Week 2: Molecular Genetics in Ecology Flashcards
What are the two main advantages of ecological genetics over observational study?
- can make inferences that cannot be gained from observation alone
- observations are clouded by unclear phenotypes
What kinds of inferences can’t be made with observational study?
- are individuals dispersing?
- are populations isolated?
- genetic diversity?
- inbreeding?
- adaptation?
What kinds of inferences are clouded by unclear phenotypes?
species identification
What is phenotypic plasticity?
when individuals with the same genotype exhibit a different phenotype
(ex. house finch plumage depends on environment, banaquit plumage depends on genes)
What are the 3 sources of genetic variation?
- mutation
- recombination
- epigenetics
What is mutation?
the most fundamental source of genetic variation
What are two characteristics of a majority of mutations?
- occur during replication
- are neutral or deleterious
Which mutations are heritable?
germline mutations
What are point mutations?
a single base pair change
What are transposable elements?
- a type of chromosomal mutation
- rearrange genes within or between chromosomes
What are the 2 kinds of mutation?
- point mutations
- chromosomal mutations
How do mutations lead to beneficial traits?
- a random mutation is beneficial
- over time, random beneficial mutations accumulate and create a new trait
- ex snake venom
How is the trait of snake venom diverse?
- trait developed separately many times
- Viperidae venom attacks cardiovascular system
- Elapidae venom targets nervous system
What is recombination? What does it do?
recombination of alleles between homologous chromosomes during meiosis
- produces novel genotypes
What is epigenetics?
- changes in gene expression without changing gene sequences
- one mechanism of phenotypic placticity
What are two epigenetic mechanisms?
- DNA methylation
- Histone modification
Where does DNA methylation typically occur?
on the cytosine base
What factors influence DNA methylation?
- temperature
- diet
- stress
What is a wildlife application of DNA methylation (epigenetics)?
assessing stress in populations
How is genome size measured?
- base pairs (BP)
- Megabse (Mb) = 1 mill bp
- Gigabase (Gb) = 1 bill bp
How big is the human genome?
~3Gb
How big is the Ambystoma mexicanum genome?
~32Gb
What are n and 2n
n = haploid state
2n = diploid state
in humans:
- n = 23
- 2n = 46
Why do Eukaryotes have multiple genomes?
because of endosymbionts
What are the two kinds of endosymbiont DNA?
- Mitochondrial DNA (mtDNA)
- Chloroplast DNA (cpDNA)
What are the two types of chromosomes?
- autosomes
- sex chromosomes
How does polyploidy happen?
errors in meiosis (unreduced gametes)
What are the two kinds of polyploidy?
- autopolyploidy: all chromosomes from same species
- allopolyploidy: multiple sets of chromosomes originating from several species (hybridization)
What are the two types of sex determination?
- environmental sex determination
- genetic sex determination
What is the difference between homogametic and heterogametic sexes?
- Homogametic: have two copies of the same sex chromosome
- Heterogametic: have two different sex chromosomes
Name a taxon where females are the heterogametic sex
Birds
Name a taxon where males are the heterogametic sex
- Mammals
- some dioecious plants
How large is an animal’s mtDNA genome?
16-18kb
Why is the mitochondrial genome useful?
- small, well-described
- non-repetitive
- structure/size/arrangement are well-conserved
How large is a plant’s mtDNA genome?
200-2500kb
How does plant mtDNA differ from animal mtDNA?
- plants have more repeat sequences, variable gene numbers
- less conserved
What are some features of plant cpDNA?
- ~150,000kb
- more recombination thatn mtDNA
- fairly conserved
What are two main modes of inheritance?
- biparental inheritance: get a nrDNA copy from each parent
- uniparental inheritance: genetic material from only one parent
What types of genetic material undergo maternal inheritance?
- mtDNA in most plants/animals
- cpDNA in angiosperms
What types of DNA are paternally inherited?
- cpDNA in gymnosperms
- rarely mtDNA
Why is most endosymbiont DNA maternally inherited?
egg cells are larger than sperm cells
What are 4 benefits of mtDNA and cpDNA studies?
- low recombination
- relatively high mutation rate
- lots of copies in each cell
- uniparentally inherited
Why is low recombination in mtDNA/cpDNA helpful?
- the arrangement of genes across individuals is conserved
- we can use UNIVERSAL PRIMERS
Why is a low mutation rate in cpDNA/mtDNA helpful?
we can detect multiple lineages
Why is having lots of mtDNA/cpDNA copies helpful?
means old/bad/degraded DNA samples can still be usable
Why is uniparental inheritance of mtDNA/cpDNA helpful?
- offspring will have same mtDNA/cpDNA as parents
- we can track lineages through time and space
What are 5 limitations of cpDNA/mtDNA
- sex-specific patterns
- effectively are a single locus
- greater probability of haplotype extinction
- reduced genomic representation (missing full diversity)
- oversimplification of genetic diversity (past & present)
What are some sources of DNA samples?
- body bits (leaves, seeds, toeclips, hair, urine, pollen, insect legs, etc>)
- remote ve non-lethal sampling
- museum specimens
How are DNA samples preserved?
- ethanol
- lysis buffer
- freezing
What are 3 steps in studying wildlife DNA?
- DNA extraction
- DNA amplification
- DNA sequencing
What is DNA extraction?
- isolate and purify DNA
- always the first step, often taxon-specific
What is DNA amplification?
- PCR, qPCR
- can give genotype or abundance information
can be targeted or genome-wide
What is DNA sequencing?
- determining the genetic code of DNA
- functional information, must first be amplified
- can be targeted or genome-wide
What are the 4 steps in DNA extraction?
- Lysis: break open cells, release DNA
- Bind DNA to spin column
- Wash DNA: remove proteins/impurities
- Elution: release DNA from spin column into final buffer
What is PCR?
- Polymerase Chain Reaction
What 2 molecules let us do PCR?
- oligonucleotide primers (to target specific known sequences)
- Taq polymerase (thermostable, necessary for annealing step)
What temperatures are required for each step of PCR?
- Denaturing: 95C
- Annealing: 55C
- Synthesizing: 72C
What is qPCR?
- quantitative PCR
- fluorescent dye probes allow for quantifying as reaction occurs
What are some applications of qPCR?
- abundance during wildlife detection
- severity of pathogen infection
- gene expression (up-regulation and down-regulation)
What does DNA sequencing give us?
- actual genetic code
- functional information beyond genotypes
What are the 3 kinds of genetic sequencing?
- Sanger sequencing (small fragments)
- High-throughput sequencing (Mb-Gb)
- Whole genome sequencing (increasingly possible)
What was the cost of the Human Genome Project? What would it cost today?
- Was $3bil, took 13yrs
- now would cost $300-600
What are molecular markers?
- specific segments of DNA associated with one part of a genome
- most fundamental tool for discerning genetic diversity
What are adaptive markers?
genomic regions that have an adaptive function (true genes)
- (less commonly used, requires sequencing)
What are neutral markers?
- genomic regions that do not alter the fitness of a phenotype (ex. non-coding loci)
- common in population genetics
- more variation
- with or without sequencing
What are the two broad types of molecular markers?
- protein markers (allozymes)(obsolete)(only co-dominant)
- DNA markers (dominant, co-dominant)
What is the ultimate type of remote sampling?
eDNA
What are the two types of dominant markers?
- RAPDs
- ALFPs
(DNA fragments)
What are the 4 types of dominant markers?
(DNA fragments)
- RLFPs
- Microsatellites
(DNA sequencing)
- SNPs
- Targeted-sequencing primers
What kind of genetic marker represents genetic diversity (without phenotypic implications)?
Neutral markers
What are RAPD and AFLP?
- Randim amplified polymorphic DNA
- Amplified fragment-length polymorphism
What are dominant markers?
can identify only one allele at a locus (presence/absence)
What are co-dominant markers?
can identify different alleles at a locus (heterozygous/homozygous)
(and allele frequencies)
What are universal primers often developed from?
Orthologous genes (genes from a common ancestor shared between different species)
What does gel electrophoresis give us?
information about DNA fragments
What kind of marker does gel electrophoresis show (dominant or co-dominant)?
co-dominant (shows 2 alleles)
What does a homozygote look like in gel electrophoresis?
A single band
When is gel electrophoresis useful?
when you know that different alleles have different lengths
What are microsatellites?
repetitive non-coding DNA sequences (STRs)
How long is a microsatellite sequence?
10-100bp
What is a STR?
Short Tandem Repeat
- eg. microsatellites
Why are microsatellites useful for tracking genetic variation?
- high mutation rate (stepwise mutations 1bp at a time)
- alleles have different lengths, so no need to sequence
What is the advantage of high mutation rates in microsatellites?
- many alelles at one locus (more variation)
- show subtle/recent variation
What is a disadvantage of high mutation rates in microsatellites?
Size homoplasy: different lineages can mutate and converge to look very similar
What is an example of microsatellites showing subtle genetic variation?
- Pyrenean desman
- mtDNA shows 1 pop
- microsats show 3 pops
What is a microsatellite motif?
The short sequence that gets repeated
(ex. TA, CAG)
What is a PCR multiplex?
amplifying multiple (microsat) loci at once
What are SNPs?
- Single Nucleotide Polymorphisms
How many SNP alleles are possible in a population?
4 (ATCG)
What is a difficulty in microsatellite study?
need to design primers for each microsat locus, need to make markers de novo for every species
What is Rad-seq? What is it used for?
Restriction site associated DNA sequencing
- used to generate hundreds of SNP markers de novo for genotyping
- type of reduced-representation sequencing
How many SNP markers can RAD-seq identify across a genome?
tens of thousands!
What do restriction enzymes do?
fragment genome and target a specific allele for genotyping
