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149 Cards in this Set

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What kind of Fst is there for humans (high/low)? What does this indicate?
low; prominent gene flow
If 2 populations have similar alleles and w/ similar frequencis, what kind of fst value is this?
low
What can restrict gene flow, as is shown by the human population strucutre?
distance; most gene flow is between enighboring populations
What is meant by denes as a stepping stone?
new mutation can spread through an entire species through gene flow eve in no individuals move long distances. Genes can take many generations to cross stepping stones. Populations must remain interconccected.
What is the best predictor of differentiation between human populations?
geographical distance
What kind of trait is skin color?
adaptive trait to proctect against UV
How is ancient gene flow/ population structure reconstructed? Can rare one do this?
haplotype trees; yes!
Averace coalescences time for genes at a locus due to genetic drift?
2X, where X is the # of genes in gene pool
Avg. time to coalesce in autosomal diploid?
4N: 2N genes in gene pool x 2
Avg. time to coalesce x chromosomal?
3N: 2(1/2N)+1(1/2N)=3/2N
3/2nx2
Avg. time to coalesce y chromosomal?
N: 1(1/2)N=1/2N x 2
How is mitochondiral DNA inhereited? What is its avg. time to coalesce?
Maternal hapoild, N
What is the lemba?
tribe of bantu speaking Africans, descendent from a group of Jews
What is the origin of the lemba
A boat of jewish men sailed from Yemen to S. Africa and married local bantu women
What do you see when you look at a haplotype tree comparing lemba bantu and Yemen's?
The bantu aren't the same as Lemba or Yemen. The lemba are an intermediate, and have a particular Y chromosome haplotype that only jews have.
Is the Y-DNA of lemba similiar or different to Bantu? What about the mtDNA?
different, same
What does the haplotype tree show? What do you overlay it with to test for paterns
space, geography types to get time
Do you expect older or younger haplotypes to be more widespread?
older
What happens to new mutations when a population spreads to a new area? What theory does this contradict?
it can become geographically side spread, and located far from the geographical center of ancestor. It can be yonger, but still more widespread!
Where are all human lineage fossils found prior to 1.9 MYA?
africa
What is the wet phase of the sahara called?
savanah
What type of organism is the human?
a savanah organish
When was the first expansion out of Africa?
1.9 MYA
When was the 2nd expansion out of Africa? What shows this?
.65 MYA; genetic data, the acheuleen hand ax took, increase in brain size, and climate data.
When was the 3rd out of Africa expansion?
.096-.169 MYA, spread of many modern fosil traits
What is the modern theory? Why is it unlikely
Modern human killed off all the "brute" humans;
1.Fossils don't agree and they show that traits are continous.
2.Gene flow and interbreeding are necesesary for a trait to spread. 3.Coalesecences wouldn't even been possible with replacement.
5. VARIATION HAS NOT BEEN DESTROYED! HUMANS ARE POLYMORPHIC FOR MANY TRAITS.
How do we know most expansion was male mediated?
doesn't involved mtDNA, only Y and nuclear DNA
Can you look at a single gene to get a complete view of human evolution?
No
1. much variation in coalscence time
2. don't observe gene trees so we needmutations to be marked at the right place and time
3. geographical sampling may be incomplete
does mtDNA coalece early or late? What does this mean?
early; recent
What is a race? Dpes this exist in humans?
Morphological distinct things from destinct evolutionary lineages? No!
What does DNA do?
it encodes information that interacts w/ the environment to influence phenotype
Name 3 traits that can be influenced by genetically determined responses to the environment
1. viablility 2. mating suces 3. fertility and fecundity

all in the environement
Which Beta Hb locus is resistant to malaria?
A/S
Which beta HB locus give anemia?
s/s
What is the fecundity of people with H/+ in a society w/ no birth control, genetic literacy, and low expecty normal life span?
normal
What is the fecundity of people with H/+ in a society w/ birth control, genetic literacy, and high expecty normal life span?
low
whay are viability, mating sucess, and fecundity/fertilityu important phenotypes in evolution?
they influence the chances for sucessful DNA replication/getting gamete to the next generation
What is the phycial basis of evolution?
DNA can replicate, DNA can mutate and recombine, DNA enodes information that interacts with the environment.
What makes up fitness?
viability, mating sucess, fecundity/fertility
Define natural selection?
heritable variation in fitness. The genes borne by a gamete influence the probability of the gamete being passed on to the next generation.
Why is Natural selection not cirular?
because information come from the environment, which is outside the genetic system! (You adapt to the enviroment, phenotypes don't come from the genotype.
What would happen if phenotypes came fromt the genotype?
there would be no evolution
When can a praying mantis mate?
whene its head is eaten off
What are the requirements for natural selection to occur?
1. there must be genetic variation (p not equal to 0 or 1) and average excess can't be equal to 0 ( heritability would be 0)
What is the actual mutation of sicke cell?
a substitution @ the 6 codon of a single nucleotide, which changes the amino acid from glutamic acid to valine
How does the sickle cell allele resist malarioa? What kind of allele is it for malaria resistance.
Cells sickle under low oxygen. Sicke cless are filtered out preferentially by the spleen. Malaria infected cells are often filtered out b/c of sickling. Therefore, parasite can't complete its life cycle.

2. Autosomal, Dominant
If viability is the phenotype of living to adult hood, what is the s allele dominant or recessive in the non-malarial environment?
recessive, only homozygotes get sicke cel anemia
If viability is the phenotype of living to adult hood, what is the s allele dominant or recessive in the malarial environment?
overdominant, b/c only heterozytoe are reistant to malaria and don't get sicke cell.
What is the 3rd allele involved in adaptation to malaria in africa?
hemoglobin c
Whatis the epidemic malaria in Africa?
colonly estabilshed in madagascar that introduced malaysian agricultural of the root fruit system. Bantu picked it up, them moved it across africa. The need to slash and burn created an envrionment for mosquitos in Africa, making malaria a common disease.
What is the hemoglobin c mutation?
at the 6th codon, the glutamic acid (GAG) is changed to Lysine (AAG) creating a 1 locus, 3 allele system
What kind of allele is Hb-C for malaria? What genotype is malaria resistant?
autosomal recessive, cc
What is the heritability of an austosomal recessive allele as long as the disease is rare?
0
What does natural selection do to an allele that defines an autosomal recesive disease?
It will insure that is is rare but it is dificult to eliminate it in a randomly mating population
Can naturally selesction eliminate an allele of an autosomal recessive genetic disease?
no! natrual selection is based on selection of heritibilaty variation, which is 0 for these types of alles
What dentermines the frequencies of nuetral alleles?
genetic drift in mutation
Do nuetral alleles evolve?
yes, genetic drifr and mutation
What does natural selection favor?
the alleles w/ the highest average excess of fitness
Is natural selection survival of the fittest? why?
no! it selects the gamete w/ the highest average excess of fitness, which may not increase the frequency of the most fit genotype
What does natural selection do to autosmal rare alleles?
It doesn't eleiminate them, it makes sure they are not heritable.
Can genetic variance exist w/ out heritibility?
yes
What does natural selection do to heritability?
It can eliminate it
What does natural selection do to non-varaible traits?
Natural selection will not occur
What does it mean to be at selective equilibrum
the change in p=0 under natural selection for all alelles.

all average excesses are equal
What does reaching equilibrium do to heritibility?
It makes traits no longer heritiable b/c every gamete has the same genotypic variation
What creates a balanced polymorphism?
reaching equilibrium allele frequencies, then maintaining them by natural selection
What type of variation can you not have at equilibrium?
additive genetic variation
Is there genotypic variation in fitness at equilibrium?
yes, broad sense heritibaility
Where is ther a high frequency of allele c?
in the upper volta of the sahara desert
What is the correlation between s and c?
Both alleles can't be increased b/c cs is deleterious from gametes point of view.
Basic lifecycle of HIV?
Look in notes (#13 pgs 1-2)
What does AIDS stand for?
Acquired Immune deficiency disease
what type of HIV can be passed on?
M-tropic HIV
What to protiens in humans allow HIV into the system? Where are they located?
CD4 and CCR5; on the macrophage
what is GP120
it is the part of HIV that interact with the receptor
What is important about the elvolved for of HIV (t-tropic)
it can attack t cells, a critical component on the immunse sistem
Can the HIV that infects a patient cause aids?
No, only the one that evolves in each patient can cause aids. Therefore, the goal is to stop evolutionary potential of age
What region and gene are important to consider w/ HIV?
V3 region of envelope gene
What does the V3 region do?
1. transforms it from m form to t form
2. transition from NSI to SI (more virulent form)
3. Presents one of primary targets to the immunse system
Intra visit tip branch?
nuetral, recent/w/ no known desecendents (no proven evolutionary sucess)
Itravisist interior brang
sucessful evolutionarily b/c an internal node has 2 or more descendant haplotypes (impact on selection)
Intervisit brances
sucessfull evolutionarily b/c it has displayed temporal persistence (at least 2 months) (impact on selection)
What is redundancy o the genetic code mean towards mutations?
a lot of mutations @ the dNA level have no impact at the protein level
Which type of mutations are more likely to be under natrual selection
nonynonymous
replacement/nonynonymous mutation?
amino acid change
silent or synonymous mutation
no amino acid change
what is true about the rate of substitution under selective nuetrality?
it is equal to the mutation rate
what is true about the releative rate of evolution of classes of nuetral mutations?
they should be constant, b/c they are trying to get rid of deleterious mutations. Their relative portions should be the same in all parts of the gene's evolutionary tree.
What is the expected number in a contigency table?
(row sum)(column sum)/N
What is the degrees of freed in a contingency table?
(no of rows-1)(no. of columns-1)
What kind of ratio ratio of replacement to silent substitutions is expeceted from the degeneracy of the genetic code?
2 replacement :1 silent (drives AA changes)
2 ways to classify HIV one as SI?
1. either arg or lys at AA position 306
2. glycine at 306 and arg or lys at 320
Can test of hypotehes about natural selection be used within a species? Between a speicies?
Yest to both
What types of branches fits into the polymorphic category?
tip and intraspecific interior
What types of branches fit into the interior category?
fixed and intraspecific entrior
What gene is affected by the evolution of cytochrome oxidase II?
mtDNA gene
Under nuetrality what do we expect nonsynonymous/synonymous to be?
1
Under purifying(neg) slecting what do we expect nonsynonymous/synonymous to be?
less than 1 b/c nonysnonymous sites are be eliminate
Under directional(pos) slecting what do we expect nonsynonymous/synonymous to be?
greater than 1 excess of nonsynonymous
What is the ASPM locus?
loss of function mutations in this gene cause sever reduction in the cerebral cortical size of affected humans
What are the most important biological themes?
1. host-pathogen interactions
2. reproduction
3. DNA metabilism/cell cycle
4. neuronal function
What are the varities of sickle back fish?
armor (habitats w/ large predators) and unarmored
What is ectodyplasin (EDA)?
canidate gene that determines if stickle back fish will have armor or not
What type of adaption is it if there is a strong correlation between habitaty types and position in the haplotype tree?
adaption to the environment
What does maximum parsimony do?
It allows you to infer the state of extinct ancestral state (reconstruct and synthesize the ancient type by distinct nucelotide changes)
What is the relation ship between mineralocorticoid receptor (MR) and glucocorticoid receptor (GR)?
they descend from a gene duplication deep in the vertebrate lineage and now have distinct signaling functions
What is mineralocorticoid receptor (MR)? What's special about it?
activated by aldosterone, controls electrolye homeostatis.
The homrone it uses didn't evovle until well after it began existing
What is glucocorticoid receptor (GR)?
activated by stress hormone, cortisol. Regulates metabolism, inflammation, and immunity.
What is the process of MR/GR evolution?
see slides (#13 pg 16)
Isocitrate Dehydrogenases?
group of enzyems at the core of metabolism that are very different at the nuceltide level

Only 8 AA are resposible for all the functions of this important enzyme family,
Consensus vacine?
chose the most common nucleotide state at every postion on all proteins. Often creates a protein that never existed and has no evolutional basis
Cetner of the tree vacine?
It is an acenestor to part, but not all of the tree. It mimiizes the distance btween the current form and the diseas.
Acestor vacine?
preserves the most conserve and univerisal aspect of protein function, so the vaccine can evovle to fight the diesaes
What i the comparitive method
test hypotehses about causes of variation by examining patterns across populations in the context of the evolutionary history (phylogeny)
What 2 things are directly associated when using comparitive method?
tested paterns and the canidate locus that provides the evolutionary tree.
What does the comparitive method require?
an evolutionary history (not a canidate loci directly related or specific genetics of a trait)
What is the problem w/ the comparitive method?
The evolutionary tree needed to implement the comparitive method can be confused w/ the paterns to be tested.
What is unique about anolis lizrd?
species on different islands show simiilar morphological adaptions associated w/ similar habitats
grass/bush lizard
slender short limbs, green color
trunk/ground lizrd
powerful hind legs, brown color
trunk/crown lizrd
elongated hind legs
twig lizrd
tiny limbs
What do anolis lizard species in similar habitats on different islands look like ?
The same
What is the solution to the comparitive method? Who proposed it
you have to look a the genetics/ stream of heredity based on DNA. They could only do this w/ inversions in drisophila

George Gaylord Simpson
What is the hypothesis of Developmental rigity? What rejected this hypothes?
That big morphological changes only happen once
Anolis lizrds have flexibility in basic body shape and limb morpholoty and repeatidy evolution in response to habitat
Is DNA a blueprint? Why?
No
1. it would be impossible to have beneficial changes
V
What kind of small changes can be large changes in the output process w/ out latering the process?
timing, duration, or extent of the process
What is the difference btween human and macaque (monkey) brain process?
same proces, human just start growth earlier and keep it going longer
why does the human face look like a baby mokey face?
humans retain fetal/newborn growth porccess over a longer portion of their life.
Pleitropy and slelection?
not all traits that evolve under natural selection ar adaptive, some traits are just affected as a by product
When 2 or more developmentally correlated traits are separately selected, what happens to the correlation?
it deviates from the expected correlation and gets a new one
Why did the shape of the head change?
diet was adapted to tools, not teeh, so that jaws are a meutual trait, despite evolution
2 major features of evolution?
adaptation and diversification of life
morphological species concept?
look the same w/ in species, and different than other species
-Used most often
-Bad becomes it depends on what you look at and the method of analysis and the judgement of the analysizer
sibling species? example?
-look alike but have distinct biological attributes (iecan't interbreed)
-drosoplila melangaster and drosophila simulans
Polytipic Species?
look different, but can interbreed freely
What are the 3 species concepts relating to evolutionary role of species?
-species as a reproductive community
-species as an ecological community
-species as an evolutionary lineage
types of isolating mechanisms for specieas as a reproductive community?
prezygotic isolation and postzygotic isolation
prezygotic isolation?
prevents fertilization
post zygotic isolation
prevents zygote from developing into a viable, fertile adult
How can a new species be created from allopolyploids?
1.different species come together
2.Make zygoe that is sterile
3. Endoduplication (whole genome duplication) creates tetrapoloid that is stable, but only to itself
Why cant the majority of life be put into the biological species concpet?
the majority is asexual
Why can't poplars and cottonwoods be put into the bioolgical species concept?
They can mate despite all their differences. They create a hybird leaf that is not well adapted to either habitat, but sometimes still exists, despite strong selection against it. H/e poplars and cottonwoods are definetly genetically and morphologically distinct trees (have been for 12 MY)
evolutionary species concept?
species is a distic evolutionary lineage
problem w/ evolutionary species concept?
neste hieaachy! lineages w/ in lineages
Cohesion Species concept?
cohesive evolutionary lineage and is capable of exchanging gamete/ ecological community adaptation
What is 1st in defining a cohesion species?
they must be an evolutionary lineage
Are all lineages cohesion species?
no...genetic exchangabilit/shared derived adpatations considered
Which species concept can fall outside of all the species concepts?
ecological species concept