Phylodynamics is a term coined to describe how pathogen

Pathogen

A pathogen gignomai "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host...

 genetic variation

Genetic variation

Genetic variation, variation in alleles of genes, occurs both within and among populations. Genetic variation is important because it provides the “raw material” for natural selection. Genetic variation is brought about by mutation, a change in a chemical structure of a gene. Polyploidy is an...

 is affected by—and itself affects—influences such as host

Host (biology)

In biology, a host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. In botany, a host plant is one that supplies food resources and substrate for certain insects or other fauna...

 immunity

Immunity

-Medicine:* Immunity , resistance of an organism to infection or disease.* Immunity , a scientific journal published by Cell Press-Law:*Amnesty law, immunity from past crimes...

, transmission

Transmission (medicine)

In medicine and biology, transmission is the passing of a communicable disease from an infected host individual or group to a conspecific individual or group, regardless of whether the other individual was previously infected...

 and epidemic

Epidemic

In epidemiology, an epidemic , occurs when new cases of a certain disease, in a given human population, and during a given period, substantially exceed what is expected based on recent experience...

 dynamics. For example, host immunity modulates what pathogen phylogenies are observed within individual hosts and transmitted to other hosts; at the same time, the evolutionary trajectory of pathogen populations within individual hosts affects those hosts' immune response to infection, and hence transmission.

Viral phylodynamics

Viruses can evolve rapidly: genetic variation is generated by processes such as recombination

Genetic recombination

Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...

 and reassortment

Reassortment

Reassortment is the mixing of the genetic material of a species into new combinations in different individuals. Several different processes contribute to reassortment, including assortment of chromosomes, and chromosomal crossover. It is particularly used when two similar viruses that are infecting...

; this variation can be acted on by natural selection

Natural selection

Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

. For instance, a host's immune system

Immune system

An immune system is a system of biological structures and processes within an organism that protects against disease by identifying and killing pathogens and tumor cells. It detects a wide variety of agents, from viruses to parasitic worms, and needs to distinguish them from the organism's own...

 can dramatically affect the type and number of virions available for transmission to another host. RNA Viruses

RNA virus

An RNA virus is a virus that has RNA as its genetic material. This nucleic acid is usually single-stranded RNA but may be double-stranded RNA...

 are particularly suited to phylodynamical study, thanks to "high mutation rates, large population sizes and short generation times".

Example of phylodynamics: Influenza virus evolution and epidemics in humans

Historically, the Influenza A virus has caused annual winter epidemics in human populations

Flu season

Flu season is a annually-recurring time period characterized by the prevalence of outbreaks of influenza . The season occurs during the cold half of the year in each hemisphere. Influenza activity can sometimes be predicted and even tracked geographically...

, resulting in considerable morbidity and mortality. A simple mathematical model has indicated how evolutionary changes in the virus can result in epidemics of influenza, and vice versa.
The model, which allowed the degree of host immunity to the virus to vary depending on how much the virus had changed antigenically, could account for many features of Influenza A epidemics in humans. For example, the model predicted the "boom and bust" pattern we observe in influenza virus evolution, in which a large antigenic change (a "cluster jump") is followed by a marked drop and subsequent rise in genetic diversity.