Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

BIOL*3040 Methods > Test 2 > Flashcards

Test 2 Flashcards

1
Q

Biological Species Concept

A

A group of organisms that can reproduce with each other and produce fertile offspring

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Phylogenetic Species Concept

A

Defines a species as the smallest group of organisms that share a unique evolutionary history

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Morphological Species Concept

A

Defines a species by their physical characteristics or morphology

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Genotypic Species Concept

A

Defines species as groups of organisms that share similar genetics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

____ contain DNA suitable for species identification

A

Mitochondria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How is species level identification achieved using DNA barcoding?

A

It is achieved by using a marker gene sequence with appropriate rate of evolution that can differentiate between species
- CO1 is a species level marker for animals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Interspecific

A

Between species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Intraspecific

A

Within species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

When is it hard to detect species with barcoding?

A

When species have overlapping COI barcodes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

When can we see possibilities of new species when barcoding?

A

When species have two or more distinct barcode clusters showing covariation in biological traits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How much information is needed when identifying species from a barcode, and how do you obtain this information? (2)

A
  1. Location with 2 different nucleotides = good for differentiating species
  2. Rather than sequencing the entire codon use smaller fragments to identify
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

DNA Metabarcoding

A

Allow researchers to understand the biodiversity of an entire ecosystem soley through DNA information, and transforming the way we view the living world around us

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Higher resolution gained from DNA-based analysis as compared to morphology has…

A

increased ability to discriminate sites under different stressors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Primer choice affects ____ and ____ of indicator taxa in freshwater systems

A

Richness and Recovery

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Metabarcode identification - Sequence similarity

A

Unknown metabarcode identification based on sequence similarity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Metabarcode identification - Taxonomic assignment

A
  • Breaks sequence into k-mer and calculates frequencies in query
  • Taxonomic assignment is based on the probability that query comes from a taxon
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Population genetics deals with…

A

genetic changes that occur in populations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

in a population _____ may be present a a locus

A

More than one

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Allele/gene frequency

A

The relative proportion of an allele

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Gene Pool

A

The set of all alleles existing in a population at all loci

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

The 2 major factors affecting allele frequencies in populations are…

A
  1. Natural Selection
  2. Random genetic drift
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Natural Selection

A

The fitness of a genotype is the measure of the individuals ability to survive and reproduce and is usually measured relative to other genotypes in the population

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Mutations that reduce the fitness of organisms are called…

A

Purifying or negative selection
- most common

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Mutations that do not change the fitness of an organism are called…

A

Neutral
- Occasionally occur

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Mutations that increase the fitness of carriers are called...
Advantageous or positive selection - very rare
26
Codominance
When homozygotes have different fitness values, and heterozygote is the mean of the fitness of two homozygotes
27
Dominance
When homozygotes have different fitness values, and heterozygote has the fitness of one of the two homozygotes
28
Overdominance
When heterozygote has the highest fitness
29
Underdominance
When heterozygote has the lowest fitness
30
Random Genetic Drift
Random sampling of gametes during the process of reproduction - fluctuate randomly due to chance events
31
In evolution and population genetics only individuals ____ are considered
Actively participating in reproduction
32
Effective population size
The number of individuals participating in reproduction
33
Population Bottleneck
Severe temporary reduction in population size, Can cause strong influence on Ne and therefore genetic variance
34
Fixation Probability
The probability a new mutant allele to become fixed in a population by replacing the wildtype allele
35
Fixation Probability depends on... (3)
1. Frequency 2. Selective advantage or disadvantage 3. The effective population size
36
As population size becomes larger chance effects become ___
smaller
37
Fixation Time
The time for a mutant allele to become fixed in a population
38
In small populations, number of mutations arising in each generation is ___, their probability of fixation is ___
Low, high Also works vise versa
39
Mean expected heterozygosity/ gene diversity
The probability that two alleles chosen at random from the population are different from each other
40
Nucleotide Diversity
Measure of genetic diversity at sequence level considering all polymorphic sites among sequences from a population
41
When does population structure occur?
When a species is divided into more than one population and individuals in one population are more likely to interbreed amongst themselves than with individuals from another populations. - Leads to differences in allele and or haplotype frequencies
42
If allele or haplotype frequencies differ among two or more of the sampled sites, then this indicates there is...
Population Structure
43
Microsatellite Locus
A region in a genome that has repeated sequence that is short - usually 2-5 nucleotides in length
44
Microsatellite alleles have a ___ rate of mutation
high
45
Why do microsatellites have a high rate of mutation?
It is difficult for DNA replication to faithfully copy repetitive DNA. - often causes replication slippage
46
What are good markers for population analysis?
Microsatelites
47
Why are microsatellites good markers for population analysis? (2)
1. High mutation rate is useful in studies of pops because it allows genetic change to occur within a relatively short time period 2. Microsatelites do not generally affect the fitness of an individual, so their frequencies in a pop reflect past demography of a species, instead of determine past demography
48
What is AMOVA?
Analysis of Molecular Variance An AMOVA seeks to estimate the effects of group, subpopulation, individual and within individual on allelic state
49
What question does AMOVA seek to answer?
How much variation does each level of organization contribute to allelic variation, and is this variation significantly different from zero?
50
What is Fst
a standardized measure of variation in allele frequencies across sites or subpopulations of a study
51
Fst = 0 then...
There is no variation in allele frequencies across sites = no population structure
52
As Fst increases...
Bigger variation in allele frequencies across sites indicating increasing levels of population structure
53
4 types of baseline statistics that are used in study of population statistics:
1. Measure of allelic diversity 2. Expected heterozygosity 3. Observed heterozygosity (level of inbreeding) 4. Linkage disequalibrium
54
a simple measure of allelic diversity is...
The number of unique alleles at a locus
55
Observed Heterozygosity
Is the frequency of genotype in a sample that are heterozygous at a locus
56
Expected Heterozygosity
The value of heterozygosity expected if the frequency of heterozygotes followed Hardy-Weinberg expectations, such that alleles at a locus were independently inherited
57
Inbreeding is a process that causes...
a difference between observed and expected heterozygotes
58
Inbreeding tends to ___ the level of homozygotes relative to heterozygotes
increase
59
Linkage disequalibrium
Measure the degree of association between alleles at two different loci - deviation in the observed frequency from expected frequency indicates linkage disequalibrium
60
If linkage disequilibrium is common, then alleles across loci are...
not independent - meaning information at one locus is correlated with information at another locus
61
LD can be a result of...
population structure
62
Why is LD relevant in population analysis
Natural selection ca indirectly cause alleles at teo microsatellite loci to be associated - Strong selection for an allele at a locus can cause the simultaneous increase in frequency of physically linked alleles at other loci Generally rare
63
Mantel Test
Used to test isolation by distance for a species - +ve correlation between genetic differentiation and/or pop structure and geog distance between sites
64
How does Mantel test differ from simple linear regression and correlation?
By accounting for non-independence in data points in the regression and correlation
65
What makes Mantel test valid?
When geographic distances and Fst are regressed or correlated, data points are not independent. - Mantel test adjusts the p-value associated with regression or correlation, accounting for lack of independence
66
The rate of nucleotide substitution in most genes and non-genic regions of the genome can be due to a combination of... (3)
1. Mutational input 2. Random genetic drift of neutral alleles 3. Purifying selection against deleterious alleles
67
Are these any cases of positive selection in genes?
Yes, there are a few
68
How do you detect positive selection in DNA
The rate of non-synonymous substitutions should be higher than synonymous substitutions if advantageous/positive selection plays a major role in protein evolution - Therefore you can show that the number of substitutions per synonymous site is significantly more than the number of substitutions per synonymous sites
69
True or False: Non-synonymous changes in DNA are more likely to improve the function of a protein
True Non-synonomous changes in DNA will result in amino acid change in the protein, and therefore are more likely to improve the function of a protein
70
Advantageous mutations are either quickly ___ in a population or quickly ___
Lost, fixed
71
The contribution to genetic polymorphism of advantageous mutations is...
Small
72
There are ___ types of possible substitutions
12, and each can be assigned a probability
73
In simple models (Jukes Cantor) how do we assign substitution probabilities
The probability for all of them is the same
74
Is rate of substitution uniform across sites?
No
75
Sliding Window Analysis
- Commonly used method for studying the properties of molecular sequences - Data are plotted as moving averages of a particular criterion for a window of certain length slid along a sequence alignment
76

BIOL*3040 Methods (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions