FNR 305 Exam 2

gene pool

gene pool

all alleles in a population

genetic diversity

the number and kind of genes (alleles) in a population; usually refers to a single species

genetic markers include:

microsatellites, mitochondrial DNA, allozymes, SNPs, etc.

genetic markers

most are codominant; serve as proxies for studying individual genes; allow us to estimate genetic diversity across entire genome

DNA typing

to genotype individuals by means of DNA extracted from tissue samples

population genetic structure

alleles at polymorphic loci may differ in frequency among subpopulations

genetic variation

allelic variation and heterozygosity are often assessed at microsattelite loci (genetic markers used for DNA fingerprinting)

genotype frequency

refers to the proportion of individuals in a population with a specific genotype

allele frequencies

count the # of times an allele occurs and divide by the number of chromosomes (2n in diploids); frequencies will sum to 1; basis for determining HE

average heterozygosity

the percentage of individuals that are heterozygous at a particular locus

Heterozygosity (H)

observed (H0), expected (HE)

allelic diversity (A)

mean number of alleles per locus

microsatellite genotyping

1. extract DNA sample, 2. characterize microsatellites if none described, 3. amplify each locus using PCR, 4. electrophorese to sperate alleles based on size

mtDNA markers

mitochondrial DNA: haploid, maternally inherited DNA marker; endosymbiont; evolves rapidly

Heterozygote superiority

when the fitness (measurment of viability and fertility) of heterozygotes is greater than homozygotes

overdominance

in sickle cell anemia, overdominance of the heterozygote carriers is observed because they are more resistant to malaria

Hardy-Weinberg Principle (HW)

analyzes the factors which may affect the frequencies of alleles in a population; uses a simple equation to calculate allelic frequencies: p+q=1

HWE assumptions/conditions:

1. Mating is random, 2. allelic frequencies are the same in males and females, 3. all genotypes have equivalent viability and fertility (i.e. no selections), 4. Mutation does not occur, 5. Migration into the population is absent, 6. Population is large so that allelic variations do not occur by chance (i.e. no genetic drift)

HWE calculating expected genotype frequencies:

p^2 +2pq+q^2=1
pp=homozygous dominant
qq=homozygous recessive
2pq=heterozygous

HWE calculating multiple allele frequencies:

p^2+2pq+2pr+q^2+2qr+r^2=1

Deviations from HWE

mutation, migration, selection, drift (or sampling error)

genetic drift

greater effects seen on smaller populations; sampling error that occurs at low population sizes; rare alleles may never get to next generation

microevolution

allele frequency change over time

macroevolution

refers to changes in the gene pool which produce phenotypic changes subject to the forces of natural selection

Causes of evolution:

mutation, migration, natural selection, random genetic drift

Under HWE, evolution...

would not occur and allele frequencies would remain unchanged over time

Principles of Evolution

1) more young are born that can survive, 2) heritable variation occurs within populations, 3) genetic variation may be beneficial, detrimental, or neutral, 4) organisms with genotypes most compatible with their environment are overrepresented in the next generation 5) populations change in genetic composition over time 6) over time, genetic differentiation of populations can give rise to new species

What can lead to speciation?

A reduction in gene flow between populations, accompanied by divergent selection or genetic drift.

Lack of gene flow and divergence

evolution of genetic reproductive barriers between discrete populations; may be caused by topography, habitat or climate then populations evolve separately

What is the evolutionary fate of gene pools in independent bison herds?

divergence

Divergence

can arise because of geographic barriers; can restrict gene flow; ultimately can lead to reproductive incompatibility

Rates of speciation are variable

1) instantaneous (polyploidy) 2)rapid (Drosophilia, cichlids) 3) 3 million years (estimated average time to full reproductive isolation) 4) > 20 million years for full reproductive isolation

Factors that promote rapid speciation

1) low dispersal rates 2) abundant opportunities for isolation of populations 3) strong sexual selection 4) opportunity for ecological specialization 5) bottlenecks in population size

Genetic diversity increases with

increasing population size

genetic drift

causes random changes in allele frequency in small populations; one allele may become fixed; loss of allelic diversity and lower H

Loss of genetic diversity

is related to the average increase in inbreeding, leading to reduction in fitness called inbreeding depression

Bottlenecks

longer the bottleneck, more diversity lost; rate of loss depends on population size

Mechanisms that decrease genetic diversity

Extinction of populations, fixation of favorable alleles by selection, genetic drift, inbreeding

Inbreeding

the mating of individuals related by ancestry; increases homozygosity, reduces heterozygosity; exposes rare deleterious recessive alleles; measured as the probability that 2 alleles at a locus are identical-by-descent (IBD)

inbred populations

will have a lowered mean fitness called inbreeding depression (i.e. Isle Royale wolves)

genetic load

the cumulative burden of deleterious recessive alleles found in a genome

coefficient of inbreeding, F

the probability that 2 alleles of a given gene in an individual are identical because they are descended from the same single copy of the allele in an ancestor

F

the probability that an individual carries alleles that are identical by descent (IBD); F=0 is completely outbred, F=1 is completely inbred

Inbreeding vs. Relatedness

inbreeding (F) is calculated for 1 individual; relatedness (r) between pairs and refers to the portion of genome shared btw. individuals

Inbreeding is cumulative

large populations accumulate inbreeding very slowly; smaller the population, more rapidly inbreeding accumulates

Inbreeding Depression (ID)

a reduction in fitness associated with inbreeding; Increases probability of extinction via the extinction vortex

extinction vortex

Measuring ID

= 1- (fitness inbred/fitness outbred)

10% increase in inbreeding leads to

10% reduction in fitness

Effective population size (Ne)

the size of an idealized population that would lose genetic diversity at the same rate as the actual population

Factors that reduce Ne/N

1)fluctuation in population size 2) variation in family size (few indv. monopolize mating, this skews the ratio) 3) variation in operation sex ratio

Other factors influencing Ne/N

overlapping generations and nonrandom mating

average ratio of Ne/N

0.10

Effective population size predict the effects on the population of:

random genetic drift, natural selection, mutation-selection equilibrium, inbreeding, genetic diversity

habitat fragmentation

leads to decreased Ne and reduced migration, may lead to genetic differentiation

small Ne

more drift, fewer immigrants

isolation-by-distance

the farther apart two populations are, the more likely they will differ; factor in allopatric speciation

F IT

is inbreeding of individuals in the total population

F IS

the probability that two alleles in the same individual are identical by descent

Fst

the probability that two alleles drawn at random from a subpopulation are identical by descent; widely used measure of divergence

If gene flow is high, Fst is generally:

low

Wind-pollinated trees have greater dispersal capacity than arboreal rodents such as squirrels. Given two woodlots separated by a very large field of row crops, would you expect Fst to be higher in the tree or the squirrel?

squirrel

m and Nm

m=migration rate Nm= number of migrants per generation

Consequences of fragmentation

1) fragmented populations genetically differ by chance 2)Cumulative diversification through inbreeding and drift within population fragments

How is Fst affected by dispersal rate?

Fst decreases as dispersal rate increases

How is Fst affected by habitat fragmentation?

Fst increases as habitat becomes more fragmented; Fst increases the more distant the habitat subdivisions

How is Fst affected by divergence time?

Fst increases with a longer divergence time

How is Fst affected by population size?

Fst increases when populations are smaller

How is FST generally affected by adaptive differences?

Fst increases with adaptive differences between populations

Self-fertilization

a form of inbreeding common in plants; increases homozygosity rapidly

Florida panther

isolated population that experienced a long-term bottleneck; 60-70 animals; Inbreeding depression: high incidence of abnormalities (heart defects, poor semen quality)

Minimal viable population size

minimum size required to retain reproductive fitness and evolutionary potential over thousands of years

According to Bailey, the more we intervene to manage wild populations, the more ______________________ will occur.

artificial selection

Bailey relates how a Russian geneticist selectively bred foxes for coat color. In so doing, he inadvertently selected for animals with mottled fur, floppy ears, and shorter tails. This is an example of:

linked traits

The International Union for Conservation of Nature lists what as a major obstacle for bison restoration?

regulatory status (most states recognize bison as livestock)

Population Viability Analysis (PVA)

a species specific risk assessment based on ecology and statistics; used as management tool to compare different options to recover a species

Deterministic factors

habitat loss, over-exploitation, pollution, introduced species

stochastic factors

demographics (sex ratio, birth rates), environmental variation (temperature, rainfall, competitors, predators), genetic (ID, loss of GD, divergences, etc.), catastrophes (hurricanes, floods, etc.)

Limitations of PVAs

-PVAs do not encompass the full genetic impacts on population viability
-Insufficient life-history data for most species
-Poisson variation in family sizes generally assumed (biased Ne estimates)
-May assume environmental conditions remain unchanged
-The process of conducting a PVA may be more important to conservation than the PVA output!
-mostly, species biology!

Goals for managing wild populations

-managing population size
-alleviate the effects of fragmentation
-alleviate genetic swamping due to hybridization between species
-minimize the impacts of harvesting

Hardy-Weinberg Equilibrium

a model that can be used to predict stable genotype frequencies from allele frequencies if certain assumptions are true: -no mutation, -no migration, -no selection, -no drift, -random mating

Which evolutionary force is most likely to cause genome-wide convergence in two different geographic bison populations?

migration

Biological Species Concept

group of populations that exchange (or have the potential to exchange) genes by interbreeding AND do not interbreed with other populations because of biological differences

Evolutionary "Options"

1) stasis
2) undergo gradual phyletic evolution (anagensis) to become a new species
3) undergo cladogensis to give rise to two distinct and independent daughter species

How does speciation occur?

mostly due to allopatry, but also sympatry, and some due to instant speciation (polyploid)

According to the biological species concept, the major criterion for determining whether two population are part of the same species is:

reproductive compatibility

Neutral Theory of molecular evolution

mutations leading to amino acid substitutions are rare, because they are usually detrimental; mutations that are neutral will be effected by other mutations and by genetic drift; most variation is the result of neutral mutations

Three primary questions when diagnosing genetic problems:

-Has a threatened species lost its genetic diversity?
-Is it suffering from inbreeding depression?
-Is it genetically fragmented?

Diagnosing Genetic Problems

often involves collecting tissue samples, then DNA is extracted and used to estimate allelic diversity (A), heterozygostiy (H), and the similarity of gene pools.

Recover small inbred populations

introduce individuals from other populations (outbreeding not always possible)

Genetic management of fragmented populations

-increase population size
-establish populations in several locations
-maximize reproductive rate
-insulate from environmental change
-translocation
-alternatives (aritificial insemination)
-re-establish gene flow (corridors)

Impacts of harvesting

directional selection occurs due to harvesting based on quality of individuals

Effective Population Size Equation

Ne = t/ (∑1/Nei)

Mammoths on Wrangel Island (at the tail end of mammoth existence)

Due to evolution occurring at low effective population sizes, detrimental mutations occurred such as deletions and premature stop codons. Also evolved to have a satin coat?

FOXQ1 locus

pleiotropic: satin coat and mucin secretion in GI tract, leading to gastic irritation

Nearly neutral theory

under small effective population sizes, detrimental mutations can accumulate in genomes.