lecture 17 Flashcards
conservation genetics
aims to maintain as much genetic variation as possible so that evolutionary and ecological processes may be allowed to continue.
genetic diversity is functional in conservation:
- correlated with short-term fitness.
- correlated with long-term evolutionary potential.
the goal is to:
protect diversity, adaptive potential, and evolutionary heritage.
solutions:
manage wild populations, reintroductions, captive breeding, and habitat corridors.
processes that shape genetic variation in natural populations:
mutation, selection, migration, and genetic drift.
small populations lead to loss of
genetic diversity and extinction.
polymorphism
frequency of loci with > 1 allele.
- if 2 out of 4 loci are polymorphic, then P=0.5.
allelic diversity
average number of alleles per locus, averaged over all loci sampled.
- (2+4+1+1)/4 = 2.0
observed heterozygosity
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
expected heterozygosity
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
census population size versus effective population size:
- N = census population size; number of individuals in a population.
- Ne = effective population size; size the population contributing offspring to the next generation.
Ne/N ranges from
- 02 to 0.4 with a mean of 0.1
- interpretation - about 10% of individuals contribute to genetic changes.
in an ideal population, N = Ne
- sex ratio 1:1
- random family size
- random mating
- constant size through time
- non-overlapping generations
Effect of sex ration on Ne
Ne = 4 NmNp / (Nm + Np)
effect of family size on Ne
- 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.
polygynous
lower Ne
monogamous
higher Ne
effect of cluctuating population size on Ne:
- 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.
genetic drift is the
dominant evolutionary force in small populations and selection in small populations becomes ineffective.
- s = selection coefficients.
solutions to managing small Ne:
captive breeding, reintroductions, wild population management, and habitat corridors.
methods for surveying genetic variation:
- 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.
allozyme
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.
allozyme advantages
codominant markers (both alleles are expressed); easy to replicate; no genetic information about the species necessary (just need some tissues).
allozyme disadvanges
few loci; laborious; several steps removed from the genome (DNA –> mRNA –> 1º –> 2º –> 3º enzyme)
other allozyme info
- 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)
Application of Alloyzmes
- 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
Mitochondrial DNA (mtDNA)
mitochondrial genome sequences. Commonly used to identify evolutionarily significant units (ESUs) and management units (MUs).
mtDNA advantages
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
mtDNA disadvantages
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.
Evolutionarily significant unit (ESU)
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
Management Unit
populations with significant divergence of allele frequencies, regardless of the phylogenetic distinctiveness of the alleles
Microsatellites
di-, tri-, or tetra nucleotide tandem repeats in DNA sequences. The number of repeats is highly variable.
microsatellites advantages
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
microsatellites disadvantages
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
Single nucleotide polymorphisms (SNPs)
variable nucleotide position in the genome; most widespread type of sequence variation in genomes
SNPs advantages
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
SNPs disadvantages
fewer alleles (why?); need many SNPs for accurate inferences
conservation genetics
- 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
