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Biodiversity and Conversation > L10 Conservation Genetics > Flashcards

L10 Conservation Genetics Flashcards

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1
Q

What is conservation genetics?

A

Is the application of genetics to preserve species as dynamic entities capable of coping with environmental change

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2
Q

What does conservation genetics encompass?

A

-Genetic management of small populations
-Resolution of taxonomic uncertainties
-Definition of management units within species
-Molecular genetic analysis in forensics
-Understanding of species biology

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3
Q

What does DNA stand for?

A

DeoxyriboNucleic Acid

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4
Q

What are the 4 basic nucleotides in DNA?

A

G, A,T,C
Are arranged in sequence and packed in chromosomes

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5
Q

How is DNA the foundation of an organism’s function?

A

DNA->RNA->Proteins->Metabolites->Function

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6
Q

What are two key features about DNA?

A

-Inherited from generation to generation
-Variable at intra and inter specific levels

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7
Q

How can genetic data be used?

A

To analyse diversity at different taxonomic levels

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8
Q

What is a gene pool?

A

The total array of genes in a population

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9
Q

Define a population genetically

A

-Species can be made up of different spatially or reproductively separated populations
-Each population is composed of many individuals

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10
Q

What is a genome?

A

The totality of all genetic material of an individual

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11
Q

What is a genotype?

A

The partial or entire genetic information (genes, variants and relative function) of an individual

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12
Q

What is a phenotype?

A

-An organism’s observable traits and characteristics, which the is expression of its genotype and the influence of environmental factors

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13
Q

What is genetic diversity?

A

Individuals within a population that are genetically different to each other because they each have slightly different variants of the same (homologous) genes.

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14
Q

What are alleles?

A

Each of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.

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15
Q

What factors affect genetic diversity?

A

-Genetic drift
-Mutations
-Gene flow (migration)

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16
Q

What are mutations?

A

Are changes in the DNA sequence of an organism, which occur during DNA replication or due to exposure to mutagenic substances or viral pathogens

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17
Q

What is genetic drift?

A

Corresponds to random changes in allele frequency between generations

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18
Q

What is gene flow?

A

Is the movement of genes from one population to another (dispersal or migration)

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19
Q

What is natural selection?

A

The mechanism by which some (the fittest) individuals are more successful than others at passing on their genes to the next generation

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20
Q

What are adaptations?

A

Is a (short term) processes by which individuals’ characteristics (traits) change to become better suited to different environments (diadromous life cycles)

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21
Q

What does diadromous mean?

A

Fish that migrate between salt water and fresh water

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22
Q

What is evolution?

A

Is a (long term) process by which heritable characteristics change over generations leading to new distinct entities which share a common origin (speciation)

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23
Q

What is speciation?

A

the formation of new and distinct species in the course of evolution.

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24
Q

What are two types of genetic variation?

A

-Adaptive
-Neutral

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25
Q

What are the main processes of adaptive genetic variation?

A

-Selection
-Local adaptation

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26
Q

What are the main processes of neutral genetic variation?

A

-Gene flow
-Genetic drift

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27
Q

What are two strategies in conservation genetics?

A

-Increasing gene flow
-Preventing population admixture

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28
Q

What is population admixture?

A

occurs when individuals from two or more previously isolated populations interbreed

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29
Q

What are the pros of increasing gene flow?

A

-Increases overall genetic diversity
-Increases potential for future adaptations
-Reduces the risk of local extinction

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30
Q

What are the cons of increasing gene flow?

A

-Loss of local adaptation
-Outbreeding depression
-Loss of fitness

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31
Q

When is it advised to increase gene flow?

A

-If strong selection maintains adaptation

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32
Q

What are the pros of prevent admixture?

A

-Preserves local adaptations

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33
Q

What are the cons of preventing admixture?

A

-Loss of genetic diversity

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34
Q

When is prevention of admixture advised?

A

When isolation favours adaptation

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35
Q

How is genetic diversity measured?

A

PCR, Gel electrophoresis, Sanger sequencing, qPCR, High Troughput sequencing (HTS)

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36
Q

What does PCR stand for?

A

Polymerase Chain Reaction (PCR)

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37
Q

After DNA extraction, what two different steps could be performed?

A

-Direct Sequencing
-Amplicon generation

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38
Q

What are genetic markers?

A

Are tools that enable the investigation of DNA sequence variation or lack of.

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39
Q

What are the two types of genetic markers?

A

Indirect
Direct

40
Q

What are indirect genetic markers?

A

-A phenotype controlled by a gene

41
Q

What are direct genetic markers?

A

-DNA sequence

42
Q

What are examples of genetic markers?

A

-Single point mutations (SNPs)
-Genome wide random fragments (AFLP)

43
Q

How was genetic variation measured in the 1960s?

A

-Allozymes
-Changes in DNA sequence causes changes in aminoacids sequence and hence change in electric charge that can be detected using gel electrophoresis.

44
Q

How was genetic variation measured in the 1990s?

A

-Random Amplified Polymorphic DNA (RAPD)
-Series of random primer pairs are used to generate multi-band patterns on gels.

45
Q

What is another method of measuring genetic variation?

A

-Amplified Fragment Length Polymorphism AFLP
-Restriction enzymes cute genomic DNA, with pieces of DNA being attached to adapters prior to PCR (more repeatable than RAPD)

46
Q

What are microsatellites and minisatellites?

A

-Tandem repeats of short (1-6 for micro)
-Or long (10-100 for mini) DNA fragments
-Highly variable, nuclear co-dominant inheritance and non-invasive sampling

47
Q

What are Single nucleotide Polymorphisms (SNPs)?

A

-Variation at specific sites due to point mutations
-Many can be detected by sequencing or DNA chips

48
Q

What are examples of DNA sequence databases?

A

GenBank
BOLD

49
Q

What is GenBank?

A

Collection of publicly available DNA sequences resulting from the International Nucleotide Sequence Database Collaboration
-Includes DNA Databank of Japan, the European Nucleotide and the GenBank

50
Q

What is BOLD?

A

-Cloud based data storage and analysis platform developed at the Centre for Biodiversity Genomics in Canada

51
Q

What is biodiversity?

A

Is the variety of life, including all genes, species and ecosystems and the ecological processes of which they are part of.

52
Q

Why is conserving genetic diversity important?

A

Numerous benefits and economic value from other species
Direct and Indirect benefits
-Loss of genetic diversity leads to inbreeding
-Could lead to collapse of ecosystems

53
Q

What are direct benefits from genetic resources?

A

-Food
-Medicine
-Clothing
-Building supplies
-Shelter
-40% of prescription and non-prescription drugs have ingredients extracted from plants and animals

54
Q

What are indirect benefits from genetic resources?

A

-Ecosystem services
-Maintaining water quality
-Persevering soils
-Buffers against storms and droughts
-Mitigate pollution
-Assist in breakdown of organic wastes and cycling of minerals

55
Q

What is the census population size (n)

A

Is the number of individuals in the population

56
Q

What is the effective population size (Ne)

A

Is the actual number of individuals that successful contribute to the next generation

57
Q

Why is it important to understand genetic diversity in declining populations?

A

-Reduction in reproductive fitness
-Adaptation and viability
-Re-introduction
Taxonomic uncertainty
-Invasive species

58
Q

What can cause populations to become small?

A

-Following drastic demographic events
-Sudden climatic events
-Disease
-Anthropogenic pressures
-Overharvesting
-Habitat loss
-Such drastic declines can lead to a loss of genetic diversity

59
Q

What can cause small populations to genetic variability faster?

A

Genetic drift

60
Q

How can genetic drift override natural selection?

A

-Loss of adaptive potential
-Divergence of populations in fragmented habitat
-Fixation of deleterious alleles

61
Q

What are genetic bottlenecks?

A

Is a drastic reduction in effective population size leading to a significant loss of genetic variability

62
Q

What is a founder event?

A

Is a variant of a bottleneck event except that it is directly related to a colonisation even by a small number of individuals

63
Q

What can cause genetic bottlenecks?

A

-Natural causes like floods, storms, ice melt, disease outbreaks
-Anthropogenic causes like overharvesting, habitat loss, competition from invasives

64
Q

What are the consequences from genetic bottlenecks?

A

-Reduced gene pool
-Inbreeding
-Loss of competitive advantage
-May lead to positive effect of loss of deleterious alleles (if bottleneck event was selective and not random)

65
Q

What species experienced a genetic bottleneck?

A

-Northern elephant seal (Mirounga angustirostris)
-Driven close to extinction in 19th century for fur and oil
-20-30 individuals survived on pacific island Isla Guadalupe
-Protection from hunting led to species recovery, numbers now 175,000

66
Q

What was the genetic consequences of the bottleneck event for northern elephant seals?

A

-20 allozyme loci- no variation (Bonnell and Selander, 1974)
-2 forms of genetic marker in mitochondrial DNA compared in 24 in southern elephant seals.

67
Q

What is the difference in heterozygosity in DNA microsatellites comparing Northern and Southern elephant seals?

A

0.167 Northern
0.875 Southern
(Weber et al. 2000)

68
Q

What other species experienced genetic bottlenecks?

A

The North Atlantic right whale, hunted to near extinction
-465 whales in October 2013
Mountain sheep, declined to 100 individuals

69
Q

What are Irish examples of genetic bottlenecks?

A

The Irish red grouse
-small and fragmented populations
Inbreeding found in British populations of Bechstein’s bat from habitat loss and fragmentation

70
Q

What is the founder effect?

A

-Known to drive the genetic structure of passively dispersed aquatic invertebrates (eg. water fleas)
-Evident in plant and animal populations that recolonise an area where life was wiped out. Krakatoa volcano

71
Q

What is a human example of the found effect?

A

-Amish community of eastern Pennsylvania
-Established by around 200 Swish
-1/200 suffer from Ellis-van Creveld Syndrome and 1/8 are carriers
-National average is 1/60000 and 1/1000

72
Q

What is inbreeding?

A

Is defined as the mating among relatives

73
Q

What does inbreeding result in?

A

-Increased homozygosity
-Inbreeding depression
-Reduced fecundity
-Reduced size, growth and survival of offspring
-Increased frequency of deformities

74
Q

What is an example of species heavily impacted by inbreeding?

A

Endangered sub species of cougar (Puma concolor)
-Only in 5% of former range
-Threats- illegal hunting, habitat loss and fragmentation
-Bottleneck, only 6 in Everglades, 1 female

75
Q

What have been the effects of inbreeding on the Florida panther?

A

Late 20th century panthers had 1/3 of genetic diversity compared to 19th century
-Morphological abnormalities (kinked tails)
-Cardiac defects
-Poor sperm quality
-High incidence of undescended testicles
-High prevalence of infectious disease

76
Q

What was done to diversify genetics in the Florida panthers?

A

-1995 8 females from closely related sub-species in Texas introduced, (gene exchange between two groups has occurred in the past)
-2004, 54 hybrid kittens
Hybrids more robust, no tail kinks and 3 times more likely to become adults

77
Q

What is another species that has been impacted by inbreeding?

A

Cheetah
1900:100,000, now less than 12,500
-Captured as pets and hunters for thousands of years
-Low genetic diversity, share 99% of same genes
-In non-inbred species siblings share 50% of genes

78
Q

How has inbreeding affected cheetahs?

A

-Low survival rates 30% die before one month
90% of cubs die before 3 months
-Poor sperm quality
-10% of sperm count and 70% more genetic abnormalities compared to related species

79
Q

What has been done to help cheetahs?

A

-Ex-situ conservation to recover genetic diversity
-AI and Embryo transfer used to mate unrelated individuals from zoos across the world
-Cheetah studbook: each animal has a stud number and record card, all births and pairings are recorded

80
Q

Where might inbreeding be encouraged?

A

-Selective breeding programmes with desirable phenotypes are chosen
-Often heavily inbred

81
Q

What are some some problems with intentional inbreeding?

A

-Carrots, hayfield show inbreeding depression
-Plants produced by selfing do not survive
-Reduced yields compared to open pollinated varieties
-Corn shows moderate inbreeding
-Onion, rye, sunflower, hemp only show small degree of inbreeding depression

82
Q

Is inbreeding always negative?

A

-Some populations do recover from bottlenecks
-May be due to purging of deleterious alleles
-After many generations, deleterious alleles are weeded out due to natural selection
-If population can survival initial reduction in fitness, if may recover from effects of inbreeding depression

83
Q

What does NIS stand for?

A

Non-indigenous species

84
Q

What are NIS?

A

Are organisms that have been introduced outside their natural distribution range by means of anthropogenic activities
eg. tourism, food, transportation

85
Q

What does IAS stand for?

A

Invasive alien species

86
Q

What are IAS?

A

What are NIS that have an adverse effect on ecosystems and/or people

87
Q

How many alien species have been recorded in Europe?

A

14,000 with several being invasive

88
Q

What was the estimated cost of inessive species to the Irish economy in 2013?

A

€202,894,406

89
Q

What was the estimated cost of inessive species to the UK economy in 2013?

A

€2.3 billion

90
Q

What are the most important impacts of invasive species?

A

-Loss of native biodiversity
-Environmental degradation and ecosystem services
-Human health
-Financial costs

91
Q

What are the three main pathways for invasive species to enter ecosystems?

A

-Intentional, releases and escapes
-Unintentional, transports, stowaways
-Corridor and dispersal, corridor and unaided

92
Q

How many non-native species are in Ireland?

A

1280

93
Q

How many non-natives in Ireland are harmful and invasive?

A

13% out of 377 assessed species

94
Q

What are some examples of Irish invasive species?

A

-American mink
-Chub
-Chinese mitten crab
-Pacific oyster
-Canadian waterweed

95
Q
A

Biodiversity and Conversation (12 decks)

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