allele: An allele is a particular sequence for a gene. For example, most people have the normal allele for hemoglobin, but in people carrying the sickle cell trait one of their hemoglobin genes has a different sequence, the sickle allele.

autosome: A chromosome that is not required for sex determination.

bottleneck: The sudden, catastrophic reduction of a population’s size. This opens the doors for the founder effect to permanently change the frequency of alleles in the population, since the surviving members of the drastically reduced population will not have allele frequencies representative of the original population. An example of this is the cheetah, which experienced a population bottleneck approximately 10,000 years ago resulting in such a severe reduction of genetic variation that cheetahs fail to reject skin grafts from other cheetahs, not recognizing them as foreign.

clade: A group of organisms containing an ancestral organism and all of its descendants. Clades by definition are monophyletic.

drift: Genetic drift refers to the process by which rare alleles are eliminated or propagated by the action of mere chance. While by Mendelian rules we would expect a parent with one rare allele to transmit that to 2 out of 4 of its offspring, by chance that allele might be passed on to 3 out of 4. On the other hand, the allele might be passed on to 1 out of 4, or even 0 of 4! The effects of chance variations in transmission over generations can lead to an allele drifting into extinction, or even drifting to such high frequency that it becomes fixed in the population, meaning every member of the population has only that allele. However, more often drift tends to erase minor alleles. All alleles are subject to drift, but positive and negative selection act either to fight against drift in amplifying the frequency of the allele (positive selection) or work with it to eradicate the allele (negative selection). While an allele is rare genetic drift is the most powerful force, but with an increase in frequency of the allele positive and negative selection have greater strength.

exon: A sequence of a gene that is included in the final gene product, as opposed to introns.

founder effect: A particular type of genetic drift in which a small population with allele frequencies not representative of the parent population colonize a new area. The initial allele imbalance is passed on to the offspring, and may even be amplified further by genetic drift. An example of this is Ellis van Crevald syndrome, which causes dwarfism and polydactyly, and occurs at unusually high frequency in the Amish. This is due to an abnormal allele carried by one of the original Amish colonists, and has since spread through the population.

homing endonuclease: These are selfish genetic elements present either as an intron or an intein in a “parasitized” gene. The endonuclease is made either from translation of the usually discarded intron or from splicing out the intein from the mRNA transcript’s mature protein. The endonuclease is highly specific for a short sequence in its host gene, and during meiosis will cut its host chromosome’s partner in that gene. This triggers DNA repair using the host chromosome as a template, and copying the intron or intein sequence onto the second chromosome.

ichnotaxon: When paleontologists find a characteristic mark left behind by an extinct organism (a footprint, burrow, groove, or other marking left in sediment or on an object) this is assigned a genus and species name. This makes it easier to discuss this particular type of trace fossil with others. Because the marks are typically named without us knowing the species that left them, the name of the ichnotaxon does not match the name of the organism that left those marks.

intein: Normally mRNAs are spliced to remove introns, but the transcript is then used to make the final protein. Sometimes the protein is then synthesized from the mRNA transcript and then the protein splices out a portion of itself, called the intein, and releases the rest of the protein, the extein. Most inteins contain a self-splicing domain and an endonuclease domain, and are homing endonucleases.

intron: A sequence of DNA that is not included in the final gene product, but is spliced out of the mRNA following transcription. Introns are unique to eukaryotes. Most genes have multiple introns, and different routes of splicing of a single mRNA transcript can produce different protein variants in a process called alternative splicing.

monophyly: The description for a clade containing a common ancestor and all of its descendants.

Muller’s ratchet: The gradual irreversible buildup of mutations in nonrecombining DNA, whether in an asexually reproducing organism or a non-recombining chromosome. This occurs from the failure to repair mutations through recombination and the gradual loss of the least-mutated genotype through genetic drift.

ontogeny: The development of an organism from embryo through adulthood.

paraphyly: The description for a group that excludes some organisms even though they do descend from that group’s common ancestor. For instance, the birds are excluded from the reptiles in spite of being descended from them.

polyphyly: The description for a group that contains organisms that do not share a common ancestor in that group. An example is the pachyderms, hoofed animals with thick skin grouped together based upon this superficial similarity. Phylogeneticists seek to eradicate polyphyletic groups wherever they are discovered.

Sauropsida: The sister clade to Synapsida, contains the reptiles and their descendants, the birds. Sauropsida also contains many extinct groups, one of the most notable being the dinosaurs.

Synapsida: A clade containing organisms having a single opening in the skull behind each eye, the temporal fenestra. The sole surviving synapsids are the mammals, but there were many odd and highly successful non-mammalian synapsids in the past. The synapsids were highly successful in the Permian before the Permian-Triassic extinction, the worst mass extinction that the world has ever seen.

transcription: In order to be expressed, a gene must be transcribed. Transcription is the process of copying DNA into RNA. In some cases the RNA transcript is the final gene product, while in others the mRNA is then translated into protein. If the RNA is translated into protein, the RNA is called a messenger RNA, or mRNA.

translation: Translation is the decoding of mRNA to produce a protein.