POPULATION GENETICS
W1-W6

WEEK 1

MARKER
1) what is pop genetic
2) relate concept
3)how pop genetics change

DEF: GENETIC MARKER is a gene/DNA sequence with a known location


USES: 1. study polymorphism 2. identify species/organism 3. study diseases

3) MOLECULAR MARKERS based on inheritance

  1. Dominant
    multilocus, single allelic
    detect presence of homozygote or not
    band is from only one parent

"Variable number of tandem repeat."
in a gene, the marker is tandem, agtcagtcagtc ,
repeated because the agtcagtcagtc repeated many times in the species.
but the number, how many the sequence repeated is differ in every specience, sebabtu its called variable.

non coding
heritable
differ from person to person
repeated in genome

  1. Codominant
    Single locus, multiallelic
    identify heterozygote
    band is from both parent

AFLP

MICROSATELLITE

RAPD

RFLP

types: 1) bichemical marker 2) morphological

snp

snp vs mutation
mutation occur less 1% snp occurs more in popu
snp occur at same location mutation at diffent many loaction

short, repeated tandem sequnce on a loci. ex: (CA)n STR.
Polymorph bcs number of repeats varies


1) Designed primer is needed for one specific locus.
2) reproducible . use same primer for all individual.

EPS

What is?
how GD change allele frequency
number of individual in ideal population that have the same GD value as GD in actual population.

factors influenced
↓ 1) variation in population size
↓ 2) unequal males & females
3)age structure
4)family size in skewed distribution

VARIATION

Def: differences between members/individuals of same species

types

continuouse like height

discontinuose blood type, tougue rolling

influence by

inherited like hair colour. follow mendel's law

environmental factor like habitat, diet, climate

POLYMORPHISM

if there is more allele located on locus at a gene. at least more than 1% have the polymorphism if less is considered mutation

use southern blotting

POLYmorphism many loci reproducible

PROS
prob can be unknown


CONS slow labour intensive(susah) high quality bcs uses of RE radioactive costly

HW

  1. HW in 2 and multiple allele
  2. calculate freq, estimate from sexes, haploid-diploid organism
  3. measure of variation

Hardy-Weinberg

freq remain constant throuout generation if population in equilibrium.
if G1 has 5 A, G2 also 5 A
(5 conditions)

  • Big n size
  • RM
  • no Mutation
  • No GF
  • no NS

big n: so chance dont distrupt the equilibrium. small popu can show mutation quick. 100-1000

RM: @ panximia every person same chance to mate. so individuals dont choose mate, dont choose special characteristics. in assortive mating, few heterozygous will be.

no M: so no allele frequency changes, no new allele introduced

no GF: no new allele come in or out of population

no NS: no allele are selected. if do, that allele will be more common which lead to fixation.

CALCULATE FREQ

DIPLOID
allele p + q = 1.0 {proportion all alles in population}
p = AA + (1/2)(Aa)
genotype p2 = AA 2pq = Aa q2 = aa
{proportion of individuals in population}

ADDITIONAL ASSUMPTIONS:
diploid: 2N
sexual reproduce
non-overlap

STAGES for HW Equilibrium to be true:
1) Parents Gene frequency [segregation normal]
2)ZYGOTE genotype freq
3) PROGENY genotype freq
4) PROGENY Gene freq

HW CASES

(1) 1 locus 2 Alelles

general eq yg we studied.
P=(p2 value) + (1/2)(2pq value)
BCS this is HW ;
A = p ; a = p
AA + 2Aa + aa ---- (p)(p) + 2(p)(q) + (q)(q) >>> progeny pop
➥ progeny pop depends on initial freq.

(2) multiple allele
∑𝐩𝐢𝟐

∑𝐩𝐢𝟐
A1 , A2 , A3 , ... An
homozygote AiAj = pᵢ2
heterozygote AiAj = 2pᵢpⱼ @ 1- ∑pi2

after ONE generation of RM ,
reaches equilibrium.
SHOWN BY...

2) Genotype RM
EX: blood group bcs each of 4 group is a combination of diff genotype
CALC start from recessive freq ; * P + Q + R = 1

1) Gametes RM (allele) Genes: A , a' , a their freq: p , q , r
//refer slide// ** Pᴬ = p

AFFECTING HW

(1) X-Linked

LINKAGE DISEQUILIBRIUM
more loci

BY:
Population mixturee have different gene freq
by chance
selection

HW 2 locus

EWUILIBRIUM after many generation
because of sex-dependant in tranmission of x-linked gene. X of a male is same as mother

W ; FITNESS
1) selection impact equilibrium
2)it impact fitness
3) types of selection: hetero etc
4) dom , hetero adv , hetero disadv

Absolute W: { survival rate x offspring }

Unfitness = Selection Co ; S=1-W selection to be 'eaten'

Relative W : rate of changes avrg: FREQ X FITNESS

NS

components
VSFGC

VIABILITY ; HIDUP

SEXUAL : MATE

FECUNDITY : BABY

GAMETIC

COMPABILITY

GD LOSS
1) effect of GD
2) def EPS
3) estimate EPS
4)Selection effect in finite pop

GD is stochastic@ RANDOM process , causes changes in freq
if n 🡣small , stochastic impact 🡡

DEME.
small population. have small breeding units : limited genetic exchange , inbreeding occur

EPS
no of individuals in deme that exchange gene,

Ne
= individuals capable of reproduce and contribute offspring. in ideal population

  • determine rate potential loss/change gene freq by GD
    Determine effectiveness of selection relative to drift

Factors affecting
SVSD
// compounding effect//

SeX RATIO 🢃EPS

  • can through social status.
    100 EPS if ratio 50:50
    Ne = 4 (Nm x Nf)
    Nm + Nf

VARIATION IN REPRODUCTIVE OUTPUT 🢃 85% EPS

  • number of offspring produced.
  • in species with many offspring but low survival
    Not all will reproduce tho theyre able to
    1) age 2) healt 3) sterile 4) social status

FLUACTUATING POP SIZE
GD can erodes diversity

  • in 4 seasons, ada cycle. EPS determined at smallest pop size point in the cycle
  • rate of GD is highly influenced by the lowest population size in a series of generations. ​
    1/Ne = 1/t (1/N0 + 1/N1 + ...)

DEMES 🢃EPS

EFFECTS

Because of the SVSD,
large popu act as small popu
GD erodes diversity.
effect is longterm

EVOLUTIONARY POTENTIAL
loss when popu small , diversity 🢃
evolution option like alllele are lose.
extinction rate 🢁

EXTINCTION VORTEX (6)
small pop ➟ inbreed/GD ➟ loss genetic diversity ➟
loss fitness/adaptability➟low reproduction/high mortatlity➟more smaller size
N IG D F R M N
⬇⬇⬇
major cause by
1) Environment Variation
2) DEmographic Var
3) Genetic diversity loss

OCCURS
in evolutionary genetics

(1) fitness often changes bcs environment (summer-winter)
(2) NO SELECTION

SELECTION FIXATION

division

Bottleneck Effect

Founder Effect

DEF

  • the drastic loss genetic variation
    -small portion of the initial population is lucky enogh to be alive
    -this new populationcontain generic variation that is not represent the initial population

DEF

  • small portion of the original population isolated
  • then colonize a new area
  • this new founder population doesnt represent the allelic frequency of the original population

POPULATION GENETICS
W7-W8

W8 INBREEDING

Forum

HUMANS
123 consanguineous marriages were revealed from data of 1930 matings of Garia population in India. the article revealed the inbreeding coefficient of 0.0064 ± 0.001 based on consanguineous matings. the inbreeding result in the female having low reproductive performance, 4.80 compare to non-consanguineous matings where it is 5.40 per mother. the Pre-reproductive deaths among live births were also found to be high (0.46 percent) from unions of consanguineous spouses. [1]



ANIMALS Norwegian Lundehund dog were threatened by severe inbreeding. the remaining Lundehund world-wide today appear to descend from only two individuals after underwent severe bottlenecks. disease such as gastrointestinal disease are common in their population to which all the remaining dogs may be predisposed. thus, the article discussed about rescuing their population by outcrossing the individuals with multiple breeds [1]


PLANTS
Barley pedigree figure above shows how individuals are related to one another. as a result, Harrington Barley lack of leaf disease resistance and susceptible to stem rust, net blotch and root rot .
plant breeder need to be careful so that disease resistance, yield and commercial value can be maintained and improved. with pedigree structure breeders are able to make better decision on crossing the plants. [1]

DEF

  • mating between close relatives that causes changes in genetic variances
  • proportion reduction in heterozygosity relative to random mating

relationship

fitness
cause depletion in fitness because arise of delterious alleles
if F=1 , fitness decrease

drift
drift cause small population

selection
affect the outcome of selection

GENE FLOW
POP GENETIC

DEFINE

GENE FLOW IN POPULATION

MODELS

click to edit

MUTATION

TYPES

click to edit

CHROMOSAMAL
INVERSION
TRANSLOCATION

BASE

EVOLUTION RESULT OF CHANGES IN ALLELE FREQ

Isozymes

macromolecule compound

  • proteins

CONS
mostly locate at one chromosome
tissue sensitive

DNA - USE RANDOM PRIMER - PCR - AMPLIFY


PROS
whole genome can be amplified
using single and random primer
High polymorp
quick to conduct

use re enzyme - attach adapter to the fragement - selective fragemnt - Pcr amplification


PROS
very strong n reliable
Does not require sequence information because primer is specific with adapter

use re enzyme - fragment produced - insert electrophorasis - blot