Ecological Genomics Flashcards
What is ecological genomics
study of structure and functioning of genome in order to understand relationship btw org and biotic and abiotic environments
examples of environment shaping genotypes to similar phenotype
Chinese and Indian Muntjac have very similar phenotype yet contrasting genotypes.
Cryptic species - Eurasian and short toed tree creeper.
Cichlids in African lakes
why can different genotypes in a similar environment be so identical
phenotype is under strong selection by the environment.
Makes morphology an unreliable observation
Convergent evolution
example of environment influencing a species to have polymorphic phenotype
snails - Cepea nemoralis
Colour and banding correlates with habitat
what is phenotypic plasticity
ability of an individual’s genotype to respond to environmental influences
Does not change genotype
study of plasticity in beetle.
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.
examples of molecular markers
What are they for?
- 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.
old school method of molecular marking
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
what are minisatellites
repetitive variant repeats that range in length 10-60bp at 1000 locations in genome Hypervariable regions used in paternity testing
why are micro satellites preferred now to minisatellites
Shorter and can be amplified using PCR
what is RAD sequencing
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
What is output of RAD sequencing
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.
advancements in 3 things which drove genomics revolution
Computing,
microtechnology
communication technology
advances in microtechnology
advances in laser tech dev of gene chips new seq methods mol tools possibility of working on mols of nm scale
what is microfluidics technology
tiny chip which can isolate individual cells in chambers on chip. can apply specific environments to chambers.
acclimation and adaptation
acclimation - response of individual in their lifetime
adaptation - over generations. evolutionary.
ecological genomics balances what
focus on single genome in detail
studying few genes in many species
What is a model organism?
any organism which has been studied as an example of many others. general principles may be established
qualities of a model org
long history in biological research easy to culture inexpensive to house short life cycle generate loads of offspring
yeast as model organism
Saccharomyces cervisiae
First introduced in 60s
gen time 1.5-2h
asexual and sexual
Drosophila as model org
1902
10d gen time
700eggs /female
C elegens as model org
60s
3d gen time
300 eggs./female
arabidopsis thaliana
60s
5-6 weeks gentime
10000 seeds/plant
how can we get an ultimate answer about gene function
studies involving
knockout
down regulation
overexpression
questions as to whether a potential model org will be significant
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)
how can a model org be useful for comparisons
in comparative genomics
help to assign function to genes
recognizing promoter regions
bioinformatic tools eg phylogenetic foot printing, shadowing and synteny analysis
Model SYSTEMS should..
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
