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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
What are the main processes of adaptive genetic variation?
-Selection -Local adaptation
26
What are the main processes of neutral genetic variation?
-Gene flow -Genetic drift
27
What are two strategies in conservation genetics?
-Increasing gene flow -Preventing population admixture
28
What is population admixture?
occurs when individuals from two or more previously isolated populations interbreed
29
What are the pros of increasing gene flow?
-Increases overall genetic diversity -Increases potential for future adaptations -Reduces the risk of local extinction
30
What are the cons of increasing gene flow?
-Loss of local adaptation -Outbreeding depression -Loss of fitness
31
When is it advised to increase gene flow?
-If strong selection maintains adaptation
32
What are the pros of prevent admixture?
-Preserves local adaptations
33
What are the cons of preventing admixture?
-Loss of genetic diversity
34
When is prevention of admixture advised?
When isolation favours adaptation
35
How is genetic diversity measured?
PCR, Gel electrophoresis, Sanger sequencing, qPCR, High Troughput sequencing (HTS)
36
What does PCR stand for?
Polymerase Chain Reaction (PCR)
37
After DNA extraction, what two different steps could be performed?
-Direct Sequencing -Amplicon generation
38
What are genetic markers?
Are tools that enable the investigation of DNA sequence variation or lack of.
39
What are the two types of genetic markers?
Indirect Direct
40
What are indirect genetic markers?
-A phenotype controlled by a gene
41
What are direct genetic markers?
-DNA sequence
42
What are examples of genetic markers?
-Single point mutations (SNPs) -Genome wide random fragments (AFLP)
43
How was genetic variation measured in the 1960s?
-Allozymes -Changes in DNA sequence causes changes in aminoacids sequence and hence change in electric charge that can be detected using gel electrophoresis.
44
How was genetic variation measured in the 1990s?
-Random Amplified Polymorphic DNA (RAPD) -Series of random primer pairs are used to generate multi-band patterns on gels.
45
What is another method of measuring genetic variation?
-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
What are microsatellites and minisatellites?
-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
What are Single nucleotide Polymorphisms (SNPs)?
-Variation at specific sites due to point mutations -Many can be detected by sequencing or DNA chips
48
What are examples of DNA sequence databases?
GenBank BOLD
49
What is GenBank?
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
What is BOLD?
-Cloud based data storage and analysis platform developed at the Centre for Biodiversity Genomics in Canada
51
What is biodiversity?
Is the variety of life, including all genes, species and ecosystems and the ecological processes of which they are part of.
52
Why is conserving genetic diversity important?
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
What are direct benefits from genetic resources?
-Food -Medicine -Clothing -Building supplies -Shelter -40% of prescription and non-prescription drugs have ingredients extracted from plants and animals
54
What are indirect benefits from genetic resources?
-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
What is the census population size (n)
Is the number of individuals in the population
56
What is the effective population size (Ne)
Is the actual number of individuals that successful contribute to the next generation
57
Why is it important to understand genetic diversity in declining populations?
-Reduction in reproductive fitness -Adaptation and viability -Re-introduction Taxonomic uncertainty -Invasive species
58
What can cause populations to become small?
-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
What can cause small populations to genetic variability faster?
Genetic drift
60
How can genetic drift override natural selection?
-Loss of adaptive potential -Divergence of populations in fragmented habitat -Fixation of deleterious alleles
61
What are genetic bottlenecks?
Is a drastic reduction in effective population size leading to a significant loss of genetic variability
62
What is a founder event?
Is a variant of a bottleneck event except that it is directly related to a colonisation even by a small number of individuals
63
What can cause genetic bottlenecks?
-Natural causes like floods, storms, ice melt, disease outbreaks -Anthropogenic causes like overharvesting, habitat loss, competition from invasives
64
What are the consequences from genetic bottlenecks?
-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
What species experienced a genetic bottleneck?
-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
What was the genetic consequences of the bottleneck event for northern elephant seals?
-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
What is the difference in heterozygosity in DNA microsatellites comparing Northern and Southern elephant seals?
0.167 Northern 0.875 Southern (Weber et al. 2000)
68
What other species experienced genetic bottlenecks?
The North Atlantic right whale, hunted to near extinction -465 whales in October 2013 Mountain sheep, declined to 100 individuals
69
What are Irish examples of genetic bottlenecks?
The Irish red grouse -small and fragmented populations Inbreeding found in British populations of Bechstein's bat from habitat loss and fragmentation
70
What is the founder effect?
-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
What is a human example of the found effect?
-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
What is inbreeding?
Is defined as the mating among relatives
73
What does inbreeding result in?
-Increased homozygosity -Inbreeding depression -Reduced fecundity -Reduced size, growth and survival of offspring -Increased frequency of deformities
74
What is an example of species heavily impacted by inbreeding?
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
What have been the effects of inbreeding on the Florida panther?
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
What was done to diversify genetics in the Florida panthers?
-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
What is another species that has been impacted by inbreeding?
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
How has inbreeding affected cheetahs?
-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
What has been done to help cheetahs?
-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
Where might inbreeding be encouraged?
-Selective breeding programmes with desirable phenotypes are chosen -Often heavily inbred
81
What are some some problems with intentional inbreeding?
-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
Is inbreeding always negative?
-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
What does NIS stand for?
Non-indigenous species
84
What are NIS?
Are organisms that have been introduced outside their natural distribution range by means of anthropogenic activities eg. tourism, food, transportation
85
What does IAS stand for?
Invasive alien species
86
What are IAS?
What are NIS that have an adverse effect on ecosystems and/or people
87
How many alien species have been recorded in Europe?
14,000 with several being invasive
88
What was the estimated cost of inessive species to the Irish economy in 2013?
€202,894,406
89
What was the estimated cost of inessive species to the UK economy in 2013?
€2.3 billion
90
What are the most important impacts of invasive species?
-Loss of native biodiversity -Environmental degradation and ecosystem services -Human health -Financial costs
91
What are the three main pathways for invasive species to enter ecosystems?
-Intentional, releases and escapes -Unintentional, transports, stowaways -Corridor and dispersal, corridor and unaided
92
How many non-native species are in Ireland?
1280
93
How many non-natives in Ireland are harmful and invasive?
13% out of 377 assessed species
94
What are some examples of Irish invasive species?
-American mink -Chub -Chinese mitten crab -Pacific oyster -Canadian waterweed
95

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