*Most of these definitions are adapted from the oxford dictionary modified for the context of this course.

*biology is dizzyingly and fascinatingly diverse. This poses a unique challenge and need for naming in biology. We need to name things in order to study phenomena across across organisms but it also means that there is almost always an exception to every definition. Definitions are only as useful as we let them be. So rather than stressing about the exact meaning, embrace the diversity!

locus: the position, usually of a gene or mutation, on a chromosome.

gene a unit of heredity which is transferred from a parent to offspring and is held to determine some characteristic of the offspring. The bounds of a gene can be defined by many alternative measures including by function or by recombination.

allele: one of two or more alternative forms of a gene/locus that arise by mutation and are found at the same place on a chromosome

chromosome: A segment of DNA, sets of which make up the genome of an organism. Confusingly a chromosome can refer to either a single haploid chromosome or a diploid/polyploid pair. The plural chromosomes refer to distinct haploid/diploid pairs that constitute the genome.

genome: thee complete set of genes or genetic material present in a cell or organism. A genome can consist of the nuclear genome as well as other genetic material such as that found in the mitocondria, plasmids, or chloroplasts.

quantitative trait/phenotype: a quantitative characteristic of an organism.

ploidy (haploid/diploid): The number of sets of chromosomes or other replicon. Individuals carrying a single copy of each chromosome is called haploid, an individual carrying two sets typically with one materially and one paternally inherited is called diploid. Alternative ploidies are possible and common in biology including triploids, tetraploids, octaploids, with some DNA segments (e.g., plasmids) carried in as many as 200 copies. The majority of classical population genetics focuses on evolution in haploids and diploids as we will in this class.

fitness: the expected number of offspring produced by individual. Note that fitness must be calculated from life stage x of an individual to the corresponding life stage x of its offspring. As such fitness captures variation in survival (viability) and reproduction (fecundity)

selection: variation in fitness among different types of organisms. There are many forms of selection. For example selection may be "artificial" or "natural" depending on whether it arises as a result of natural or human-mediated processes. It can be termed "abiotic" or "biotic" depending on if the variation is a result of the environment or due to interactions among organisms of the same or different species. It can be termed "sexual" if it arises due to differential mating success. It may be termed "viability" or "fecundity" depending on when it arises in the life cycle. And it can be described by numerous terms describing classic patterns in the relative fitnesses of genotypes/phenotypes (e.g., directional, stabilizing, linear, additive, overdominant, balancing etc.) Note that this is an incomplete list of descriptors.

genetic drift: evolution (changes in allele frequency. or phenotypes) resulting from the random sampling, often of gametes, in a finite population.

recombination: the rearrangement of genetic material, especially by crossing over in chromosomes or by the artificial joining of segments of DNA from different organisms. Recombination often refers to the rearrangment of maternal and paternal genes along a chromosome.

gametes: cells (often haploid) produced by meiosis. In organisms with two sexes maternal gametes are termed eggs and paternal gametes are termed sperm.

segregation: the separation of pairs of alleles at meiosis and their independent transmission via separate gametes.

meiosis: A form of cell division that halves the number of chromosomes resulting in the production of gametes. Meiosis is essential for the completion of the "alternation of generations" in sexually reproducing organisms

inbreeding: nonrandom mating of individuals due to an excess of matings between relatives. Note that inbreeding is context dependent. A population is inbreed relative to _____.

assortative mating: nonrandom mating based on the genotypes/phenotypes of the mates.

migration/gene-flow: while these two words are not always interchangeable in all fields we will use them interchangeably in this class as they are typically used in evolution. This denotes the movement of individuals and more importantly their genes between subpopulations.

metapopulation: a set of subpopulations connected by (incomplete) gene-flow. Metapopulations where migration is random is known as panmictic

life history: refers the set of characteristics/traits or an organism that determine the demography of the population.

allelic dominance: The relative phenotype of a heterozygote. Fitness is often expressed with a quantity $h$, where dominance for fitness is given by: $$w_{aa}=1\quad w_{Aa}=1+hs \quad w_{AA}=1+s$$. If $h=0$ then the $A$ mutant allele is recessive if $0\geq h\geq 1$ the mutation is co-dominant. If $h=1/2$ the mutation is additive, if $h>1$ the mutation is overdominant and $h<0$ the mutation is underdominannt.

Named Models

Wright-Fisher Model A model of neutral genetic drift in discrete-time. Each generation ofspring pick their parents resulting in stochastic variation in the number of $A$ alleles in the population. The transition probability for having $i$ alleles in generation 1 to $j$ alleles in generation 2 is binomial.

Hardy-Weinberg Frequencies Genotype frequencies after random mating

Two-Patch Model A model of migration between two patches/demes. Migration can assumed to be symmetric or assymetric.

Metapopulation Model (aka Island Model) A model of a finite or infinite number of interconnected demes. Migration is often assumed to be random among the demes (puff ball migration) or follows a specific migration matrix.

Lattice Model A specific case of a metapopulation model where demes are arrayed along a regular grid.

Island-Continent(Mainland) Model A model of migration between an island of small size and an infinitely large/dense mainland. Mainland immigrants impact island allele frequencies/demography but island migrants are assumed to have no effect on the mainland. Note that this model is often equivalent to a metapopulation model with an infinite number of demes.