Population Structure and Conservation Genetics

Question 1

what is meant by panmixia?

Answer 1

population is completely homogenous and mixing - no genetic differences

Question 2

what is population structure?

Answer 2

species don’t mix across their entire ranges - there are allele frequency differences (subpopulations)

Question 3

what is the wahlund effect?

Answer 3

subdivided population has fewer heterozygotes than expected

Question 4

what is Fst?

Answer 4

genetic differentiation.

Question 5

what is He?

Answer 5

expected heterozygosity

Question 6

what is Ht?

Answer 6

total He from average p + q across all subpopulations. always positive between 0 - 1.

Question 7

what is Hs?

Answer 7

average He across each subpopulation

Question 8

how does gene flow affect population structure?

Answer 8

reduces population structure. homogenesises gene frequencies

Question 9

how does selection affect population structure?

Answer 9

could do either. different selection pressures (increase). universally adaptive genes (decrease).

Question 10

how does genetic drift affect population structure?

Answer 10

random mutations in genes. by chance. increases population structure.

Question 11

define clade

Answer 11

sequences all descended from a single ancestor (grouping)

Question 12

define sister taxa

Answer 12

most closely related sequences

Question 13

define outgroup

Answer 13

information as to where the base of the tree is gives direction

Question 14

define scale bar

Answer 14

percentage sequences divergence

Question 15

define branch length

Answer 15

how different the sequences are

Question 16

what is PCA?

Answer 16

principal component analysis

Question 17

what is the function of PCA

Answer 17

• describing variation in complex multidimensional data sets

- helps visualise genetic distances and relatedness between populations

Question 18

in a PCA what does it mean if they’re further apart?

Answer 18

the more genetically different they are

Question 19

what is the result of a barrier?

Answer 19

reduces gene flow

Question 20

what is the function of wildlife corridoors?

Answer 20

promotes gene flow between populations

Question 21

describe isolation by distance

Answer 21

• populations closer together = more genetically similar
• further away = more genetically different
• gene flow wont occur

Question 22

when is a higher Fst expected?

Answer 22

at loci under divergent selection comapred to neutral/universally adaptative traits

Question 23

what factors create a need for conservation?

Answer 23

human eg habitat destruction. environment eg fires

Question 24

what happens when a population is under threat?

Answer 24

can become small and fragmented

Question 25

outline the extinction vortex

Answer 25

1. genetic drift much stronger in small populations 2. get inbreeding 3. less able to adapt 4. reduced fitness 5. reduces population further 6. could become extinct

Question 26

what is the consequence of inbreeding?

Answer 26

- low genetic diveristy - inbreeding depression - more homozygous

Question 27

what is inbreeding depression?

Answer 27

reduced fitness in offspring | - more exposed to deleterious recessive alleles

Question 28

what are ESUs?

Answer 28

evolutionary significant units

Question 29

why are historical differences important?

Answer 29

- defined by reciprocal monopylyl for mtDNA alleles | - significant divergence of nuclear allele frequencies

Question 30

what is DNA barcoding?

Answer 30

- short section of DNA to identify a species

Question 31

what would you use for animal DNA barcoding?

Answer 31

650 bp of mitochodnrial cytochrome oxidase 1

Question 32

what would use for plant DNA barcoding?

Answer 32

chloroplast genes (rbcL and matK)

Question 33

what are the advantages?

Answer 33

- no taxonomic knowledge required - discovery of crypt species - potentially very fast

Question 34

what are the disadvantages?

Answer 34

- based on mitochondrial DNA not nuclear DNA - need a lab - cant distinguish species in rapidly evolving taxa - can be little/no difference between intra and interspecific genetic variation

Question 35

what are the forensic applications?

Answer 35

- DNA amplified from tiny bits - tracking individuals - sexing individuals - identifying species