Topic 1 Flashcards
(30 cards)
1
Q
Gene
A
a unit of inheritance (DNA) occupying a fixed position on a chromosome
2
Q
Allele
A
an alternative form of a gene at a given locus
3
Q
Locus
A
A fixed position on a chromosome where a gene and its alleles are located
4
Q
Haploid
A
Having one complete set of chromosomes
5
Q
Diploid
A
Having two complete sets of chromosomes
6
Q
Homozygous
A
having two copies of the same allele at a locus
7
Q
heterozygous
A
having two different alleles at a locus
8
Q
what is a population
A
- An Aggregation of individuals of the same species in the same place and time
- A collection of organisms that we have lumped together because we think they function as a unit
9
Q
why are populations difficult to define
A
- Species exhibit non-random patterns of spatial distribution, or geographic structure, giving rise to population subdivision
- Population subdivision arises as a result of several factors: Physical Barriers, Non-Random Mating resulting from proximity effects, Behavioral effects etc.
10
Q
ideal population
A
- Non-Overlapping Generations
- Diploid
- Sexual Reproduction
- Mating occurs at Random, Panmictic: every male has equal probability of mating with every female and vice versa
- Population is Large
- Migration is Negligible
- Genetic Mutations Don’t Occur
- Unaffected by Natural Selection
11
Q
phenotype
A
- refers to the observable characteristics of an individual
- Individuals within populations exhibit phenotypic variation
- An individual’s phenotype arises as a result of interactions between its genetic characteristics (genotype) and the environment
12
Q
Monomorphic
A
a locus at which all individuals in a population possess the same allele (no variation)
13
Q
polymorphic
A
a locus at which two or more alleles (or haplotypes) are present in a population
14
Q
molecular markers
A
- Any segment of DNA, or a product of DNA that can be assayed to determine levels of population genetic variability
- Common Molecular Markers include allozymes, microsatellites, nuclear gene sequences, mitochondrial DNA sequences, chloroplast DNA sequences, single nucleotide polymorphisms
15
Q
biparental inheritance
A
Typically applies to the nuclear genome of diploid sexually reproducing organisms, where one allele comes from the mother, the other from the father
16
Q
uniparental inheritance
A
Important exceptions to biparental inheritance include the inheritance of mitochondrial DNA, which in animals and plants is usually inherited from the mother (matrilineal), and plastids e.g., Chloroplasts (also usually matrilineal), and the y chromosome (usually paternal inheritance)
17
Q
allozymes
A
- Allozymes were the workhorse molecular marker in population genetics and molecular ecology for about 40 years.
- They became much less frequently used in the early to mid 2000s, when they were largely replaced by microsatellites
18
Q
microsatellites (biparentally inherited)
A
- Also known as Variable Number of Tandem Repeats
- Consist of repetitive short DNA sequences (e.g., AT repeated many times)
- Assayed by Polymerase Chain Reaction (PCR) amplification and fluorescent analysis, Codominant, Mendelian Inheritance
- Microsatellites are non-coding and their function is uncertain- Rapidly Evolving
19
Q
microsatellites
A
- Microsatellites are a workhorse marker in population genetic and molecular ecology studies. They exhibit a high degree of variability as a result of their rapid rates of evolution.
- This renders them ideally suited to discriminate between populations, identify different stocks, and even discriminate between different family lines
20
Q
Sanger DNA sequencing
A
- Extract DNA from individual
- Target specific DNA region in a Polymerase Chain Reaction (few Copies-many copies)
- Incorporate Dye into DNA copies
- Sequence
20
Q
Nuclear DNA
A
- Generally assayed directly by PCR followed by sequencing
- Can also be assayed indirectly using methods such as Restriction Fragment Length Polymorphisms (RFLPs), Amplified Fragment Length Polymorphisms (AFLPs), and Single Stranded Conformational Polymorphism (SSCP)
21
Q
Next generation sequencing
A
- NGS has replaced Sanger sequencing in many applications. DNA is first fragmented by sonication or restriction enzymes, followed by PCR amplification of all, or targeted DNA regions to produce sequencing libraries.
- Many fragments in these libraries (50- 300 bp long) are then simultaneously sequenced with the addition of nucleotides to complementary strands
22
Q
Single nucleotide polymorphisms
A
- Single nucleotide polymorphisms are the most abundant polymorphisms in the genome, with one occurring every 500 nucleotides (on average) in many wild animal populations.
- In the case of SNPs, we consider a single DNA nucleotide position to be a locus, and each locus can have a maximum of four alleles (A,G,C,T). However, since rates of change at single nucleotide positions are low on average (about 10-8 per nucleotide per generation), most SNPs consist of two alleles. SNPs are one of the more commonly employed molecular markers today
23
Q
Mitochondrial DNA
A
- Small (37 genes in animals)
- Circular
- Haploid
- Maternal inheritance
24
Chloroplast DNA
- Like mitochondrial DNA, chloroplast DNA is a single circular molecule, but is larger (around 130 genes that are involved in photosynthesis).
- In most plants, chloroplast DNA is maternally inherited, but it is paternally inherited (patrilineal) in conifers. Chloroplast DNA evolves about 5-6 times faster than plant mitochondrial DNA (on average)
25
disadvantages of mitochondrial and chloroplast DNA
1. Pseudogenes: occasionally, a mitochondrial or chloroplast gene can be integrated into the nuclear genome, where it becomes a nonfunctional pseudogene
2. All mitochondrial and chloroplast genes are linked and inherited as non-independent units
3. Heteroplasmy: occasionally, paternal ‘leakage’ can occur, and you can get two different copies of mtDNA in an individual
26
haploid chromosomes
- The Y chromosome is small and contains few genes. Because of its paternal transmission in most animals (uniparental Inheritance), it can be used to track patrilines (patterns of male descent).
- It has few genes compared to other chromosomes, and its small size results in little recombination. It has low mutation rates, but has some noncoding regions that have higher rates
27
assessing population genetic variation
- Population Genetic studies depend on determining the amount of genetic variation within and among populations
- If a population has no genetic variation, there is very little that we can learn or say. If this is the case, population geneticists pack up and spend the rest of the day at the beach.
28
standard error
- The standard error provides us with a measure of precision, not a measure of accuracy.
- Accuracy: How close an estimated value is to the real or true value in a population, the closer the estimate, the greater the accuracy
- Precision: A measure of repeatability or reproducibility. How similar inferred values would be if we repeatedly estimated them using identical sample sizes and methodologies
29
how much genetic variability exists within populations
- The Classical Hypothesis: Populations contain very little variation, and selection maintains a single best allele at any locus and heterozygotes are rare. Heterozygotes result from rare deleterious mutations that are quickly eliminated by selection
- The Balance Hypothesis: Individuals are heterozygous at many loci, and balancing selection maintains lots of genetic variability within populations
