Ecological Genomics

Question 1

What is ecological genomics

Answer 1

study of structure and functioning of genome in order to understand relationship btw org and biotic and abiotic environments

Question 2

examples of environment shaping genotypes to similar phenotype

Answer 2

Chinese and Indian Muntjac have very similar phenotype yet contrasting genotypes.
Cryptic species - Eurasian and short toed tree creeper.
Cichlids in African lakes

Question 3

why can different genotypes in a similar environment be so identical

Answer 3

phenotype is under strong selection by the environment.
Makes morphology an unreliable observation
Convergent evolution

Question 4

example of environment influencing a species to have polymorphic phenotype

Answer 4

snails - Cepea nemoralis

Colour and banding correlates with habitat

Question 5

what is phenotypic plasticity

Answer 5

ability of an individual’s genotype to respond to environmental influences
Does not change genotype

Question 6

study of plasticity in beetle.

Answer 6

Nutrition dependent variation in body and horn size in beetles Proagoderus lanista.
No variation in genetalia with nutrition status or body size.
Decided in larval nutritional state - reflected in insulin levels in imaginal discs, which will grow into limbs.

Question 7

examples of molecular markers

What are they for?

Answer 7

• polymorphic proteins eg Allozymes
• polymorphic DNA sequences eg mini satellites, micro satellites, SNPs.
• must be polymorphic, to indicate extent of diversity in a pop, to infer pop structure and gene flow. To tell if orgs are genetically the same or not.

Question 8

old school method of molecular marking

Answer 8

RFLP
restriction enzymes cleave DNA samples at specific points. run on gel and compare fragments between species
- better resolution using allozymes and can combine with other markers

Question 9

what are minisatellites

Answer 9

repetitive variant repeats that range in length
10-60bp
at 1000 locations in genome
Hypervariable regions
used in paternity testing

Question 10

why are micro satellites preferred now to minisatellites

Answer 10

Shorter and can be amplified using PCR

Question 11

what is RAD sequencing

Answer 11

Restriction site Associated DNA markers
cut sample with RE and add P1 adaptor and shear.
Selectively sequence frags with adaptor on Illumina (indexed)
Can do many at once and easily identify significant SNPa

Question 12

What is output of RAD sequencing

Answer 12

Structure plot.
Each line is output of assumption that there is a different no populations. colors show how each population fits into the total population. whichever color pattern fills the space best is the most fitting number of populations.

Question 13

advancements in 3 things which drove genomics revolution

Answer 13

Computing,
microtechnology
communication technology

Question 14

advances in microtechnology

Answer 14

advances in laser tech
dev of gene chips
new seq methods
mol tools
possibility of working on mols of nm scale

Question 15

what is microfluidics technology

Answer 15

tiny chip which can isolate individual cells in chambers on chip. can apply specific environments to chambers.

Question 16

acclimation and adaptation

Answer 16

acclimation - response of individual in their lifetime

adaptation - over generations. evolutionary.

Question 17

ecological genomics balances what

Answer 17

focus on single genome in detail

studying few genes in many species

Question 18

What is a model organism?

Answer 18

any organism which has been studied as an example of many others. general principles may be established

Question 19

qualities of a model org

Answer 19

long history in biological research
easy to culture
inexpensive to house
short life cycle
generate loads of offspring

Question 20

yeast as model organism

Answer 20

Saccharomyces cervisiae
First introduced in 60s
gen time 1.5-2h
asexual and sexual

Question 21

Drosophila as model org

Answer 21

1902
10d gen time
700eggs /female

Question 22

C elegens as model org

Answer 22

60s
3d gen time
300 eggs./female

Question 23

arabidopsis thaliana

Answer 23

60s
5-6 weeks gentime
10000 seeds/plant

Question 24

how can we get an ultimate answer about gene function

Answer 24

studies involving
knockout
down regulation
overexpression

Question 25

questions as to whether a potential model org will be significant

Answer 25

medical, agricultural or ecological significance
biotech significance - valuable products, capacity to degrade environmental pollutants
evolutionary interesting - not sensu stricto
phylogenetic key position - eg Ciona (Sea squirt, break of chordates)

Question 26

how can a model org be useful for comparisons

Answer 26

in comparative genomics
help to assign function to genes
recognizing promoter regions
bioinformatic tools eg phylogenetic foot printing, shadowing and synteny analysis

Question 27

Model SYSTEMS should..

Answer 27

embrace diverse phylogenetic lineages
complement our genomic knowledge of primary production
Reflect the diversity of life histories
Be involved in critical ecological interactions
… be ecologically relevant