observed data is selected as the best estimate.
A related statistical method is Bayesian inference. While maximum likelihood asks about the probability of the data given a tree, Bayesian inference asks what the probability is that a particular tree is correct, given the data and a model of evolution. This method combines the likelihood of the data with prior knowledge about the evolutionary process. The result is a distribution of possible trees, each with an associated posterior probability, providing a clear measure of confidence in different parts of the tree.
Interpreting a Phylogenetic Tree
The output of a phylogenetic analysis is a diagram that visually represents the inferred evolutionary history. Understanding the components of this tree is necessary to accurately extract the information it contains about the connections between different life forms.
A phylogenetic tree is composed of several parts. The tips of the tree, or terminal nodes, represent the organisms being studied. The lines connecting them are the branches, which represent evolutionary lineages changing over time. Where branches split, a node represents an inferred common ancestor. A rooted tree has one node at the base, the root, which represents the most recent common ancestor of all organisms included.
The most common mistake in reading a phylogenetic tree is to interpret relatedness based on how close the tips are to one another. True evolutionary relatedness is determined by tracing the branches back to find the most recent common ancestor. Two species are more closely related if they share a common ancestor that is more recent in time. The branches can be rotated around any node without changing the relationships it depicts, much like a mobile can spin without changing how its parts are connected.
Real-World Applications of Phylogenetics
In epidemiology, phylogenetics is used to track the spread and evolution of infectious diseases. By sequencing the genomes of viruses from different patients, researchers can build a phylogenetic tree that shows how the virus is moving through a population and mutating over time. This approach helps identify transmission chains and inform public health strategies for diseases like COVID-19, influenza, and HIV.
Conservation biology relies on phylogenetic analysis to make informed decisions about protecting biodiversity. By analyzing the DNA of different populations, conservationists can determine if they are genetically distinct species or subspecies that merit separate conservation efforts. For example, phylogenetics can help settle whether two groups of turtles in different locations are separate species, each requiring its own management plan.
Phylogenetics has also found a place in forensics. In legal cases, a phylogenetic tree can be used as evidence to trace the source of an infection or a contaminated product. One well-known example involved a case where a dentist was accused of transmitting HIV to his patients. A phylogenetic analysis of the HIV strains from the dentist and patients helped to confirm the epidemiological link.