Term
|
Definition
| A statistic that tests for recombination. Coalescent history of nucleotides close to each other should be more similar than those further apart, on average, if recombination occurs. |
|
|
Term
| Absolute fitness (W, λ, r) |
|
Definition
| A parameter that predicts or predicts in part the increase in growth in numbers of a genotype. Predicts in part means that in some situations one cannot predict exactly, such as the number of offspring. Genotype-specific growth rate that predicts the absolute number of individuals of a given genotype in a population over time. Assume that it remains constant. Includes growth rate and finite rate of increase. |
|
|
Term
| Ancestral population phase |
|
Definition
| A phase of demographic expansion and spatial expansion. |
|
|
Term
|
Definition
| A locus in Drosophila melanogaster and D. simulans with a π value of 0.0044 and 0.0062, respectively. |
|
|
Term
|
Definition
| One of the most important medical inventions in human history. Its use in medicine and agriculture is increasing spread of resistant pathogenic bacteria. May be fond in wastewater in low concentrations. Found in the environment at high concentrations around 1 - 2 μg/L. It creates some of the strongest selection pressures in nature, with high selection coefficients. |
|
|
Term
| Average fitness (w-bar, λ-bar) |
|
Definition
| The frequency-weighted sum of the relative fitness values of each genotype in the population. Changes as frequencies of genotypes change. If a genotype has an absolute fitness greater than the average fitness, it will increase in frequency. |
|
|
Term
|
Definition
A frequency-weighted average, depending on the sum of the product of frequency and relative fitness for each genotype.
ptwA + qtwB |
|
|
Term
|
Definition
| Based on the idea that changes at the DNA sequence level occur with different probabilities. A true estimator because it seeks to infer the pattern of shared common ancestry. |
|
|
Term
|
Definition
| A layer of bacteria which may live on hydrothermal hot springs, and freshwater rivers. |
|
|
Term
|
Definition
| In the Moran model, a point in time when an individual reproduces by mitosis, and then another individual dies. Population size is unchanged. Genotype frequency changes by 0, +1, or -1. The probability of each of these possibilities adds up to 1. The magnitude in genotype frequency change is greater in a smaller population. |
|
|
Term
|
Definition
| The bacteria which causes Lyme disease. It is transmitted by ticks of the genus Ixodes. It is not transmitted from adult tick to its eggs; the tick must acquire the bacteria from vertebrate hosts, and can transmit it to subsequent hosts in its lifetime. It was introduced to North America from Europe, first arriving on the Eastern coast, and expanded westward into its current range. In the last 50 years populations have expanded, leading to spread of Lyme disease. |
|
|
Term
|
Definition
| A locus in Drosophila melanogaster and D. simulans with a π value of 0.0170 and 0.510, respectively. |
|
|
Term
|
Definition
| Mates by self-fertilization. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| A locus in Arabidopsis thaliana and A. lyrata ssp. Petraea with a π value of 0.0042 and 0.0135, respectively. |
|
|
Term
|
Definition
| An H1-receptor antagonist. Range of effluent is 1,300 - 1,400 μg/L. |
|
|
Term
|
Definition
| In 1859, stated the process of natural selection can be summarized as three basic observations about populations: all species have more offspring than could possibly survive and reproduce, individual organisms vary in phenotypes that influence their ability to survive and reproduce, and within each generation, individuals possessing phenotypes that confer greater survival and reproduction will contribute more to offspring to the next generation. |
|
|
Term
|
Definition
| An antibiotic-fluoroquinolone. Range of effluent is 28,000 - 31,000 μg/L. |
|
|
Term
|
Definition
| A serotonin reuptake inhibitor. Range of effluent is 770 - 840 μg/L. |
|
|
Term
|
Definition
Coalescence
"Grow together"
"Fuse"
The point in time where a pair of lineages or genealogies trace back in time to a single common ancestral lineage. |
|
|
Term
|
Definition
| Models that look at patterns among individuals available to us in the present, and try to reconstruct versions of events such as inbreeding, gene flow, or natural selection in the past that could have led to the individuals in the present. Tries to trace back through time to coalescent events. |
|
|
Term
|
Definition
| A locus in Caenorhabditis elegans and C. remanei with a π value of 0.0102, and 0.0228, respectively. |
|
|
Term
|
Definition
| Occurs when FST is significantly greater than zero. |
|
|
Term
|
Definition
| An area is divided into a grid of discrete cells, and invidiauls can potentially occupy these cells, being of different genotypes. If a cell is empty, the rate at which it is filled is proportional to the rate of births among its nearest neighbors. If there are no neighbors, there is no likelihood of an individual occupying that point. An individual in an occupied cell dies at a particular rate. Gives rise to spatial patterns in genotypes; there are regions in the area where there is only one genotype. |
|
|
Term
|
Definition
| The total number of individuals in a population. |
|
|
Term
|
Definition
| A local, small area within a larger population. When there are two demes with two genotypes, time for a genotype to get in the same deme is (1/2m), where m is the probability an individual migrates. |
|
|
Term
|
Definition
| Historical expansion from an ancestral population of small size. With no geographic structure, the population expands. Phases include expansion phase and ancestral population phase. |
|
|
Term
|
Definition
| Assumes population size is infinite. With an infinite population size, there is no genetic drift. In reality all populations have a finite size. |
|
|
Term
|
Definition
| Rate of nonsynonymous substitution at nonsynonymous sites. |
|
|
Term
|
Definition
| A measure of the type of selection occurring on a protein. The ratio of nonsynonymous substitution and synonymous substitution. If it equals 1, no selection is occurring. Calculated by estimating the coalescent tree for individuals, and estimating the ancestral sequence of the tree. Changes that have happened are figured out by comparing individuals with the ancestral sequence. |
|
|
Term
|
Definition
| Rate of synonymous substitution at synonymous sites. |
|
|
Term
| Empirical coalescent tree |
|
Definition
| An estimate backwards in time, using empirical data. |
|
|
Term
|
Definition
| An antibiotic-fluorquinolone. Range of effluent is 150 - 300 μg/L. |
|
|
Term
|
Definition
| An antibiotic-fluoroquinolone for veterinary use. Range of effluent is 780 - 900 μg/L. |
|
|
Term
|
Definition
| A locus in Arabidopsis thaliana and A. lyrata ssp. Petraea with a π value of 0.0192 and 0.0276, respectively. |
|
|
Term
|
Definition
| Diploid. Population genetics uses different tools and concepts than in prokaryotes. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| A phase of demographic expansion. |
|
|
Term
| Expected number of segregating sites (E(S)) |
|
Definition
| The expected number of mutations on a tree. In the infinite sites model, each mutation occurs at a unique site. |
|
|
Term
|
Definition
A statistical measure of population structure. A measure of the variation in genotype frequency among subpopulations. Measures the extension of population structure at different levels: subpopulations, individuals within subpopulations, and within individuals. The lower the value, the less strong the differentiation between populations, and less population structure. The greater the value, the more there is local adaptation.
0 - 0.05 = Small divergence among subpopulations
0.05 - 0.15 = Moderate divergence among subpopulations
0.15 - 0.25 = Large divergence among subpopulations
> 0.25 = Very large divergence among subpopulations |
|
|
Term
| Finite rate of increase (λ) |
|
Definition
| Absolute fitness in models where time is discrete. A multiplier that represents the net difference between the number of individuals lost from the population due to death and the number of new individuals recruited to the population by reproduction each generation. Units are per generation or time step. If the number of births and deaths are equal, then it is equal to 1, and population size does nto change. If it is greater than 1, population grows. If it is lesser than 1, population shrinks. |
|
|
Term
|
Definition
| Needed in order for bacteria to evolve resistance to high concentrations of antibiotic. |
|
|
Term
|
Definition
| A gene in HIV. An internal structure protein. |
|
|
Term
|
Definition
Allele copy
A replicated DNA sequence that has passed from ancestor to a descendant; used synonymously with the term lineage. |
|
|
Term
|
Definition
| The record of ancestor-descendant relationships for a family or locus. |
|
|
Term
|
Definition
| Typically characterized by the frequency of genotypes. Informs us about processes in the population, provided that there is a model, conceptual or theoretical, that links the two. |
|
|
Term
|
Definition
| A unique sequence of DNA encompassing all or part of a species' genome. |
|
|
Term
|
Definition
| A locus in Caenorhabditis elegans and C. remanei with a π value of 0.0009 and 0.0188, respectively. |
|
|
Term
|
Definition
| Continuous growth rate. Absolute fitness in models where time is continuous. Units are h-1 or min-1. |
|
|
Term
|
Definition
| An example of random genetic drift. The centre of a petri dish was inoculated with approximately 106 E. coli individuals with two genotypes, green and red, at a 1:1 ratio. The population expanded outwards across the face of the dish, and even though the central region was well-mixed, discrete areas of genotypes were observed near the edges. At the periphery of expansion there are a small number of individuals reproducing to fill large regions of the dish. |
|
|
Term
| Haplotype frequency distribution |
|
Definition
Site frequency spectrum
The distribution of the frequency of each sequence haplotype in a population, assuming that individuals are haploid or homozygous. Shows the proportion of sequences in a population that represent each of the observed sequence alleles. |
|
|
Term
| Height of a coalescent tree |
|
Definition
| The total time from the present to the point in the past where all k sampled lineages find their MRCA. The sum of the coalescence waiting times as coalescent events reduce the number of lineages from k, to k-1, to k-2, down to 1. |
|
|
Term
|
Definition
| This virus will adapt to different parts of an organism's body. Mechanisms for local adaptations within an individual may be due to local differentiation of cells involved in immune response, or in antiviral drug levels. |
|
|
Term
|
Definition
| Genes that are important in basic functions. Have a slower rate of evolution. |
|
|
Term
|
Definition
| A process which determines the frequencies of genotypes within the population. Relevant to diploids. |
|
|
Term
|
Definition
| A tick which lives on the west coast of North America. Transmits Borrelia burgdorferi. |
|
|
Term
|
Definition
Blacklegged tick
The tick which transmits Lyme disease to humans. Has a three-stage life cycle which takes at least two years to complete, and requires feeding on one vertebrate host per stage. Larvae and nymphs feed on small mammals or birds. Adults feed almost exclusively on white-tailed deer. Lives on the east coast of North America. Borrelia burgdorferi is not transmitted from adult ticks to eggs; it is acquired from hosts. |
|
|
Term
| Limited dispersal/migration |
|
Definition
| A process which determines the frequencies of genotypes within the population. Can lead to pronounced genetic drift, even when population size is large. |
|
|
Term
|
Definition
| A line of descent or ancestry for a homologous DNA sequence or a locus, regardless of whether or not copies of the locus are identical or different. |
|
|
Term
|
Definition
| An antibiotic-fluoroquinolone. Range of effluent is 150 - 300 μg/L. |
|
|
Term
|
Definition
Lyme borreliosis
A disease caused by the bacteria Borrelia burgdorferi. The bacteria is carried on ticks in the Ixodes genus. Affects various vertebrate species. The most common vector-borne disease in North America. First diagnosed in Lyme, Connecticut in 1976, and incidence and geographic extent in USA has incrased dramatically since that time. |
|
|
Term
|
Definition
| An angiotensin II receptor antagonist. Range of effluent is 2,400 - 2,500 μg/L. |
|
|
Term
|
Definition
| Correlates genetic and geographic distance. If there is population structure, then we expect more genetically dissimilar individuals to be geographically more distant from each other. Differs from ordinary correlation because it accounts for non-indepdendence between data points. |
|
|
Term
|
Definition
| Based on the idea that changes at the DNA sequence level occur with different probabilities. A true estimator because it seeks to infer the pattern of shared common ancestry. |
|
|
Term
|
Definition
| A large petri dish with bands of different concentrations of antibiotic. Used to show how bacteria evolve resistance quickly. |
|
|
Term
|
Definition
| A β1-adrenoreceptor antagonist. Range of effluent is 800 - 950 μg/L. |
|
|
Term
|
Definition
| Causes genotypes to become more similar. |
|
|
Term
|
Definition
| Individuals in different demes can coalesce with each other before coalescing with individuals from the same deme. |
|
|
Term
|
Definition
| Individuals in different demes can coalesce with each other before coalescign with individuals from the same deme. |
|
|
Term
| Minimal inhibitory concentration (MIC) |
|
Definition
| The lowest concentration of antibiotic yielding no visible growth of a genotype. Selection above the MIC of a strain selects even mutations with very high costs; susceptible bacteria are eliminated. Selection below the MIC of a strain causes susceptible bacteria to grow slower, but can select for resistant mutants de novo from a susceptible population, and fitness costs of the selected mutations will be considerably lower. |
|
|
Term
| Minimal selection concentration (MSC) |
|
Definition
| The concentration of antibiotic where the susceptible and resistant genotypes have the same fitness and growth rate. Fitness cost of resistance is balanced by the antibiotic-conferred selection for the resistant mutant. Coincides with a point where the selection coefficient is zero; no selection occurs at this point. A larger MSC is good because it means a larger concentration of antibiotic is needed before resistant strain has higher relative fitness than the susceptible strain. |
|
|
Term
|
Definition
| The number of pairwise differences. |
|
|
Term
|
Definition
| Distribution of pairwise differences. The frequency distribution of the number of nucleotide sites that differ between all unique pairs of DNA sequences in a sample from a single species. Can be used to infer the history of the population that gave rise to a sample of DNA sequence. Invovles calculating the number of nucleotide differences between each pair of individuals in a sample, then generating a histogram of these pairwise differences. On the x-axis is the mismatch, and on the y-axis is the frequency that a particular number of mismatches occurs in a sample. A "goodness-of-fit"-like test done to test whether the observed distribution is different from an expected distribution under a model. One can exclude a model of demographic history if it fits the distribution poorly. |
|
|
Term
|
Definition
Neo-Darwinian synthesis
Once particulate inheritance was understood, genetics was unified with the principle of natural selection. Develops expectations for the genetic changes that are caused by natural selection. |
|
|
Term
|
Definition
| Assumes that overall birth and death rates of a population are equal, so a population is stable in size. One birth-death event occurs every instantaneous point in time. Average magnitude of change in genotype frequency per birth-death event is a negative function of population size. Can be used for random genetic drift, or selection. With no selection, the average magnitude of change is an inverse function of population size. With a smaller population there are greater fluctuations, and selection has less effect. |
|
|
Term
|
Definition
| Similar to Mantel's test and test for special autocorrelation in genetic variation. Seeks to determine if there is a relationship between geographic distance and genetic distance of individuals. A positive number indicates more alikeness, and negative indicates less alikeness. |
|
|
Term
| Most recent common ancestor (MRCA) |
|
Definition
| The first common ancestor of all lineages or gene copies at some time in the past for a sample of lineages taken in the present. |
|
|
Term
| Multilocus sequence typing scheme (MSLT) |
|
Definition
| Analysis of multiple loci can buffer against potentially skewed evolutionary points. Can be used to track housekeeping genes. |
|
|
Term
| Multiple sequence alignment |
|
Definition
| Made when determining DNA sequences. The homologous nucleotide sites for each sequence are lined up in the same columns. Measures used to characterize the pattern of DNA polymorphisms include number of segregating sites and nucleotide diversity. |
|
|
Term
|
Definition
| A process which determines the frequencies of genotypes within the population. Needed in order for bacteria to evolve resistance to high concentrations of antibiotic. |
|
|
Term
|
Definition
| The mutation rate for the sequenced region(s) of the genome. A high value would be arond 10-6, or one in a million. |
|
|
Term
|
Definition
| There is a correlation between genetic and geographic distances. |
|
|
Term
| Neighbor joining tree (NJ) |
|
Definition
| A distance-based approach. Seeks to find the tree that minimizes the number of DNA sequence changes in a tree. |
|
|
Term
|
Definition
| Individuals within the same deme must coalesce with each other before coalescing with individuals from other demes. |
|
|
Term
|
Definition
| Individuals within the same deme can coalesce with individuals from other demes before coalescing with individuals from the same deme. |
|
|
Term
| Nonsynonymous substitution |
|
Definition
| A change in DNA sequence that changes protein sequence, and therefore may have effects on phenotype and fitness, if there is selection. |
|
|
Term
|
Definition
| An antibiotic-fluoroquinolone. Range of effluent is 150 - 300 μg/L. |
|
|
Term
|
Definition
| Average pairwise differences. A measure used to characterize the pattern of DNA polymorphisms in a multiple sequence alignment. Equivalent to the heterozygosity measured using alleles represented by DNA sequences, assuming random mating and the infinite sites model of mutation. Averages the number of nucleotide site differences found when each unique pair of DNA sequences in a sample is compared. Sensitive to the frequency of each DNA sequence allele in a sample. |
|
|
Term
|
Definition
| The number of mutations on a coalescent tree. |
|
|
Term
| Number of segregating sites (S) |
|
Definition
| A measure used to characterize the pattern of DNA polymophisms in a multiple sequence alignment. A segregating site is any of the L nucleotide sites that maintain two or more nucleotides within the population. |
|
|
Term
|
Definition
| An antibiotic-fluoroquinolone. Range of effluent is 150 - 160 μg/L. |
|
|
Term
|
Definition
| A gene in Borrelia burgdorferi which encodes an outer surface protein. It can be used for strain typing of the bacteria. |
|
|
Term
|
Definition
| Not known to be the truth; it is only a best approximation. |
|
|
Term
|
Definition
| Genetic variation over a geographic area. Understanding historical patterns of movement and colonization of a species. Explains current distributions. |
|
|
Term
|
Definition
| A gene in HIV. A reverse transcription protein for reproduction. |
|
|
Term
|
Definition
| A group of individuals of the same species that occupy a defined area. |
|
|
Term
|
Definition
| The study of the genetic composition of a population. |
|
|
Term
|
Definition
| The non-random distribution of genotypes geographically due to limited dispersal or local adaptation. The population has differetn geographic groups with different genes. |
|
|
Term
|
Definition
| A protein is undergoing adaptive evolution. Selection for different functional properties of a protein relative to an ancestral protein. Only changes at nonsynonymous sites can generate adaptive protein sequences. dN is greater than dS, so dN/dS is greater than 1. |
|
|
Term
| Principal component analysis (PCA) |
|
Definition
| Allows for visualization of high dimensional data on a lower dimensional surface. Finds axes that explain from the most to the least amount of variation in a dataset. Useful because it can qualitatively indicate whether the genotypes of individuals from the same deme cluster together on a 2D surface, which would indicate population structure. Can condense 500,000 dimensions into 2 dimensions. Finds a plane which cuts through the most variation, and projects all points onto this plane. |
|
|
Term
|
Definition
| Population genetics uses different tools and concepts than in eukaryotes. Generally reproduce asexually. |
|
|
Term
|
Definition
| Selection that maintains existing functional properties of a protein. Nonsynonymous substitutions are deleterious. dN/dS is lesser than 1. |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| A proess which determines the frequencies of genotypes within the population. No forces is causign genotype frequencies to change, but it changes anyway. Changes in genotype frequencies are due to random sampling in finite populations. Eventually one genotype consists of 100% of the population. All populations experience random genetic drift. Extent of drift is greater in smaller populations, and genotype fixes faster. Larger populations are more resistant to declines in frequency of a beneficial genotype. |
|
|
Term
|
Definition
| An H2-receptor antagonist. Range of effluent is 90 - 160 μg/L. |
|
|
Term
|
Definition
| A locus in Arabidopsis thaliana and A. lyrata ssp. Petraea with a π value of 0.0012 and 0.0013, respectively. |
|
|
Term
|
Definition
| A process which determines the frequencies of genotypes within the population. Genetic material from a genotype is incorporated into another genotype. Two genomes interchange parts, and form a new lineage. The upstream and downstream regions have different coalescent histories. |
|
|
Term
|
Definition
Darwinian fitness
Malthusian fitness
Absolute fitness of one genotype, relative to the absolute fitness of a standard or reference genotype, often the genotype with the highest absolute value. A more general term, unitless and useful for comparisons aross species. You do not need to known the population growth rates of each genotype; you can find the outcome of the growth process in terms of relative frequencies. If it equals one, the two genotypes have identical growth rates and the proportion of each genotype remains constant. If it is greater than one, genotype B will grow faster than A, and will represent a larger proportion of the population over time. Symbolized as w in models were time is discrete, and m in models where time is continuous. It is sometimes easier to measure experimentally than absolute fitness. Use is universal.
w = λB / λA |
|
|
Term
|
Definition
| The frequency of a genotype in a population. May be used for populations of any size. |
|
|
Term
|
Definition
| The ancestral recombination graph. A theoretical model of the ancestral history of a population that includes recombination. Parallel edges indicate possible points of recombination in the past. |
|
|
Term
|
Definition
| The number is drawn from the number of demes in teh population. |
|
|
Term
|
Definition
| A nucleotide site that is variable in a sample. |
|
|
Term
|
Definition
| A process which determines the frequencies of genotypes within the population. |
|
|
Term
| Selection coefficient (s) |
|
Definition
| The proportional increase or decrease in fitness relative to the standard/reference genotype. Magnitude ranges from 0 to 1. In nature values are generally between 0.001 and 0.01. Larger numbers occur with high antibiotic selection. May be directly estimated, such as in competition experiments. Use is universal. Fitness is unitless, and can be compared across species. |
|
|
Term
|
Definition
| Spatial expansion into multiple demes. Phases include spatial expansion phase and ancestral population phase. Can lead to pronounced genetic drift, even when population size is large. There are initially a small number of individuals in a local area at the front of expansion. By chance, one of the genotypes can reach high frequency in this small area due to drift. Combined with subsequent growth into the unoccupied region, this leads to a large region containing only a single genotype. |
|
|
Term
| Spatial expansion phase (td) |
|
Definition
| A phase of spatial expansion. |
|
|
Term
|
Definition
| Concentrations below the MIC, where there can be selection. |
|
|
Term
|
Definition
| A change in DNA sequence that does not change a protein sequence, and therefore does not change the phenotype and likely does not have fitness effects. |
|
|
Term
| Time to reach frequency of 0.5 (T50) |
|
Definition
| A proportional negaitve function of the selection coefficient. |
|
|
Term
|
Definition
| A locus in Caenorhabditis elegans and C. remanei with a π value of 0 and 0.0112, respectively. |
|
|
Term
| Traditional selective window |
|
Definition
| The range of antibiotic concentration above the MIC, previously thought to be the only concentration where there can be selection for the resistant strain. |
|
|
Term
|
Definition
| A locus in Drosophila melanogaster and D. simulans with a π value of 0.0051 and 0.252, respectively. |
|
|
Term
|
Definition
| A change from a purine to a purine, or from a pyrimidine to a pyrimidine. More common than transversions. |
|
|
Term
|
Definition
| A change from a purine to a pyrimidine, or from a pyrimidine to a purine. Less common than transitions. Lead to changes in amino acids, thus protein sequence, thus phenotype, thus sequence. On average they are deleterious. |
|
|
Term
|
Definition
| The mean or expected time back in the past until a single coalescence event in a sample of lineages. |
|
|
