population genetics Flashcards
heterozygosity
defined as the mean percentage of loci heterozygous per individual (the mean percentage of individuals heterozygous per locus)
population structure
patterns of heterozygosity can be predicted from the ecological processes experienced by organisms, including differences in life history
organisms that tend to breed with close relatives (interbreeding) within their immediate populations have more
homozygous loci in their genomes
organisms that tend to breed with individuals that are not closely related to them have greater levels of
heterozygosity
F statistics
a way to describe genetic population structure in diploid organisms in terms of three allelic correlations (Fis, Fit, Fst)
(1-Fit)
(1-Fst)(1-Fis)
Fis
is the correlation between homologous (same) alleles within individuals with reference to the local population
Fit
the corresponding allelic correlation with reference to the total population
Fi
fixation indices (Fi) this means that they are measuring the tendency of loci to be fixed at only one allele for the entire population (no genetic diversity)
Fi=
1-(hobs/hexp)
postive Fi values indicate
fixation indices could indicate inbreeding
negative Fi values
more heterozygotes than expected from excess outbreeding
Fst
can be interpreted as the proportion of genetic variation among (as opposed to within) subdivided populations
Fst=
(ht-hs)/ht
hs
expected heterozygosity at a locus within subpopulations
Ht
the overall expected heterozygosity given allele frequencies in the total population
Fst number interpretation
0.0-1.0
0 (subpopulations genetically identical)
1 (subpopulations fixed for different alleles)
Fst population subdivision
the proportion of the total genetic variation that can be accounted for by the subdivision of populations
population subdivisions account for
50% of total genetic variation
<.05
little genetic difference
.05-.15
moderate genetic difference
.15-.25
great genetic difference
> .25
very great genetic difference
gene flow interpretation
Fst is expected to be low between populations that are conned by high gene flow
first parameter in a data set
heterozygosity
population bottlenecks
metapopulation dynamics that severely reduced the level of genetic variation relative to that expected or found in comparable mammals
heterozygosity is maximal when the
allele frequencies are equal
two allele system is described by
a concave down parabola that starts at zero
heterozygosity peaks at a value of
.05
for a multi-allelic system
heterozygosity is greatest when allele frequencies are equal
F stats
are a general stats tool for analyzing variances in gene frequencies
F is
inbreeding coefficient (global variation in individuals relative to their subpopulation)
NEGATIVE= OUTBRED, excess of heterozygotes
POSITIVE= INBRED, more homozygotes
Fst inter
assess the variation in the subpopulations relative to that in the total population)
0-1
0- subpopulations have the same gene frequencies
1- subpopulations have completely non overlapping sets of alleles (subpopulations are fixed for different alleles)
natural populations tend to have
Fst values that range between zero up to .05
values of Fst above
.2 are considered high
Fit
assesses the variation in individuals relative to the variation in the total set of subpopulations
H1
average observed heterozygosity in individuals
Hs
expected heterozygosity (gene diversity) of subpopulations, calculated as the weighted average across a set of subpopulations
Ht
the expected heterozygosity over the whole set of populations
molecular markers
Information-rich molecules- DNA, RNA, proteins
PCR
polymerase chain reaction
a lab procedure in which millions of copies of a specific piece of DNA are made
it is essentially an amplification method whereby the tiniest amounts of DNA that may be present in blood, hair, or tissues
DNA polymerase
the name of this method is derived from the key component in the process that carries out the replication of DNA
Taq polymerase
most commonly used polymerase
Thermus aquaticus
optimal at 70 degrees
primers
it can create a new DNA strand, using DNA single stranded oligonucleotides
short sequences of DNA that are made to match exactly the ends of DNA region to be copied
how many times are steps in PCR repeated
30-40 times
DNA template
the DNA to be copied usually extracted and purified from blood or other tissues
dNTPs
building blocks from which taq polymerase can synthesize new DNA, added in excess amount
buffer solution
creates an optimal chemical environment for the reaction to occur in
thermal cycler
automated machine that carries out PCR
denaturation temp
95- separates the DNA strands separated
annealing temp
40-60 primers attach to matching sequence in each strand
extension temp
72 degrees taq polymerase attaches to primer and adds complement nucleotides
then process is repeated 20x
microsatellite
is a tract of tenderly repeated DNA motifs that range in length from one to five or more nucleotides and are typically repeated 5-50x
where are micros located
non-coding parts of the genome and do not produce proteins but can be in regulatory and coding regions
what are microsatellites used
genetic fingerprinting
DNA profiling
kinship analysis
select desirable traits in plant breeding
to study population dynamics based on the theories of population genetics and in species conservation projects
mapping locations in the genome
