ECCB 400 Exam 2

What do DNA repair systems do?

They correct DNA damage before it becomes a mutation. They are required to maintain DNA functionality

Explain the stickleback mutation

Freshwater ones developed more teeth and less armor. evolution can occur fast when cryptic variants are present, the mutant allele Bmp6 changed the gene regulation for # of teeth.

Neanderthal DNA

They analyzed mtDNA (mitochondrial) from the fossil and found the difference in substitutions (27.2). Using this they were able to date when the last common ancestor of modern humans and neanderthals lived.

Why can we use molecular markers to infer genetic relationships

Because genetic material is transmitted from parent to offspring in predictable manner.

Biparental inheritance (and uniparental inheritence)

In a genome of diploids, one allele from each locus is inherited from mother and one from the father.

Two possible uniparentally inherited organelle genomes:

1. mtDNA

2. plastids (includes cpDNA/chloroplasts)

shared organelle features

circular chromosome, smaller genome than nuclear genome, located outside nucleus, chloroplasts only in green plants

function of mtDNA

cellular respiration (process where energy is extracted from food)

Animal mtDNA features

• very compact (only 16k compared to nuclear 3.2 billion)

• 13 protein coding genes, several other genes code for RNA

• mostly non-repetitive sequences

• most animals have mtDNA that is maternally inherited

why is animal mtDNA a useful and popular molecular marker to use? (5 reasons)

• mutation rates are relatively high

rate of synonymous subs are 10x the rate in nuclear genes, showing polymorphisms/genetic differences within and among populations

• tends to evolve neutrally

neutral substitutions common, beneficial and deleterious rare 

• generally lacks recombination

offspring usually have same mt genome as mother, making mtDNA a single haplotype

• haploid and uniparentally inherited

mtDNA has ¼ pop size of nuclear DNA, making it more sensitive to bottlenecks

• easy to work with (small size, many copies in a cell, conserved arrangement of genes)

allele vs haplotype

allele is the version of DNA at one locus, while haplotype is the combination of alleles across loci on one chromosome

substitutions vs mutations

mutations: genetic change within species, often deleterious

substitutions: changes between species, often neutral/beneficial

plant mtDNA unique features

(mostly maternally inherited)

1. regularly undergo recombination (gene duplications and rearrangements)

2. high genome size variation

3. slow evolving/rate of nucleotide substitutions are 100x slower

Chloroplast DNA (cpDNA) & advantages

often used as a molecular marker.

• in ANGIOSPERMS, maternally inherited (gymnosperms differ)

Advantages:

1. uniparentally inherited

2. structurally more stable than mtDNA

3. synonymous sub rate is faster than in plant mtDNA but slower than in nuclear genes

4. cpDNA contains MICROSATELLITES that evolve fast

Explain the Park Grass Experiment (PGE)

Adjacent plots receive diff types and amts of nutrients, causing populations to locally adapt. This allows us to study the role of natural selection in reproductive isolation in earliest stages of speciation.

Also introduced the selective mechanism reinforcement aka the Wallace effect, which is where low fitness of hybrids select reprod isolation between diverging pops.

PGE experiment with sweet vernal grass

They expected that pollen flow between plots would be higher than seed flow. cpDNA is only inherited via seeds, while nuclear DNA is inherited via pollen and seeds.

RESULTS:

pops were more similar on basis of cpDNA, showing that seed flow is higher than pollen flow.

WHY?

There were likely difference in flowering times, bc plots w diff flowering times cant exchange pollen, but can exchange seeds so natural selection has reinforced reprod. isolation

Mammalian Y chromosome features

1. patrilineal descent (father to son)

2. only effectively haploid mammal chromosome

3. mutation rate is higher than other chromosomes

4. recombination occurs in two small pseudoautosomal regions (PARs) at the tips and recombine with the X chromosome

using molecular markers with hybrids

comparing nuclear vs mtDNA can help find past hybridization events bc mtDNA doesn’t recombine and can be retained for long time after hybridization unless hybrids back cross to parental species

Introgression

movement of genes from one species into the gene pool of another. usually thru repeat backcrossing of hybrids between two species with one of its parent species

explain the study of Hyla treefrogs and introgression and hybridization

when looking at nDNA, there shows no evidence of hybridization. cant rule out introgression bc small # of genes analyzed has low power to detect introgression in nDNA.

using mtDNA, some haplotypes of the brown H. arenicolor are more similar to haplotypes of green H. wrightorum than their own species, suggesting hybridization that lead to introgression of mtDNA from green frog to brown frog, but not vise versa bc not all brown frogs have green frog DNA.

what is a molecular marker

a specific DNA sequence within an organisms genome that can be used to identify and distinguish between individuals or pops.

Codominant vs Dominant markers

Codominant:

identify all the alleles at a particular locus (precise). in diploid individuals, can distinguish homo vs heterozygous. can calculate ALLELE FREQUENCIES

• DNA sequencing like single nucleotide polymorphisms (SNPs) and microsatellites.

• using allozymes and RFLPS are extinct

Dominant:

reveals only a single dominant allele; methods are rarely used.

• AFLPs and RAPDs

What are microsatellites

they are simple sequence repeats (SSRs) or stretches of DNA that consist of tandem repeats. They are located in nDNA and cpDNA.

• they mutate much faster than other types of sequences

• useful for inferring evolutionary events in the past (intraspecific markers)

DNA fingerprinting 

uses the polymerase chain reaction which amplifies microsatellites. Individuals are analyzed based on occurrence and length of repetitive sequences in genome. (Size and order of bands)

Single nucleotide polymorphisms (SNPs)

• single base pair positions along a DNA sequence that vary between individuals

• most SNPs have only two alleles, although six are possible (AGCT, insertion, deletion)

• advantageous bc more numerous than microsatellites and found within or close to genes

modes of speciation (Allopatric, peripatric, parapatric, sympatric)

1. Allopatric: new species formed from geographically isolated pops

2. Peripatric: new species formed from small pop isolated at edge of larger pop

3. Parapatric: new species formed from continuously distributed pop

4. Sympatric: new species formed from within range of ancestral pop

adaptive radiation

rapid increase in the # of species descending from a common ancestor w great ecological diversity

population

potentially interbreeding group of individuals that belong to the same species and live within a restricted geographical area.

why is genetic diversity important to populations

1. environments are always changing and genetic diversity is necessary for evolving and adapting

2. low genetic diversity means higher inbreeding, which reduces fitness

how does genetic diversity impact an ecosystem

it influences survival of pops, genetically diverse plant communities support diverse animal communities and are more resistant to disturbances. Genetic diversity can be based on allele or genotype frequencies.

Hardy-Weinberg Equilibrium and assumptions (5)

under certain conditions genotype frequencies can follow a predictable pattern

1. Allele frequencies: only two alleles at locus (A or a) so p+q=1

2. Genotype frequencies: AA + Aa + aa = 1

3. genotype freq: p² + 2pq + q² = 1

ASSUMPTIONS:

• random mating/mating is equally likely between all combos

• no selection on any genotype

• pop size is infinite

• alleles segregate following normal Mendelian inheritance

• Migration/mutation on allele frequencies are insignificant

factors that cause deviation from HWE

1. asexual reproduction

2. natural selection

3. inbreeding

4. improper sampling

5. wahlund effect (inadvertently sampling from more than one pop, leads to substantial overestimate of H_e)

nucleotide diversity

measure of polymorphism in a sample of gene sequences. represents average # of nucleotide differences per site between any two DNA sequences chosen randomly

what influences genetic diversity

1. Genetic drift

2. Demography (sex ratios, fluctuating pop size, reprod success variation)

3. Bottlenecks

4. Natural selection

5. Founder effects and invasive species

Genetic Drift: consequences and pop size

It is a populations allele frequencies change from one generation to the next by chance.

Consequences:

1. allele frequencies fluctuate and not all alleles will be reproduced to the same extent

2. results in non-adaptive evolutionary change

SMALL POPS: drift decreases genetic diversity; allele becomes fixed or extinct in short period of time

LARGE POPS: limited effect, longer time needed before pronounced effects. natural selection has a stronger effect.

Census pop size (Nc) vs. Effective pop size (Ne)

Nc: # of individuals in a particular population

Ne: rate at which genetic diversity will be lost following genetic drift

Why Ne is lower than Nc: Sex ratios

unequal sex ratios reduce Ne. Even if overall sex ratio is close to 1, unequal sex ratio of BREEDING adults decreases Ne but has no effect on Nc

Why Ne is lower than Nc: variation in reprod success (VRS)

it is the variation in numbers of viable offspring produced throughout an individuals lifetime. Higher VRS decreases Ne relative to Nc

Why Ne is lower than Nc: fluctuating pop size

fluctuating pop sizes are estimated to reduce the Ne of wild pops by 65%