Module 2 - Adaptive variation

Question 1

Name some management objectives regarding genetic variation

Answer 1

• the evolutionary potential need to be conserved (To improve chances of population survival)
• Loss of evolutionary potential greatest in small populations
• Ecotype variation (local adaptation) and problems of translocation (we can’t swap individuals between populations that are highly adapted to unique environments)
• Adaptation to captivity

Question 2

What is the phenotype?

Answer 2

Physical attributes

Question 3

What is the genotype?

Answer 3

Genetic attributes

Question 4

Qualitative phenotypes?

Answer 4

Phenotypes with a discrete character that we can describe
e.g. colour genes (simple, mendelian inheritance, albinism), blood types e.g. A, B, AB, O

Question 5

Quantitative phenotypes

Answer 5

Phenotypes that need to be measured - complex trait (Comprised of alleles from many genes and can either add or subtract from the final phenotype (Measurable traits that are normally distributed))
e.g. weight, length disease resistance, fecundity
Bristle number in flies
Beak size in Darwin’s finches

Question 6

Why is it important to study quantitative genetic traits?

Answer 6

The ultimate goal of many genomic studies is to understand genetics behind complex traits (morphology, life-history, variation, disease resistance/suceptibility)

Question 7

What is the essence of quantitative genetics?

Answer 7

Traits are controlled by 10’s to 100’s of genes each with a small effect.

It’s hard to predict exact animal phenotype the more genes are impacting the phenotype

Selection increases the allele frequencies of favorable genes for the trait in the population

Question 8

What are some metrics that could be used to infer reproductive fitness?

Answer 8

Litter size, lifetime number of litters, clutch size, days to flowering

Question 9

What is heritability?

Answer 9

Heritability = the proportion of phenotype variance it attributed to additive genetic variation.

Determines the extent to which a character is passed on from parent to offspring in a population. Beneficial traits will only be passed on if they are heritable.

“The heritability of a trait within a population is the proportion of observable differences in a trait between individuals within a population that is due to genetic differences”

Heritability of a character in a population determines the response to selection.

Question 10

If a trait has low heritability in a population most of the phenotypic variance is due to

Answer 10

environmental influence and it is hard to change the trait via selection forces

Question 11

If a trait has high heritability in a population most of the phenotypic variance is due to

Answer 11

additive genetic variation and not the environment. The trait can easily be changed via selection forces.

Question 12

What is the heritability range for morphological traits?

Answer 12

Usually 0.3-0.8

Question 13

What is the heritability of life-history/fitness traits in wild vertebrates?

Answer 13

Below 0.4

Question 14

Why do morphological traits typically have higher heritability than life-history traits?

Answer 14

Selection has a larger impact on fitness traits compared to morphological traits (these may not give any advantage, and thus have low selection pressure), which removes the additive genetic variation from the population.

Question 15

Is heritability for a trait constant?

Answer 15

Heritability for a trait is not constant, but varies among different populations that are genetically divergent

It is something you report for a particular point in time, since it may change.

Question 16

Can you use neutral markers to measure levels of adaptive variation in a population

Answer 16

People do it, they use limited numbers of neutral markers (like microsatellites) to say something about variation in a population, expecially of small populations of endangered species, however, the relationship is NOT ROBUST

This method is only useful with very low genetic diversity

“Molecular measures using small numbers of neutral loci have only a very limited ability to predict quantitative genetic variability”

Question 17

What is the best way of obtaining information on a populations short term evolutionary potential?

Answer 17

We need to measure quantitative variation directly

However, this can be difficult in wild populations and we need to use advanced molecular tools to detect this information e.g. Population genomics

Question 18

What is the difference between Fst and Qst?

Answer 18

Fst is a measure of neutral molecular markers, it describes neutral genetic variation.
Theoretically it reflects the action of drift and geneflow.

Qst is a measure of morphological and life history traits, it describes quantitative variation.
It reflects the action of drift, gene flow AND selection.

Question 19

What is the usual relationship between Fst and Qst

Answer 19

Qst is usually larger than Fst in natural populations

Question 20

What are the traits of importance to conservation primarily?

Answer 20

Quantitative e.g. fitness

Question 21

What is variation in quantitative characters due to?

Answer 21

Both genetic and environmental effects

Question 22

What is the evolutionary potential of a character determined by?

Answer 22

It’s additive genetic variation / heritability

Question 23

Why are heritabilities lower for fitness traits compared to morphological traits?

Answer 23

Due to selection, which impacts fitness traits more

Question 24

What do we measure with Qst?

Answer 24

Quantitative variation

Question 25

How is the correlation between Qst and genetic variation?

Answer 25

It can be poor, which is why we have to use advanced genomic approaches to identify genes or regions of genome underlying traits and use them directly instead of using Qst

Question 26

Name the four microevolutionary processes

Answer 26

Mutations, Migration, Natural Selection, Genetic Drift

Question 27

Heritability determines the

Answer 27

response to selection

Question 28

Genotype-Environment interactions are important in conservation biology when translocating animals because

Answer 28

We need to understand how local adaptations will progress to the next generations, we wish to have animals that are well suited to the new environment they get moved to. We do not want outbreeding depression!

Question 29

Genetic variation is linked to adaptive potential. Often limited numbers of neutral markers e.g. microsatellites in neutral loci are used to measure levels of genetic variation in small populations of endangered species. Is that a good method to measure genetic variation?

Answer 29

Not really, there is no robust relationship between neutral loci and overall genetic variation. However, the smaller the population the better it works..

It can be useful if it is the only data we have available

If we need information on a population’s short-term evolutionary potential, quantitative variation should be measured directly. This can be difficult and we need advanced molecular tools (Population genomics)

Question 30

Strong selection can limit

Answer 30

a populations capacity to evolve

Question 31

What is stabilising selection?

Answer 31

A type of selection (on a quantitative trait) that favours phenotypic intermediates, due to the removal of the extremes e.g. birth size.
Most frequently seen in non-fitness-related traits

Question 32

What is directional selection?

Answer 32

A type of selection (on a quantitative trait) that happens due to a specific influence that directs the phenotype in some way. Can either be an advantage or a disadvantage for the species

Question 33

What is disruptive selection?

Answer 33

Pretty much the opposite to stabilising selection. A type of selection (on quantitative traits) that is caused by different influences, but it favours the extremes e.g. fragmented populations in different environments.
If the selection is removed you get a normal distribution again.

Question 34

What is a cline?

Answer 34

When there is a balance between selection and migration a cline forms. It is a local adaptation. Common for morphological and quantitative traits.

Reflect changes in selection across environmental gradients (think of the different morphotypes of koalas).

Question 35

What impacts the steepness of a cline?

Answer 35

Dispersal rates: If limited dispersal, the cline is steep. If high dispersal, clines are more gradual.

Question 36

Give a definition of selection

Answer 36

Differential success of genotypes in next generation. The favourable alleles will build up in frequency and the unfavourable will drop

Question 37

In a simplistic model, what 2 life history components affect genotypes?

Answer 37

Viability (Do they survive?)
Fertility (Do they reproduce?)

Question 38

What is the allelic state?

Answer 38

Can be dominant, intermediate or recessive

Question 39

Why is selection less effective in small populations

Answer 39

1. Because there is low initial genetic diversity, and thus not a lot of material for selection to work on
2. Genetic drift is random and has a lot more impact on small population sizes.

Question 40

Migration and selection can result in one of two things:

Answer 40

A balance or a cline

Question 41

What is conservation genomics and what can it do?

Answer 41

Conservation genomics is using new genomic techniques to solve problems in conservation biology.
It allows us to examine genomic patterns within and among populations to make inferences about phenotypic variation, adaptation and evolution.

We can link complex genotypes and phenotypes by comparing genotypic and phenotypic information in breeding and natural populations.

We do this by using genome-wide, multi-locus data sets to identify non-neutral outlier loci by contrasting patterns of population divergence among genetic regions.

Question 42

Neutral markers are used in conservation genetics. They can give us:

Answer 42

Gives us unbiased estimates of genetic variation, population structure and gene flow.
However, there is no direct biological meaning of these loci, e.g. survival, fecundity, and we can therefore only use them to infer biological activity based on assumptions and expectations that are not always true.

Question 43

Non-neutral markers are used in conservation genomics. They are better than neutral markers to provide an insight into the role of evolutionary processes that influence populations and species, because:

Answer 43

They are loci under selective pressure and can therefore be measured as a direct biological measurement, i.e. less guess work (e.g. adaptive or deleterious genes). They also give us a better understanding of phenotypic differences.

Question 44

One outlier test approach is the Candidate Gene Approach. What is a candidate gene?

Answer 44

A candidate gene is a gene that we suspect to regulate or control the phenotype expression of interest.
We can then target our analysis to the regions where we know these genes are situated.
If we don’t know anything when starting the analysis we have no candidate genes and have to take a different approach

Question 45

What type of markers do we use to delineate ESUs?

Answer 45

Both neutral and outlier markers

Question 46

What type of markers do we use to delineate MUs?

Answer 46

Neutral only! Not outliers.

Question 47

What microevolutionary processes do neutral markers tell us about?

Answer 47

Genetic drift, geneflow

Question 48

What microevolutionary process does adaptive markers tell us about?

Answer 48

Selection