Bio 2970 Exam 3

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alignment

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permits identification of SNPs in homologous DNA sequenes

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ApoE haplotype tree

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branches denote base substitutions

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biological species concept

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also called the isolation species concept

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exaptation

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describes utility of feathers for flying in birds

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founder-effect speciation

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kind of allopatric speciation

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gradualism

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accumulation of small quantitative changes leads to qualitative change

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identity by descent

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DNA replication without mutation

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mathematical models

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typically make unrealistic assumptions to facilitate study

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measured genotype approaches

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used to find quantitative trait loci

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p

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frequency of the homozygous genotype plus half the frequency of heterozygous genotypes for a particular allele

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parsimony-informative character

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two or more ingroup taxa share a derived state

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randomness in natural selection

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new variation does not necessarily favor organismal survival and reproduction

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reinforcement

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dubious claim that postzygotic isolation leads to evolution of premating isolation

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system of mating

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guides calculation of genotype frequencies given allelic frequencies; must be specified to calculate genotypic frequencies from frequencies of alleles in a population

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Tay-Sachs disease

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a genetically transmitted but not heritable phenotype

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haplotype

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set of identical haploid genomes for a specified unit of measurement

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clade/monophyletic group

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a group of two or more species that includes the most recent common ancestor of all group members and all descendants of that ancestor

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adaptation

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a trait that evolved by natural selection for a particular biological role

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mutation and genetic drift

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a pair of evolutionary forces that explain most evolutionary change measured in the hemoglobin beta pseudogene; a pair of evolutionary forces that explain most evolutionary change measured in fibrinopeptides

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dominance variance/ dominance genetic variance

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genetic variance minus the additive genetic variance for a single-locus model; nonadditive genetic variance in a single-losuc model

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fitness

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sufficient parameter for a quantatitive phenotype whose additive variance measures evolution by natural selection

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linkage disequilibrium

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populational parameter that permits SNP markers in a genome to scan to identify chromosomal regions that contribute to variation in a quantitative phenotype; allows genome scans to identify where QTLs occur in a genome but can be misleading in identifying which variable site within a locus actually causes phenotypic variation; non random association between allelic states of two SNP markers in haplotypes

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unit evolutionary period (UEP)

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evolutionary time needed for accumulation of 1% amino-acid sequence divergence of homologous proteins in diverging lineages; the separation time in millions of years required to evolve 1% amino acid sequence divergence between homologous proteins

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isolation by distance

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sewall wright's term for a geographic population structure in which most gene flow is between neighboring demes, and many generations are required for new mutations to become geographically widespread in a species; model of population structure in which geographically distant populations do not exchange alleles directly but may do so indirectly using intervening populations as "stepping stones"

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hardy weinberg equilibrium

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common name for the mathematical demonstration that mendelian heredity does not cause evolutionary change

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drosophila pseudoobscura

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branches of a haplotype tree of chromosome-3 gene orders denote paracentric inversions

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gene pool

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population of gene copies collectively shared by individuals of a deme; defined as either the gene copies collectively shared by individuals of a deme or the deme's population of potential gametes

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genotypic deviation

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average amount by which individuals of a specified genotype differ from the mean value of their population for a quantitative phenotype

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heritable phenotype

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often has no discrete alternative categories and no single gene necessary or sufficient to produce it

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inbreeding effective size

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inversely related to the prevalence of identity by descent among copies of homologous DNA in a population; populational parameter that measures strength of genetic drift on rates of identity by descent of copies of homologous DNA; a mathematical parameter used to measure the ave rate of coalescence of alleles in a population

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measured genotype approach

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permits estimating epistatic genetic variance for a quantitative trait only if genotypes are measured at two or more loci

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Mendelian inheritance

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hardy weinberg equilibrium shows that this does not cause evolution

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norm of reaction

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each six ApoE genotypes shows a wide range of cholosterol levels, with values overlapping among genotypes; the range of phenotypes associated with a particular genotype under varying environmental conditions and genetic backgrounds

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randomness of mutation

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newly arising alleles are not predominantly ones advantageous to the possessors

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sickle-cell anemia

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hemoglobin S allele is necessary but not sufficient for this disease

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SNP

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used in a genome scan to mark an entire genome in 10cM intervals

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mutation

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evolutionary force responsible for introducing the tay-sachs allele into the human population; destroys identity by descent of copies of homologous DNA; an evolutionary force whose main consequence is to introduce many rare alleles into a population

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epistasis/ genetic epistasis

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presence of an A1 allele at the LDLR locus prevents expression of phenotypic differences between the e3 and e4 alleles in genotypes at the ApoE locus

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heritability/ narrow-sense heritability

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additive genetic variance divided by total phenotypic variance

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ideal population

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characterized by constant size, even sex ratio, nonoverlapping generations, random mating, poisson-distributed fecundity, and no selection; mathematical reference point for evaluating effective population sizes of natural populations

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variance effective size

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populational parameter that measures strength of genetic drift on rates of random change of allelic frequency

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neutral alleles

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alternative sequences of homologous DNA that have no impact on any phenotype related to reproductive success

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functional density

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denotes the proportion of amino acid sites that perform specific function (including substrate recognition, active site for catalysis, ligand binding, and allosteric shifts) in a protein

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average (x-meanx)(y-meany)

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covariance between parent and offspring used by fischer to estimate additive genetic variance for a quantitative phenotype

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dn=do(1-2m)^n

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recurring migration between demes across many generations keeps their allele frequencies similar

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epistatic genetic variance

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measurable in candidate-locus studies only if genotypes at two or more loci are studied together

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gAB*gab does not equal gAb*gaB

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linkage disequilibrium

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genetic architecture

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number of varying loci affecting a quantitative trait and amounts of additive and nonadditive genetic variance

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genetic drift

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evolutionary properties include no direction, cumulative across generations, loss of alleles, and genetic divergence among isolated demes; evolutionary change caused by sampling error inherent of finite population size

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hemoglobin A/S genotype

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shows codominance of alleles for protein electrophoretic mobility

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inbreeding

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populational measure of the probability that gametes united in fertilization are identical by descent at a locus

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protein functional density

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inversely proportional to the probability that amino acid substitutions produce neutral alleles

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s^2

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measures width of the normal distribution of a quantitative phenotype in a population

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tree scan

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used to determine which of the SNP sites that differ among haplotypes for a candidate locus associate most strongly with phenotypic variation in a population

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(2Nmu)(1/2N)= mu

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describes the long-term rate of neutral evolution of a protein sequence

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phenylketonuria

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a human disease caused by interaction between a dietary condition and homozygosity for an enzyme deficiency, for which the dietary condition is common and the genetic condition rare

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scurvy

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a human disease caused by interaction between a dietary condition and homozygosity for an enzyme deficiency, for which the dietary condition is rare and the genetic condition common

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coronary artery disease

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a human disease of varying severity, which has heritability of 65% but for which no single environmental or genetic factor is either necessary or suffieient

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standard deviation

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square root of variance

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bottleneck

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general term for one or more generations of small size in the history of a population

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paracentric inversion

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kind of genetic change denoted by each branch of Dobzhansky and Sturtevant's haplotype tree of gene orders for chromosome 3 of drosophilis persimilis and D. pseudoobscura

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additive genetic variance

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equals the narrow-sense heritability multiplied by the total phenotypic variance

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average excess

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analytical assignment of a phenotype to a gamete

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bonellia

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illustrates the importance of environment on development of the adult phenotype

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broad-sense heritability

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ratio of the total genetic variance to phenotypic variance within a generation

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g(AB)g(ab)=g(Ab)g(aB)

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linkage equlibrium

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1/2N

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measures the strength of genetic drift in a population for an autosomal locus

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persistence of fetal hemoglobin

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shows epistatic interaction with the sickle-cell allele in some human populations

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(p^2 + 2pq)/ q^2

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ratio of a dominant to recessive phenotype in a population at HW equilibrium

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synonymous substitutions

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evolve more rapidly than nonsynonymous substitutions for protein-coding genes

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mean and variance/ mean and standard deviation

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two parameters needed to describe a normal distribution

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correlation/ correlation coefficient

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a standardized measure of covariance that varies from -1 to +1

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quantitative trait loci (QTL)

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varying genes that each make a small contribution to variation of a quantitative phenotype in a population

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single nucleotide polymorphism (SNP)

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a site in the genome at which two different bases occur as the common alternative alleles in a population

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gene flow

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movement of genes among demes of the same species by migration of individuals prior to mating

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founder effect/ founder event

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occurrence of a population bottleneck associated with establishment of a new geographic deme in the history of a population

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heterozygosity

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a name for the probability that two alleles selected at random from a population are not identical by descent

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F(sub ST)

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Sewall Wright's statistic used to express the proportion of allelic diversity partitioned among rather than within local populations of a species