Ade Lectures 4 - 9

Front 1

Heritability

Back 1

Proportion of total phenotypic variance controlled by additive genetic variance
Measured by slope of average parents vs average offspring value
Lowest in fitness related traits

Front 2

Breeders equation

Back 2

R = h2 S
Predicts response to selection
Assumes environment the same

Front 3

S in Breeders equation

Back 3

Selection differential
Difference between mean of all parents and mean of selected parents
Useful for artificial selection

Front 4

Phenotypic value (P) =

Back 4

Genotypic value (G) + environment (E)

Front 5

Va

Back 5

Additive genetic variance
Alleles which are codominant
Cause small increase/decrease in trait value
Largest component of Vg

Front 6

Vd

Back 6

Dominance variance
Can cause inbreeding depression

Front 7

Vi

Back 7

Epistatic variance
Due to allele interactions from other loci

Front 8

H2

Back 8

Broad sense heritability
Vg/Vp
All types of genetic variance

Front 9

h2

Back 9

Narrow sense heritability
Va/Vp
Just additive variation

Front 10

Selection Gradient

Back 10

Beta = S / Variance in trait
Estimate relative fitness (w) by diving fitness by mean fitness

Front 11

Traits closely related to fitness

Back 11

Have the greatest phenotypic variance
Greatest environmental input

Front 12

Plasticity

Back 12

Trait responds to environmental conditions
One off or ongoing

Front 13

Causes of covariance with relatives

Back 13

Shared environment, shared rearing environment, shared mother, shared birth year

Front 14

Variation in red deer antler mass

Back 14

Age: 51%
Year of growth: 14%
Year of birth: 1%
Va: 17%

Front 15

Counter gradient variation

Back 15

Environment declined so genetic response masked

Front 16

Inbreeding depression

Back 16

Lower fitness in inbred individuals or lower values of traits related to fitness

Front 17

Deleterious recessive

Back 17

Rarely shown
Homozygous recessive least fit
Hetero fitter than average of homo

Front 18

Dominant deleterious

Back 18

Immediately selected out

Front 19

Overdominance

Back 19

Heterozygous advantage

Front 20

Identical by descent

Back 20

Alleles inherited from replication of the same allele in a common ancestor

Front 21

Inbreeding coefficient

Back 21

f, probability that 2 alleles at a randomly-chosen locus are ibd
Affected by relatedness of parents

Front 22

f of half-sibling mating

Back 22

0.125

Front 23

f of full-sibling mating

Back 23

0.25

Front 24

f of selfing

Back 24

1
No heterozygous

Front 25

Interspecific questions

Back 25

Identity: same species?
Relatedness: how close are species?
Structure: relationship between species?

Front 26

Intraspecific questions

Back 26

Identity: same individual?
Relatedness: how close are 2 individuals?
Structure: relationship between populations?
Rates and patterns of evo change?

Front 27

Basic DNA techniques

Back 27

Restriction enzymes, electrophoresis, annealing

Front 28

Electrophoresis

Back 28

Measures length of fragments, move through gel at rate proportional to length, in single or double helix

Front 29

Southern Blotting

Back 29

Electrophoresis of DNA fragments onto filter blot, denature and create single strand, probe

Front 30

Methods to reveal variation

Back 30

RFLPs using Southern blotting, PCR amplification, DNA sequencing

Front 31

RFLPs

Back 31

DNA cut with restriction enzymes, Southern blot, probed, detects point mutations and indels between sites

Front 32

PCR

Back 32

Double strand DNA separated, primers hybridised and extended, separated and repeated, majority are unit length strands bound by 2 primers

Front 33

PCR-RFLP

Back 33

Isolated DNA amplified using PCR, cut with enzyme, electrophoresis, stain and score

Front 34

Sanger Sequencing

Back 34

dATP has dideoxy add-on that causes synthesis to stop, polymerase drops off, creates different length strands and shows sequence

Front 35

Automatic sequencing

Back 35

Dyes fluoresce when hit by laser, detected as they pass a detector

Front 36

Next-generation sequencing

Back 36

Short fragments stuck to surface and amplified, new base addition measured at each cycle using fluorescent bases, massively parallel, align fragments and detect variation, errors high, hard to assemble genome

Front 37

SNPs

Back 37

Isolated DNA sequenced, chips use data from Sanger to select primers that can detect 2 alleles at a site, bead arrays with primer for sequence, presence of each allele at each bead tested for hybridisation

Front 38

Dominant markers

Back 38

Can't distinguish hetero from homo
Need multiple polymorphic loci

Front 39

Polymorphic

Back 39

Areas of strong selection maintaining variation, non-expressed regions

Front 40

Satellite

Back 40

DNA with tandem repeated sequences, repeats have high mutation rate and number of alleles, informative markers

Front 41

Mini-satellites used in:

Back 41

Multi-locus DNA fingerprinting

Front 42

Micro-satellites

Back 42

Used in Single-locus DNA profling
2-5 bases, varies
Bound by unique sequence DNA
Non-invasive samples
Genotype by radioactive labelling
aka Simple tandem/sequence repeats
Mutation mainly replication slippage

Front 43

Higher allele even-ness

Back 43

More heterozygosity

Front 44

Uses of identifying individuals micro-satellite data

Back 44

Forensics, trade in endangered species, population size estimates, paternity, understanding mating systems, measure fitness, pedigrees

Front 45

Freq of AB =

Back 45

2 x freq A x freq B

Front 46

Expected number with matching profile =

Back 46

World population x probability of matching locus

Front 47

Crude method of relatedness

Back 47

Count shared alleles, repeat with a sample of loci to get an average, take into account allele freq