Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
130 Cards in this Set
- Front
- Back
|
How do genes on the same chromosome behave?
|
uneven distribution of phenotype/genotypes is found
- genes on the same chromosome do no assort independently |
|
|
In Cis
|
When alleles together on the same homolog, said to be in cis or in coupling
|
|
|
In trans
|
when alleles are on different homologs - said to be: in trans or in repulsion
|
|
|
linkage
|
association of genes together on the same chromosome
|
|
|
Recombination
|
process of generating new gametic types (produce non-parental types)
|
|
|
Recombination Frequency
|
non parental gametes/total gametes
*constant and re-produceable value between 0% and 50% |
|
|
Phases of Prophase I
|
1. lepotene
2. zygotene 3. pachytene 4. diplotene |
|
|
Lepotene
|
"thin thread"
- chromatin condensation begins |
|
|
Zygotene
|
"paired thread"
- homologs pair with one another --> synapsis - bead like regions of local condensation called chromomeres - produces bivalents |
|
|
chromomeres
|
bead like regions of local condensation
|
|
|
synapsis
|
precise pairing of 2 homologs
|
|
|
pachytene
|
"thick thread"
- chromosomes continue to condense - begins when synapsis is completed |
|
|
diplotene (diakinesis)
|
"two thread"
- becomes clear that each homolog has 2 chromatids - homologs seem to repel on another but held together by chiasmata |
|
|
Recombination frequency
|
nonparentals/total * 100
2T + 4NPD/4total sco+dco/total |
|
|
Interference
|
a crossover at one loci interferes with a crossover at another loci
1-coc |
|
|
Coefficient of Coincidence
|
observed doubles/expected doubles
|
|
|
Expected number of doubles
|
(recombo freq) * (number of progeny)
|
|
|
Gene-Centromere Distance
|
(# of second division segregations)/(total) * (1/2)
|
|
|
if a gene is very far from its centromere
|
1/3 will be 1st division segregation
2/3 will be 2nd division segregation |
|
|
1st division segregation
|
4:4
|
|
|
2nd division
|
2:4:2 or 2:2:2:2
*crossover between a gene and its centromere |
|
|
What does the Holiday Model tell us?
|
- No an accurate representation of why we get 50% recombination
- looks at 2 chromatids (1 strand of DNA) - crossing over 100% of time would get 50% recombinants...but only for one chromosome |
|
|
Chiasmata Frequency
|
2* recombination frequency
|
|
|
Why do we have 50% recombination
|
- There is no chromatid interference, so there is equal chance we will get a 1 strand, 2 strand, 3 strand or 4 strand double crossover
- Single cross over --> 50% recombination - Double cross over --> no chromatid interference, averaged over all double crossovers, get 50% |
|
|
Tetratype Formed by...
|
single cross over
3 strand double cross over |
|
|
Parental Ditype formation
|
no cross over
|
|
|
NPD formation
|
4 strand double crossover
No crossover, opposite alignment |
|
|
PD = NPD
|
unlinked
|
|
|
PD>>NPD
|
linked
|
|
|
Gene conversion
|
1/1000 - 5:3 ratio
1/200 - 6:2 ratio * due to the removal of bulky mutations |
|
|
Chromatid Interference
|
*influence of one crossover on chromatids selected for another
i.e. double strand vs. triple strand dco NOT REAL |
|
|
Centromere Interference
|
related to one crossover suppressing the likelihood of another happening
*sco vs. dco REAL |
|
|
For a chromosome to be stable transmitted through cell division, it must have...
|
1. one and only one centromere
2. telomeres - normal chromosome ends 3. linear/circular shape (NO branching) 4. Can't be too big or too small |
|
|
Deficiencies
|
- helpful for determining locations of genes
- Usually bad when heterozygous leading to developmental delay, mental retardation etc - lethal when homozygous usually (1/3 of genes are essential) |
|
|
Duplications
|
- deleterious effects when heterozygous
- important in evolution - can get pairing out of register (unequal crossing over) |
|
|
When Evaluating Spores/Asci
|
- look at one allele or pair of alleles at a time
- |
|
|
Mulitgene gamily
|
family of genes that encodes related proteins that presumably arose by duplication and divergence
|
|
|
Inversions
|
- pericentric or paracentric
- You would see an inversion loop under a microscope - crossing over (drosophila dont cross over, so no issues) you get issues - anaphase bridge - crossovers are inviable, noncrossovers are viable |
|
|
Paracentric inversion
|
*inversion does not include the centromere
1. Appear to suppress crossing over 2. Doesn't reduce fertility because non crossovers are directed to viable egg positions |
|
|
Pericentric Inversion
|
* Crossovers that include the centromere
1. Appear to suppress crossing over because the zygotes die 2. heterozygosity does decrease fertility |
|
|
Translocations
|
*involves two nonhomologous chromosomes
*assumes centromeres are near the middle and interchanged regions are large * 1/2 time there is adjacent segregation *1/2 of time there is alternate segregation Conclusions: 1. heterozygote x normal --> 50% zygote death (semisterility) 2. pseudolinkage --> apparent linkage of nonhomologous chromosomes due to death of gametes that do not inherit chromosomes together |
|
|
alternate segregation
|
T1 + T2 and N1 + N2
*only ones that survive |
|
|
Adjacent Segregation
|
T1 + N2 and T2 + N1 (usually)
- 1 is normal and 1 is not |
|
|
Euploid
|
integral number of whole haploid sets
- odd n numbers are usually sterile |
|
|
Colchicine
|
stops polymerization of spindle
- if you add it to a chromosome after duplications, the cell does not divide and you can keep duplicating the chromosome numbers |
|
|
autopolyploid
|
all haploid sets from the same organism
|
|
|
allopolyploid
|
chromosome sets from different species
|
|
|
Aneuploid
|
not an integral number of chromosome sets
|
|
|
Dosage compensation
|
mechanisms that ensures effective dosage of X is same in males and females
- only 1 active X in each cell - inactivated by becoming heterochromatin (facultative) - bar bodies = # x's -1 |
|
|
Facultative heterochromatin
|
sometimes condensed
|
|
|
constitutive heterochromatin
|
always condensed
|
|
|
5:1 ratio of progeny
|
AAaa x aaaa
|
|
|
Polymorphism
|
presence of more than 1 common form in a population
|
|
|
SNP
|
single nucleotide polymorphism
|
|
|
Indels
|
polymorphisms that are small insertions of deletions
|
|
|
Psuedolinkage and full fertility
|
homozygous for a translocation
|
|
|
Anticipation
|
when a disease seems to get worse one generation to the next (non-mendelian)
|
|
|
Huntington Disease (HD)
|
- autosomal dominant condition (100% penetrance)
- form of polymorphism - 42-121 repeats of CAG at the end of allele (glumatine) is the disease condition - 10-15 repeats is normal |
|
|
Propagation of Disease
|
- during replication, GAC --> GTC to form hairpins that, if large, can lead to increased number of repeats that cannot be digested by flap endonuclease (FEN)
- overrun but okazaki fragments - explained instability of high number of repeats (threshold repeats to form a hairpin) - more frequency in males due to high number of replications |
|
|
Polytene chromosomes
|
salivary chromosomes of Drosophila
- 2^10 chromatids perfectly synapsed |
|
|
G-bands
|
trypin + hen stain with giemsa
- dark = AT rich - light = GC rich |
|
|
R bands
|
"reverse" banding
dark = GC rich light = AT rich |
|
|
Q bands
|
bright Q bands = dark G bands
|
|
|
RFLP
|
due to polymorphic restriction sites
|
|
|
Haeckel's biogenetic law
|
assumes terminal addition and condensation
|
|
|
uniformity of law
|
Lyell's methodological assumption that principles of chemistry and physics have not changed throughout history
|
|
|
pseudolinkage
|
due to death of zygotes not receiving chromosomes together
|
|
|
alignment
|
shows hypotheses of site homology among homologous DNA sequences
|
|
|
univalent
|
unpaired chromosome in meiosis I
|
|
|
66.6% meiosis II segregation
|
gene far from centromere
|
|
|
homoplasy
|
character-state changes on a phylogeny exceed the number of derived character states
|
|
|
indel
|
deletion or insertion of a few base pairs
|
|
|
common descent
|
empirically highly corroborated component of Darwinism
|
|
|
postmeiotic segregation
|
5:3 or abnormal 4:4
|
|
|
Branch Migration
|
changes amount of hybrid DNA
|
|
|
Heterotropy
|
comparative studies of vertebrate development indicate that a caudal development modules was recruited for evolution of paired pectoral and pelvic appendages in an ancestor of quadrupedal vertebrates
*evolutionary change in the physical location of a developmental process |
|
|
Heterochrony
|
a population of salamanders that retains an aquatic larval morphology throughout life is inferred to have evolved from metamorphosing forms by decreasing the rate of somatic development relative to attainment of sexual maturity
*evolutionary changes in developmental rates and timing |
|
|
Clade
|
a taxonomist defines the taxonomic family Hominidae as the most recent common ancestor of humans and orangs and all descendants of that ancestor
*diagnosed by the sharing of homologies |
|
|
synapomorphy
|
shared derived character
|
|
|
endosymbiotic theory
|
theory tested and verified by showing that the rRNA genes of mitochondria and chloroplasts are closer phylogenetically to bacterial rRNA genes than to those of eukaryotic nuclear genomes
*Eukaryotic organelles descend from prokaryotic organisms taken inside an ancestral host cell |
|
|
Bootstrapping
|
To test support for a branch in a parsimony tree, an investigator samples sites from the alignment replacement to generate 1,000 synthetic data sets equal in size to the original one, applies parsimony analysis to each new data set, and finds the percentage of resulting trees that contain the clade in question
*statistical analysis of branch support |
|
|
Bootstrapping
|
To test support for a branch in a parsimony tree, an investigator samples sites from the alignment replacement to generate 1,000 synthetic data sets equal in size to the original one, applies parsimony analysis to each new data set, and finds the percentage of resulting trees that contain the clade in question
*statistical analysis of branch support |
|
|
Outgroup (comparison)
|
an investigator conducting a molecular phylogenetic analysis of birds adds a crocodilian sample to the analysis to permit determining character polarity and rooting the phylogenetic tree
- |
|
|
Allopatric speciation
|
a taxonomist studying the geographical distributions of rodent species observes that the closest relative of any particular species tends to be located in a nearby region separated by a geographic area
*geographic isolation of population PRECEDES evolution of species level differences |
|
|
Multiplication of Species
|
Geographic splitting of a population followed by evolutionary divergence of the separated parts
|
|
|
Homology
|
comparisons of the forelimbs of various mammals reveal that all have a proximal long bone, called a humerus, despite some variation in its exact form and function
*forms derived from an equivalent characteristic of a common evolutionary ancestor - molecular = homologous DNA - cellular - chromosomes |
|
|
Falsification
|
Potential fate shared by all scientific hypotheses when tested against data
|
|
|
Complementary Principle
|
When asked to estimate the mutation rate of a gene associated with human disease, an investigator inquires whether the desired rate is for origin of harmful phenotypes or total base substitution measured at the DNA-sequence level
*both subjective and objective components to measurements -subjective (volition) - questions asked, concepts chosen, measurements chosen, structure of study system must be described - objective (cognition) - dynamics of the system being studied |
|
|
Niche
|
set of resources actually or potentially used by a species
|
|
|
Biological Species Concept
|
a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature
|
|
|
Neo-Darwinism
|
General term describing darwinian evolutionary theory after its original Lamarckian components were purged and the chromosomal theory of inheritance added in their place
|
|
|
Divergence of character
|
darwin's term for the concept, illustrated by the only figure in The Origin of Species, that separate lineages often accumulate differences from their common ancestor and from each other
|
|
|
Cladogram
|
a tree diagram that presents the nested hierarchy of clades diagnosed by the sharing of homologies across species but whose branches are not interpreted as evolutionary lineages
|
|
|
Parallelism
|
at a site in aligned homologous DNA sequences of humans and apes, homoplastic sharing of a derived state by humans and orangs is attributed to seperate substitutions occurring in their terminal lineages
*lineages diverge from their common ancestor but not from one another (type of homoplasy) |
|
|
PCR primers
|
source of specificity in obtaining homologous DNA from multiple species for phylogenetic analysis
|
|
|
Bayesian methods
|
statistical approach for finding the phylogenetic tree most likely to have produced the observed variation in a set of aligned DNA sequences using a model of base substitution and reporting branch support as posterior probabilities
|
|
|
Parsimony
|
Methodological principle illustrated by a claim that if "silent" substitutions in a DNA sequence can be explained as neutral variation, we would not test the more complicated hypothesis that natural selection maintains this variation in a populations
|
|
|
Transversion
|
general term for a base substitution in DNA that replaces a purine with a pyrimidine on one strand and a pyrimidine with a purine on the complementary strand
|
|
|
Transitions
|
purine -> purine
pyramidine -> pyramidine |
|
|
Two Threats posed to Darwinis
|
1. fit of hostility - creationism
2. fit of enthusiasm - expands explanatory scheme to account fo human culture and ideas |
|
|
Lyell's Principle of Geology
|
Uniformitarianism
1. Uniformity of law - laws of science have been constant throughout history 2. Uniformity of process - use of familiar geological processes to explain past events 3. Gradualism - changes occur in small increments which accumulate over time to produce large changes 4. nondirectionalism - dynamic steady state of change |
|
|
Walter Alvarez - Theory of Impact Crises
|
studied amount of iridium - small, relatively constant amount entering atmosphere/year due to meteorites
- due to large spikes in some of the layers, proposed an asteroid impacted and caused 1 of 5 major extinctions |
|
|
Domain of Darwinism
|
diversity of plant and animal life, NOT origin of life
|
|
|
Active doubt
|
test Darwin's explanations, correct errors by gathering new data
|
|
|
Hypothetico deductivism
|
*construct theory - explanation based on measurable phenomenon
1. potentially falsifiable - makes empirical predictions 2. parsimony - simplest explanation is best working hypothesis 3. no positive proof - best rational explanation is not positive proof 4. empirical verification and power 5. no magic, supernatural or inherently unknowable factors |
|
|
subjective (volition)
|
questions asked, concepts chosen, measurements chosen, structure of study system must be described
|
|
|
objective (cognition)
|
dynamics of the system being studied
|
|
|
Darwinian Theories of Evolution
|
1. Evolution as such
2. common descent 3. Multiplication of Species 4. Gradualism 5. Natural Selection |
|
|
Evolution as Such
|
the biological world is neither constant nor perpetually cycling, but is steadily and perhaps directionally changing
- perpetual change with continuity from past to present life |
|
|
Common Descent
|
All plants and animals have descended from some one form into which life was first breathed
- Lineages: series of ancestor-descendent populations through time |
|
|
Lineages
|
series of ancestor-descendent populations through time
a. persist without change b. persist with change c. branch (biforcation) d. extinct |
|
|
Divergence of character
|
separate lineages accumulate differences from their common ancestor and from each other
|
|
|
Phylogeny tree
|
branching tree of lineages. The structure of evolutionary history is a branching tree of lineages
|
|
|
Ontogeny recapitulates phylogeny
|
= biogenetic law
- organismal development repeats adult stages of ancestral forms. Assumes: 1. terminal addition 2. condensation |
|
|
Terminal Addition
|
Part of Haeckel's idea of ontogeny
*new features are added to the end of ontogeny |
|
|
condensation
|
part of Haeckel's idea of ontogeny
*older features are displaced to earlier and shorter developmental occurrences |
|
|
Exceptions to "ontogeny recapitulates phylogeny"
|
1. caenogenesis
2. heterochrony 3. heterotropy |
|
|
caenogenesis
|
- evolution of new characters restricted to pre-adult stages (like organisms that undergo metamorphism)
|
|
|
heterochrony
|
evolutionary change in developmental rates and timing
|
|
|
heterotropy
|
evolutionary change in the physical location of a developmental process (geccos)
- modularity |
|
|
modularity
|
characteristic, semi-autonomous patters of gene expression and cellular proliferation and differentiation (formation of "toe pads" of a gecco)
|
|
|
homology
|
forms derived from an equivalent characteristic of a common ancestor
i.e. bat wings vs bird wings - homologous as forelimbs, not wings |
|
|
HIstorical structure of homologies
|
sharing of homologies among species forms a nected hierarchy of groups within groups
|
|
|
Monophyletic group (clade)
|
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
- diagnosed by the sharing of homologies |
|
|
cladogram
|
branches denote the nested hierarchy of clades as diagnosed by synapomorphies
|
|
|
Phylogenies from DNA sequences
|
1. identify a study group (=ingroup) and a close relative (=outgroup)
2. amplify and sequence homologous genes for all species 3. align homologous sequences to get site homologies (=positional homology) --> ALIGNMENT 4. identify sites variable in the ingorup 5. determine character polarity of step 4 6. identify shared derived characters - "parsimony informative sites" 7. parsimony criterion - find the tree topology that requires smallest # of changes 8. apply stat tests of branch support |
|
|
Distance based methods
|
1-3 same as parsimony
4. calculate genetic distances for all pair wise comparisons of data (% seq difference and % seq similarity) 5. use algorithm to convert the matrix distance to a tree (UPGMA or neighbor joining - averaging algorithms) 6. stat tests |
|
|
Maximum likelihood method + bayesian Approaches
|
* can use complex models of base substitution to find the tree most likely to have produces the data
*1-3 same 4. identify a stat model of base substitution (transitions to transversions or codon position for protein coding - silent vs. replacement) 5. Determine likelihood of the data for the molecular evolutionary model and each contrasting topology and branch length 6. identify topology with highest likelihood Bayesian analysis - each branch has a posterior probability, p> 0.95 indicates strong support |
|
|
bootstrappin
|
*stat analysis of branch support
1. sample sites in the alignment with replacement to produce a new data set equal in size to the original one 2. construct a phylogenetic tree from the new data set using the same method as the original analysis 3. repeat steps 1+2 1000+ times 4. for each clade/branch, what percent of the 1000+ trees contain the clade/branch? values > 70% constitute strong support |
|
|
If internal branch is shorter relative to external...
|
parallel substitution in external is more likely that substitution in small internal branch
|
