Phenotype Vs Genotype
P: Observable characteristic
G: Individuals complete set of genes
Types of Inheritance
simple
incomplete dom
co-dom
polygenic
epistasis
sex-linked
mitochondrial
multiple alleles
What are allozymes, why are they not typically used in modern molecular ecology
allelic forms of the same protein-coding locus (also molecular marker
- very invasive to retrieve from specimens
- not all variations in protein-coding DNA seq translates to variable protein-coding locus
- info is in genome and these only have small portrion from genes
What was the DNA technological advancement in 1980 and what were the steps for it
Sanger sequencing
1. generates frags of diff lengths (via PCR w/fluorescent chain-terminating ddNTPs) that are visualized on lanes (via size separation by cappillary gel electrophoresis
- laser excitation on automated sequencers show coloured peaks on a graph
What was the genetic understanding in 20th century (60’s-80’s), what do we know about it now.
no understanding of
- genetic variation
- links between phenotypes and genotypes
- roles of functional genes
- 98% of human genome is actually none-coding genes
- we have large genetic variability
- we have inheritable genes
What was the DNA technological advancement in 1985
polymerase chain reaction
What was the DNA technological advancement in 1990
quantitative PCR
- monitors PCR in real time
the frags produced in it are labelled w/fluorescent dye probs and DNA binding which can be quantified after
can quantify DNA and RNA relatively
- amount a gene is expressed
- identifies conditions that result in up or down regulation of a gene
What was the DNA technological advancement in 2005
next gen sequencining
(seq millions of DNA)
characterization gene expression
(transcriptons and their functions)
what are genetic markers, give their characteristics, what are they in molecular ecology
a molecular sample that gives info on source (biomarkers eg. hemoglobin)
- diff characteristics that will provide diff info (eg postal code vs telephone area code)
- could tell us ancestry, susceptibility to disease. phenotypes
- DNA sets used to identify species, genetic variation, gene flow etc.
what makes a good genetic marker, what characteristics do you have to consider when choosing which one to assay
- heritable
- not influenced by environment
- variable
- neutral or adaptive
- mode of inheritance
- level of variability
-prior genomic resources needed - ease, use, cost
- what kid of tissue samples needed
- number of independent markers/coverage of genome
adaptive vs neutral biomarkers , what do you have to be aware of?
Adaptive:
- functional (serves purpose)
- may experience selection
- alleles have diff fitness
neutral:
- non-functional junk DNA
- doesn’t experience selection
- diff alleles have equal fitness
linkage disequilibrium: non-random allele association from diff loci
selective sweepL increase in frequency of neutral allele due to proximity w/target allele
mode of inheritance diff between nuclear DNA and organelle dna
nuclear:
- biparental
- milti chromosome
-large
- recombination
organelle
- uniparental
- simple, supercoiled circle
- small
- no recombination
- conserved seq
what’re the variability between molecular markers
- amt of allele at each loci (mutation rate)
- high variability needed to detect relationship within pop and low variability to detect relationship amongst distant pops
low variability:
- low mute rate
-low polymorphism
- long-term evol signal
- uniparental inheritance
- stable, less informative for recent events (used to examine historical process
high variability:
- high mute
- high polymorphism
- short-term evolutionary signal
- biparental inheritance
- responsive to recent events (monitors conservation efforts)
what’re the costs and ease of use for biomarkers
costs:
- initial investment
- sample throughout
- data processing costs
- low-cost markers are ideal for broad population studies
- higher cost deliver high-resolution data but are more expensive to develop
ease of use:
- technical complexity
- time
- reproductibillity
- simpler markers are more accessible but sometimes less reproducible
- complex ones require advanced tech/expertise but provide higher resolution
what are used to identify individuals (bear case study)
case 1: used molecular markers (microsatellites) to assign to population
case 2: used molecular tools to identify by individuals/sex/species
key points:
- hair samples were distinguishable via genotypes at microsatellite loci
- 6 unique loci worked for both grizzly/black bear bears
- each locus had alleles in both grizzly (4-8) and black (6-13)
How do we identify individuals? what’re the variables to calculate it
calc probs of both:
homo for A
homo for a
hetero for Aa
any given genotype
probability of two random at BOTH loci
By calculating Probability of identity (probs that 2 individuals have the same genotype)
AA = pA^2
aa = pa^2
Aa = 2pApa
homo A = pA^2 * pA^2 = pA⁴
homo a = pa^2 * pa^2= pa⁴
hetero Aa = 2pApa * 2pApa= (2pApa)^2
any = pA^2 + pa^2 + 2pApa = pA⁴ + (2pApa)^2
simple:
p random = sum of all homo possibilities + sum of all hetero possibilities
p both = pRandom1 * pRandom2…
why is calculating the variability of loci important for identifying individuals
calculating enough variable loci results in the probability of an individual being so low that it’s impossible to mistake 2 individuals due to same genotype (two bears will not be the same just cause of brown fur, will have other unique loci)
how do we identify populations, calculate probs of homo aa, BB chances and hetero chances aa/BB if
pop1:
pA = 0.8
pa = 0.2
pB = 0.4
pb = 0.6
pop2:
pA = 0.1
pa = 0.9
pB = 0.8
pb = 0.2
aa:
pop1 = 0.2 * 0.2 = 0.04
pop2 = 0.9 * 0.9 = 0.81
BB:
pop 1 = 0.4 *0.4 = 0.16
pop 2 = 0.8 * 0.8 = 0.64
aa/BB: take the top answers not the given
pop 1 = 0.04 *0.16 = 0.0064
pop 2 = 0.81 * 0.64 = 0.52
How do you identify sex bears vis birds case study
bears:
- used hair samples
- coamplification of ZFx/ZFy/SRy
SRY = sex determining region on y-chromosome
- PCR should show
band = male
no band = female
ZFx/ZFy = zinc finger protein gene on both x/Y chromosome
- PCR should show
band = for both male/female as positive control
birds:
Males = homogametic ZZ = 1 band on PCR
females = heterogametic ZW = 2 bands on PCR
both should have = diff size CHD locus on both Z and W chromosomes
what is a species?
what are the limitations of this concept?
how do you differentiate between species?
Definition:
bio concept- group of actually/potentially interbreeding natural pops that are reproductively isolated from other groups
limitations:
- doesn’t account for hybridization or introgression
phylo concept: group sharing min 1 uniquely derived trait (mostly to speciate asexually reproducing organisms)
limitation:
- oversplitting = erroneous conservation efforts
genetic species concept: interbreeding natural pops that’s genetically distinct from other similar groups via DNA barcodes (focus on genetic isolation rather than reproductive)
limitations:
- doesn’t acc for hybridization cause samples are from animal mtDNA and plat cpDNA
- barcodes absent in rapidly evolving lineages w/low diversity
- requires gap reflecting greater genetic similarity within rather than between species
what is population genetics
the study of genetic variation/changes within populations
- gene behaviour in pop
- allele freq changes/evolution over time
how do you calculate the genotype frequency and how do you calculate allele freq
genotype freq:
- # individuals/total
= AA/total
= aa/total
=Aa/total
allele freq:
- calculate for singular allele not pair
eg.( #Ax2 for homo) + #A in hetero) / (total x 2)
what is the hardy Weinberg principle and how do you calculate it
a null hypothesis - genetic variation is constant across generations w/no disturbances
- no mutations
- no gene flow
- random mating
- infinite pop size
- no selection
p^2 + 2pq + q^2
calc the hardy Weinberg for this example:
Small island w/pop of 100 lizards exhibit a trait (single gene with two alleles):
* B (Black stripes) and b (no stripes)
* Stripes are dominant
You found:
* 60 striped
* 40 plain
Is this population in Hardy-Weinberg Equilibrium
- Calculate allele frequencies
* q^2 = 0.4
q = √0.4 = 0.632
* p = 1 – q
* p = 1 – 0.632 = 0.368 p = frequency of B allele - Predict genotype frequencies
* BB:
= p^2 = 0.135
* bb:
= q2 = 0.4
* Bb
= 2pq
= 2 (0.632)(0.368) = 0.465
therefore expected is:
BB: 13.5
bb: 40
Bb: 46.5
Actually observed:
BB: 15
bb: 40
Bb: 45
- Chi-squared test (don’t square root from the X^2)
X^2 = sum of all (O - E)^2 / (E)
BB: = (15 - 13.5)^2 / 13.5
= 0.167
bb = 0
Bb = 0.048
X^2 = BB + bb + Bb
= 0.167 + 0.048 + 0
= 0.215 > 5.99 (the 0.05 value from chi chart)
= pop is in hardy Weinberg
under the 2 degrees of freedom, check if the value is lower than the value under 0.05 column
