BIOL 201 Study Guide - Midterm Guide: Inbreeding Depression, Population Bottleneck, Allele Frequency
Chapter 10: Migration and Inbreeding
Assumptions of Hardy-Weinberg Model
no selection
○
no mutation
○
no migration
○
random mating
○
infinite population size
○
•
Mainland-Island Model of Migration
deltaP = k(Pm-Pi)
Pm and Pi are the allele frequencies on the mainland and the island
§
k is the (migrating population)/(total population w migrants)
§
○
At equilibrium, the island population will reach the allele frequency of the
mainland.
○
•
Non-random Mating
Inbreeding
Leads to a decrease in heterozygotes
§
Genotype frequencies change under inbreeding, but allele
frequencies dont
§
○
Identity by Descent: When say two cousins mate, the offspring can end up
having 2 copies of the same allele
○
•
F statistics: statistically expected level of heterozygosity in a population
F= 1- [(observed heterozygotes)/(2pq)]
○
•
Effects of Population Genetics
•
Inbreeding depression
Deleterious recessives are usually at low frequency, so most are found in
heterozygotes.
○
HOWEVER, inbreeding inc proportion of homozygotes, so there is
stronger selection AGAINST deleterious recessives in an inbreed
population.
○
•
Chapter 11: Genetic Drift
Wright-Fisher Model: all assumptions are held except for the infinite population,
the population is finite.
•
Many generations of drift results in the spread of frequencies to the 2 extremes,
p=0 and p=1. After a few generations, you are likely to see something that looks
along the lines of a bell-curve. You wouldn’t see all of the allele frequency on
either of the ends (p=0 or p=1) because there is no selection acting in genetic
drift.
•
Smaller populations drift in frequency more dramatically and reach fixation faster
than larger ones
•
All subpopulations will go to fixation or loss eventually, with no other forces, it is
just a matter of how long.
•
Heterozygosity (H)
Observed: Ho: 1- f(homozygotes)
Based on the actual count of genotypes in the population
§
○
Expected: He: 1 -[(p^2 +q^2)] or (2pq)
Predicted HWE genotype proportions using allele frequencies
§
○
The direction of drift in any population is unpredictable, but the avg speed
with which heterozygosity (genetic variation) declines can be predicted
based only on population
Ht= (1 -(1/(2N))^t x Ho
t is the number of generations
□
§
○
•
Chapter 12: Conservation Genetics
Conservation Genetics: the effects of drift, inbreeding, and migration on
endangered species
•
Some endangered species may incur a population bottleneck -a dramatic
reduction in population
Key factors to this include overhunting or habitat fragmentation
○
•
A bottleneck effect increases the effects of genetic drift - leading to reduction in
genetic variation, and inc in inbreeding, leading to more homozygotes, including
deleterious recessive alleles
Inbreeding is evident because of many recessive traits that are found in no
other populations of a given species - phenotypic evidence
○
•
Actual Ht may be a little lower than the predicted Ht bc:
Initial heterozygosity, Ho may have been lower
○
the loci may have drifted faster than most
○
the census population size may have been an overestimate of Ne bc:
fluctuating pop size
§
uneven sex ratio
§
○
•
Effective population size is greatly reduced by bottlenecks
Ne = {k / [(1/N1)+(1/N2)+(1/N3)+…+(1/Nk)]}
k = # of generations
§
○
•
Territoriality means relatively few mating males compared to females
•
Effective population size, Ne
with dif # of males and females
Ne = 4(Nm)(Nf) / (Nm+Nf)
§
Unequal sex ratio leads to faster decline in heterozygosity and
faster divergence among populations
§
○
with same # of males and females
Ne = Nm + Nf
§
○
•
The founder effect is the reduced genetic diversity that results when a population
is descended from a small number of colonizing ancestors - for example, when a
population results from a bottleneck population.
•
Selection in a finite population is not deterministic
•
Chapter 13: Sexual Selection
Anisogamy: the fusion of gametes that differ (ex in size)
•
Fecundity: the ability to produce offspring
Female fecundity is limited by ability to gain resources for producing eggs
and rearing young - resources limited
○
Male fecundity is limited by ability to attract mates - higher variance
○
•
Fundamental Asymmetry of Sex
Competition between males for access to females
○
Females preference for males perceived to be of high quality
○
•
Male-Male Competition demonstrated by:
Elaborate Mating Displays
Ex: Birds
§
○
Direct combat (before mating)
Ex: Seals
§
○
Sperm competition (during or after mating)
Ex: scooping out other males sperm from female
§
○
•
Female Preference
Choosy females may benefit their offspring directly through acquisition of
resources and improve their fitness
Good genes, that confer higher fitness in both sexes
For ‘good genes’ mate choice to work, sexual displays need
to be honest signals of genotype fitness
□
§
Sexy sons, that lead to the male offspring having traits that are
more likely to confer better luck with sexual reproduction
AKA runaway selection
□
§
○
The better the nuptial gift, the longer the duration of copulation, up to a
certain point, and the longer the duration of copulation, the more sperm
transferred, also up to a certain point
○
•
Polygamous species are more likely to be sexually dimorphic, (ex: the male
having some sort of secondary sexual trait such as bright colors or big wings),
than monogamous species because they need the sexual dimorphism to win
serial mate choice conquests.
•
Sexual selection affects only reproductive fitness, but not all differences in
reproductive fitness are sexual selection
•
Male-Male competition is intrasexual
•
Mate choice (females) is intersexual
•
Chapter 14: Cooperation
Altruism is behavior of an animal that benefits another at its own expense
•
Cooperative brooding (ants) occurs through brood raiding, stealing of the young,
because more individuals available to work increases the probability of nest
survival
•
Reciprocity, or reciprocal altruism: a behavior where an organism acts in a
manner that temporarily reduces its fitness while increasing another organism's
fitness, with the expectation that the other organism will act in a similar manner
at a later time
Can be favored if there are many opportunities for mutual aid between
unrelated individuals
Ex: mobbing in birds
§
Birds are going to help those who have helped them before over
those who haven’t helped them before
§
○
•
Kin Selection: natural selection in favor of behavior by individuals that may
decrease their chance of survival but increases that of their kin (who share a
proportion of their genes)
Direct Fitness: the individuals own probability of survival and # of offspring
that live to reproductive age
○
Indirect Fitness: the fitness received by helping non-descendent kin
○
•
Inclusive fitness: individuals should be more wiling to perform altruistic acts for
kin than for non-kin
Hamilton's Rule: Altruistic behaviors are favored when:
B x r -C > 0
§
B: indirect benefits of the behavior to ones relatives
§
r: coefficient of relatedness
§
C: direct costs to the individual
§
○
Inclusive fitness includes both the direct and indirect contributions to an
individual’s fitness
○
•
Coefficient of Relatedness (r): the probability that a gene from one individual is
identical by descent to one from another individual
(0.5) from each parental to offspring that is related between the 2
○
•
Coalitions work together to defend territories and engage in elaborate displays to
attract females - only the dominant brother in the coalition actually mates
•
Eusociality
Features:
Reproductive division of labor
§
Cooperation rearing of young
§
Overlapping generations
§
○
•
Haplodiploidy is a sex-determination system in which males develop from
unfertilized eggs and are haploid, and females develop from fertilized eggs and
are diploid.
A female has higher relatedness to a full sister than to either parent
○
•
Chapter 15: Molecular Genetics
Neutral alleles are much more likely to be at intermediate frequencies in a
population than deleterious or beneficial because those are lost or fixed quickly
•
Beneficial Mutations are rare
•
Deleterious Mutations are common but quickly lost
•
Neutral Mutations fate are determined by genetic drift alone
Polymorphisms and divergence will be dominated by neutral mutations
○
•
Polymorphism: two or more alleles within a population or species
•
Substitution: sequence divergence between species
•
Neutral Theory:
Large amount of deleterious or neutral
○
# of mutations are related to mutation rate (u) and population size (2Ne)
# mutations = u(2Ne)
§
○
Probability of fixation = 1/(2Ne) (1 over total individuals in population)
○
We only expect neutral mutations to fix. - Null Hypothesis
○
Ka/Ks
k = (# of sub)/(# sites)
§
1st and 2nd are non-synonymous
§
3rd is synonymous because there is some redundancy in the amino
acid coded for the last nucleotide in codons
Synonymous sites are always created by genetic drift
□
§
Ka is deleterious (non-synonymous) (1st and 2nd) - only ones that
can be positively or negatively selected
§
Ks is neutral (synonymous) (3rd)
§
When Ka = Ks, Non-synonymous mutations are equal to
synonymous and there is no selection - Neutrality
§
Ka>Ks, more nonsynonymous than expected - positive selection
§
Ka<Ks, fewer nonsynonymous than expected - purifying selection
§
○
•
Most protein coding sequences are predominantly under purifying selection
•
Rate of divergence = substitutions per synonymous sites per year x lineages
•
Nearly Neutral Theory (updated version)
Still large amount of deleterious or neutral, but a more distributed around
neutral to allow for some neg/beneficial mutations that are around neutral
○
Helps w predictions bc proportion of effectively neutral corresponds w
pop size
○
Prop of mut that are effectively neutral
|s| << 1/(2Ne) - if pop is large, less drift, less selection
proportion around neutral becomes wider to neg/beneficial
□
§
|s| >> 1/(2Ne) - if pop is small, more drift, more selection
proportion around neutral becomes narrower against
neg/beneficial
□
§
○
Purifying selection is accounted for within neutral theory, but not positive
selection
○
Neutral theory serves as a null model
○
More generations = more mutations
○
Heterozygosity will be relatively insensitive to population size bc
organisms w large population sizes will have proportionally smaller rates
of neutral mutations
○
Molecular clock will tick in years
Based on observation that long-lived organisms tend to have
smaller population sizes, and thus proportionally higher neutral
mutation rates
§
○
•
Molecular Clock Stuff: If some sites mutate more often than others, using long
term, there is the issue of saturation bc you may get a lower number of mutations
than actually occurring. If short term, you want a site that mutates more
frequently or you most likely wont be able to see much.
•
The role of drift in molecular evolution is considerable and likely more important
than at the organismal level.
•
Chapter 16: Speciation
Evolutionary species concept: a species is a lineage of populations which
maintains its identity from other such lineages and which its own evolutionary
tendencies and historically fate
•
Isolation allows evolution to act independently on dif populations
•
Mutation, genetic drift, and selection lead to divergence
•
Different Species Concepts
Phenetic: a cluster of phenotypically similar individuals in multivariate
space
○
Biological: a group of actually or potentially inbreeding populations which
are reproductively isolated from other such groups
○
Phylogenetic: the smallest monophyletic group distinguished by a shared
derived character
○
○
•
Geographic Modes of Speciation:
Allopatric: geographic barrier (think two separate circles)
○
Parapatric: partial spatial isolation (think Venn diagram)
○
Sympatric: genetic polymorphism (think green and blue mixed green)
○
○
•
Pre-zygotic Isolating Mechanisms
Habitat Isolation
○
Temporal Isolation
○
•
Post-zygotic Isolating Mechanisms
Hybrids are inviable
○
Hybrids survive but are sterile
○
Low hybrid fitness
○
•
Character Displacement occurs when differences among similar species whose
distributions overlap geographically are accentuated in regions where the
species co-occur, but are minimized or lost where the species' distributions do
not overlap
•
Chapter 17: History of Life
5 Main types of fossils
Carbon Films: two-dimensional image imprinted delicately into rock
○
Molds and Casts: imprints in rock
○
Trace Fossils: a footprint, trail, burrow, or other trace of an animal rather
than of the animal itself
○
Petrified Fossils: actual bone remains
○
Preserved Remains: remains preserved in sap
○
•
Endosymbiosis led to chloroplasts, mitochondria, and apicoplasts
•
Common Features of Species Transitions
Shared reproductive fate among formerly autonomous units
○
Economies of scale and efficiencies of specialization (ie divisions of labor)
○
Novel ways of acquiring, processing, transmitting and/or storing info
○
•
For every living species, there may be thousands of extinct fossil species not
noted/recognized
•
Chapter 18: Human Evolution and Senescence
Polymorphisms are better preserved through larger population sizes
•
Phylogenetic incongruence, the inability to diverge into 2 unique species can be
due to coalescence, in which 2 smaller parts come together to form one larger
one.
•
LOOK AT THOSE QUIZ Qs
•
Serial founder effects: occurs when a new colony is started by a few members if
the original population
•
Senescence: an inc in the rate of mortality, and a decline in fecundity, with age
Due to:
Mutation Accumulation: harmful mutations are accumulated along a
lifetime
§
Antagonistic Pleiotropy: when one gene controls for more than one
trait where at least one of these traits is beneficial to the organism's
fitness and at least one is detrimental to the organism's fitness
§
○
•
Exam%2%Review
Wednesday,+ February+28,+2018
3:08+PM
Chapter 10: Migration and Inbreeding
Assumptions of Hardy-Weinberg Model
no selection
○
no mutation
○
no migration
○
random mating
○
infinite population size
○
•
Mainland-Island Model of Migration
deltaP = k(Pm-Pi)
Pm and Pi are the allele frequencies on the mainland and the island
§
k is the (migrating population)/(total population w migrants)
§
○
At equilibrium, the island population will reach the allele frequency of the
mainland.
○
•
Non-random Mating
Inbreeding
Leads to a decrease in heterozygotes
§
Genotype frequencies change under inbreeding, but allele
frequencies dont
§
○
Identity by Descent: When say two cousins mate, the offspring can end up
having 2 copies of the same allele
○
•
F statistics: statistically expected level of heterozygosity in a population
F= 1- [(observed heterozygotes)/(2pq)]
○
•
Effects of Population Genetics
•
Inbreeding depression
Deleterious recessives are usually at low frequency, so most are found in
heterozygotes.
○
HOWEVER, inbreeding inc proportion of homozygotes, so there is
stronger selection AGAINST deleterious recessives in an inbreed
population.
○
•
Chapter 11: Genetic Drift
Wright-Fisher Model: all assumptions are held except for the infinite population,
the population is finite.
•
Many generations of drift results in the spread of frequencies to the 2 extremes,
p=0 and p=1. After a few generations, you are likely to see something that looks
along the lines of a bell-curve. You wouldn’t see all of the allele frequency on
either of the ends (p=0 or p=1) because there is no selection acting in genetic
drift.
•
Smaller populations drift in frequency more dramatically and reach fixation faster
than larger ones
•
All subpopulations will go to fixation or loss eventually, with no other forces, it is
just a matter of how long.
•
Heterozygosity (H)
Observed: Ho: 1- f(homozygotes)
Based on the actual count of genotypes in the population
§
○
Expected: He: 1 -[(p^2 +q^2)] or (2pq)
Predicted HWE genotype proportions using allele frequencies
§
○
The direction of drift in any population is unpredictable, but the avg speed
with which heterozygosity (genetic variation) declines can be predicted
based only on population
Ht= (1 -(1/(2N))^t x Ho
t is the number of generations
□
§
○
•
Chapter 12: Conservation Genetics
Conservation Genetics: the effects of drift, inbreeding, and migration on
endangered species
•
Some endangered species may incur a population bottleneck -a dramatic
reduction in population
Key factors to this include overhunting or habitat fragmentation
○
•
A bottleneck effect increases the effects of genetic drift - leading to reduction in
genetic variation, and inc in inbreeding, leading to more homozygotes, including
deleterious recessive alleles
Inbreeding is evident because of many recessive traits that are found in no
other populations of a given species - phenotypic evidence
○
•
Actual Ht may be a little lower than the predicted Ht bc:
Initial heterozygosity, Ho may have been lower
○
the loci may have drifted faster than most
○
the census population size may have been an overestimate of Ne bc:
fluctuating pop size
§
uneven sex ratio
§
○
•
Effective population size is greatly reduced by bottlenecks
Ne = {k / [(1/N1)+(1/N2)+(1/N3)+…+(1/Nk)]}
k = # of generations
§
○
•
Territoriality means relatively few mating males compared to females
•
Effective population size, Ne
with dif # of males and females
Ne = 4(Nm)(Nf) / (Nm+Nf)
§
Unequal sex ratio leads to faster decline in heterozygosity and
faster divergence among populations
§
○
with same # of males and females
Ne = Nm + Nf
§
○
•
The founder effect is the reduced genetic diversity that results when a population
is descended from a small number of colonizing ancestors - for example, when a
population results from a bottleneck population.
•
Selection in a finite population is not deterministic
•
Chapter 13: Sexual Selection
Anisogamy: the fusion of gametes that differ (ex in size)
•
Fecundity: the ability to produce offspring
Female fecundity is limited by ability to gain resources for producing eggs
and rearing young - resources limited
○
Male fecundity is limited by ability to attract mates - higher variance
○
•
Fundamental Asymmetry of Sex
Competition between males for access to females
○
Females preference for males perceived to be of high quality
○
•
Male-Male Competition demonstrated by:
Elaborate Mating Displays
Ex: Birds
§
○
Direct combat (before mating)
Ex: Seals
§
○
Sperm competition (during or after mating)
Ex: scooping out other males sperm from female
§
○
•
Female Preference
Choosy females may benefit their offspring directly through acquisition of
resources and improve their fitness
Good genes, that confer higher fitness in both sexes
For ‘good genes’ mate choice to work, sexual displays need
to be honest signals of genotype fitness
□
§
Sexy sons, that lead to the male offspring having traits that are
more likely to confer better luck with sexual reproduction
AKA runaway selection
□
§
○
The better the nuptial gift, the longer the duration of copulation, up to a
certain point, and the longer the duration of copulation, the more sperm
transferred, also up to a certain point
○
•
Polygamous species are more likely to be sexually dimorphic, (ex: the male
having some sort of secondary sexual trait such as bright colors or big wings),
than monogamous species because they need the sexual dimorphism to win
serial mate choice conquests.
•
Sexual selection affects only reproductive fitness, but not all differences in
reproductive fitness are sexual selection
•
Male-Male competition is intrasexual
•
Mate choice (females) is intersexual
•
Chapter 14: Cooperation
Altruism is behavior of an animal that benefits another at its own expense
•
Cooperative brooding (ants) occurs through brood raiding, stealing of the young,
because more individuals available to work increases the probability of nest
survival
•
Reciprocity, or reciprocal altruism: a behavior where an organism acts in a
manner that temporarily reduces its fitness while increasing another organism's
fitness, with the expectation that the other organism will act in a similar manner
at a later time
Can be favored if there are many opportunities for mutual aid between
unrelated individuals
Ex: mobbing in birds
§
Birds are going to help those who have helped them before over
those who haven’t helped them before
§
○
•
Kin Selection: natural selection in favor of behavior by individuals that may
decrease their chance of survival but increases that of their kin (who share a
proportion of their genes)
Direct Fitness: the individuals own probability of survival and # of offspring
that live to reproductive age
○
Indirect Fitness: the fitness received by helping non-descendent kin
○
•
Inclusive fitness: individuals should be more wiling to perform altruistic acts for
kin than for non-kin
Hamilton's Rule: Altruistic behaviors are favored when:
B x r -C > 0
§
B: indirect benefits of the behavior to ones relatives
§
r: coefficient of relatedness
§
C: direct costs to the individual
§
○
Inclusive fitness includes both the direct and indirect contributions to an
individual’s fitness
○
•
Coefficient of Relatedness (r): the probability that a gene from one individual is
identical by descent to one from another individual
(0.5) from each parental to offspring that is related between the 2
○
•
Coalitions work together to defend territories and engage in elaborate displays to
attract females - only the dominant brother in the coalition actually mates
•
Eusociality
Features:
Reproductive division of labor
§
Cooperation rearing of young
§
Overlapping generations
§
○
•
Haplodiploidy is a sex-determination system in which males develop from
unfertilized eggs and are haploid, and females develop from fertilized eggs and
are diploid.
A female has higher relatedness to a full sister than to either parent
○
•
Chapter 15: Molecular Genetics
Neutral alleles are much more likely to be at intermediate frequencies in a
population than deleterious or beneficial because those are lost or fixed quickly
•
Beneficial Mutations are rare
•
Deleterious Mutations are common but quickly lost
•
Neutral Mutations fate are determined by genetic drift alone
Polymorphisms and divergence will be dominated by neutral mutations
○
•
Polymorphism: two or more alleles within a population or species
•
Substitution: sequence divergence between species
•
Neutral Theory:
Large amount of deleterious or neutral
○
# of mutations are related to mutation rate (u) and population size (2Ne)
# mutations = u(2Ne)
§
○
Probability of fixation = 1/(2Ne) (1 over total individuals in population)
○
We only expect neutral mutations to fix. - Null Hypothesis
○
Ka/Ks
k = (# of sub)/(# sites)
§
1st and 2nd are non-synonymous
§
3rd is synonymous because there is some redundancy in the amino
acid coded for the last nucleotide in codons
Synonymous sites are always created by genetic drift
□
§
Ka is deleterious (non-synonymous) (1st and 2nd) - only ones that
can be positively or negatively selected
§
Ks is neutral (synonymous) (3rd)
§
When Ka = Ks, Non-synonymous mutations are equal to
synonymous and there is no selection - Neutrality
§
Ka>Ks, more nonsynonymous than expected - positive selection
§
Ka<Ks, fewer nonsynonymous than expected - purifying selection
§
○
•
Most protein coding sequences are predominantly under purifying selection
•
Rate of divergence = substitutions per synonymous sites per year x lineages
•
Nearly Neutral Theory (updated version)
Still large amount of deleterious or neutral, but a more distributed around
neutral to allow for some neg/beneficial mutations that are around neutral
○
Helps w predictions bc proportion of effectively neutral corresponds w
pop size
○
Prop of mut that are effectively neutral
|s| << 1/(2Ne) - if pop is large, less drift, less selection
proportion around neutral becomes wider to neg/beneficial
□
§
|s| >> 1/(2Ne) - if pop is small, more drift, more selection
proportion around neutral becomes narrower against
neg/beneficial
□
§
○
Purifying selection is accounted for within neutral theory, but not positive
selection
○
Neutral theory serves as a null model
○
More generations = more mutations
○
Heterozygosity will be relatively insensitive to population size bc
organisms w large population sizes will have proportionally smaller rates
of neutral mutations
○
Molecular clock will tick in years
Based on observation that long-lived organisms tend to have
smaller population sizes, and thus proportionally higher neutral
mutation rates
§
○
•
Molecular Clock Stuff: If some sites mutate more often than others, using long
term, there is the issue of saturation bc you may get a lower number of mutations
than actually occurring. If short term, you want a site that mutates more
frequently or you most likely wont be able to see much.
•
The role of drift in molecular evolution is considerable and likely more important
than at the organismal level.
•
Chapter 16: Speciation
Evolutionary species concept: a species is a lineage of populations which
maintains its identity from other such lineages and which its own evolutionary
tendencies and historically fate
•
Isolation allows evolution to act independently on dif populations
•
Mutation, genetic drift, and selection lead to divergence
•
Different Species Concepts
Phenetic: a cluster of phenotypically similar individuals in multivariate
space
○
Biological: a group of actually or potentially inbreeding populations which
are reproductively isolated from other such groups
○
Phylogenetic: the smallest monophyletic group distinguished by a shared
derived character
○
○
•
Geographic Modes of Speciation:
Allopatric: geographic barrier (think two separate circles)
○
Parapatric: partial spatial isolation (think Venn diagram)
○
Sympatric: genetic polymorphism (think green and blue mixed green)
○
○
•
Pre-zygotic Isolating Mechanisms
Habitat Isolation
○
Temporal Isolation
○
•
Post-zygotic Isolating Mechanisms
Hybrids are inviable
○
Hybrids survive but are sterile
○
Low hybrid fitness
○
•
Character Displacement occurs when differences among similar species whose
distributions overlap geographically are accentuated in regions where the
species co-occur, but are minimized or lost where the species' distributions do
not overlap
•
Chapter 17: History of Life
5 Main types of fossils
Carbon Films: two-dimensional image imprinted delicately into rock
○
Molds and Casts: imprints in rock
○
Trace Fossils: a footprint, trail, burrow, or other trace of an animal rather
than of the animal itself
○
Petrified Fossils: actual bone remains
○
Preserved Remains: remains preserved in sap
○
•
Endosymbiosis led to chloroplasts, mitochondria, and apicoplasts
•
Common Features of Species Transitions
Shared reproductive fate among formerly autonomous units
○
Economies of scale and efficiencies of specialization (ie divisions of labor)
○
Novel ways of acquiring, processing, transmitting and/or storing info
○
•
For every living species, there may be thousands of extinct fossil species not
noted/recognized
•
Chapter 18: Human Evolution and Senescence
Polymorphisms are better preserved through larger population sizes
•
Phylogenetic incongruence, the inability to diverge into 2 unique species can be
due to coalescence, in which 2 smaller parts come together to form one larger
one.
•
LOOK AT THOSE QUIZ Qs
•
Serial founder effects: occurs when a new colony is started by a few members if
the original population
•
Senescence: an inc in the rate of mortality, and a decline in fecundity, with age
Due to:
Mutation Accumulation: harmful mutations are accumulated along a
lifetime
§
Antagonistic Pleiotropy: when one gene controls for more than one
trait where at least one of these traits is beneficial to the organism's
fitness and at least one is detrimental to the organism's fitness
§
○
•
Exam%2%Review
Wednesday,+ February+28,+2018 3:08+PM
Chapter 10: Migration and Inbreeding
Assumptions of Hardy-Weinberg Model
no selection
○
no mutation
○
no migration
○
random mating
○
infinite population size
○
•
Mainland-Island Model of Migration
deltaP = k(Pm-Pi)
Pm and Pi are the allele frequencies on the mainland and the island
§
k is the (migrating population)/(total population w migrants)
§
○
At equilibrium, the island population will reach the allele frequency of the
mainland.
○
•
Non-random Mating
Inbreeding
Leads to a decrease in heterozygotes
§
Genotype frequencies change under inbreeding, but allele
frequencies dont
§
○
Identity by Descent: When say two cousins mate, the offspring can end up
having 2 copies of the same allele
○
•
F statistics: statistically expected level of heterozygosity in a population
F= 1- [(observed heterozygotes)/(2pq)]
○
•
Effects of Population Genetics
•
Inbreeding depression
Deleterious recessives are usually at low frequency, so most are found in
heterozygotes.
○
HOWEVER, inbreeding inc proportion of homozygotes, so there is
stronger selection AGAINST deleterious recessives in an inbreed
population.
○
•
Chapter 11: Genetic Drift
Wright-Fisher Model: all assumptions are held except for the infinite population,
the population is finite.
•
Many generations of drift results in the spread of frequencies to the 2 extremes,
p=0 and p=1. After a few generations, you are likely to see something that looks
along the lines of a bell-curve. You wouldn’t see all of the allele frequency on
either of the ends (p=0 or p=1) because there is no selection acting in genetic
drift.
•
Smaller populations drift in frequency more dramatically and reach fixation faster
than larger ones
•
All subpopulations will go to fixation or loss eventually, with no other forces, it is
just a matter of how long.
•
Heterozygosity (H)
Observed: Ho: 1- f(homozygotes)
Based on the actual count of genotypes in the population
§
○
Expected: He: 1 -[(p^2 +q^2)] or (2pq)
Predicted HWE genotype proportions using allele frequencies
§
○
The direction of drift in any population is unpredictable, but the avg speed
with which heterozygosity (genetic variation) declines can be predicted
based only on population
Ht= (1 -(1/(2N))^t x Ho
t is the number of generations
□
§
○
•
Chapter 12: Conservation Genetics
Conservation Genetics: the effects of drift, inbreeding, and migration on
endangered species
•
Some endangered species may incur a population bottleneck -a dramatic
reduction in population
Key factors to this include overhunting or habitat fragmentation
○
•
A bottleneck effect increases the effects of genetic drift - leading to reduction in
genetic variation, and inc in inbreeding, leading to more homozygotes, including
deleterious recessive alleles
Inbreeding is evident because of many recessive traits that are found in no
other populations of a given species - phenotypic evidence
○
•
Actual Ht may be a little lower than the predicted Ht bc:
Initial heterozygosity, Ho may have been lower
○
the loci may have drifted faster than most
○
the census population size may have been an overestimate of Ne bc:
fluctuating pop size
§
uneven sex ratio
§
○
•
Effective population size is greatly reduced by bottlenecks
Ne = {k / [(1/N1)+(1/N2)+(1/N3)+…+(1/Nk)]}
k = # of generations
§
○
•
Territoriality means relatively few mating males compared to females
•
Effective population size, Ne
with dif # of males and females
Ne = 4(Nm)(Nf) / (Nm+Nf)
§
Unequal sex ratio leads to faster decline in heterozygosity and
faster divergence among populations
§
○
with same # of males and females
Ne = Nm + Nf
§
○
•
The founder effect is the reduced genetic diversity that results when a population
is descended from a small number of colonizing ancestors - for example, when a
population results from a bottleneck population.
•
Selection in a finite population is not deterministic
•
Chapter 13: Sexual Selection
Anisogamy: the fusion of gametes that differ (ex in size)
•
Fecundity: the ability to produce offspring
Female fecundity is limited by ability to gain resources for producing eggs
and rearing young - resources limited
○
Male fecundity is limited by ability to attract mates - higher variance
○
•
Fundamental Asymmetry of Sex
Competition between males for access to females
○
Females preference for males perceived to be of high quality
○
•
Male-Male Competition demonstrated by:
Elaborate Mating Displays
Ex: Birds
§
○
Direct combat (before mating)
Ex: Seals
§
○
Sperm competition (during or after mating)
Ex: scooping out other males sperm from female
§
○
•
Female Preference
Choosy females may benefit their offspring directly through acquisition of
resources and improve their fitness
Good genes, that confer higher fitness in both sexes
For ‘good genes’ mate choice to work, sexual displays need
to be honest signals of genotype fitness
□
§
Sexy sons, that lead to the male offspring having traits that are
more likely to confer better luck with sexual reproduction
AKA runaway selection
□
§
○
The better the nuptial gift, the longer the duration of copulation, up to a
certain point, and the longer the duration of copulation, the more sperm
transferred, also up to a certain point
○
•
Polygamous species are more likely to be sexually dimorphic, (ex: the male
having some sort of secondary sexual trait such as bright colors or big wings),
than monogamous species because they need the sexual dimorphism to win
serial mate choice conquests.
•
Sexual selection affects only reproductive fitness, but not all differences in
reproductive fitness are sexual selection
•
Male-Male competition is intrasexual
•
Mate choice (females) is intersexual
•
Chapter 14: Cooperation
Altruism is behavior of an animal that benefits another at its own expense
•
Cooperative brooding (ants) occurs through brood raiding, stealing of the young,
because more individuals available to work increases the probability of nest
survival
•
Reciprocity, or reciprocal altruism: a behavior where an organism acts in a
manner that temporarily reduces its fitness while increasing another organism's
fitness, with the expectation that the other organism will act in a similar manner
at a later time
Can be favored if there are many opportunities for mutual aid between
unrelated individuals
Ex: mobbing in birds
§
Birds are going to help those who have helped them before over
those who haven’t helped them before
§
○
•
Kin Selection: natural selection in favor of behavior by individuals that may
decrease their chance of survival but increases that of their kin (who share a
proportion of their genes)
Direct Fitness: the individuals own probability of survival and # of offspring
that live to reproductive age
○
Indirect Fitness: the fitness received by helping non-descendent kin
○
•
Inclusive fitness: individuals should be more wiling to perform altruistic acts for
kin than for non-kin
Hamilton's Rule: Altruistic behaviors are favored when:
B x r -C > 0
§
B: indirect benefits of the behavior to ones relatives
§
r: coefficient of relatedness
§
C: direct costs to the individual
§
○
Inclusive fitness includes both the direct and indirect contributions to an
individual’s fitness
○
•
Coefficient of Relatedness (r): the probability that a gene from one individual is
identical by descent to one from another individual
(0.5) from each parental to offspring that is related between the 2
○
•
Coalitions work together to defend territories and engage in elaborate displays to
attract females - only the dominant brother in the coalition actually mates
•
Eusociality
Features:
Reproductive division of labor
§
Cooperation rearing of young
§
Overlapping generations
§
○
•
Haplodiploidy is a sex-determination system in which males develop from
unfertilized eggs and are haploid, and females develop from fertilized eggs and
are diploid.
A female has higher relatedness to a full sister than to either parent
○
•
Chapter 15: Molecular Genetics
Neutral alleles are much more likely to be at intermediate frequencies in a
population than deleterious or beneficial because those are lost or fixed quickly
•
Beneficial Mutations are rare
•
Deleterious Mutations are common but quickly lost
•
Neutral Mutations fate are determined by genetic drift alone
Polymorphisms and divergence will be dominated by neutral mutations
○
•
Polymorphism: two or more alleles within a population or species
•
Substitution: sequence divergence between species
•
Neutral Theory:
Large amount of deleterious or neutral
○
# of mutations are related to mutation rate (u) and population size (2Ne)
# mutations = u(2Ne)
§
○
Probability of fixation = 1/(2Ne) (1 over total individuals in population)
○
We only expect neutral mutations to fix. - Null Hypothesis
○
Ka/Ks
k = (# of sub)/(# sites)
§
1st and 2nd are non-synonymous
§
3rd is synonymous because there is some redundancy in the amino
acid coded for the last nucleotide in codons
Synonymous sites are always created by genetic drift
□
§
Ka is deleterious (non-synonymous) (1st and 2nd) - only ones that
can be positively or negatively selected
§
Ks is neutral (synonymous) (3rd)
§
When Ka = Ks, Non-synonymous mutations are equal to
synonymous and there is no selection - Neutrality
§
Ka>Ks, more nonsynonymous than expected - positive selection
§
Ka<Ks, fewer nonsynonymous than expected - purifying selection
§
○
•
Most protein coding sequences are predominantly under purifying selection
•
Rate of divergence = substitutions per synonymous sites per year x lineages
•
Nearly Neutral Theory (updated version)
Still large amount of deleterious or neutral, but a more distributed around
neutral to allow for some neg/beneficial mutations that are around neutral
○
Helps w predictions bc proportion of effectively neutral corresponds w
pop size
○
Prop of mut that are effectively neutral
|s| << 1/(2Ne) - if pop is large, less drift, less selection
proportion around neutral becomes wider to neg/beneficial
□
§
|s| >> 1/(2Ne) - if pop is small, more drift, more selection
proportion around neutral becomes narrower against
neg/beneficial
□
§
○
Purifying selection is accounted for within neutral theory, but not positive
selection
○
Neutral theory serves as a null model
○
More generations = more mutations
○
Heterozygosity will be relatively insensitive to population size bc
organisms w large population sizes will have proportionally smaller rates
of neutral mutations
○
Molecular clock will tick in years
Based on observation that long-lived organisms tend to have
smaller population sizes, and thus proportionally higher neutral
mutation rates
§
○
•
Molecular Clock Stuff: If some sites mutate more often than others, using long
term, there is the issue of saturation bc you may get a lower number of mutations
than actually occurring. If short term, you want a site that mutates more
frequently or you most likely wont be able to see much.
•
The role of drift in molecular evolution is considerable and likely more important
than at the organismal level.
•
Chapter 16: Speciation
Evolutionary species concept: a species is a lineage of populations which
maintains its identity from other such lineages and which its own evolutionary
tendencies and historically fate
•
Isolation allows evolution to act independently on dif populations
•
Mutation, genetic drift, and selection lead to divergence
•
Different Species Concepts
Phenetic: a cluster of phenotypically similar individuals in multivariate
space
○
Biological: a group of actually or potentially inbreeding populations which
are reproductively isolated from other such groups
○
Phylogenetic: the smallest monophyletic group distinguished by a shared
derived character
○
○
•
Geographic Modes of Speciation:
Allopatric: geographic barrier (think two separate circles)
○
Parapatric: partial spatial isolation (think Venn diagram)
○
Sympatric: genetic polymorphism (think green and blue mixed green)
○
○
•
Pre-zygotic Isolating Mechanisms
Habitat Isolation
○
Temporal Isolation
○
•
Post-zygotic Isolating Mechanisms
Hybrids are inviable
○
Hybrids survive but are sterile
○
Low hybrid fitness
○
•
Character Displacement occurs when differences among similar species whose
distributions overlap geographically are accentuated in regions where the
species co-occur, but are minimized or lost where the species' distributions do
not overlap
•
Chapter 17: History of Life
5 Main types of fossils
Carbon Films: two-dimensional image imprinted delicately into rock
○
Molds and Casts: imprints in rock
○
Trace Fossils: a footprint, trail, burrow, or other trace of an animal rather
than of the animal itself
○
Petrified Fossils: actual bone remains
○
Preserved Remains: remains preserved in sap
○
•
Endosymbiosis led to chloroplasts, mitochondria, and apicoplasts
•
Common Features of Species Transitions
Shared reproductive fate among formerly autonomous units
○
Economies of scale and efficiencies of specialization (ie divisions of labor)
○
Novel ways of acquiring, processing, transmitting and/or storing info
○
•
For every living species, there may be thousands of extinct fossil species not
noted/recognized
•
Chapter 18: Human Evolution and Senescence
Polymorphisms are better preserved through larger population sizes
•
Phylogenetic incongruence, the inability to diverge into 2 unique species can be
due to coalescence, in which 2 smaller parts come together to form one larger
one.
•
LOOK AT THOSE QUIZ Qs
•
Serial founder effects: occurs when a new colony is started by a few members if
the original population
•
Senescence: an inc in the rate of mortality, and a decline in fecundity, with age
Due to:
Mutation Accumulation: harmful mutations are accumulated along a
lifetime
§
Antagonistic Pleiotropy: when one gene controls for more than one
trait where at least one of these traits is beneficial to the organism's
fitness and at least one is detrimental to the organism's fitness
§
○
•
Exam%2%Review
Wednesday,+ February+28,+2018 3:08+PM
Document Summary
Assumptions of hardy-weinberg model no selection no mutation no migration random mating infinite population size. Pm and pi are the allele frequencies on the mainland and the island k is the (migrating population)/(total population w migrants) At equilibrium, the island population will reach the allele frequency of the mainland. Genotype frequencies change under inbreeding, but allele frequencies dont. Identity by descent: when say two cousins mate, the offspring can end up having 2 copies of the same allele. F statistics: statistically expected level of heterozygosity in a population. Deleterious recessives are usually at low frequency, so most are found in heterozygotes. However, inbreeding inc proportion of homozygotes, so there is stronger selection against deleterious recessives in an inbreed population. Wright-fisher model: all assumptions are held except for the infinite population, the population is finite. Many generations of drift results in the spread of frequencies to the 2 extremes, p=0 and p=1.
