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Biology 2970 Final (Larson)
Larson's section of the final (population genetics)
199
Biology
Undergraduate 2
12/10/2008

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Term
Lewontin's two wars over evolution
Definition
"fit of hostility" and "fit of enthusiasm"
Term
"fit of hostility"
Definition
religious creationism
Term
"fit of enthusiasm"
Definition
social and political misuses
Term
uniformitarianism
Definition
from Lyell's "Principles of Geology":

1) uniformity of law
2) uniformity of process
3) gradualism
4) nondirectionalism
Term
uniformity of law
Definition
laws of chemistry and physics have not changed during earth's history (assumption of science - not a testable hypothesis)
Term
uniformity of process
Definition
use familiar geological processes to explain past events (assumption of science - not a testable hypothesis)
Term
gradualism
Definition
accumulation of quantitative change leads to qualitative change (opposite - catastrophism; testable hypothesis)
Term
nondirectionalism
Definition
dynamic steady state
Term
neodarwinism
Definition
Darwinism + chromosomal tehory of inheritance
Term
Darwin's 5 Theories of Evolution
Definition
1) evolution as such
2) common descent
3) multiplication of species
4) gradualism
5) natural selection
Term
evolution as such
Definition
life has a long history of change
Term
common descent
Definition
all plants and animals have descended from one form into which life was first breathed
Term
phylogeny
Definition
structure of evolutionary history is a branching tree of species lineages; ancestor descendant population through time
Term
lineage fates
Definition
they either:
1) persist without change
2) persist with change (divergence of character)
3) branch
or 4) go extinct
Term
biogenetic law
Definition
ontogeny recapitulates phylogeny; organismal development repeats adult stages of ancestral forms
Term
two assumptions of biogenetic law
Definition
1) terminal addition
2) condensation
Term
terminal addition
Definition
organisms acquiring new features at adult stages
Term
condensation
Definition
earlier stages become condensed into shorter time periods
Term
notochord
Definition
becomes intervertibral discs; no descendants have ever lost the notochord because it is so critical - example of common descent
Term
caenogenesis
Definition
evolution of new characters restricted to pre-adult stages
Term
heterochrony
Definition
evolutionary change in developmental rates and timing
Term
heterotopy
Definition
evolutionary changes in physical location of a developmental process
Term
mosaic development
Definition
evolutionary change occurs independently in different areas of the body
Term
homology (Owen)
Definition
the same organ in different organisms under every variety of form and function
Term
homology (evolutionary)
Definition
forms derived from an equivalent characteristic of a common evolutionary ancestor
Term
homologies can be...
Definition
morphological, chromosomal, or molecular
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
Term
synapomorphy
Definition
shared derived character
Term
clades are diagnosed by...
Definition
sharing of homologies
Term
phylogenetic tree/cladogram
Definition
shows nested hierarchy of clades (groups within groups) diagnosing shared derived characters
Term
parsimony
Definition
simplest hypothesis is the favored working hypothesis (the tree topology that requires the smallest amount of evolutionary changes is the favored working hypothesis)
Term
alignment
Definition
identifies positional homology of site homology (easy in protein coding sequences but difficult in indels)
Term
indel
Definition
length variation (insertion or deletion)
Term
parsimony informative characters
Definition
have different minimum numbers of changes on contrasting topologies (hypotheses)
Term
homoplasy
Definition
character similarity that does not represent common ancestry
Term
parallelism
Definition
lineages diverge from common ancestor but not from each other (type of homoplasy)
Term
character reversal
Definition
evolutionary return to ancestral character formerly lost of changed (type of homoplasy)
Term
convergence
Definition
origin of superficially similar features by dissimilar evolutionary processes (type of homoplasy)
Term
endosymbiotic hypothesis
Definition
bacteria came to reside within another cell and became so symbiotic they stayed
Term
multiplication of species
Definition
geographic splitting of a population followed by evolutionary divergence of the separated parts
Term
allopatric speciation
Definition
geographic barriers precede reproductive barriers
Term
nonallopatric speciation
Definition
sympatric-

parapatric-
Term
biological species concept
Definition
a reproductive community of populations (reproductively isolated from other) that occupies a specific niche in nature
Term
reproductive community
Definition
populations that can exchange genes (interbreed), evolves as a single unit, new mutation can spread through the species at a given time
Term
niche
Definition
set of resources actually or potentially used by a species' members
Term
realized niche
Definition
set of resources that is actually used by a species' members
Term
fundamental niche
Definition
set of resources that is potentially used by a species' members
Term
reproductive barriers
Definition
intrinsic obstacle to the exchange of genes between populations; can be prezygotic or postzygotic
Term
prezygotic barriers
Definition
prevent formation of a zygote; examples: temporal (timing of flowering), ecological (very different niches), behavioral (courtship ritual), mechanical (incompatible genatalia), gametic
Term
postzygotic barriers
Definition
hybrid inviability, hybrid sterility, hybrid breakdown (viable and fertile but their offspring are not always viable/fertile/competent)
Term
reinforcement
Definition
controversial theory; idea that selection acting on hybrids with postzygotic isolation leads to evolution of prezygotic isolation between populations
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
species diagnosis
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
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
Term
sources of allopatry
Definition
vicariance and founder effect
Term
vicariance
Definition
geographically subdividing a formerly continuous habitat
Term
founder effect
Definition
rare dispersal across pre-existing barrier
Term
gradualism
Definition
the variations are supposed to be extremely slight, but of the most diversified nature; "natura non facit saltum"
Term
"sport"; "monster"
Definition
organisms with distinctly different look from parental population
Term
pigeons
Definition
used to study gradualism because they are monogamous
Term
natural selection
Definition
most controversial theory; a population-based mechanism of evolutionary change invoked to explain adaptation
Term
adaptation
Definition
observation that many organisms appeared to be there for a purpose; a trait that evolved by natural selection for a particular biological role
Term
heritable variation
Definition
an organism resembles its parents more closely than it does individuals chosen at random from a population
Term
random component of natural selection
Definition
variation is produced at random with respect to the needs of the organism
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
Term
teleology
Definition
opposes by natural selection because it has no pre-set goal or direction
Term
altruism
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)
Term
sexual selection
Definition
traits that might detriment survival but favor mating/reproduction
Term
progressive adaptation
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
Term
fitness
Definition
ability to convert resources into survival and reproduction
Term
exaptation
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)
Term
"cranes making cranes"
Definition
Dennett: explanation of relationship between adaptation and exaptation
Term
biodiversity
Definition
rates of multiplication just barely higher than rates of extinction
Term
mode of inheritance
Definition
Darwin was wrong about this - believed Lamarck's use and disuse of parts
Term
catastrophism
Definition
geological history of earth explained through catastrophies
Term
ingroup vs. outgroup
Definition
a study group (ingroup) and close relative with polarized characters that roots the tree (outgroup)
Term
phylogeny reconstruction
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
Term
exceptions of common descent
Definition
caenogenesis, heterochrony, heterotopy, mosaic evolution - now all are central concepts of evolution
Term
abstraction and simplification
Definition
identify essential aspects of reality and remove distracting elements
Term
sufficient parameters
Definition
minimum number of summary variables
Term
assumptions
Definition
use unreal conditions to facilitate study (i.e. ideal gas law)
Term
we want models to...
Definition
1) reflect reality
2) have generality
3) be precise
Term
coalescence
Definition
all copies of homologous DNA trace to a common ancestral molecule
Term
identity by descent
Definition
replication without mutation
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
haplotype
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
Term
common forms of haploid data
Definition
DNA sequence, restriction map
Term
single nucleotide polymorphism (SNP)
Definition
Term
to create haplotype tree
Definition
compare number of inversions between gene orders, treating each gene order as a haplotype (not always SNPs)
Term
deme
Definition
local population of reproducing individuals that has physical continuity over time and space; lowest biological level that can evolve
Term
gene pool
Definition
population of gene copies collectively shared by individuals of a deme; a population of potential gametes
Term
system of mating
Definition
rules at the level of the deme by which gametes are united in fertilization, thereby defining the transition from haploidy to diploidy
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
Term
degrees of freedom for Hardy-Weinberg
Definition
number of categories - 1 - 1 more for estimated parameter
Term
p=q=0.5
Definition
Mendelian ratios observed
Term
ratio of dominant:recessive phenotypes
Definition
(p^2 + 2pq) : q^2
Term
rate of elimination of lethal allele
Definition
a=q^2
Term
ratio of creation of lethal allele
Definition
a= Mu (as in, the Greek letter "Mu")
Term
at equilibrium q^2 =
Definition
q^2=Mu
Term
~1000 loci
Definition
number of loci known to yeild lethal alleles
Term
phenotype
Definition
any measurable trait, either discrete or continuous
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
coronary artery disease
Definition
genetic disorder with a heritability of ~65% with no discrete phenotypic categories (a complex heritable phenotype)
Term
sickle cell anemia
Definition
the mutated allele is overdominant; there are different phenotypes associated with different genes
Term
PKU
Definition
environmental factors influence phenotype more than the genotype does
Term
quantitative genetics
Definition
continuously varying phenotypes in a population
Term
discrete genotypes can yield continuous phenotypes through:
Definition
1) polygenic inheritance
2) environmental variation
Term
norm of reaction
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
variance
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
sigma^2 (genetic) = ?
Definition
sum((HW freq.)(x-Mu)^2)
Term
broad-sense heritability
Definition
portion of phenotypic variance that can be explained by the model genetic variation among individuals
Term
h^2 (B) = ?
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
average excess
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
breeding value
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
dominance variance
Definition
genetic dominance is necessary but not sufficient for it
Term
epistatic variance
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
evolutionary forces
Definition
factor or process that can change the frequency of an allele in the gene pool
Term
genetic drift
Definition
sampling error associated with finite population size
Term
genetic drift is:
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
ideal population
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
inbreeding
Definition
measures probability that gametes united in fertilization are identical by descent for the locus of interest
Term
bottleneck effect
Definition
a large population today has had one or more generations of small size in the past
Term
founder effect
Definition
the bottleneck that coincides with new geographic settlement
Term
genetic architecture
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
neutral alleles
Definition
no impact on any phenotype related to reproductive success
Term
rate of loss of alleles
Definition
1/2N
Term
rate of origin by mutation
Definition
2N*(Mu), where Mu is the mutation rate to neutral alleles
Term
molecular clock
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
general functions
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
gene flow
Definition
most matings occur within demes, but some individuals mate outside their local deme
Term
m = ?
Definition
fraction of a population that migrates to another one before mating
Term
d(0) = ?
Definition
p1-p2 (the difference in allele frequencies between the demes at generation 0)
Term
p1' = ?
Definition
p1 - m*d(0)
Term
p2' = ?
Definition
p2 + m*d(0)
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
gene flow
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
candidate loci
Definition
prior knowledge relates gene function to the phenotype
Term
genome scan
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
tree scan
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
heritability
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
Pioneer Fund
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
D(max) = ?
Definition
lower value of p1q2 or p2q1
Term
D' = ?
Definition
D/D(max)
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
genetic variance = ?
Definition
freq*(gen. dev.)^2
Term
h^2 (N) = ? (narrow sense heritability)
Definition
(sigma^2 (a))/(sigma^2 (p))
Term
sigma^2 (p) = ?
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
balanced polymorphism
Definition
selection maintains a polymorphism in a population
Term
selective peaks
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
HIV genome
Definition
evolves 10^6 times faster than nuclear; sampled 285 bp region of V3 region of envelope gene
Term
ALIVE study
Definition
studied the evolution of HIV-1 by examining HIV-1 sequence data over a period of 3-4 years
Term
M-tropic
Definition
attracted towards macrophage then becomes dual-tropic
Term
nonsynonymous site
Definition
replacement; new amino acid
Term
synonymous site
Definition
silent; same amino acid
Term
d(N)
Definition
number of nonsynonymous substitutions per nonsynonymous site
Term
d(S)
Definition
number of synonymous substitutions per synonymous site
Term
neutral prediction
Definition
d(N)/d(S) = 1
Term
under directional selection
Definition
d(N)/d(S) > 1
Term
under conservative selection
Definition
d(N)/d(S) < 1
Term
artificial selection
Definition
humans decide which traits are desirable and choose the parents accordingly
Term
natural selection
Definition
certain variants within a given population have traits that result in the production of more offspring
Term
variable trait
Definition
leaf shape, trichome number
Term
invariable trait
Definition
green color, yellow flower color
Term
trichome
Definition
small epidermal "hairs"; function to absorb water and minerals
Term
petiole
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
response to selection
Definition
measures heritability with respect to the mean
Term
parent-offspring regression
Definition
measures heritability by looking at the data as a whole
Term
Fisher statistic (Fst)
Definition
qualitatively assesses change in allele frequency in a population
Term
gene flow predominates
Definition
if Fst is close to 0
Term
genetic drift predominates
Definition
if Fst close to 1
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