Term
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Definition
| This describes an “ideal” population, which will maintain the same allele and genotype frequencies over time, due to the absence of any of the phenomena that drive evolution (mutation, migration, selection, drift). |
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Definition
| Having more than one allele of a single gene present in a population. |
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Definition
| Having only a single allele for a single gene present in a population. |
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Definition
| Having the same allele present on both parental chromosomes (found in diploid organisms). |
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Definition
| Having different alleles on each of the parental chromosomes (diploid). |
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Definition
| Different enzymes that are encoded by different alleles present at a single locus. |
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Definition
| Mating between individuals in a population is not influenced by the genotype of either partner. |
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Term
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Definition
| A genotype that is identical to the genotype of one parent that presents due to recombination not occurring between two linked loci. If the loci are closely linked, the nonrecombinant offspring will far outnumber the recombinant offspring. |
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Term
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Definition
| A genotype resulting from the recombination of parental alleles at linked loci. This genotype will differ from the parental genotype, and will occur at a much lower rate than either parental genotype. If the loci are not linked, the same genotype will occur 50% of the time, not because of recombination but simply because of independent assortment. |
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Term
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Definition
| A deviation from independence seen in an individual’s gametes, in which certain alleles are more frequently represented than expected by chance. This can occur from linkage between loci, as well as from occurrences like “selfish genes,” which will occur more frequently than expected by chance in a gametic population. |
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Definition
| A deviation from independence seen in the assortment of two loci, which is caused by the two loci being physically close together on the chromosome, and thus inherited together more often than separated by recombination. |
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Term
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Definition
| This is the log10 of D, which is the likelihood ratio (linkage likelihood over independence likelihood). |
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Term
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Definition
| This is the genes that are inherited from a single parent (in diploid organisms). |
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Term
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Definition
| This is a test that evaluates the goodness of fit of a set of data relative to the null hypothesis. In this course, the null hypothesis is that the population is in Hardy-Weinberg proportions. By assessing allele frequencies and comparing them to a Chi-squared distribution with the same degrees of freedom, we can determine how likely it in that the population is in HW proportions or not. |
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Term
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Definition
| This is a statistical distribution that gives the probability of an event occurring when there are two possible outcomes. In the case of p and q in a population, the allele frequencies in Hardy-Weinberg proportions is derived from the binomial distribution, and comes out to (p+q)(p+q)=p2+2pq+q2 |
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Term
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Definition
| This is caused by the random sampling that comes from a population of finite size. Allele frequencies will change over time in a finite population due to some alleles being passed on to the next generation in higher or lower frequencies simply due to random chance. A powerful example of this is the bottleneck effect. |
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Term
| Identical by descent (i.b.d.) |
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Definition
| When the same allele is found in two individuals due to their sharing a common ancestor. The allele is the same one that was found in the common ancestor, and was passed down through generations into both of the individuals’ DNA. |
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Term
| Effective population size |
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Definition
| The number of individuals in a population that contribute alleles to the next generation. The size of the effective population can be changed by several factors, including sex ratio and mating systems. The effective population size is more appropriate to use for calculations involving drift, since only the individuals that mate will contribute to the allele composition of the next generation. |
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Term
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Definition
| An event in which effective population size is suddenly and dramatically decreased. The alleles that remain were randomly selected from within the finite population, and thus will likely occur is a much different frequency than in the original population. This will likely push many alleles to fixation or loss and lower genetic diversity. |
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Definition
| The theory that most of the genetic evolution that occurs is due to random genetic drift, since most alleles have neutral fitness scores and will not be subject to selection. |
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Term
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Definition
| An organism’s likelihood of surviving to reproductive age and reproducing to contribute offspring to the next generation. This is also used for individual genotypes, as in the degree to which they will contribute to the organism’s likelihood to survive and reproduce. |
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Term
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Definition
| The average fitness of all genotypes containing a given allele weighted by the number of alleles contained in each genotype, for p it is w1 = p(w11) + q(w12) |
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Term
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Definition
| A situation in which two alleles are maintained in a population of organisms because heterozygotes are better able to survive than either homozygote. |
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Term
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Definition
| When the heterozygote is more fit than either homozygote, the population will experience balancing selection and will reach an equilibrium point between the two alleles, in which any deviation from the equilibrium will be reversed in following generations. |
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Term
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Definition
| When the heterozygote is less fit than either of the homozygotes, the population will reach an unstable equilibrium. If the allele frequency ever deviates from the equilibrium value, the allele that is higher at this point will be pulled to fixation and the other will be lost. |
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Definition
| When the heterozygote is more fit than either homozygote. |
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Term
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Definition
| When the heterozygote is less fit than either homozygote. |
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Term
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Definition
| The same as underdominance, but generally refers to hybrid inferiority, in which two diverging populations have offspring that are less fit than the offspring of either of the separate populations. |
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Term
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Definition
| Selection coefficients, s and h, give the relative fitness of the other homozygote and the heterozygote when compared to a homozygote with a fitness set at 1. The heterozygote’s fitness is equal to 1-hs, and the homozygote’s is equal to 1-s. |
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Term
| Fisher's Fundamental Theorem of Natural Selection |
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Definition
| "The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time." Natural selection will always tend to lead to increased fitness. |
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Term
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Definition
| A graph of allele frequency vs. mean fitness of the population. In directional selection, the slope will always be positive as the more fit homozygote increases in frequency. In balancing selection with a stable equilibrium, the peak of the graph occurs at the equilibrium value. |
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Term
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Definition
| Sewall Wright’s theory of evolution (contrasts with Fisher’s theory). Describes the way in which adaptive landscapes can be traversed by populations as they diverge and drift changes allele frequency randomly. A population at an adaptive peak can be pushed through drift to the base of a new adaptive peak (into an adaptive valley), then natural selection will push the population to the new peak. |
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Term
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Definition
| A mutation occurring at the same nucleotide base more than one time. It is incredibly unlikely, and can essentially have its likelihood estimated to be zero. |
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Term
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Definition
| A model which considers any new mutation to be a new allele, regardless of its effect on phenotype. |
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Term
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Definition
| Mutation model which assumes that alleles are represented by integer values and that a mutation either increases or decreases the allele value by one. For variable number tandem repeats loci (VNTR), the allele value is generally taken as the number of tandem repeats in the DNA sequence. |
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Term
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Definition
| A model which considers any new mutation within a gene to be changing the gene from the ancestral allele A to the new allele B. This is useful for calculating the equilibrium state between mutations to B and back to A, but is likely not quite as accurate on a molecular level as the infinite alleles model. |
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Term
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Definition
| The nearly neutral theory of molecular evolution is a modification of the neutral theory of molecular evolution that accounts for the fact that not all mutations are either so deleterious such that they can be ignored, or else neutral. Slightly deleterious mutations are reliably purged only when their selection coefficient is greater than one divided by the effective population size. In larger populations, a higher proportion of mutations exceed this threshold for which genetic drift cannot overpower selection, leading to fewer fixation events and so slower molecular evolution. These nearly neutral mutations will only be selected against when s > (1/Ne). |
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Term
| Mutation-selection balance |
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Definition
| The equilibrium value at which deleterious alleles enter the population through mutation at an equal rate to the same alleles being removed from the population by selection. |
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Term
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Definition
| The difference between the average individual in a population and a theoretical optimal individual. A very low genetic load indicates that the individual being compared has a low chance of survival compared to the best possible individual. L = (Wopt – mean fitness) / Wopt |
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Term
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Definition
| Positive feedback cycle, in which the accumulation of mutational load causes a decrease in population size, which causes an increase in inbreeding depression (that is, deleterious recessive alleles are expressed in homozygous state after mating of related individuals), which causes a further decrease in population size and so on. Computer models suggest that such a mutational meltdown can lead to population extinction. |
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Term
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Definition
| In asexual populations, deleterious alleles will continue to be accumulated in the genome without being removed by selection. This is a hypothesis to explain why sexual selection has been favored by evolution. |
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Term
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Definition
| The loss of genetic diversity that comes from a population derived from a small number of migrant ancestors. The effect on genetic diversity is like that caused by a population bottleneck. |
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Term
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Definition
| The likelihood that an allele will become fixed in a population of a given size N. This probability is determined by mutation rate, selection coefficients, and effective population size. |
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Term
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Definition
| The likelihood that an allele will become fixed in a population. This probability is determined by mutation rate, selection coefficients, and effective population size. |
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Term
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Definition
| The number of generations that are required for an allele to be fixed or lost from a population. The time varies by the mutation rate, selection, and effective population size. |
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Term
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Definition
| Mating between closely-related individuals. |
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Term
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Definition
| Mating between unrelated individuals. |
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Term
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Definition
| Assortative mating is a mating pattern and a form of sexual selection in which individuals with similar phenotypes mate with one another more frequently than would be expected under a random mating pattern. |
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Term
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Definition
| Increased fitness found in a crossbred/outbred/hybrid individual. |
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Term
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Definition
| Same as heterosis - increased fitness found in a crossbred/outbred/hybrid individual. |
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Term
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Definition
| The decreased fitness, sterility, or inviability of offspring resulting from a hybrid cross. These effects increase and maintain speciation between populations of similar organisms. |
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Term
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Definition
| When crosses between genetically distant or unrelated individuals are less fit than crosses between more closely related individuals. |
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Term
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Definition
| Several genetic mechanisms which prevent the successful fertilization of a plant with an individual that is too closely related (self) and promote outbreeding. In plants with SI, when a pollen grain produced in a plant reaches a stigma of the same plant or another plant with a similar genotype, the process of pollen germination, pollen-tube growth, ovule fertilization and embryo development is halted at one of its stages and consequently no seeds are produced. |
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Term
| Sporophytic incompatibility |
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Definition
| Self-incompatibility in which the SI phenotype of the pollen is determined by the phenotype of the anther/sporophyte. |
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Term
| Gametophytic incompatibility |
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Definition
| SI in which the SI phenotype of the pollen is determined by its own gametophytic haploid phenotype. |
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Term
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Definition
| Populations of a single species live physically apart from each other, meaning that breeding between populations is reduced or eliminated. |
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Term
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Definition
| Species share an environment. Often used to describe multiple distinct species living in the same place, but can refer to a single species living in one place that is diverging based on choice of ecological niche. |
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Term
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Definition
| Tandem array of short (1-6 base pairs) repeated sequences, with a total degree of repetition of five to about one hundred at each locus, and usually scattered randomly throughout the genome. For example, the repeat unit can be simply CA, and might exist in a tandem array of, for instance, 50 repeats, denoted by (CA)50. The number of repeats in an array can be highly variable, giving rise to extensive polymorphism. |
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Term
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Definition
| The capability of surviving, often in the sense of the viability of offspring. If the offspring of a cross are inviable, then they will not survive. This is the most dramatic effect of speciation. |
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Term
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Definition
| Fertility, the ability to produce gametes and mate to create viable offspring. |
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Term
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Definition
| A.K.A. fixation indices, these describe the deviation in heterozygosity from Hardy-Weinberg expectations in a population undergoing changes in allele frequency. |
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Term
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Definition
| A model of migration in which a source population is considered to have an infinite population which is donating migrants to a much smaller island population. In the absence of strong selection, the island population's allele frequency will eventually become equal to that of the mainland population. |
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Term
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Definition
| A model of migration in which multiple "islands" exist, in which gene flow between adjacent islands is more common than between more distant islands. |
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Term
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Definition
| A model of migration in which many islands exist, all of which have an equal chance of contributing migrants to any other island. |
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Term
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Definition
| The movement of genes between populations, otherwise known as migration. |
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Term
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Definition
| A mutation in which one nucleotide is changed to another. |
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Term
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Definition
| A mutation that does not affect the phenotype of the organism. Can be a synonymous mutation or one that is outside of a functional region. |
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Term
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Definition
| A substitution that does not change the amino acid being coded for. |
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Term
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Definition
| Same as substitution mutation. |
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Term
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Definition
| A mutation that causes a change in the amino acid coded for, and possibly a change in phenotype. |
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Term
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Definition
| The idea that mutations will occur at regular intervals over time within a species, which can then be counted to determine species divergence. It is not always accurate, since mutations can occur at different rates. |
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Term
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Definition
| Also known as purging or negative selection, this is selection that removes deleterious alleles from the population. |
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Term
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Definition
| This type of selection occurs when advantageous alleles arise in a population and are selected for until they sweep the population. |
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Term
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Definition
| A form of selection in which polymorphism is conserved at a locus, often due to the heterozygotes at that locus having higher fitness than either of the homozygotes. |
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Term
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Definition
| The reduction in genetic variance around the site of a strongly positiviely selected mutation. |
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Term
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Definition
| This occurs when neutral or slightly deleterious alleles are swept to fixation due to their close physical proximity to a strongly positively selected mutation. |
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Term
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Definition
| This is a test of the neutral theory, in which observed homozygosity is compared to expected homozygosity under the neutral theory. If the difference between the two is large enough, the null hypothesis of neutrality can be rejected. |
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Term
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Definition
| This is a test of the neutral theory, in which multiple DNA sequences are compared. The mean number of pairwise differences and the number of segregating sites, which should be equal under neutral theory, are compared. If they are significantly different, the neutral theory can be rejected. |
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Term
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Definition
| This is a test of the neutral theory, in which polymorphisms within a species are compared to the divergence between species. If a species shows high polymorphism but low divergence at a site (or vice-versa), the neutral theory can be rejected. |
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Term
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Definition
| This is a test of the neutral theory, in which polymorphism within a species is compared to the divergence between species at neutral (synonymous/silent) and non-neutral (non-synonymous) sites. |
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Term
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Definition
| A gene tree depicts the evolutionary history of a gene, including duplication events and mutations. They can include paralogues within a single species as well as orthologues between species and the differences they include. |
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Term
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Definition
| Operational taxonomic unit, a working definition for grouping closely-related organisms based on genetic similarity. |
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Term
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Definition
| Most recent common ancestor, the most recent ancestor of two or more species that have now diverged. It is represented on a phylogenetic tree as a node connecting two or more branches that end in a single species. |
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Term
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Definition
| Arranging a DNA, RNA, etc. sequence against a related species' homologous sequence to find regions of homology and divergence and in some cases to determine the region's function based on the annotation of the other's organism's sequence. |
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Term
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Definition
| A method of hierarchical clustering in which species are grouped by pairwise comparisons starting with the most similar pair and moving to the least similar pair. It is an unweighted calculation, so branch length is not determined by species relatedness. |
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Term
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Definition
| A hierarchical clustering method based around creating a tree with the least possible genetic distance. |
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Term
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Definition
| The simplest scientific explanation for the evidence. In tree-building, it means that the model with the least mutation is the most likely. |
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Term
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Definition
| A method of taxonomic tree selection that maximizes the probability of the observed genetic data. |
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Term
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Definition
| Site that is useful to determine relatedness between 4 indidividuals. Need 3 different alleles. 2 individuals will share an allele (A), and the other two individuals will share another allele. |
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Term
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Definition
| An allele has become fixed - there is no variation at this site in the population. |
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Term
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Definition
| An allele or trait that is unique to a single species on a tree, ie the mutation causing this trait occurred on the branch leading to this species. |
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Term
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Definition
| When two species share a mutation on their ancestral line, while the other species being compared have different alleles at that site. |
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Term
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Definition
| An invariant, autoapomorphic, simple isomorphic, or extremely variable site - cannot be used to make phylogenetic assumptions. |
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Term
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Definition
| The use of DNA testing in combination with traditional genealogy and traditional genealogical and historical records to infer relationships between individuals. |
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Term
| Spatially varying environments |
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Definition
| The habitat varies over space, like the example of the birds that live in either the trees or the savannah but never interbreed. |
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Term
| Temporally varying environments |
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Definition
| The habitat varies over time, for example seasonally, so that mating and survival challenges change within the same space. |
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Term
| Frequency dependent selection |
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Definition
| A situation in which the fitness associated with a given allele is a function of the proportion of other alleles in the population. |
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Term
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Definition
| One gene controls for more than one trait, where at least one trait is beneficial and at least one is detrimental to the organism. |
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Term
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Definition
| A form of selection in which individuals choose a mate based on desirable characteristics, often those which indicate greater fitness. |
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Term
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Definition
| Overall variance in traits for a population. It results from a combination of genetic and environmental variance. |
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Term
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Definition
| Phenotypic variance that is due to genetics. |
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Term
| Additive genetic variance |
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Definition
| The only form of genetic variance that is included in narrow-sense heritability. It is the variance that can be seen where the addition of a particular allele always adds a quantifiable amount to a trait. |
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Term
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Definition
| Variance due to heterozygotes not being exact midpoints of homozygote parents. |
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Term
| Narrow sense heritability |
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Definition
| The ratio of additive genetic variance to phenotypic variance. |
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Term
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Definition
| The ratio of total genetic variance to total phenotypic variance. |
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Term
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Definition
| The average effect a given allele has on phenotype or phenotypic value. |
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Term
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Definition
| The mean phenotypic value of an individual's offspring. |
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Term
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Definition
| The change in phenotypic value from the base population when individuals with a trait of interest are selected and crossed. |
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Term
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Definition
| A section of DNA (locus) that directly corresponds to a change in the individual's phenotype. |
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