This page is intended to provide definitions to commonly used terms and explain abbreviations. I’ll add new terms sporadically as topics come up in my posts.

aDNA = ancient DNA; DNA extracted from pre-modern biological specimens.

Antigens= any molecule that our immune system will mount a specific response against. Each antigen may have multiple locations, or epitopes, where antibodies actually bind. Antigens can be proteins, lipids (fats), carbohydrates, glycoproteins or lipoproteins.

Basic Reproduction Number (R0) = an epidemiological term meaning that number of persons an average infected person transmits the infection to in a  population of totally susceptible people. For example, an R0 of 2.0 means that the average infected person transmits the infection to two susceptible persons;  the number of infections is doubling with each round of transmission.

Biogeography = concerned with the geographic distribution of species over time.

Clade = a section of the phylogenetic tree that reaches to modern organisms and includes all descendants from a common ancestor.

A hypothetical phylogenetic tree. The blue and red boxes are clades. The green box is not a clade because it does not include all descendants of a common ancestor. (Source: Wikipedia commons)

Endemic = A disease that usually occurs within a given population at a relatively steady rate.

Epidemic =An outbreak of disease in humans above the baseline of the usual incidence of that disease in the population.

Epizootic = An outbreak of disease among animals.

Germline DNA = heritable DNA passed from parent to offspring in gametes (eggs and sperm). In bacteria, all of their chromosomal DNA is heritable.

Molecular clock = uses the number of nucleotide base changes (mutations/polymorphisms), generation time, and the mutation rate to estimate how much time has passed since two species or strains descended from a common ancestor.

Morbidity = rate of illness. It is usually listed as morbidity and mortality which translates into sickness and death rates.

Mutation =  a change in one or more nucleotides of DNA. If it is a neutral change (does not effect the gene product) then it is usually called a polymorphism. If it is a harmful change then it is called a mutation. A point mutation changes a single nucleotide base. A frameshift mutation occurs when bases are added or deleted.

Mutation rate = the rate at which heritable (germline) nucleotides (bases) change in the DNA of a species, often expressed in generation times. Mutation rate varies among species.

Normal flora = microbes that are normally found on or in the human body without causing disease. Some of these microbes, like intestinal residents,  are necessary for normal human function.

Opportunistic pathogen = a microbe that normally co-exists with humans without causing disease but will take advantage of gaps in our immune defense. There are three primary reasons for opportunistic infections: 1) an immune compromised host, 2) finding itself in a new location such as through a break in the skin, or 3) suppression of our normal flora by antibiotics. The yeast Candida albicans is a good example of an opportunistic pathogen.

Pandemic = a outbreak of diseases with a wide geographic coverage (usually two or more continents). Most pandemics are causing by a novel or reemerging organism that moves along trade routes and against which humans have little or no immunity. See my defining pandemic post.

Panzootic = a pandemic in animals.

Pathogen = A disease causing organism.

PCR = polymerase chain reaction, an enzymatic reaction that amplifies one specific section of DNA.

Phylogenetic tree = a diagram illustrating the relationship between organisms. Phylogenetic trees can be constructed to show the relationship between species or within a species. Today phylogenetic trees are constructed primarily by comparative genetics.

Plague pit = a mass grave believed to contain plague victims. The skeletons are often not in uniform orientation and may be in disarray. There will likely be remains of mixed gender and age with no obvious signs of pre-mortem mass trauma, like battle injuries.

R0 = see basic reproduction number above.

SNP / single nucleotide polymorphism = An SNP is a place, a single base, in the genome where individuals of a species vary. These changes are not necessarily considered mutations. Many SNPs make no change in the gene products of the organism either because it is a non-coding region or because it doesn’t change the amino acid coded for in a gene.

Sylvatic host = a wild animal that hosts a microbe away from humans. Domestic animals and others closely associated with humans are not considered to be sylvatic.

Zoonosis: An infectious disease that is transmitted from an animal to a human. Some of our worst infectious diseases like the plague are zoonoses.