Conservation genetics Flashcards
What is conservation genetics?
The use of genetic theory and techniques to reduce extinction risk in threatened species.
What can genetics contribute to conservation of threatened species or ecosystems?
- Loss of genetic diversity, inbreeding
- Resolving fragmented population structures
- Defining management units within a species
- Identifying viable sites for r reintroductions
- Detecting hybridisation
- Resolving taxonomic problems, forensics
- Unravelling species biology (sex determination, mating systems)
How do you measure genetic variation?
- Actually trying to measure/estimate DNA sequence variation
- Can be done directly (sequencing) or indirectly (variation in protein structure)
- Model of inheritance is an important factor
- Methods that reveal a high level of genetic diversity generally give better precision for conservation genetics
- Often need to analyse large numbers of individuals so cost is an important factor.
What does the Hardy Weiberg theory assume?
Large population
Random mating
No mutation, migration or selection
Mendelian segregation of alleles
Equal fertility of parental genotypes
Equal fertilizing capacity of all gametes
Equal survival of all genotypes
How can you test if there is a significant difference between expected alleles and observed?
Chi Squared.
What happens when there is a frequent reduction in population size?
There is a reduction in heterozygosity - genetic diversity.
What does a high heterozygosity mean?
Lots of genetic variability.
If observed is lower than expected, it might be due to inbreeding.
Higher than expected could be due to mixing populations.
Variance between observed and expected heterozygosity reduces with increasing population size.
What can happen in small populations?
Random genetic drift can cause a greater loss of alleles in small populations.
In a simulation of size 20, lots of alleles either fix or are lost.
In a simulation of size 100, they fluctuate a lot more.
How can heterozygosity be affected by genetic drift?
There can be a massive and quick reduction in heterozygosity per generation as a result of drift, this happens faster in smaller populations.
Effects on HW equilibrium by genetic drift or inbreeding?
Genetic drift:
Loss of heterozygosity results in alleles being in approx HW equilibrium frequencies
Inbreeding:
Lower heterozygosity than expected.
What can indicate threatened taxa?
77% of threatened taxa have a lower heterozygosity than non threatened taxa.
Example of a threatened taxa with low heterozygosity?
Northern Hairy Nosed Wombat.
Lives in Queensland and New South Wales. Has low heterozygosity.
One of the rarest mammals in the world. Used to have a wide range across NSW, now just 3km^2.
Much lower number of alleles/heterozygosity than the southern species which has a wider range.
Describe how inbreeding results in reduced genetic variation?
Inbreeding is the production of offspring from mating of individuals related by ancestry
Offspring have an increased probability of inheriting alleles that are identical by descent (autozygous)
The probability of both alleles at a locus uniting in an individual that are identical by descent is termed the inbreeding coefficient (F)
Inbreeding is a major issue with threatened populations both in the wild and also for ex-situ conservation
At F = 1, fully inbred
As population size increases, F goes down over time
F = 1/2N is the probability that an individual has two alleles identical by descent
Increases more rapidly in smaller populations
Example of inbreeding depression?
Survival of progeny in mammals.
Juveniles mortality amongst inbred and non-inbred lines varies significantly. Higher values in most species for inbred animals.
Chondrodystrophy in Californian Condors.
All were taken into captivity in 1987 and the current population was founded by 14 individuals.
Suffer from a lethal condition called chondrodystrophy which impacts on the bone development of chick, caused by a lethal recessive mutation.
Frequency of this allele is about 9%.
What is genetic rescue?
Introduction of outbred individuals or captively reared individuals to restore genetic variability and mitigate the negative effects of inbreeding.
Introduction of outbred individuals in Swedish Adders.
Why is identification of species an issue for conservation biology?
- Un-recognised endangered species could go extinct.
- Endangered species denied legal protection whilst common species are given protection.
- Incorrectly identifying species that may be hybridised with other species, reducing reproductive fitness or defeating conservation objectives.
- Populations that could be used in genetic rescue may be overlooked.
issues with defining species?
Biological species concept is the most widely accepted species concept, but there are at least 22 other species concepts.
Most species have been identified based on morphological characters as groups that are distinct from other groups.
What is a cryptic species?
Group of organisms that initially appear indistinguishable but comprise of more than one species.
What is the fixation probability?
Chance that a new mutant appears in individuals in the population
What is the fixation time?
Time it takes for a new allele to become fixed in a certain population.
What is the neutral theory of molecular evolution?
Genetic drift causes allele frequencies to change over time and wander randomly. Some alleles go extinct, others become fixed.
Time to fixation/loss varies with effective population size and initial allele frequency. Depends on whether an allele has a selective advantage.
Example: in an effective pop size of 1 million individuals, mean gen time of 2 years. Takes 8 mil years for neutral mutation to fix, selective advantage of 1% takes 5,803 years.
Emergence of molecular data indicated variation in proteins that had little effect on function. Proposed that most mutations which fix are neutral and that any differences between species at these sites evolve by random genetic drift.
Evidence for neutral evolution?
The rate of molecular evolution and the degree of polymorphism is too high to be explained by selection.
The constancy of molecular evolution.
Functionally less constrained parts of molecules evolve at higher rates.
Can be shown that the rate of mutation = rate of neutral mutation
Evidence against neutral evolution?
Inconstancy of the molecular clock.
Levels of heterozygosity which are too constant between species and too low in species with high population sizes.
Observed levels of genetic variation and evolutionary rates which are not related in the expected way
Example of a cryptic species?
Northern sportive lemur in N Madagascar.
Dry and humid forests, where populations are fragmented and subject to hunting.
Sequence analysis of the mitochondrial d loop. Significant number of differences suggesting that the lemur exists as two separate cryptic species caused by chromosomal rearrangements.
Issues with spotting cryptic species?
Mitochondrial and nuclear DNA phylogenies can differ and so may miss cryptic species.
What is the barcoding gap?
In a specific data set, the difference between the greatest intraespecific distance and the smallest interespecific distance is called “Barcoding Gap”.
If it exists, it means that you can establish a cut value for the species delimitation in your data because there are no overlap between the intra and interespecific distances.
For example, if the greatest intraespecific distance is 1%, and the smallest interespecific distance is 4%, two sequences that differ 1% should be of the same species.
Example of a use for the barcoding gap?
Right Whales.
Right whales used to be classified by area (N vs S). No morphological criteria distinguished the species, and hunting was the main cause of decline.
Barcoding gap, consistent with the two being distinct species.
Are some groups of organisms more likely to harbour cryptic species than others?
Species rich ecosystems
Poorly studied organisms
Groups poor in morphological characters
Organisms with species recognition and mate choice systems that rely on non-morphological characteristics.
Example of cryptic species in Amphibians?
Around 1/3 of Amphibians are globally threatened - disease spread or habitat loss.
2 species in SE Asia actually represented 14 species.
Issues with hybridisation?
Affects protected status.
Ethiopian wolf - fewer than 250 mature adults. Microsatellites indicate inbreeding between Ethiopian female wolves and male dogs.
Genetic impacts of population fragmentation?
Atlantic Forest in Brazil from 82% cover in 1500 to 3% in 2000. Genetic impacts depend on whether there are changes in gene flow among fragments.
Decreased gene flow (increased genetic structure) can lead to inbreeding, loss of genetic diversity and elevated extinction risk. Range from random mating (F=0) to isolation (F=1).
Describe some of the types of population structure?
Source-sink population structure with mainland (source) providing migrants to island (sink) populations
Island structure with equal levels of migration among populations
Stepping stone model where only neighbouring populations exchange migrants
Two-dimensional stepping stone structure
Metapopulation structure where empty circles indicate (temporarily) extinct populations and grey-shaded circles are newly founded populations
How do we estimate levels of gene flow and inbreeding in populations?
-Population fragmentation results in heterozygote deficiency (Wahlund effect) when compared to Hardy-Weinberg expectations
-Thus inbreeding in a total population can be partitioned into
Inbreeding of individuals relative to their fragment
Inbreeding due to differentiation among subpopulations relative to the total population
-F is effectively the inbreeding coefficient averaged across all individuals from all population fragments. Values above 0.25 indicate very great genetic differentiation.
What is the Wahlund effect?
Reduction of heterozygosity in a population caused by subpopulation structure.
E.g. one population all homozygous for one allele, and the other for another. Techinically HW-equilibrium frequencies, but all homozygous.
