Conservation genetics

Question 1

What is conservation genetics?

Answer 1

The use of genetic theory and techniques to reduce extinction risk in threatened species.

Question 2

What can genetics contribute to conservation of threatened species or ecosystems?

Answer 2

1. Loss of genetic diversity, inbreeding
2. Resolving fragmented population structures
3. Defining management units within a species
4. Identifying viable sites for r reintroductions
5. Detecting hybridisation
6. Resolving taxonomic problems, forensics
7. Unravelling species biology (sex determination, mating systems)

Question 3

How do you measure genetic variation?

Answer 3

1. Actually trying to measure/estimate DNA sequence variation
2. Can be done directly (sequencing) or indirectly (variation in protein structure)
3. Model of inheritance is an important factor
4. Methods that reveal a high level of genetic diversity generally give better precision for conservation genetics
5. Often need to analyse large numbers of individuals so cost is an important factor.

Question 4

What does the Hardy Weiberg theory assume?

Answer 4

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

Question 5

How can you test if there is a significant difference between expected alleles and observed?

Answer 5

Chi Squared.

Question 6

What happens when there is a frequent reduction in population size?

Answer 6

There is a reduction in heterozygosity - genetic diversity.

Question 7

What does a high heterozygosity mean?

Answer 7

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.

Question 8

What can happen in small populations?

Answer 8

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.

Question 9

How can heterozygosity be affected by genetic drift?

Answer 9

There can be a massive and quick reduction in heterozygosity per generation as a result of drift, this happens faster in smaller populations.

Question 10

Effects on HW equilibrium by genetic drift or inbreeding?

Answer 10

Genetic drift:
Loss of heterozygosity results in alleles being in approx HW equilibrium frequencies

Inbreeding:
Lower heterozygosity than expected.

Question 11

What can indicate threatened taxa?

Answer 11

77% of threatened taxa have a lower heterozygosity than non threatened taxa.

Question 12

Example of a threatened taxa with low heterozygosity?

Answer 12

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.

Question 13

Describe how inbreeding results in reduced genetic variation?

Answer 13

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

Question 14

Example of inbreeding depression?

Answer 14

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%.

Question 15

What is genetic rescue?

Answer 15

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.

Question 16

Why is identification of species an issue for conservation biology?

Answer 16

1. Un-recognised endangered species could go extinct.
2. Endangered species denied legal protection whilst common species are given protection.
3. Incorrectly identifying species that may be hybridised with other species, reducing reproductive fitness or defeating conservation objectives.
4. Populations that could be used in genetic rescue may be overlooked.

Question 17

issues with defining species?

Answer 17

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.

Question 18

What is a cryptic species?

Answer 18

Group of organisms that initially appear indistinguishable but comprise of more than one species.

Question 19

What is the fixation probability?

Answer 19

Chance that a new mutant appears in individuals in the population

Question 20

What is the fixation time?

Answer 20

Time it takes for a new allele to become fixed in a certain population.

Question 21

What is the neutral theory of molecular evolution?

Answer 21

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.

Question 22

Evidence for neutral evolution?

Answer 22

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

Question 23

Evidence against neutral evolution?

Answer 23

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

Question 24

Example of a cryptic species?

Answer 24

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.

Question 25

Issues with spotting cryptic species?

Answer 25

Mitochondrial and nuclear DNA phylogenies can differ and so may miss cryptic species.

Question 26

What is the barcoding gap?

Answer 26

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.

Question 27

Example of a use for the barcoding gap?

Answer 27

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.

Question 28

Are some groups of organisms more likely to harbour cryptic species than others?

Answer 28

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.

Question 29

Example of cryptic species in Amphibians?

Answer 29

Around 1/3 of Amphibians are globally threatened - disease spread or habitat loss.

2 species in SE Asia actually represented 14 species.

Question 30

Issues with hybridisation?

Answer 30

Affects protected status.

Ethiopian wolf - fewer than 250 mature adults. Microsatellites indicate inbreeding between Ethiopian female wolves and male dogs.

Question 31

Genetic impacts of population fragmentation?

Answer 31

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).

Question 32

Describe some of the types of population structure?

Answer 32

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

Question 33

How do we estimate levels of gene flow and inbreeding in populations?

Answer 33

-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.

Question 34

What is the Wahlund effect?

Answer 34

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.