lecture 17

Question 1

conservation genetics

Answer 1

aims to maintain as much genetic variation as possible so that evolutionary and ecological processes may be allowed to continue.

Question 2

genetic diversity is functional in conservation:

Answer 2

• correlated with short-term fitness.

- correlated with long-term evolutionary potential.

Question 3

the goal is to:

Answer 3

protect diversity, adaptive potential, and evolutionary heritage.

Question 4

solutions:

Answer 4

manage wild populations, reintroductions, captive breeding, and habitat corridors.

Question 5

processes that shape genetic variation in natural populations:

Answer 5

mutation, selection, migration, and genetic drift.

Question 6

small populations lead to loss of

Answer 6

genetic diversity and extinction.

Question 7

polymorphism

Answer 7

frequency of loci with > 1 allele.

- if 2 out of 4 loci are polymorphic, then P=0.5.

Question 8

allelic diversity

Answer 8

average number of alleles per locus, averaged over all loci sampled.
- (2+4+1+1)/4 = 2.0

Question 9

observed heterozygosity

Answer 9

frequency of heterozygote individuals per locus, averaged over number of loci sampled.
- (0.2+0.4+0.0+0.0)/4 = 0.6/4 = 0.15

Question 10

expected heterozygosity

Answer 10

can calculate the expected heterozygosity under HWE.
- for a locus with 2 alleles:
> heterozygosity (Hexp) = 2pq
> homozygosity (Fexp) = 1-2pq
> Fexp = p^2 + q^2
- for a locus with > 2 alleles:
> Fexp = sum of p^2 with p = frequency of allele i and n = number of alleles.
> Hexp = 1-Fexp
> Hexp = 1 - sum of p^2

Question 11

census population size versus effective population size:

Answer 11

• N = census population size; number of individuals in a population.
• Ne = effective population size; size the population contributing offspring to the next generation.

Question 12

Ne/N ranges from

Answer 12

0. 02 to 0.4 with a mean of 0.1

- interpretation - about 10% of individuals contribute to genetic changes.

Question 13

in an ideal population, N = Ne

Answer 13

• sex ratio 1:1
• random family size
• random mating
• constant size through time
• non-overlapping generations

Question 14

Effect of sex ration on Ne

Answer 14

Ne = 4 NmNp / (Nm + Np)

Question 15

effect of family size on Ne

Answer 15

• variation in family size when some pairs have 0 or few offspring, and others have many offspring.
• decrease in Ne as variance in family sizes increases above 2.
• Ne = (4N-2)/(Vk + 2) where Vk = variance in family size.

Question 16

polygynous

Answer 16

lower Ne

Question 17

monogamous

Answer 17

higher Ne

Question 18

effect of cluctuating population size on Ne:

Answer 18

• Ne = t / sum of (1 / Ne) where t = number of generations and Ne = effective size for generation i.
• population bottlenecks:
  > census size (N) will recover much faster than Ne.
  > the longer the bottleneck, the more variation lost.

Question 19

genetic drift is the

Answer 19

dominant evolutionary force in small populations and selection in small populations becomes ineffective.
- s = selection coefficients.

Question 20

solutions to managing small Ne:

Answer 20

captive breeding, reintroductions, wild population management, and habitat corridors.

Question 21

methods for surveying genetic variation:

Answer 21

• allozymes (1960s): measure genetic variation within and between species.
• mitochondrial DNA (1980s): male vs. female gene flow; identify evolutionary significant units (ESUs).
• microsatellites (1990s): bottlenecks; effective population size; assignment tests.
• SNPs (2000s): identify genomic regions under selection.

Question 22

allozyme

Answer 22

allelic forms at the same protein-coding locus detected with electrophoresis. protein variants from allelic variants will have slightly different electrical charges, and can be visualized using electrophoresis.

Question 23

allozyme advantages

Answer 23

codominant markers (both alleles are expressed); easy to replicate; no genetic information about the species necessary (just need some tissues).

Question 24

allozyme disadvanges

Answer 24

few loci; laborious; several steps removed from the genome (DNA –> mRNA –> 1º –> 2º –> 3º enzyme)

Question 25

other allozyme info

Answer 25

• Ht is the total expected heterozygosity in a species.
• Hs is the mean expected within population heterozygosity averaged over all populations.
• Fst is the proportion of total heterozygosity in a species due to genetic divergence among populations. Fst = (Ht - Hs) / Ht (Fst = fixation index)

Question 26

Application of Alloyzmes

Answer 26

• Identify the subpopulation composition of mixed stocks of salmon captured in the ocean and freshwater
• Rapid genetic analysis allows managers to close the fishery if too many fish are harvested from any single breeding population
• Crucial to prevent over fishing, longer term closures of fishing, and extinction of source populations

Question 27

Mitochondrial DNA (mtDNA)

Answer 27

mitochondrial genome sequences. Commonly used to identify evolutionarily significant units (ESUs) and management units (MUs).

Question 28

mtDNA advantages

Answer 28

maternally inherited; effectively haploid; smaller effective population size (Ne); sensitive to genetic drift; evolves quickly (compare to nuclear DNA); no recombination; 16,000+ characters; easy to sequence

Question 29

mtDNA disadvantages

Answer 29

inherited as a single locus; introgression leads to conflicting patterns; biased measure of gene flow (female only);
- “Significant” differences in mtDNA easy to detect with large sample sizes because of the greater divergence expected at loci with smaller Ne such as mtDNA.

Question 30

Evolutionarily significant unit (ESU)

Answer 30

genetically distinct unit that is considered a priority for conservation. This term can apply to any species, subspecies, geographic race, or population.


• aim to ensure that evolutionary heritage is recognized and protected and that the evolutionary potential inherent across the set of ESUs is maintained.
• Thus, the term ‘significant’ is a recognition that the set of populations are historically isolated and likely to have a distinct potential.
• The emphasis is on historical population structure Reciprocal monophyly typically used with mtDNA

Question 31

Management Unit

Answer 31

populations with significant divergence of allele frequencies, regardless of the phylogenetic distinctiveness of the alleles

Question 32

Microsatellites

Answer 32

di-, tri-, or tetra nucleotide tandem repeats in DNA sequences. The number of repeats is highly variable.

Question 33

microsatellites advantages

Answer 33

codominant; fast mutation rate; screen many loci and select highly variable loci (many alleles); PCR enabled non-destructive sampling from nontraditional sources (scat, fur, pollen, swabs); ability to detect recent genetic bottlenecks; individual assignment tests; parentage tests

Question 34

microsatellites disadvantages

Answer 34

null alleles (missing allele because primer/ PCR fails) appear as homozygous; requires species-specific or even population-specific primers (hard to develop); huge amount of upfront work required for developing loci

Question 35

Single nucleotide polymorphisms (SNPs)

Answer 35

variable nucleotide position in the genome; most widespread type of sequence variation in genomes

Question 36

SNPs advantages

Answer 36

easy to obtain genome-wide variation; fundamental unit of variation (nucleotide differences); can work with degraded samples; common throughout genome; analyze 100s or 1000s of samples; automated sample processing

Question 37

SNPs disadvantages

Answer 37

fewer alleles (why?); need many SNPs for accurate inferences

Question 38

conservation genetics

Answer 38

• Understand and manage the genetic consequences of small population sizes

• Determine evolutionary relationships among populations and prioritize groups for conservation & management

• Protect genetic diversity, adaptive potential, & evolutionary heritage