Evolutionary Biology Modules 1-17 Review

Comprehensive vocabulary flashcards covering the key concepts of Modules 1 through 17, including evolutionary algorithms, population genetics, phylogenetics, speciation, and genome evolution.

Algorithm

A finite set of well-defined instructions for accomplishing some task which, given an initial state, will terminate in a recognizable end state.

Deterministic algorithm

An algorithm that has the same output every time.

Stochastic algorithm

An algorithm that is more random; the approximate frequency of different outcomes can be predicted.

Digital encoding of information

The process of turning text, images, or audio of a computer into binary format.

Linear regression models

A fundamental statistical and machine learning tool used to predict a continuous numeric outcome based on one or more input variables.

Common garden experiment

A test of different ecotypes under identical environmental conditions.

Reaction norm

The reaction of a given genotype to different conditions, representing the phenotypes it produces in different environments.

Genotype-by-environment interaction

A phenomenon where different genotypes respond differently to the same changes in the environment, resulting in different reaction norms.

Heritability ($h^2$)

A scaling factor estimated as the transition of response ($R$) over selection differential ($S$); higher heritability indicates a larger response to selection.

Nucleotide diversity (\text{\pi})

The average proportion of nucleotides that differ between two randomly chosen sequences in a population.

Synonymous mutation

A molecular event where a nucleotide change occurs but there is no change in the resulting amino acid.

Nonsense mutation

A mutation that results in the creation of a stop codon.

Missense mutation

A mutation that results in the replacement of one amino acid with another.

Frameshift mutation

A molecular event caused by an insertion or deletion (indel) that shifts the reading frame.

Autozygous

An individual that carries two alleles that are identical by descent.

Inbreeding coefficient ($F$)

The probability that a randomly chosen individual in the population is autozygous.

Assortative mating

A mating pattern where similar individuals are more likely to mate specifically because they are similar.

Social homogamy

A mating pattern where similar individuals are more likely to mate because they are more likely to meet.

Genetic drift

Random variation in survival and reproductive success leading to random changes in allele frequencies in finite populations.

Coalescence

A consequence of genetic drift where all alleles present in a population today eventually trace back to a single ancestral allele.

Effective population size ($N_e$)

The number of individuals in an idealized population in which the rate of genetic drift would be the same as in the actual population.

Bottleneck effect

A severe reduction in population size that accelerates genetic drift and leads to a loss of heterozygosity.

Relative fitness

A standardized measure of reproductive success among different genotypes measuring how well an organism passes on genes compared to the most successful individuals.

Selection coefficient ($s$)

A population genetics metric that quantifies the relative fitness disadvantage of a specific genotype compared to a standard, more fit genotype.

Muller’s Ratchet

A process where the mean number of mutations per genome increases from generation to generation in the absence of recombination.

Selective sweep

A result of a beneficial mutation dragging linked neutral or slightly deleterious mutations to fixation.

Hardy-Weinberg equilibrium

A state where genotype frequencies remain constant indefinitely in the absence of evolutionary forces such as mutation, selection, and migration.

Stabilizing selection

A mode of selection that applies pressure on outliers, causing the trait distribution to peak in the middle.

Negative frequency-dependent selection

A mode of selection where the rarer the phenotype, the higher its fitness.

Terminal nodes

The tips of a phylogenetic tree representing extant (currently existing) taxa.

Monophyletic taxa

A group that includes all descendants of their last common ancestor.

Paraphyletic taxa

A group that includes some, but not all, descendants of their last common ancestor.

Synapomorphies

Shared derived characters that provide the only useful source of phylogenetic information.

Homoplasies

Independently evolved characters that lead to similarities not reflecting shared descent.

Principle of maximum parsimony

The assumption that the best estimate of the true phylogeny requires the smallest number of evolutionary changes.

Incomplete lineage sorting (ILS)

A phenomenon that causes conflict between gene trees and species trees, often occurring more likely in species with larger population sizes.

Mitochondrial Eve

The woman from whom the mtDNA of all living humans originated approximately $140,000$ to $200,000$ years ago.

Biological Species Concept (BSC)

The definition of species as groups of actually or potentially interbreeding natural populations that are reproductively isolated from other groups.

Phylogenetic Species Concept (PSC)

The definition of a species as the smallest monophyletic group of common ancestry.

Dobzhansky-Muller Incompatibilities

Reproductive isolation caused by the accumulation of genetic differences where interacting alleles at different loci are unfit in hybrids.

Sympatric speciation

Speciation occurring without a physical barrier, which requires very strong selection to overcome the effects of gene flow.

Ring species

A series of populations that disperse around a circular barrier where end populations behave as different species upon meeting, despite gene flow between neighbors.

Positional cloning

A method of mapping a trait with increasing resolution until reaching a single-gene density.

LOD score

The logarithm of odds; used to compare the probability of obtaining data under a linkage hypothesis ($H_1$) versus a null hypothesis ($H_0$).

Genome-Wide Association Study (GWAS)

An observational approach scanning complete genomes of large populations to find statistical associations between genetic variants and traits.

Cis-regulatory elements (CREs)

Tissue-specific enhancers that determine when and where a gene will activate expression based on transcription factor binding.

Pleiotropy

A condition where a single gene or mutation influences multiple, seemingly unrelated phenotypic traits.

Gene cooption

A mechanism of phenotypic evolution where ancestral genes are recycled to facilitate the evolution of new traits.

Stratigraphy

The study of the composition, arrangement, and distribution of sedimentary and layered volcanic rocks to determine relative ages.

Half-life

The constant rate at which it takes for $50_{\%}$ of a radioactive isotope to decay into a stable daughter isotope.

Crown group

A group including all descendants of the latest common ancestor of all extant taxa.

Stem groups

Extinct lineages that branch below the crown group in a phylogeny.

Exaptation

A biological adaptation where the current function was not the function performed while the trait originally evolved under earlier selection pressures.

Punctuated equilibrium

An evolutionary theory characterized by periods of stasis suddenly interrupted by rapid, brief bursts of significant morphological change.

Four-fold degenerate sites

Positions in the genetic code where all four possible nucleotides specify the same amino acid, making any mutation at that site synonymous.

Pseudogenes

Genomic sequences that lack regulatory sequences, are not transcribed, and cannot perform functions in the organism.

C-value paradox

The lack of correlation between genome size and organismal complexity.

Exon shuffling

A process where new proteins with novel functions arise through the movement of exons that encode distinct functional domains.

Subfunctionalization

A possible outcome of gene duplication where the original functions of the ancestral gene are split between the two new copies.

Horizontal gene transfer (HGT)

The movement of genetic material between organisms in a manner other than traditional parent-to-offspring reproduction.