Genes Evo & Dev L6 Notes Flashcards
How many base pairs are there?
3 billion
What proportion of base pairs code for proteins?
At most 3%
What proportion of base pairs are regulatory?
10%
What proportion of base pairs are repetitive?
45%
What proportion of base pairs are non-functional/junk?
85%
What are transposons?
Mobile genetic elements Sequences DNA -> move in genome Simplest ->transposons -> transposase Enables removal & insertion of sequences from genome Do not require reverse transcriptase
What are the functions of retrotransposons?
• Retrotransposons
Produce RNA
Require reverse transcriptase -> reverse transcribe RNA
-> DNA. -> insert into target site
Describe how movement of transposons is thought to have occur
• Movement of transposons -> mutations
Tool -> Drosophila
Possibly involved -> cancers
Characters -> Prevention of transposition -> favoured
->Conflict -> host & transposition
2% -> new insertion -> L1 element -> occurred in gametes/zygote
Can be prevented by small interfering RNAs.
Outline how new genes are formed
1. Duplicate Non-coding sequence Long strings -> 3 amino acids 2. Change -> nucleotide bases Tagged as secretory 3. Translocation Moves sequence near promoter region Activates/ functionalised gene
Give an example illustrating formation of a new gene
Fish -> polar seas -> ‘Anti-freeze’ glycoproteins
Northern gaddids -> Arctic cod -> different glycoproteins to those -> Antarctic fish.
Adaptation
Protein doesn’t become functional -> last step -> gene assembly
Doesn’t require designer ->arising -> natural processes.
All parts incl. proteins -> synthesised -> translocation & duplication alone,
- Series of steps -> neutral/ slightly advantageous
Give an example of a structure thought to have arisen as a result of transposition?
Mammalian placenta -> requires syncitins
>Genes -> once encoded -> envelope -> retrovirus
Repeatedly coopted -> mammals
>Evolution of placenta
>Control gene expression -> pregnancy
Evolution -> placenta -> viviparous Mabuya lizards
Why is it thought the new structures can be formed as a result as a result of transposition.
Eg. Gravid Mabuya ->Gives birth -> Studied placental transcriptome
> Extract RNA -> tissue of interest
> Find genes expressed -> particular tissue / developmental stage
> Functional genes identified
What does information does a transcriptome provide?
Function of a genome in time (eg. developmental stage) & place (eg. organs)
What are LINE elements?
Long Interspersed Elements
What is horizontal gene transfer?
The transfer of genetic material between organisms other than parent & offspring.
What does horizontal gene transfer involve?
• Horizontal gene transfer - Widespread -> prokaryotes - Minor source -> genetic variation mitochondrial DNA genes -> integrated -> nuclear DNA - Multicellular organisms Involves parasite/symbiote - Possibly leads -> adaptations
Give an example if evidence of horizontal gene transfer.
Eg. – Aprrox. 25% cow genome -> composed -> BovB elements -> reptiles
- Long interspersed element -> 3.2 kb -> repetitive piece DNA
- Inert element -> Comparison of animal genomes
BovB closely related to element -> sheep
>Closely related -> elements -> snakes
»_space;Closer to snakes than marsupials
- 25% cows’ genomes -> from snakes.
- Explanation -> ticks.
Transfer gene from snakes -> cows -> horizontal gene transfer
Give examples of horizontal gene transfer.
Spodoptera moth -> immune barrier -> acquired through virus -> lives in parasitoid wasp.
Carotenoids -> red colouration
–> Acquired -> animals -> food.
Pea aphids -> normally green -> red form in some clones
–>Linked -> predation avoidance=
Genes -> carotenoid biosynthesis
–>Acquired -> fungus.
What did reconstruction of extinct genomes enable?
- By comparison -> genomes -> many diff taxa
->possible identification ->25 groups genes -> required to be an animal.
New genes -> appeared -> animal origin
>Homeobox developmental genes, signalling
pathways, cell adhesion molecules, receptors, etc.
How is it thought insects are crustaceans
DNA analysis -> 62 genes
Hexapods -> within Pancrustacea
Remipedes & Cephalocarids -> crustaceans -> sister group -> insects.
Most purposes; crustacea -> (not incl. insects) still valid.
Describe the spread of the Cabbage White butterfly.
• Spread of Cabbage White -> butterfly
- Rough but unclear idea of spread through history
- Asked world -> catch & send butterflies
3000 insects -> 293 localities
- Nuclear & mitochondrial DNA genotyping
European & Asian diverge -> 1200yrs
->Carried along silk road -> Coinciding -> widespread adoption -> brassica Crops
- Last 160 yrs -> trade -> dispersed butterfly
Outline the argument on the number of giraffe species.
- Traditionally -> several sub-species -> pattern morphology
- 7 nuclear genes & mitochondrial DNA sequenced
4 groups -> diverge 1-2million years ago
Argued -> 4 species -> no gene flow
->No evidence isolated
Cannot conclude species based on DNA only. -> no minimal
change in base pairs - Populations geographically isolated -> can’t use “biological species definition”
Members of different species, when present in same area, do not mate with each other, or do mate but cannot produce fertile offspring.
Found can hybridize in zoos -> but still can’t apply
->Other isolating barriers in nature -> different breeding times/genetically
based aversion -> could keep separated anyway. - Therefore must use genetic divergence -> as don’t encounter
Genetic divergence -> measures amount of sequence difference -> DNA
What are the 4 species of giraffe that are thought to exist?
i) Southern giraffe (Giaffa giraffa)
ii) Masai giraffe (G. tippelskirchi)
iii) Reticulated giraffe (G. reticulata)
iv) Northern giraffe (G. Camelopardalis) -> incl. Nubian giraffe (G. c. camelopardis) as distinct related species.
Describe eDNA
• eDNA -> Environmental DNA
Extraction DNA sequences -> no organism
>Soil, water, air
Non-invasive -> conservation & ecology
Molecules behave differently -> different situations
Requires careful amplification & bioinformatic identification
Effective -> aquatic systems.
Eg. Loch Ness Monster
Describe differences in human genomes
- Avrg. Difference -> 0.1% -> eachother
- Human genetic variation -> severely underestimated -> Only European DNA in reference
- 910 African descent -> compared
10% more DNA -> reference genome
Some variants -> protein-encoding genes
Functional significance unclear
Give genetic evidence of natural selection in humans
- -50 Tibetans -> 4000m -> 40% less oxygen -> 2750 yrs
-40 Han Chinese
EPAS1 gene -> controls production -> red blood cells
->87% -> Tibetans
->9% -> Han - Bajau people -> SE Asia -> Diving ability -> long periods
Selection on -> PDE10A gene -> larger spleens -> reservoir blood cells
->BDKRB2 gene -> diving reflex
Describe variation in skin colour
• Skin colour
Darker skin -> protects -> UV
Light skin -> enables biosynthesis -> Vitamin D -> sun is weaker.
Skin colouration -> 15 genes
Substantial variation in Africa
Indigenous peoples -> South Africa
>Large colour variation
>Large variation -> Underlying genes -> incl. genes coding -> lighter skin
Complex underlying local evolutionary pressures
Doesn’t correlate with any other trait
