Term
| Lewontin's two wars over evolution |
|
Definition
| "fit of hostility" and "fit of enthusiasm" |
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Term
|
Definition
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Term
|
Definition
| social and political misuses |
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Term
|
Definition
from Lyell's "Principles of Geology":
1) uniformity of law
2) uniformity of process
3) gradualism
4) nondirectionalism |
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Term
|
Definition
| laws of chemistry and physics have not changed during earth's history (assumption of science - not a testable hypothesis) |
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Term
|
Definition
| use familiar geological processes to explain past events (assumption of science - not a testable hypothesis) |
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Term
|
Definition
| accumulation of quantitative change leads to qualitative change (opposite - catastrophism; testable hypothesis) |
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Term
|
Definition
|
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Term
|
Definition
| Darwinism + chromosomal tehory of inheritance |
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|
Term
| Darwin's 5 Theories of Evolution |
|
Definition
1) evolution as such
2) common descent
3) multiplication of species
4) gradualism
5) natural selection |
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Term
|
Definition
| life has a long history of change |
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Term
|
Definition
| all plants and animals have descended from one form into which life was first breathed |
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Term
|
Definition
| structure of evolutionary history is a branching tree of species lineages; ancestor descendant population through time |
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Term
|
Definition
they either:
1) persist without change
2) persist with change (divergence of character)
3) branch
or 4) go extinct |
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Term
|
Definition
| ontogeny recapitulates phylogeny; organismal development repeats adult stages of ancestral forms |
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Term
| two assumptions of biogenetic law |
|
Definition
1) terminal addition
2) condensation |
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Term
|
Definition
| organisms acquiring new features at adult stages |
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Term
|
Definition
| earlier stages become condensed into shorter time periods |
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Term
|
Definition
| becomes intervertibral discs; no descendants have ever lost the notochord because it is so critical - example of common descent |
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Term
|
Definition
| evolution of new characters restricted to pre-adult stages |
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Term
|
Definition
| evolutionary change in developmental rates and timing |
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Term
|
Definition
| evolutionary changes in physical location of a developmental process |
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Term
|
Definition
| evolutionary change occurs independently in different areas of the body |
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Term
|
Definition
| the same organ in different organisms under every variety of form and function |
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Term
|
Definition
| forms derived from an equivalent characteristic of a common evolutionary ancestor |
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Term
|
Definition
| morphological, chromosomal, or molecular |
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|
Term
| clade (monophyletic group) |
|
Definition
| a group of two or more species/lineages that includes the most recent common ancestor (MRCA) of all members of the group and all of its descendants |
|
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Term
|
Definition
|
|
Term
| clades are diagnosed by... |
|
Definition
|
|
Term
| phylogenetic tree/cladogram |
|
Definition
| shows nested hierarchy of clades (groups within groups) diagnosing shared derived characters |
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Term
|
Definition
| simplest hypothesis is the favored working hypothesis (the tree topology that requires the smallest amount of evolutionary changes is the favored working hypothesis) |
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Term
|
Definition
| identifies positional homology of site homology (easy in protein coding sequences but difficult in indels) |
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Term
|
Definition
| length variation (insertion or deletion) |
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|
Term
| parsimony informative characters |
|
Definition
| have different minimum numbers of changes on contrasting topologies (hypotheses) |
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Term
|
Definition
| character similarity that does not represent common ancestry |
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Term
|
Definition
| lineages diverge from common ancestor but not from each other (type of homoplasy) |
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Term
|
Definition
| evolutionary return to ancestral character formerly lost of changed (type of homoplasy) |
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Term
|
Definition
| origin of superficially similar features by dissimilar evolutionary processes (type of homoplasy) |
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Term
|
Definition
| bacteria came to reside within another cell and became so symbiotic they stayed |
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|
Term
| multiplication of species |
|
Definition
| geographic splitting of a population followed by evolutionary divergence of the separated parts |
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Term
|
Definition
| geographic barriers precede reproductive barriers |
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Term
|
Definition
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|
Term
| biological species concept |
|
Definition
| a reproductive community of populations (reproductively isolated from other) that occupies a specific niche in nature |
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Term
|
Definition
| populations that can exchange genes (interbreed), evolves as a single unit, new mutation can spread through the species at a given time |
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Term
|
Definition
| set of resources actually or potentially used by a species' members |
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Term
|
Definition
| set of resources that is actually used by a species' members |
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Term
|
Definition
| set of resources that is potentially used by a species' members |
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Term
|
Definition
| intrinsic obstacle to the exchange of genes between populations; can be prezygotic or postzygotic |
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Term
|
Definition
| prevent formation of a zygote; examples: temporal (timing of flowering), ecological (very different niches), behavioral (courtship ritual), mechanical (incompatible genatalia), gametic |
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Term
|
Definition
| hybrid inviability, hybrid sterility, hybrid breakdown (viable and fertile but their offspring are not always viable/fertile/competent) |
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|
Term
|
Definition
| controversial theory; idea that selection acting on hybrids with postzygotic isolation leads to evolution of prezygotic isolation between populations |
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|
Term
| problems of biological species concept |
|
Definition
1) applies to sexual forms only
2) there is no temporal dimension (only looks at one area of time, no fossil study)
3) there are no single units of evolution
4) it is often not practically testable |
|
|
Term
|
Definition
| geographic variation is continuous within species and discontinuous between them (does not define species by morphological, chromosomal, or molecular differences) |
|
|
Term
| phylogenetic species concept |
|
Definition
| a lineage of ancestral-descendant populations diagnosably distinct from other such lineages |
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|
Term
| differences between phylogenetic species concept and biological species concept |
|
Definition
| phylogenetic has an explicit temporal dimension (looks backwards not at slices), allows asexual reproduction, and doesn't require that reproductive isolation has occurred |
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Term
|
Definition
| vicariance and founder effect |
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Term
|
Definition
| geographically subdividing a formerly continuous habitat |
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Term
|
Definition
| rare dispersal across pre-existing barrier |
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Term
|
Definition
| the variations are supposed to be extremely slight, but of the most diversified nature; "natura non facit saltum" |
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Term
|
Definition
| organisms with distinctly different look from parental population |
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Term
|
Definition
| used to study gradualism because they are monogamous |
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Term
|
Definition
| most controversial theory; a population-based mechanism of evolutionary change invoked to explain adaptation |
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Term
|
Definition
| observation that many organisms appeared to be there for a purpose; a trait that evolved by natural selection for a particular biological role |
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Term
|
Definition
| an organism resembles its parents more closely than it does individuals chosen at random from a population |
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|
Term
| random component of natural selection |
|
Definition
| variation is produced at random with respect to the needs of the organism |
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|
Term
| nonrandom component of natural selection |
|
Definition
| differential survival and reproduction among varying organisms causes populations to accumulate favorable variants and to discard less favorable ones |
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|
Term
|
Definition
| opposes by natural selection because it has no pre-set goal or direction |
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|
Term
|
Definition
| characteristics that exist strictly for the benefit of organisms other than the ones possessing the trait at the expense of the possessor (disagrees with natural selection; i.e. suicide of lemmings) |
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|
Term
|
Definition
| traits that might detriment survival but favor mating/reproduction |
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|
Term
|
Definition
| not necessarily a consequence of natural selection; Darwin believed a modern version of an organism could "beat up" the ancestral ones |
|
|
Term
| algorithmic definition of natural selection (Dennett) |
|
Definition
a cascade of algorithmic processes feeding on chance:
1) substrate neutrality (popln with variablity in fitness that is heritable)
2) underlying mindlessness (no preconceived goal)
3) guaranteed results |
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|
Term
|
Definition
| ability to convert resources into survival and reproduction |
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|
Term
|
Definition
| a trait co-opted by natural selection for a role incidental to the trait's origin (i.e. feathers came before flight but assist in flight) |
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Term
|
Definition
| Dennett: explanation of relationship between adaptation and exaptation |
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Term
|
Definition
| rates of multiplication just barely higher than rates of extinction |
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Term
|
Definition
| Darwin was wrong about this - believed Lamarck's use and disuse of parts |
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Term
|
Definition
| geological history of earth explained through catastrophies |
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|
Term
|
Definition
| a study group (ingroup) and close relative with polarized characters that roots the tree (outgroup) |
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|
Term
|
Definition
| specify study groups and a close relative, look at DNA in homologous gene regions and look at sites of variation |
|
|
Term
| hypthetico-deductive process = active doubt |
|
Definition
| looking for falsification of explanations with data; no positive proof of explanations; leads to best-working hypothesis; verification and corroboration |
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|
Term
| exceptions of common descent |
|
Definition
| caenogenesis, heterochrony, heterotopy, mosaic evolution - now all are central concepts of evolution |
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|
Term
| abstraction and simplification |
|
Definition
| identify essential aspects of reality and remove distracting elements |
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Term
|
Definition
| minimum number of summary variables |
|
|
Term
|
Definition
| use unreal conditions to facilitate study (i.e. ideal gas law) |
|
|
Term
|
Definition
1) reflect reality
2) have generality
3) be precise |
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|
Term
|
Definition
| all copies of homologous DNA trace to a common ancestral molecule |
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|
Term
|
Definition
| replication without mutation |
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|
Term
| 3 properties of DNA that are the basis for molecular evolution |
|
Definition
1) DNA can replicate
2) DNA can mutate and recombine
3) DNA encodes RNA and proteins that interact with environmental conditions to influence phenotype |
|
|
Term
|
Definition
| set of identical haploid genomes for a specified unit of measurement |
|
|
Term
| common usage of haplotypes |
|
Definition
| bases present at polymorphic sites are genetically linked on a DNA molecule |
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|
Term
| common forms of haploid data |
|
Definition
| DNA sequence, restriction map |
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|
Term
| single nucleotide polymorphism (SNP) |
|
Definition
|
|
Term
|
Definition
| compare number of inversions between gene orders, treating each gene order as a haplotype (not always SNPs) |
|
|
Term
|
Definition
| local population of reproducing individuals that has physical continuity over time and space; lowest biological level that can evolve |
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|
Term
|
Definition
| population of gene copies collectively shared by individuals of a deme; a population of potential gametes |
|
|
Term
|
Definition
| rules at the level of the deme by which gametes are united in fertilization, thereby defining the transition from haploidy to diploidy |
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|
Term
| essential assumption of Hardy-Weinberg |
|
Definition
| non-overlapping of generations |
|
|
Term
| life cycle for a population |
|
Definition
| deme of diploid individuals -> meiosis -> gene pool of haploid gametes -> fertilization -> deme of diploid individuals |
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|
Term
| degrees of freedom for Hardy-Weinberg |
|
Definition
| number of categories - 1 - 1 more for estimated parameter |
|
|
Term
|
Definition
| Mendelian ratios observed |
|
|
Term
| ratio of dominant:recessive phenotypes |
|
Definition
|
|
Term
| rate of elimination of lethal allele |
|
Definition
|
|
Term
| ratio of creation of lethal allele |
|
Definition
| a= Mu (as in, the Greek letter "Mu") |
|
|
Term
|
Definition
|
|
Term
|
Definition
| number of loci known to yeild lethal alleles |
|
|
Term
|
Definition
| any measurable trait, either discrete or continuous |
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|
Term
| characteristics of complex heritable phenotypes |
|
Definition
1) no discrete categories
2) no single gene necessary or sufficient for a phenotype
3) interactions among multiple genetic and environmental factors
4) confoundment of frequency and causation in complex systems |
|
|
Term
|
Definition
| genetic disorder with a heritability of ~65% with no discrete phenotypic categories (a complex heritable phenotype) |
|
|
Term
|
Definition
| the mutated allele is overdominant; there are different phenotypes associated with different genes |
|
|
Term
|
Definition
| environmental factors influence phenotype more than the genotype does |
|
|
Term
|
Definition
| continuously varying phenotypes in a population |
|
|
Term
| discrete genotypes can yield continuous phenotypes through: |
|
Definition
1) polygenic inheritance
2) environmental variation |
|
|
Term
|
Definition
| set of phenotypes associated with a particular genotype in interaction with a variety of environmental conditions and genetic backgrounds |
|
|
Term
| example of norm of reaction |
|
Definition
| drosophilia have between 700 and 1000 facets depending on the temperature |
|
|
Term
| key parameters of a normal distribution |
|
Definition
| mean (Mu) and variance (sigma^2) |
|
|
Term
|
Definition
| average or expected value of the squared deviation of x from the mean [(x-Mu)^2]/n (for Mu unknown replace denominator with n-1) |
|
|
Term
| Fisher's analysis of variance |
|
Definition
| phenotypic variance = genetic variance + environmental variance |
|
|
Term
|
Definition
|
|
Term
|
Definition
| portion of phenotypic variance that can be explained by the model genetic variation among individuals |
|
|
Term
|
Definition
| (sigma^2(g))/(sigma^2(p)) |
|
|
Term
| quantitative genetic analysis of variance (in quantitative phenotypes) |
|
Definition
| identifies correlates of populational variation, not cause and effect |
|
|
Term
| steps of quantitative genetic analysis (in quantitative phenotypes) |
|
Definition
1) assume that distribution of environmental deviations is the same every generation
2) assign a "phenotype" to a gamete and calculate average excess of the gamete type
3) calculate the breeding value (additive genotypic deviation)
4) calculate the additive genetic variance |
|
|
Term
|
Definition
| the average genotypic deviation caused by a gamete bearing allele after fertilization with a second gamete drawn at random from the gene pool; measures influence of a gamete type on phenotypic variation in the next generation |
|
|
Term
|
Definition
| additive genotypic deviation; the measured influence of a diploid genotype on phenotypic variation in the next generation |
|
|
Term
| additive genetic variance |
|
Definition
| average of the squared breeding values in the population |
|
|
Term
|
Definition
| genetic dominance is necessary but not sufficient for it |
|
|
Term
|
Definition
| nonadditive genetic variance associated with genetic epistasis |
|
|
Term
| population genetic definition of evolution |
|
Definition
| a change in the allele or gamete frequency in the gene pool |
|
|
Term
|
Definition
| factor or process that can change the frequency of an allele in the gene pool |
|
|
Term
|
Definition
| sampling error associated with finite population size |
|
|
Term
|
Definition
1) cumulative over generations
2) has no direction in frequency of alleles
3) is inversely proportional to sample size (strength is proportional to 1/2N)
4) has loss of alleles
5) isolated demes become genetically differentiated from each other |
|
|
Term
| effective population number (N(e)) |
|
Definition
| the size of an ideal population whose rate of random genetic drift equals that of the real population |
|
|
Term
|
Definition
| constant size, even sex rations, non-overlapping generations, random mating, fecundity is Poisson distributed, no selection |
|
|
Term
| inbreeding effective size |
|
Definition
| size of an ideal population whose rate of accumulation of identity by descent equals that of the real population |
|
|
Term
|
Definition
| measures probability that gametes united in fertilization are identical by descent for the locus of interest |
|
|
Term
|
Definition
| a large population today has had one or more generations of small size in the past |
|
|
Term
|
Definition
| the bottleneck that coincides with new geographic settlement |
|
|
Term
|
Definition
| number of variable loci affecting a phenotype; amount of additive and nonadditive variance |
|
|
Term
| complex genetic architecture |
|
Definition
| the founder can convert nonadditive variance to additive variance; causes increase in heritable phenotypic variation for a phenotype |
|
|
Term
|
Definition
| no impact on any phenotype related to reproductive success |
|
|
Term
|
Definition
|
|
Term
| rate of origin by mutation |
|
Definition
| 2N*(Mu), where Mu is the mutation rate to neutral alleles |
|
|
Term
|
Definition
| constant rates of evolution (Mu is constant) |
|
|
Term
| rate of long-term evolution |
|
Definition
| (rate of origin)(rate of loss) |
|
|
Term
| functional density of proteins |
|
Definition
| proportion of amino acid sites that perform specific functions (i.e. substrate recognition, active site for catalysis, ligand binding, allosteric shifts) |
|
|
Term
|
Definition
| each amino acid site contributes a small amount: charge, pH optimum, solubility |
|
|
Term
| unit evolutionary period (UEP) |
|
Definition
| time needed for 1% amino acid sequence divergence between homologous proteins |
|
|
Term
|
Definition
| most matings occur within demes, but some individuals mate outside their local deme |
|
|
Term
|
Definition
| fraction of a population that migrates to another one before mating |
|
|
Term
|
Definition
| p1-p2 (the difference in allele frequencies between the demes at generation 0) |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| gene flow (m>0) is an evolutionary force when... |
|
Definition
| d(0) doesn't equal 0; when the initial gene pools are different |
|
|
Term
|
Definition
| an evolutionary force that reduces genetic differences between demes and increases genetic variation within local populations |
|
|
Term
| Sewall Wright's measuring the balance of gene flow and genetic drift |
|
Definition
| isolation by distance does not equal total isolation; gene flow occurs mainly between neighboring populations; a new mutation can spread throughout the entire species through "stepping stones" |
|
|
Term
|
Definition
| prior knowledge relates gene function to the phenotype |
|
|
Term
|
Definition
| saturated, genome-wide linkage mapping; SNP's are major analytical tool; SNP markers every 10 centimorgans |
|
|
Term
| population studied should have... |
|
Definition
1) variation for the phenotype of interest (high incidence for disease phenotypes)
2) high levels of linkage disequilibrium among polymorphic loci within 10 cM of each other |
|
|
Term
| linkage equilibrium vs. disequilibrium |
|
Definition
| relationship between allele frequencies at 2 loci (SNP sites) and frequencies of their 2-locus haplotype |
|
|
Term
|
Definition
| use the haplotype tree to test the influence of [single] base substitutions on a phenotype of interest by reducing the analysis to 2-allele categories for a candidate locus |
|
|
Term
| tree scan procedure (QTL localization) |
|
Definition
1) use each branch of the haplotype tree to designate a pair of contrasting alleles
2) measure norms of reaction for each genotype formed (A1A1, A1A2, A2A2)
3) locate branches for which genotypes in part 2 are most different for the measured phenotype |
|
|
Term
|
Definition
| offspring resemble their parents more closely than they do individuals drawn at random from teh population for phenotypic deviations from the population mean |
|
|
Term
| parent-offspring correlations |
|
Definition
| when q is very small, almost all mating under random mating in the population is one of three types |
|
|
Term
|
Definition
| "pseudoscience"; hereditarian studies of IQ; founded by Draper; wanted to demonstrate genetic differences in intelligence/ability between African Americans and whites |
|
|
Term
| D (linkage disequilibrium) = ? |
|
Definition
| abs value(g(AB)*g(ab) - g(Ab)*g(aB)) |
|
|
Term
| linkage disequilibrium = 0 |
|
Definition
| D = ? in linkage equilibrium |
|
|
Term
|
Definition
| lower value of p1q2 or p2q1 |
|
|
Term
|
Definition
|
|
Term
| QTL (quantitative trait loci) |
|
Definition
| varying genes that each make a small contribution to variation of a quantitative phenotype in a population |
|
|
Term
| total genetic variance = ? |
|
Definition
| variance (dom) + variance (add) |
|
|
Term
|
Definition
|
|
Term
| h^2 (N) = ? (narrow sense heritability) |
|
Definition
| (sigma^2 (a))/(sigma^2 (p)) |
|
|
Term
|
Definition
| sigma^2 (g) + sigma^2 (e) |
|
|
Term
| Fisher's fundamental theorem of natural selection |
|
Definition
| rate of increase in fitnesss of a population at any time equals its additive genetic variance in fitness at that time |
|
|
Term
|
Definition
| selection maintains a polymorphism in a population |
|
|
Term
|
Definition
| allele frequencies at which average fitness reaches a local optimum |
|
|
Term
| adaptive evolution by shifting balance metapopulation (many small demes connected by gene flow) |
|
Definition
| drift in allele frequency within demes can shift average excesses for fitness; demes can explore multiple selective peaks |
|
|
Term
|
Definition
| evolves 10^6 times faster than nuclear; sampled 285 bp region of V3 region of envelope gene |
|
|
Term
|
Definition
| studied the evolution of HIV-1 by examining HIV-1 sequence data over a period of 3-4 years |
|
|
Term
|
Definition
| attracted towards macrophage then becomes dual-tropic |
|
|
Term
|
Definition
| replacement; new amino acid |
|
|
Term
|
Definition
|
|
Term
|
Definition
| number of nonsynonymous substitutions per nonsynonymous site |
|
|
Term
|
Definition
| number of synonymous substitutions per synonymous site |
|
|
Term
|
Definition
|
|
Term
| under directional selection |
|
Definition
|
|
Term
| under conservative selection |
|
Definition
|
|
Term
|
Definition
| humans decide which traits are desirable and choose the parents accordingly |
|
|
Term
|
Definition
| certain variants within a given population have traits that result in the production of more offspring |
|
|
Term
|
Definition
| leaf shape, trichome number |
|
|
Term
|
Definition
| green color, yellow flower color |
|
|
Term
|
Definition
| small epidermal "hairs"; function to absorb water and minerals |
|
|
Term
|
Definition
| stalk that connects the leaf to the stem |
|
|
Term
| components required for a PCR reaction |
|
Definition
| Taq polymerase, dNTPs, 2 primers, Mg+, buffers, DNA template strand |
|
|
Term
|
Definition
| measures heritability with respect to the mean |
|
|
Term
| parent-offspring regression |
|
Definition
| measures heritability by looking at the data as a whole |
|
|
Term
|
Definition
| qualitatively assesses change in allele frequency in a population |
|
|
Term
|
Definition
|
|
Term
| genetic drift predominates |
|
Definition
|
|
