Transcript 3000_2013_2b

mutations are the
basis of diversity
we will learn THIS:
[mutations happen and add diversity to a
population. A/G, presence/absence,
red/white]
such diversity is temporary. in a
finite population a single genetic
polymorphism
will eventually disappear through
drift, but selection, non-random
mating, and migration will modify
that rate
sciencedaily.com
offspring = heredity
• bacteria, archaea
divide (literally) into
two daughter cells
• most eukaryotes
make it more
complicated: sexual
reproduction
centromere
• DNA packed into
chromatids
coiled DNA
• DNA packed into
chromatids
• sister chromatids contain
homologous stretches of
DNA and bound at
centromere
• each chromatid was
inherited from different
parent
•
ACTTCAGAT
ACTTCAGAT
•
•
GGTCATATAT
GGTCACATAT
homologous regions
(LOCUS or LOCI) found on
each chromatid are
ALLELES
they may be different at one
or more nucleotides or other
forms of mutation
so: LOCUS descended from
single ancestral region of
genome; ALLELES
represent the diversity of
that locus
so: each sexually produced
offspring is unique because:
mutations
AND
genetic recombination
this diversity is what we
are exploring!
so: each sexually produced
offspring is unique because:
mutations
AND
genetic recombination
this diversity is what we
are exploring!
diversity
• diversity of GENOTYPE (combination of
alleles at one or more LOCI) is one
contribution to the organism
PHENOTYPE (what it looks like,
manifestation of genotype)
• genes are inherited; phenotype is
complex, involving genotype at one or
more loci AND environmental
contributions
Gamete production
Independent
assortment
Expected
proportions and
Combinations
some phenotypes depend almost entirely on genotype
at single locus
(illustrated by Punnett squares)
some phenotypes are not controlled by genotype
?
normal distributions
• “bell” curves, Gaussian, tend to have a mean (location of
peak) and symmetric variance (the width of the
distribution)
• why do we see it so much? why does it apply to
quantitative traits?
• “central limit theorem”: sum of many random variables is
distributed normally
aa Aa AA
18
how do we find these
many genes?
• human body height, flower corolla
length, many genes (quantitative) but
where are they?
• quantitative trait loci (QTL)
• association studies allow us to find the
markers that tend to be found in
individuals with a given trait
LOD: log (ratio) of
odds, e.g. LOD of
2 means that a
genetic marker is
2
10 or 100 times
more likely
associated with
trait than not
meaning, marker
and trait show up
together more often
than expected by
chance
variation
matters
• dominant, recessive, homozygosity,
heterozygosity, allelic variation of all
types
• important component of variation is the
average effect
alleles
(e.g. having
additiveof
genetic
variance
symbolized
as Var(A)
allele GATGAT
generates
red pigment;
variance in phenotype due to average effects of alleles
GACGAT white pigment; heterozygotes
are pink)
• allele symbol discussion: A is not
dominant to a (necessarily), just
traditional symbols, ANY SYMBOL
models
• all models are wrong
• some are useful
•
•
science attempts to find the simplest set of
interactions that explains the most complex
observations
“How do these genes combine to determine the phenotype of an individual? The simplest model is
to assume that genes act additively with each other both within and between loci, but of course
they may interact to show dominance or epistasis, respectively.”
– Hill et al. (2008) PLOS Genetics, showing that additive genetic variance comprises the largest
component of genetic variance that contributes to phenotype, much more than gene interactions or
allelic interactions
“additional resources” on wiki
chapter 5 is done
• you should understand mutational
diversity
• what is a gene? a locus? an allele?
• how are phenotype and genotype
related?
drift and
selection
moving into Ch 6
how fast can a
population change?
• 1969: French government starts
spraying organophosphate insecticides
along Mediterranean coast
how fast can a
population change?
• what we know so far: populations are
variable (traits, alleles)...some of this
variation is heritable
• not all offspring survive; those that do
can pass along heritable traits
• if you change the environment, the
variation present may change in
response
Nice, France
how fast can a
population change?
• 1969: French government starts
spraying organophosphate insecticides
along Mediterranean coast
• mosquito population fell dramatically but
started growing again by 1972
• mosquitoes near coastline were
resistant to insecticide!
Ester locus
• encodes enzyme esterase, can detoxify
organophosphates, but not normally
enough to tolerate insecticide
• allele called Ester
esterase
1
produce more
what connections can
you make?
• Luria-Delbruck
• HIV example
• straight-up natural selection at work!
population genetics
• you cannot follow the fate of a single
allele without reference to others
• the frequency of Ester
1
increased in
some locations (meaning frequency of
others DOWN)
• we study allele frequencies through
space and time, and what causes them
to change
evolution = change
•
•
•
•
•
if allele frequencies and genotype frequencies do not
change, population is not evolving
Hardy-Weinberg equilibrium requires a set of
conditions so that population is not evolving
(if population is evolving, one or more of these is
NOT TRUE)...
random mating with respect to locus/loci being
studied
population infinitely large (very big)
•
•
•
“with respect to the
loci being studied”
the NULL hypothesis is the boring one: that
you, as a scientist, are studying a portion of
the genome that is of no evolutionary
interest
we KNOW some traits are important for
fitness and evolution, but first must reject
that null hypothesis
example: GENE 3000 students and 810
numbers
allele frequencies
•
•
•
•
•
if 9 out of 10 dentists chew sugarless gum,
there are 2 types of dentists, one type at
frequency 0.9, the other at frequency 0.1
this is algebra: d1+d2 = 0.9 + 0.1 = 1
any symbols may be used for alleles or allele
frequencies, but frequencies sum to...
ONE! (1) uno un ein etc.
important: may be >2 alleles
genotype frequencies
• genotype is just the composition of
alleles describing an individual
• if haploid, there is only one allele
• if diploid, there are 2
• above that, it gets complicated
genotype
frequencies
• diploid individual genotype indicated for a
locus by listing both alleles, e.g. A1A1 or
A1 A2
•
•
genotype frequency is just the proportion of
individuals with that genotype, AGAIN
SUMMING TO ONE (1).
1
1
AA
0.4,
1
2
A A 0.5,
2
2
A A 0.1;
freqs sum to
1
•
if Hardy-Weinberg holds, allele frequencies
and genotype frequencies predict each
other
probabilities
•
•
•
•
d1+d2 = 0.9 + 0.1 = 1
independent assortment of alleles: father has
probability 0.9 of contributing d1, 0.1 of d2
mother same odds
d1d1 genotype should be in 0.9x0.9=0.81 of
offspring, d2d2 in 0.01, what about
heterozygotes?