Genetics

Question 1

What are the 6 ways genetic tools can help environmental biology

Answer 1

Resolving taxonomic uncertainty to identify species (turtles)
Rescue populations from inbreeding
Manage captive breeding individuals
The role of sex in ecology or captive breeding
Identify pathogens
Forensics can be used to solve wildlife crimes

Question 2

What are the principles of genetic tools?

Answer 2

1. Use a site/locus on the genome that differs at the level you need to understand/ identify (level of polymorphism)
2. Generate suffcient DNA at that site/locus
3. Sequence the DNA at the site of interest

Question 3

What is a marker loci?

Answer 3

A ‘gene’ sequence located at the sequence-specific site in a genome. Can be coding or non-coding DNA

Question 4

Whats the difference between coding and non-coding DNA

Answer 4

Coding DNA is less variable: useful for comparing between species (e.g mitochondrial enzyme genes like cyctochrome b
Non-coding DNA is highly variable : useful for comparing between populations or individuals as it allows for hidden mutations (e.g microsatellites showing high variation between individuals)

Question 5

What are the 5 core ‘ingredients’ required to set up a PCR.

Answer 5

The DNA template that needs to be copied
DNA nucleotides to produce the new chains
Primers to bind to each end of the DNA that needs to be copied
Taq polymerase to add on the new bases
A buffer to ensure the conditions remain optimal

Question 6

Describe a PCR

Answer 6

DNA is denatured at 94 Celsius and the strands separate.
Temp. lowered to 54 celsius to allow synthetic primers to anneal
Temp raised back up to optimal temp 72 for taq to allow extension and DNA reforms at the locus of interest

Question 7

What is phyletic speciation

Answer 7

It is the process of gradual change in a single population.

Question 8

What is divergent speciation

Answer 8

the divergence of one species into two or more descendant species

Question 9

What is extinction

Answer 9

The end of an evolutionary lineage (population, Species, Genus, Family)

Question 10

If extinction rates are currently exceeding speciation rates , what is the result?

Answer 10

Loss of biodiversity

Question 11

How are individual and population phenotypes struggling?

Answer 11

REDUCED POPULATION SIZES
CONSTRAINED POPULATION MOBILITY
INCREASED ENVIRONMENTAL STRESS

Question 12

What does phenotypic expression depend on?

Answer 12

dominance and heterozygosity within the alleles

Question 13

Why is genetic diversity good? 2 reasons

Answer 13

Genetic variation / heterozygosity allows adaptability to environmental stress / change = evolutionary potential

prevents expression of deleterious homozygous recessive genes which prevents inbreeding depression

Question 14

How is genetic variability maintained

Answer 14

Through recombination and sexual reproduction

Question 15

What are the consequences of a highly inbred population

Answer 15

reduced heterozygosity /increased probabability of parents sharinf identical alleles

Question 16

Why is reduced heterozygosity bad

Answer 16

It increases the chance of parents sharing common alleles which will increase the expression of genes in their homozygous form

Question 17

Why are homozygous genes bad

Answer 17

Homozygous genes persisit in the genome with low expressions so they are rarely selected against so tend to code of sub=perfect phenotypic traits

Question 18

Examples of deleterious homozygosity

Answer 18

Cystic fibrosis
sickle cell anaemia
red green coour blind

Question 19

What is fitness`

Answer 19

is a measure of survival and reproductive success in the natural environment

Question 20

What are the consequences of inbreeding

Answer 20

is a measure of survival and reproductive success in the natural environment
= Inbreeding depression of fitness

Question 21

How does inbreeding depression manifest?

Answer 21

Infertility
Abnormal sperm
Reduced clutch size/hatching success 
Embryonic mortality
Offspring survival
Disease susceptibility
General survival under extreme selection
Local extinction

Question 22

Example of inbreeding not reducing fitness

Answer 22

Current population of black robins descended from 1 breeding female with a bottlenecked population of 5 birds. The descendants show no minisatellite DNA variation but overall their survival rate is normal

Question 23

What is heterosis

Answer 23

improved or increased function of any biological quality in a hybrid offspring.

Question 24

What is outbreeding depression

Answer 24

When very genetically different organisms breed. Can occur when local adaptations are disrupted within a species, or when newly-formed species are hybridised

Question 25

Example of inbreeding depression

Answer 25

Deer mice Jimenez et al. 1994 captured in wild, then inbred or not in lab n=367 inbred and n=419 non-inbred released inbred survived at rate only equal to 56% of non-inbred inbred lost weight after release, non-inbred maintained weight

Question 26

How can outbreeding depression manifest

Answer 26

Intermediate genotypes are not adapted to either parental habitat. Breakdown of biochemical or physiological compatibility.

Question 27

How can molecular makers help in conservation policy

Answer 27

mitochondrial DNA analyses was used to determine the species status for the Kemp Ridley sea turtle and the olive Ridley sea turtle. Scientists were unsure of their relatedness, but analyses showed that their mtDNA was distinct enough to be considered for separate protection under the US Endangered species act

Question 28

What is introgession?

Answer 28

It is the movement of a gene (gene flow) from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species

Question 29

Example of how genetic tools can help with the issue of introgression

Answer 29

Enzyme and mitochondrial data indicated that the cut throat salmon was hybridising with non native salmon which is contributing to their population decline and native populations become isolated from each other. Introgessed populations were removed by conservation efforts to encourage native individuals to breed with each other

Question 30

Limitations to genetic monitoring

Answer 30

added expense, particularly with non-invasive samples, owing to the need to repeat genetic analyses to reduce genotyping errors genotyping errors, if not adequately controlled, impede accurate estimates of many metrics e.g multifold overestimates in abundance genetic monitoring efforts that rely on non-invasive samples are more vulnerable than are traditional monitoring to fraud

Question 31

What is genetic monitoring

Answer 31

he use of molecular markers to (i) identify individuals, species or populations, or (ii) to quantify changes in population genetic metrics (such as effective population size, genetic diversity and population size) over time.

Question 32

example of genetic monitoring used fraudulently

Answer 32

Controversy over a lynx survey done in the U.S. rub pads were used to to collect lynx fur and sent to a lab for DNA analysis. There is some evidence to say that some of the presented data came from captive lynxes and not wild ones. It is easier to plant a spurious genetic sample than a live individual Dalton 2002

Question 33

Example of using molecular markers to define population viability

Answer 33

Mircosatellites were used to measure genetic diversity after a significant bottleneck in koalas

Question 34

Limitations to RAPD markers

Answer 34

the least informative of all known DNA markers; rarely detect heterozygosity Very sensitive to reaction conditions so results are often laboratory dependent cus enxyme reaction Amplification products are not always reproduce-able Co migration can occur

Question 35

What is RAPD

Answer 35

RAPD is a modification of the PCR in which a single, short and arbitrary oligonucleotide primer, able to anneal and prime at multiple locations throughout the genome, can produce a spectrum of amplification products that are characteristics of the template DNA

Question 36

What can RAPD be used for

Answer 36

gene mapping, population genetics, molecular | evolutionary genetics, and plant and animal breeding

Question 37

Example of saving an inbred population

Answer 37

An isolated population of adders in Sweden nearly went extinct due to inbreeding depression; a high proportion of offspring were stillborn or deformed. 20 males were introduced into the area for 4 mating seasons before being returned. In the following years the adder population grew rapidly and DNA analysis showed increased genetic variability

Question 38

What does RAPD stand for

Answer 38

Random amplified polymorphic DNA