Transcript SC435 Genetics Seminar

SC435 Genetics Seminar
• Welcome to our LAST SEMINAR
• We will continue our population genetics
and variation
• The seminar will begin at 9:00PM ET
Unit 8
• Discussion board
• Unit 9 Quiz
• Final Project
Unit Readings
Chapter 14
Chapter 15
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Molecular evolution
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Accumulation of sequence differences through time is the basis of
molecular systematics, which analyses them in order to infer
evolutionary relationships
A gene tree is a diagram of the inferred ancestral history of a group of
sequences
A gene tree is only an estimate of the true pattern of evolutionary
relations
Neighbor joining = one of the way to estimate a gene tree
Bootstrapping = a common technique for assessing the reliability of a
node in a gene tree
Taxon = the source of each sequence
Fig. 14.1
Molecular evolution
• A gene tree does not
necessarily coincide with a
species tree:
 The sorting of
polymorphic alleles in the
different lineages
 Recombination within
gene make it possible for
different parts of the
same gene to have
different evolutionary
histories
Population Genetics
• Population genetics = application of genetic principles to entire
populations of organisms
• Population = group of organisms of the same species living in the same
geographical area
• Subpopulation = any of the breeding groups within a population among
which migration is restricted
• Local population = subpopulation within which most individuals find their
mates
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Population Genetics
• Gene pool = the complete set of genetic information in
all individuals within a population
• Genotype frequency = proportion of individuals in a
population with a specific genotype
• Genotype frequencies may differ from one population
to another
• Allele frequency = proportion of any specific allele in a
population
• Allele frequencies are estimated from genotype
frequencies
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Mating Systems
• Random mating means that mating pairs are formed
independently of genotype
• Random mating of individuals is equivalent of the random union
of gametes
• Assortative mating = nonrandom selection of mating partners; it
is positive when like phenotypes mate more frequently than
would be expected by chance and is negative when reverse
occurs
• Inbreeding = mating between relatives
Hardy–Weinberg Principle
• When gametes containing either of two alleles, A or a,
unite at random to form the next generation, the genotype
frequencies among the zygotes are given by the ratio
p2 : 2pq : q2
this constitutes the Hardy–Weinberg (HW) Principle
p = frequency of a dominant allele A
q = frequency of a recessive allele a
p + q =1
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Fig. 14.10
Hardy–Weinberg Principle
• One important implication of the HW Principle is that
allelic frequencies will remain constant over time if the
following conditions are met:
• The population is sufficiently large
• Mating is random
• Allelic frequencies are the same in males and females
• Selection does not occur = all genotypes have equal in
viability and fertility
• Mutation and migration are absent
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Hardy–Weinberg Principle
• Another important
implication is that
for a rare allele,
there are many
more heterozygotes
than there are
homozygotes for
the rare allele
Fig. 14.12
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DNA Typing
• The use of polymorphisms in DNA to link suspects with samples
of human material is called DNA typing
• Highly polymorphic sequences are used in DNA typing
• Polymorphic alleles may differ in frequency among
subpopulations = population substructure
• DNA exclusions are definitive
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Allelic Variation
• Allelic variation may result from differences in the
number of units repeated in tandem = simple tandem
repeat (STR)
• STRs can be used to map DNA since they generate
fragments of different sizes which can be detected by
various methods
• Most people are heterozygous for SSR alleles
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Fig. 14.17
Inbreeding
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Inbreeding means mating between relatives
Inbreeding results in an excess of homozygotes compared with random
mating
In most species, inbreeding is harmful due to rare recessive alleles that
wouldn’t otherwise
become homozygous
Fig. 14.9
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Fig. 14.23
Evolution
• Evolution refers to changes in the gene pool of a population or in the
allele frequencies present in a population
• Evolution is possible because genetic variation exists in populations
• Four processes account for most of the evolutionary changes
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Evolution
1. Mutation = the origin of new genetic capabilities in populations =
the ultimate source of genetic variation
2. Migration = the movement of organisms among subpopulations
3. Natural selection = the process of evolutionary adaptation =
genotypes best suited to survive and reproduce in a particular
environment give rise to a disproportionate share of the offspring
4. Random genetic drift = the random, undirected changes in allele
frequencies, especially in small populations
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Natural Selection
• Natural selection is the driving force of adaptive evolution and is a
consequence of the hereditary differences among organisms and their
ability to survive and reproduce in the prevailing environment
• Adaptation = progressive genetic improvement in populations due to
natural selection
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Natural Selection
In its modern formulation, the concept of natural selection rests on
three premises:
 More organisms are produced than can survive and reproduce
 Organisms differ in their ability to survive and reproduce, and
some of these differences are due to genotype
 The genotypes that promote survival are favored and
contribute disproportionately to the offspring of the next
generation
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Fitness
• Fitness is the relative ability of genotypes to survive
and reproduce
• Relative fitness measures the comparative
contribution of each parental genotype to the pool of
offspring genotypes in each generation
• Selection coefficient refers to selective disadvantage
of a disfavored genotype
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Selection in Diploids
• Frequency of favored dominant allele changes slowly if allele is
common
• Frequency of favored recessive allele changes slowly if the allele
is rare
• Rare alleles are found most frequently in heterozygotes
• When favored allele is dominant, recessive allele in heterozygotes
is not exposed to natural selection
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Fig. 14.25
Selection in Diploids
• Frequency of very common or rare alleles changes very
slowly
• Selection for or against very rare recessive alleles is
inefficient
• The largest reservoir of harmful recessive alleles is in the
genomes of heterozygous carriers, who are
phenotypically normal
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Selection in Diploids
• Selection can be balanced by new mutations
• New mutations often generate harmful alleles and
prevent their elimination from the population by natural
selection
• Eventually the population will attain a state of equilibrium
in which the new mutations exactly balance the selective
elimination
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Maternal Inheritance
• Maternal inheritance refers to the transmission of genes
only through the female
• In higher animals, mitochondrial DNA (mtDNA) shows
maternal inheritance
• Mitochondria are maternally inherited because the egg is
the major contributor of cytoplasm to the zygote
• Some rare genetic disorders are the result of mutations in
mtDNA and are transmitted from mother to all offspring
• The severity of the disorder depends on the proportions
of normal and mutant mitochondria among affected
individuals
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Maternal Inheritance
• Recombination does not occur in mitochondrial DNA making it a
good genetic marker for human ancestry
• Human mtDNA evolves at approximately a constant rate = 1
change per mt lineage every 3800 years
• Modern human populations originated in subsaharan Africa ~
100,000 years ago
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Multifactorial Traits
• Multifactorial traits are determined by multiple genetic and
environmental factors acting together
• Multifactorial = complex traits = quantitative traits
• Most traits that vary in the population, including common human
diseases with the genetic component, are complex traits
• Genetic architecture of a complex trait = specific effects and
combined interactions of all genetic and environmental factors
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Quantitative Inheritance
• Quantitative traits = phenotypes differ in quantity rather
than type (such as height)
• In a genetically heterogeneous population, genotypes are
formed by segregation and recombination
• Variation in genotype can be eliminated by studying inbred
lines = homozygous for most genes, or F1 progeny of
inbred lines = uniformly heterozygous
• Complete elimination of environmental variation is
impossible
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Quantitative Inheritance
• Continuous traits = continuous gradation from one phenotype to
the next (height)
• Categorical traits = phenotype is determined by counting (hen’s
eggs)
• Threshold traits = only two, or a few phenotypic classes, but
their inheritance is determined by multiple genes and
environment (adult-onset diabetes)
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Fig. 15.5
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Phenotypic Variation
• Variation of a trait can be separated into genetic and
environmental components
• Genotypic variance sg2 = variation in phenotype caused by
differences in genotype
• Environmental variance se2 = variation in phenotype caused
by environment
• Total variance sp2 = combined effects of genotypic and
environmental variance
sp2 = sg2 + se2
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Fig. 15.9
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Phenotypic Variation
• Genotype and environment can interact or they can be associated
• Genotype-environment (G-E) interaction = environmental effects
on phenotype differ according to genotype
• Genotype-by-sex interaction: same genotype produces different
phenotype in males and females (distribution of height among
women and men)
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Fig. 15.10
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Genetic Variation
• Genotype-environment (G-E) association = certain
genotypes are preferentially associated with certain
environments
• There is no genotypic variance in a genetically
homogeneous population sg2 = 0
• When the number of genes affecting a quantitative
trait is not too large, the number, n, of genes
contributing to the trait is
n = D2/8sg2
D = difference between parental strains
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Broad-Sense Heritability
• Broad-sense heritability (H2) includes all genetic
effects combined
H2 = sg2 / sp2 = sg2 / sg2 + se2
• Knowledge of heritability is useful in plant and animal
breeding because it can be used to predict the
magnitude and speed of population improvement
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Heritability: Twin Studies
• Twin studies are often used to assess genetic effects
on variation in a trait
• Identical twins arise from the splitting of a single
fertilized egg = genetically identical
• Fraternal twins arise from two fertilized eggs = only
half of the genes are identical
• Theoretically, the variance between identical twins
would be equivalent to se2 , and between fraternal
twins - sg2/2 + se2
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Heritability: Twin Studies
Potential sources of error in twin studies of heritability:
– Genotype-environment interaction increases the
variance in fraternal twins but not identical twins
– Frequent sharing of embryonic membranes by identical
twins creates similar intrauterine environment
– Greater similarity in treatment of identical twins results in
decreased environmental variance
– Different sexes can occur in fraternal but not identical
twins
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Artificial Selection
• Artificial selection =“managed evolution” = the practice of selecting a
group of organisms from a population to become the parents of the
next generation
• h2 is usually the most important in artificial selection
• Individual selection = each member of the population to be selected is
evaluated according to its individual phenotype
• Truncation point = arbitrary level of phenotype that determines which
individuals will be used for breeding purposes
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Artificial Selection
There are limits to the improvement that can be
achieved by artificial selection:
• Selection limit at which successive generations show
no further improvement can be reached because
natural selection counteracts artificial selection due to
indirect harmful effects of selected traits (weight at
birth versus viability)
• Correlated response = effect of selection for one trait
on a non-selected trait (number of eggs and their
size)
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Correlation Between Relatives
• Correlation
coefficient of a trait
between relatives is
related to the
narrow- or broadsense heritability
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