Genes Evo & Dev L6 Notes

Question 1

How many base pairs are there?

Answer 1

3 billion

Question 2

What proportion of base pairs code for proteins?

Answer 2

At most 3%

Question 3

What proportion of base pairs are regulatory?

Answer 3

10%

Question 4

What proportion of base pairs are repetitive?

Answer 4

45%

Question 5

What proportion of base pairs are non-functional/junk?

Answer 5

85%

Question 6

What are transposons?

Answer 6

	Mobile genetic elements 
	Sequences DNA -> move in genome 
	Simplest ->transposons -> transposase
Enables removal & insertion of sequences from genome
	Do not require reverse transcriptase

Question 7

What are the functions of retrotransposons?

Answer 7

• Retrotransposons
 Produce RNA
Require reverse transcriptase -> reverse transcribe RNA
-> DNA. -> insert into target site

Question 8

Describe how movement of transposons is thought to have occur

Answer 8

• 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.

Question 9

Outline how new genes are formed

Answer 9

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

Question 10

Give an example illustrating formation of a new gene

Answer 10

 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

Question 11

Give an example of a structure thought to have arisen as a result of transposition?

Answer 11

 Mammalian placenta -> requires syncitins
>Genes -> once encoded -> envelope -> retrovirus
Repeatedly coopted -> mammals
>Evolution of placenta
>Control gene expression -> pregnancy
Evolution -> placenta -> viviparous Mabuya lizards

Question 12

Why is it thought the new structures can be formed as a result as a result of transposition.

Answer 12

Eg. Gravid Mabuya ->Gives birth -> Studied placental transcriptome
> Extract RNA -> tissue of interest
> Find genes expressed -> particular tissue / developmental stage
> Functional genes identified

Question 13

What does information does a transcriptome provide?

Answer 13

Function of a genome in time (eg. developmental stage) & place (eg. organs)

Question 14

What are LINE elements?

Answer 14

Long Interspersed Elements

Question 15

What is horizontal gene transfer?

Answer 15

The transfer of genetic material between organisms other than parent & offspring.

Question 16

What does horizontal gene transfer involve?

Answer 16

•	Horizontal gene transfer
-	Widespread -> prokaryotes 
-	Minor source -> genetic variation
mitochondrial DNA genes -> integrated -> nuclear DNA
-	Multicellular organisms 
Involves parasite/symbiote
-	Possibly leads -> adaptations

Question 17

Give an example if evidence of horizontal gene transfer.

Answer 17

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

Question 18

Give examples of horizontal gene transfer.

Answer 18

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.

Question 19

What did reconstruction of extinct genomes enable?

Answer 19

• 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.

Question 20

How is it thought insects are crustaceans

Answer 20

 DNA analysis -> 62 genes
 Hexapods -> within Pancrustacea
 Remipedes & Cephalocarids -> crustaceans -> sister group -> insects.
 Most purposes; crustacea -> (not incl. insects) still valid.

Question 21

Describe the spread of the Cabbage White butterfly.

Answer 21

• 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

Question 22

Outline the argument on the number of giraffe species.

Answer 22

• 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

Question 23

What are the 4 species of giraffe that are thought to exist?

Answer 23

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.

Question 24

Describe eDNA

Answer 24

• 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

Question 25

Describe differences in human genomes

Answer 25

- 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

Question 26

Give genetic evidence of natural selection in humans

Answer 26

1. -50 Tibetans -> 4000m -> 40% less oxygen -> 2750 yrs -40 Han Chinese EPAS1 gene -> controls production -> red blood cells ->87% -> Tibetans ->9% -> Han 2. Bajau people -> SE Asia -> Diving ability -> long periods Selection on -> PDE10A gene -> larger spleens -> reservoir blood cells ->BDKRB2 gene -> diving reflex

Question 27

Describe variation in skin colour

Answer 27

• 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