Molecular Methods

Question 1

DNA amplificiation

Answer 1

mimics natural process of DNA replciation

Question 2

PCR

Answer 2

polymerase chain reaction

Question 3

natural DNA replication process

Answer 3

1. helicase unspirals DNA
2. polymerase unzips DNA into ssDNA
   3.exonuclease remove mismatches bases + proof reading in 3-5’ activity
   4/ primers bind onto chain + extends to replicate chain

Question 4

process of DNA amplification

Answer 4

1.helicase replaces by denaturation
2.short primers anneal to template
3. PCR

Question 5

sanger sequencing

Answer 5

method for determining nucleotide seuqnceof DNA

Question 6

pros of mtDNA for molecular markers

Answer 6

easy to amplify (lots of copies), high mutation rates, conserved gene content, conserved regions for primer design, no recombination

Question 7

example of mtDNA being used hisyorically

Answer 7

finding whale meat trade in Japan where they came from

Question 8

DNA barcodes

Answer 8

fill knowledgeable gaps with molecular tools

Question 9

application of DNA barcoding

Answer 9

id cryptic sp., finding food fraud, illegal animal trade, slow spread of invasive sp., finding diets, id ancient sp., id hosts + vectors, asses water quality, speed up sp. id “barcode bioblitz”

Question 10

limitations of DNA barcodes

Answer 10

pseudogenes, primers for some phyla are hard to design, some sp. are so closely related they don’t have diffs, barcode sequences aren’t ideal for phylogenies, not all animals have mtDNA that would evolve at the same rate

Question 11

microsatellite

Answer 11

non-coding region of DNA composed of short repetitive sequences in tandem

Question 12

mitochondrial sequencing

Answer 12

mostly variation between closely related sp/sub-sp

Question 13

restriction enzymes

Answer 13

enzymes recognition particular DNA to ‘cut’ at specific areas

Question 14

examples of DNA fingerprinting

Answer 14

asiatic lions are very divergent from serengeti

Question 15

pros of microsatellites

Answer 15

cheap + fast process, can use small amount of material, lots of variation, markers are co-dominant

Question 16

cons of microsatellittes

Answer 16

Development of primers for new sp. are difficult

Question 17

other uses of microsatellites

Answer 17

pop structures, maternity analysis, explore pop structure in wild pops

Question 18

other sequencing methods

Answer 18

outdated: allonyms, restriction enzymes, multi loci sequencing

next-gen: single nucleotide polymorphisms, sequencing the whole genome

Question 19

what features does mendelian pops have

Answer 19

random mating, panmixia, no gene flow, no selection, infinite pop size

Question 20

example of reduced bottlenecks

Answer 20

great prairie chickens

Question 21

inbreeding

Answer 21

% that alleles in an individual will eerie from the same common ancestor

Question 22

what can cause IB

Answer 22

small pops, non-random mating

Question 23

how else can inbreeding be measured

Answer 23

use equations based on pop size, known pedigrees, path analysis

Question 24

how does hybrid vigour occur

Answer 24

high heterozygosity cause higher fitness (masks strong effects of deleterious alleles )

Question 25

example of highly inbred captive popualtion

Answer 25

golden tamarins

Question 26

how can small/inbred pops avoid IBD

Answer 26

via purging - homozygous recessives were exposed to selection + removed from pops

Question 27

outbreeding depression

Answer 27

2 genetically too-distant groups cross reducing fitness

Question 28

what is an example of outbreeding depression

Answer 28

use of alpine + Nubia ibex failed

Question 29

why is outbreeding difficult to collect evidence for

Answer 29

meta anaylsis show no impact, marine copepods can't expect inbreeding, more common in plants

Question 30

example of inbreeding causing environmental stress

Answer 30

soay sheep, song sparrow

Question 31

heterosis

Answer 31

high heterozygosity

Question 32

what is selfing in plants

Answer 32

asexual reproduction, increases autozygosity per gen, produce haploid genes

Question 33

Is Ne>50 good indicator

Answer 33

yes in plants (50 used in seed banks), very subjective in animals what

Question 34

50/500 method

Answer 34

`ne>50 for short-term conservation, Ne>500 for long-term consevatiob

Question 35

issues for genetically viable pops

Answer 35

Ne

Question 36

effective pop size

Answer 36

ne

Question 37

what does Ne need to account for

Answer 37

sexual maturity, biased sex ratio

Question 38

examp-le of high IBD created from genetic rescue

Answer 38

Isle Royale grey wolf (went through bottleneck, and introduced a new male)

Question 39

pros of genetic rescue of isle Royale wolf

Answer 39

improved future genetic health (fixed pelvic bone deformity)

Question 40

cons of genetic rescue of Isle Royale wolf

Answer 40

loss of variaiton at neutral alleles, after 2-3 gens fitness benefits of genetic rescue, beneficilffects weren't detected (due to environmental factors)

Question 41

example of successful genetic rescue

Answer 41

Florida panthers, adders, bighorn sheep, prairie chicknes, Mexican wolf

Question 42

issues with outcrossing

Answer 42

cause outcrossing depressions (Nubian + alpine ibex)

Question 43

why were Floridian panthers controversL

Answer 43

Politically (taxonomist considered Texas as separate sp.), seen as scary, habit use, validity of pop modelling, lack of objectivity

Question 44

pros fo Florida panthers gen rescue

Answer 44

now protected sp + show signs of IBD

Question 45

arguments against genetic rescue

Answer 45

only some studies show reduce pops = reduced gen variation, may not work, easy to go wrong if Indies lack adaptations OF NATIVE POPS

Question 46

Example of genetic rescue gone wrong

Answer 46

koalas

Question 47

why was koala genetic rescue failed

Answer 47

translocation success was measured at source and not impact of translocated inidivs- stress of translocation caused dehydration + death

Question 48

ways to avoid genetic rescue

Answer 48

augment gene flow

Question 49

examples of non-controversial augmented gene flow

Answer 49

african wild dogs, south African elephants, golden lion tamarin, black rhino, red cockaded woodpecker

Question 50

what is a more radical option for gen reduce other than traslocation

Answer 50

intro of new pathogen (American chestnut)

Question 51

cons of American chestnut gen rescue

Answer 51

trees tike long to grow, If more loci are involved predictions may weaken, backcrossing can lose progress quickly

Question 52

example of first cloned endangered anima;

Answer 52

black footed ferrets (suffer IBD)