Week 2: Molecular Genetics in Ecology Flashcards
1
Q
What are the two main advantages of ecological genetics over observational study?
A
- can make inferences that cannot be gained from observation alone
- observations are clouded by unclear phenotypes
2
Q
What kinds of inferences can’t be made with observational study?
A
- are individuals dispersing?
- are populations isolated?
- genetic diversity?
- inbreeding?
- adaptation?
3
Q
What kinds of inferences are clouded by unclear phenotypes?
A
species identification
4
Q
What is phenotypic plasticity?
A
when individuals with the same genotype exhibit a different phenotype
(ex. house finch plumage depends on environment, banaquit plumage depends on genes)
5
Q
What are the 3 sources of genetic variation?
A
- mutation
- recombination
- epigenetics
6
Q
What is mutation?
A
the most fundamental source of genetic variation
7
Q
What are two characteristics of a majority of mutations?
A
- occur during replication
- are neutral or deleterious
8
Q
Which mutations are heritable?
A
germline mutations
9
Q
What are point mutations?
A
a single base pair change
10
Q
What are transposable elements?
A
- a type of chromosomal mutation
- rearrange genes within or between chromosomes
11
Q
What are the 2 kinds of mutation?
A
- point mutations
- chromosomal mutations
12
Q
How do mutations lead to beneficial traits?
A
- a random mutation is beneficial
- over time, random beneficial mutations accumulate and create a new trait
- ex snake venom
13
Q
How is the trait of snake venom diverse?
A
- trait developed separately many times
- Viperidae venom attacks cardiovascular system
- Elapidae venom targets nervous system
14
Q
What is recombination? What does it do?
A
recombination of alleles between homologous chromosomes during meiosis
- produces novel genotypes
15
Q
What is epigenetics?
A
- changes in gene expression without changing gene sequences
- one mechanism of phenotypic placticity
16
Q
What are two epigenetic mechanisms?
A
- DNA methylation
- Histone modification
17
Q
Where does DNA methylation typically occur?
A
on the cytosine base
18
Q
What factors influence DNA methylation?
A
- temperature
- diet
- stress
19
Q
What is a wildlife application of DNA methylation (epigenetics)?
A
assessing stress in populations
20
Q
How is genome size measured?
A
- base pairs (BP)
- Megabse (Mb) = 1 mill bp
- Gigabase (Gb) = 1 bill bp
21
Q
How big is the human genome?
A
~3Gb
22
Q
How big is the Ambystoma mexicanum genome?
A
~32Gb
23
Q
What are n and 2n
A
n = haploid state
2n = diploid state
in humans:
- n = 23
- 2n = 46
24
Q
Why do Eukaryotes have multiple genomes?
A
because of endosymbionts
25
What are the two kinds of endosymbiont DNA?
- Mitochondrial DNA (mtDNA)
- Chloroplast DNA (cpDNA)
26
What are the two types of chromosomes?
- autosomes
- sex chromosomes
27
How does polyploidy happen?
errors in meiosis (unreduced gametes)
28
What are the two kinds of polyploidy?
- autopolyploidy: all chromosomes from same species
- allopolyploidy: multiple sets of chromosomes originating from several species (hybridization)
29
What are the two types of sex determination?
- environmental sex determination
- genetic sex determination
30
What is the difference between homogametic and heterogametic sexes?
- Homogametic: have two copies of the same sex chromosome
- Heterogametic: have two different sex chromosomes
31
Name a taxon where females are the heterogametic sex
Birds
32
Name a taxon where males are the heterogametic sex
- Mammals
- some dioecious plants
33
How large is an animal's mtDNA genome?
16-18kb
34
Why is the mitochondrial genome useful?
- small, well-described
- non-repetitive
- structure/size/arrangement are well-conserved
35
How large is a plant's mtDNA genome?
200-2500kb
36
How does plant mtDNA differ from animal mtDNA?
- plants have more repeat sequences, variable gene numbers
- less conserved
37
What are some features of plant cpDNA?
- ~150,000kb
- more recombination thatn mtDNA
- fairly conserved
38
What are two main modes of inheritance?
- biparental inheritance: get a nrDNA copy from each parent
- uniparental inheritance: genetic material from only one parent
39
What types of genetic material undergo maternal inheritance?
- mtDNA in most plants/animals
- cpDNA in angiosperms
40
What types of DNA are paternally inherited?
- cpDNA in gymnosperms
- rarely mtDNA
41
Why is most endosymbiont DNA maternally inherited?
egg cells are larger than sperm cells
42
What are 4 benefits of mtDNA and cpDNA studies?
1. low recombination
2. relatively high mutation rate
3. lots of copies in each cell
4. uniparentally inherited
43
Why is low recombination in mtDNA/cpDNA helpful?
- the arrangement of genes across individuals is conserved
- we can use UNIVERSAL PRIMERS
44
Why is a low mutation rate in cpDNA/mtDNA helpful?
we can detect multiple lineages
45
Why is having lots of mtDNA/cpDNA copies helpful?
means old/bad/degraded DNA samples can still be usable
46
Why is uniparental inheritance of mtDNA/cpDNA helpful?
- offspring will have same mtDNA/cpDNA as parents
- we can track lineages through time and space
47
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)
48
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
49
How are DNA samples preserved?
- ethanol
- lysis buffer
- freezing
50
What are 3 steps in studying wildlife DNA?
1. DNA extraction
2. DNA amplification
3. DNA sequencing
51
What is DNA extraction?
- isolate and purify DNA
- always the first step, often taxon-specific
52
What is DNA amplification?
- PCR, qPCR
- can give genotype or abundance information
can be targeted or genome-wide
53
What is DNA sequencing?
- determining the genetic code of DNA
- functional information, must first be amplified
- can be targeted or genome-wide
54
What are the 4 steps in DNA extraction?
1. Lysis: break open cells, release DNA
2. Bind DNA to spin column
3. Wash DNA: remove proteins/impurities
4. Elution: release DNA from spin column into final buffer
55
What is PCR?
- Polymerase Chain Reaction
56
What 2 molecules let us do PCR?
- oligonucleotide primers (to target specific known sequences)
- Taq polymerase (thermostable, necessary for annealing step)
57
What temperatures are required for each step of PCR?
1. Denaturing: 95C
2. Annealing: 55C
3. Synthesizing: 72C
58
What is qPCR?
- quantitative PCR
- fluorescent dye probes allow for quantifying as reaction occurs
59
What are some applications of qPCR?
- abundance during wildlife detection
- severity of pathogen infection
- gene expression (up-regulation and down-regulation)
60
What does DNA sequencing give us?
- actual genetic code
- functional information beyond genotypes
61
What are the 3 kinds of genetic sequencing?
- Sanger sequencing (small fragments)
- High-throughput sequencing (Mb-Gb)
- Whole genome sequencing (increasingly possible)
62
What was the cost of the Human Genome Project? What would it cost today?
- Was $3bil, took 13yrs
- now would cost $300-600
63
What are molecular markers?
- specific segments of DNA associated with one part of a genome
- most fundamental tool for discerning genetic diversity
64
What are adaptive markers?
genomic regions that have an adaptive function (true genes)
- (less commonly used, requires sequencing)
65
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
66
What are the two broad types of molecular markers?
- protein markers (allozymes)(obsolete)(only co-dominant)
- DNA markers (dominant, co-dominant)
67
What is the ultimate type of remote sampling?
eDNA
68
What are the two types of dominant markers?
- RAPDs
- ALFPs
(DNA fragments)
69
What are the 4 types of dominant markers?
(DNA fragments)
- RLFPs
- Microsatellites
(DNA sequencing)
- SNPs
- Targeted-sequencing primers
70
What kind of genetic marker represents genetic diversity (without phenotypic implications)?
Neutral markers
71
What are RAPD and AFLP?
- Randim amplified polymorphic DNA
- Amplified fragment-length polymorphism
72
What are dominant markers?
can identify only one allele at a locus (presence/absence)
73
What are co-dominant markers?
can identify different alleles at a locus (heterozygous/homozygous)
(and allele frequencies)
74
What are universal primers often developed from?
Orthologous genes (genes from a common ancestor shared between different species)
75
What does gel electrophoresis give us?
information about DNA fragments
76
What kind of marker does gel electrophoresis show (dominant or co-dominant)?
co-dominant (shows 2 alleles)
77
What does a homozygote look like in gel electrophoresis?
A single band
78
When is gel electrophoresis useful?
when you know that different alleles have different lengths
79
What are microsatellites?
repetitive non-coding DNA sequences (STRs)
80
How long is a microsatellite sequence?
10-100bp
81
What is a STR?
Short Tandem Repeat
- eg. microsatellites
82
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
83
What is the advantage of high mutation rates in microsatellites?
- many alelles at one locus (more variation)
- show subtle/recent variation
84
What is a disadvantage of high mutation rates in microsatellites?
Size homoplasy: different lineages can mutate and converge to look very similar
85
What is an example of microsatellites showing subtle genetic variation?
- Pyrenean desman
- mtDNA shows 1 pop
- microsats show 3 pops
86
What is a microsatellite motif?
The short sequence that gets repeated
(ex. TA, CAG)
87
What is a PCR multiplex?
amplifying multiple (microsat) loci at once
88
What are SNPs?
- Single Nucleotide Polymorphisms
89
How many SNP alleles are possible in a population?
4 (ATCG)
90
What is a difficulty in microsatellite study?
need to design primers for each microsat locus, need to make markers de novo for every species
91
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
92
How many SNP markers can RAD-seq identify across a genome?
tens of thousands!
93
What do restriction enzymes do?
fragment genome and target a specific allele for genotyping
