Week 4 Flashcards
1
Q
Who and when create the process of DNA fingerprinting?
A
Sir Alec Jeffries 1984
2
Q
What is an overview of the function of DNA?
A
DNA sequence codes for an allele
Alleles = genetic variants at specific locus (gene)
Alleles encode proteins…..and thus everything!
Pairs of chromosomes in diploid organisms
3
Q
What does both alleles impact?
A
At a locus (gene) alleles from both chromosomes combine to
produce the Genotype and its effects
4
Q
What produces the phenotype?
A
Genotype and environment
5
Q
What is polymorphic DNA?
A
Variation in some part of the genome
6
Q
How can polymorphism vary?
A
Polymorphism in, or among - individuals, groups, populations or species
7
Q
What is an overview of exons?
A
Transcribed part of genome
Nucleotide sequence variation can be mapped
Different alleles directly influence phenotype
8
Q
What is an overview of non coding DNA (neutral markers)?
A
Part of genome with no direct function (not transcribed)
Neutral to selection
Highly polymorphic
Provides many highly informative markers
9
Q
What are the different types of DNA?
A
Nuclear autosome – bi-parentally inherited
Sex chromosomes e.g. Y = males, X = both sexes
Mitochondrial - maternally inherited
10
Q
What are examples of DNA markers?
A
Microsatellite repeats, e.g. CTTT(inverse^)10
Sequence data
SNPs – single nucleotide polymorphisms
11
Q
How can you co-oridinate individuals with DNA results?
A
Place spots or tags to identify the individual
12
Q
Where can you get DNA from?
A
Blood
Tissue
Faeces
Hair follicles
Feathers
Sloughed skin
13
Q
Where can you store collected DNA?
A
100% Ethanol
Specialised buffers
Dried
14
Q
Why do we need only to collect a small amount of DNA?
A
As we can undego PCR to amplify the DNA regions we are investigating
15
Q
What are and what happens during the 3 main stages of PCR?
A
Denaturing – when the double-stranded template DNA is heated to separate it into two single strands.
Annealing – when the temperature is lowered to enable the DNA primers to attach to the template DNA.
Extending – when the temperature is raised and the new strand of DNA is made by the Taq polymerase enzyme
16
Q
How can molecular techniques be useful in the field?
A
Distinguishing similar species
Determining prey species
* Observations = difficult or time consuming
* Gut contents or faecal samples
17
Q
What is DNA barcoding?
A
Library of species barcodes
18
Q
What is used in DNA barcoding?
A
Short, easy to amplify section of DNA
That has lots variation across spp……but little within species variation
Same sections used across all (or at least whole groups of) species
In animals - e.g. 600-700bp of mitochondrial COI region
19
Q
Why are molecular techniques used for sex determination?
A
In the majority of organisms sex is genetically determined- these genes can be used to identify sex
20
Q
How can molecular techniques be used for sex determination?
A
Amplify a piece of DNA on sex chromosomes
21
Q
What is a case study of molecular techniques being used for sex determination?
A
Allele on W chromosome is shorter than on the Z
Run on a size separation electrophoresis gel
Females (ZW) have two bands - Males (ZZ) have one
Birds
22
Q
What is a case study for sex determination in whales?
A
Baleen whales lack obvious secondary sexual
characteristics.
A Y-chromosome probe used in humpback whales (identifies males)
Determine gender of free ranging whales using skin biopsies
23
Q
What can be used to determine biological age?
A
DNA methylation and Telomeres
24
Q
What is a case study of usinf DNA methylation for age determination?
A
Key DNA loci show increased methylation with age
Can be used to calculate age
Polanowski et al 2014 - humpback whales
Determine age structure of pods and populations - pods are all male or all female with calves
25
Why can telomeres be used to determine age?
Telomere attrition with cell replication
Thus telomeres shorten with age
Can be used to determine chronological age
May cause senescence /age related disease
26
What causes telomeres to shorten?
Oxidants – also erode telomeres
* Product of metabolism
* Affected by stresses
27
What can increases telomere shortening?
Higher oxidants and telomere shortening with, for example:
1) infection
2) reproductive effort
3) Psychological stress
28
What is a case study of the relationship between telomere length and post-sampling lifespan?
Seychelles warbler, Acrocephalus sechellensis
Measured teleomere length and then recorded when the birds died
Positive correlation - telomere length predicts future
lifespan after controlling for age
29
What did the experiment with the Seychelles warbler prove?
Marker of biological age
30
In Seychelles warbler what was shown to increase life span?
The cost (stress) of fighting with new and/or unrelated neighbours
Having helpers delays ageing in breeding females
31
Why are telomeres a good tool for estimating lifespan?
Telomeres as a generic currency to measure the costs of different behaviours in life
32
How can molecular tools be useful for monitering infections?
Who has an infection e.g. malaria
When they get it
How they behave when infected
Survival and reproductive success
Behavioural changes selected for
33
What bird in Hawaii escape malaria througha change in behaviour?
Hawaiian Honeycreeper
34
How did the Hawaiian honeycreeper reduce eposure to malaria?
They move nest up in the mountains where it was too cold for mosquitos before moving down in the day to find food
35
What is the overview of the spread of Wolbachia?
Detected using PCR of ribosomal DNA from the bacteria
Ca 60% of insects infected!
Transmitted in egg cytoplasm therefore only by female hosts
Cause female bias in hosts’ offspring e.g. override sex
determination, induce parthenogenesis, kill male eggs etc
36
How did the wide spread nature of Wolbachia impact mating behaviour?
Acraea butterflies:
Skews sex ratio to mainly females - reversing the sex that
competes for a mate - results in female lekking
37
What are the problems with determining parentage without genetics?
Difficult to watch individuals or groups
Matings may be secretive/difficult to observe
Females may copulate with multiple males
Offspring from multiple females may be mixed
38
What can DNA markers revel about mating systems?
Can revel the mating system used eg monogamy or polygyny or even promiscuity
39
How can did they determine the mating system of Dunnock - Prunella modularis?
Highly variable mating system including polyandry
Two males mate with, and defend the territory of, a
single female.
DNA fingerprints identify if both males contribute to
a single brood.
Match offspring bands not found in the Mum (M)
against the fingerprint profile of potential fathers
(Pa and Pb).
Both males gain paternity
40
How common is extra pair paternity?
Common in birds
Average of 15% EPP in songbirds
Superb fairy-wrens: 76% EPP
Frequent in mammals e.g. 20% in white-toothed shrews
41
What are behaviours to reduce parental care?
Inter or intrspecific brood parasitism
42
What are examples of interspecifc brood parasitism?
Cuckoos etc
Occurs in birds, fish and insects
43
What is the overview of intraspecific brood parasitism?
Take advantage of members of own species
Often only revealed using molecular markers
Common in fish and birds
44
What is cooperative breeding?
Situation where adult individuals, in addition to the genetic parents, stay within a group and regularly aid in the rearing of young
45
What are examples of cooperative breeding?
Paper wasps
Acorn woodpeckers
Meerkats
46
Why are molecular techniques important for cooperative breeding?
Test the importance of kin selection
47
Why is molecular techniques used for reproductive sucess of behaviours?
Accurate assessment of lifetime reproductive success –
to determine the adaptive significance of behaviours
Test variance in reproductive success across systems with
differing levels of sexual dimorphism
48
What is a case study of sexual dimorphism in reproductive behaviours?
Male reproductive skew drives sexual dimorphism
Theory – variance in male reproductive success is much
greater than in females
Consequently
Selection is much greater in males
Invest more in elaborate secondary sexual characteristics and behaviour
49
What is an example of 2 genes impacting a behaviour?
Oldfield mice have long tunnels to den with escape tunnel
Deer mouse - short tunnels with no escape tunnel
Bred together results in the same as Oldfield
Backcross of offspring with deer mice results in 4 outcomes
Oldfield style, deer mouse style, long tunnel with no escape or short tunnel and a escape tunnel
Example of 2 loci effecting behaviour
50
What is an example of a gene affecting behaviour?
Dopamine receptor D4 - Neurotransmitter that plays a major
role in reward-motivated behaviour
51
How can Dopamine receptor D4 impact behaviour?
Repeatable behavioural
Tendencies within an individual
Introvert / extrovert
Novelty seeking behaviour
Aggression
Seen in humans and blue tits
52
How can molecular techniques help indentify cause of behaviors?
Screening the genome for genes associated with behaviour
53
What is an example of behaviour being impact by environment with a slight influence from genetics?
Caste and behavioural differences in honey bees
- same genome…. different behaviours
Royal jelly fed to bee at certain stage of development causing development into queen
54
What impacts genes?
The environment, epigentics, gene expression, regulatory elements and herefitary genetics. With phenotype impacting response to envrionment
55
What are the 2 main processes of sexual reproduction?
Gametogenesis and Fertilisation
56
What happens in gametogenesis?
The production of haploid sperm and eggs via meiosis
Involves recombination and isolation of one set of chromosomes
57
What happens in fertilisation?
Fusion of haploid gametes from two different individuals to produce diploid embryos/offspring
58
Why is sexual reproduction a theorectical problem?
More complex and includes more processes
59
What are the stages of sexual reproduction not in asexual reproduction?
Gametogenesis and fertilisation
60
What stages are asexual reproduction and stages of sexual reproduction?
Embryogenesis and maturation
61
What is the two-fold cost of sex?
Share offspring relatedness with a male. Offspring relatedness is 0.5 rather than 1
Have to produce offspring who won’t produce any themselves (sons)
This is inefficient compared with asexually reproducing females
62
Why is reproduction a theoretical problem for sexual selection?
In a resource-limited environment, asexual lineages can rapidly outcompete sexual lineages
63
What are the costs of sexual reproduction?
Sharing genetic relatedness of offspring
Production of males
Breaking up of coadapted gene complexes through recombination
Requirement to find mates
Sexual conflict
64
When did sexual reprodiction evolve?
Recombination/syngamy (to correct/alter damaged DNA) probably evolved ~3 billion years ago
Sexual reproduction probably evolved ~1.2 billion years ago (Bangiomorpha)
65
What does the early selection of sexual reproduction mean for the process?
It means it is an advantageous phenomenon
66
How widespread is sexual reproduction?
99% of eukaryotes use it
Many prokaryotes too
67
Can organisms undergo both sexual and asexual reproduction?
Accepted across several taxa of snakes, never observed in elapid snakes but demonstrated genetically.
Observed in Komodo dragons, zebra sharks and Mollys.
68
Why are the propositions for evolution of sexual reproduction?
Drift-based model: Fisher-Muller Hypothesis
Selection-based model: Red Queen Hypothesis
69
Why did they think the Fisher-Muller hypothesis can reduce impact of mutation?
Sexual reproduction can break this ratchet, as in a diploid organism, inheritance is not 100%
Parents are likely to come from different lineages so unlikely to carry the same mutation
70
Why is sexual selection needed to reduce mutations?
In asexual lineages, any mutations that arise are passed on to clonal offspring and so accumulate in the lineage.
Mutations are almost always detrimental to fitness – essentially all mutations are accidents
In asexual reproduction the only mechanism to purge a mutation is a randomly occurring back-mutation. This is very rare
71
What is evidence for drift-based models?
Although asexual species exist, they do not tend to persist over evolutionary timescales.
That is, they could be referred to as ‘twigs on the tree of life’.
72
What is an example of the short timescale of asexual timescale?
Timema shepardi is asexual but closest two species T.californicum and T.landelsensis which are sexually reproducing
73
What is an example of exception of drift-based model asexual reproduction timescale?
These are bdelloid rotifers
They have existed for 40 million years
They have 360 species
They are asexual
74
What is the Red Queen hypothesis?
Over time and space, biotic AND abiotic selection pressures vary
Examples of this include climate change/global warming; host-parasite coevolution, or predator-prey coevolution
Due to recombination, sexual reproduction increases variation, which increases adaptability
This allows for more rapid evolutionary change/adaptation to new conditions
75
What is an example for selection-based model?
New Zealand mud snail - Potamopyrgus antipodarum
Trematode parasites - example: Microphallus
76
What is the overview of New Zealand mud snail?
Potamopyrgus are abundant in freshwater habitats throughout New Zealand.
2 forms: sexual and asexual.
Asexuals can produce twice as many daughters as sexuals – so why do sexuals exist
77
What is the outcome of the investigation into New Zealand mud snail and parasite for reproduction method?
Positive association between proportion of males in a population and parasite load
Suggests that sexually reproducing snails (measured by proportion of males in a population) are more able to cope with parasite load.
78
What is an evidence of drift-based models explaining the short term nature of asexual reproduction?
Increased mutation accumulation is associated with asexuality and occurs rapidly enough to be detected derived asexual lineages of P.antipodarum
79
What is an overview of the differences between drift based and selection based model?
Drift-based model - Sex can undo mutation accumulation and thus the associated costs (purge bad genomes)
Selection-based models - Sexual reproduction allows increased variability to combat changing selection pressures, e.g. parasites (spread good genomes)
80
What was the idea of the first gametes?
A prehistoric population of aquatic sexual reproducers, producing isogamous protogametes.
These isogamous protogamtes shed into the water and seek to fuse with another.
Naturally, there will be small amounts of variation in size/number of protogametes produced
81
What do protogametes need to do?
Fuse with other protogametes
Provision for the resulting zygote
82
What were the possibilities for the variation of protogametes?
An individual has finite resources, they can make numerous very small protogametes to be competitive for maximising the number of fusions, or they can make fewer large protogametes to produce fitter offspring
This results in disruptive selection
83
What are the outcomes for different isogametes with different sizes?
Large frequent - lots of resources but collisions very rare
Small frequent - collisions common but few resources
Middle frequent - collisions not common and few resources
Some small some large - lots of resources and common collisions
84
What was the final outcome of the disruption selection of protogametes?
Sperm where the protogametes that where selected for competitive for fusions
Eggs where the protogametes that selected for zygote provisioning
85
What is the evidence of sperm being competitive for fusions?
More sperm = more competitive for fusions.
Comparisons: Species at higher risk of experiencing sperm competition produce more sperm.
86
What was an experiment for competition leading to higher sperm?
Some mice, male could guarantee female saw no male.
Other group males couldnt guarentee female saw no other male
The results were that males that could guarentee with high likelihood that female saw no rival produced less sperm
87
What is the relationship between male crickets and spermatiform and sperm size?
Natural variation in the sperm length of male crickets
Within a male, sperm size is fairly consistent across spermatophores
Within a male, sperm number is fairly consistent across spermatophores
88
How did they investigate the sucess of spermatiform and sperm size on male cricket reproductive sucess?
1- Screen sperm number and length from spermatophore.
2- Mate two screened males with a female.
3- Identify who wins fertilisations
89
What were the results of male cricket reproductive sucess?
More sperm = more fertilisations
Smaller sperm = more fertilisations
90
What is an example of egg size impacting thick-bille murre sucess?
Larger eggs = fitter offspring
Experiment in thick-billed murre.
Eggs translocated between nests within a colony.
Larger eggs:
Fledged earlier
Wing feathers developed faster
Higher weight maintenance after fledging
91
What is an example of egg size impacting trout success?
Larger eggs:
Larger juveniles at hatching
Increased hatchling survival
Effects compounded when juvenile diet was limited (e.g. under stress).
92
Why is anisogamy evolutionarily stable?
Chicken egg volume = 50,000 microliters
Chicken sperm volume ~0.005 microlitres
Single sperm = 0.00001% volume investment of ova
But per ejaculate is 1,000,000,000 cells
93
What would happen if you doubled the size of chicken sperm?
Doubling sperm volume = insignificant increase - to 0.00002% of zygote investment
Would result in = halving of ejaculate size = significant loss of ~500 million sperm cells, reducing the likelihood of fertilisation success
94
What is anisogamy?
A form of sexual reproduction wherein males and females produce sex cells, or gametes, of different sizes
