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HELENP EE Evolution and Natural Selection > EE Lecture 10: Genome Evolution > Flashcards

EE Lecture 10: Genome Evolution Flashcards

1
Q

what is the C value paradox

A

lower end of organisms gene numbers correlates with complexity

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2
Q

what is the c value

A

the total amount of DNA in the haploid genome

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3
Q

what explains C-value paradox

A

non coeding DNA

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4
Q

how does amount of non coding DNA change

A 
transposition
replication slippage
unequal crossing over
polyploidy
chomosomal duplicationq
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5
Q

what are the processes behind changes in genome size in genic regionsq

A

gene duplication and loss

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6
Q

what are the processes behind changes in genome size in nongenic regions

A

selfish DNA

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7
Q

what are multigene families

A

groups of genes from same organism that encode protein with simillar sequences either over their full length or limited to a specific domain
can be tandemly repeated or dispersed in gene clusters

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8
Q

give an example of a gene family

A

globin gene

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9
Q

what does the multigene globin family allow for

A

the production of different types of Hb; embryonic, fetal, adult

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10
Q

how did Globins arise

A

from a single origin 800MYA

then series of gene duplications due to unequal cross over, followed by mutation and divergence in function

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11
Q

how did rDNA evolve

A

by gene duplication but also concerted evoln to produce lots of ribosomes with the same function

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12
Q

what is concerted evoln

A

explains the observation that paralogs are more closely related than orthologs

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13
Q

what are paralogs

A

genes related by duplication in a genome

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14
Q

what is concerted evoln caused by

A

gene conversion

the DNA sequence of one gene is replaced by the DNA sequence from another

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15
Q

what are homologs

A

2 genes related by common ancestry

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16
Q

what are orthologs

A

genes in different species that evolved from common ancestral gene by speciation - normally retain same function

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17
Q

what explains the observation that paralogs are more closely ewlated than orthologs

A

concerted evoln

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18
Q

what are 2 genes related by common ancestry called

A

homologs

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19
Q

what are genes in different species that have evolved from common ancestral gene by speciation called

A

orthologs

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20
Q

what are 2 genes that have evolved by duplication called

A

paralogs

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21
Q

which retain same function, orthologs or paralogs

A

orthologs

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22
Q

what evoln is caused by gene conversion

A

concerted evoln

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23
Q

how common is gene duplication

A

relatively common

0.01/gene/MYrs

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24
Q

what is the outcome of most gene duplicates

A

theyre lost or silenced, few can survive and diverge to new functions or maintain same function (dosage or regulation)

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25
Q

what is normal transmission rate of meiosis

A

d = 0.5

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26
Q

why are selfish genetic elements selfish

A

because they bias their transmission to become rapidly fixed in popns

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27
Q

how is inheritance bias caused

A

gonotaxis
interference
overreplication

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28
Q

under what circumstances would SGEs (selfish genetic elements) not become rapidly fixed in popns

A

if opposed by evolnary forces

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29
Q

what are examples of SGEs

A

chromosomes
genes
haplotypes
cytoplasmic factors like Wolbachia bacteria

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30
Q

what is Wolbachia bacteria an example of

A

a selfish genetic element

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31
Q

what is gonotaxis

A

orientating towards the germ line

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32
Q

what is interference

A

aggressive competition to get in germline

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33
Q

over-replication

A

replicating more than once during the cell cycle

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34
Q

give an example of inheritance bias caused by gonotaxis

A

Gonotaxis of B chromosomes

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35
Q

in what percentage of plants does gonotaxis of B chromosomes occur

A

10-15%plant and animal species and fungi

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36
Q

what are B chromosomes

A

genetic element that employs gonotaxis
found in the nucleus and rarely coding (unlike A chroms)
they avoid undergoing proper cell division and and seek to enter germline in as large numbers as possible

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37
Q

are B chroms essential, where do they originate from

A

no, supernumary - not all individuals possess them

they originate from A set (sex chroms)

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38
Q

how many B chroms do chives have in mitotic metaphase

A

3

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39
Q

how many B chroms do Myrmeleotettix maculatus GRASSHOPPER have in mitotic metaphase

A

2

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40
Q

what percentage of individuals in Britain have B chroms

A

50%

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41
Q

what is transmission rate of B chroms - down which lineage?

A

inherited through females

d=0.8

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42
Q

discuss fitness efrfects in grasshoppers

A

2B and above = very unfit
slows development from diapause to adult
causes sperm dysfunction

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43
Q

what can having 2Bs and above cause

A

slow development from diapause to adult

sperm dysfunction

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44
Q

why are B chroms seen as genomic parasites

A

theyre detrimental to their carriers by reducing fitness

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45
Q

what does the parasitic model of B chrom evoln show

A

stable frequencies of B chrom gonotaxis maintained due to an eqbm between B chrom accumulation and deleterious effects of B chrom on its carriers

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46
Q

how is inheritance bias caused by over-replication

A

increased rate transmission due to being copied more than once during cell cycle

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47
Q

where does inheritance bias caused by over replication occur

A

in germ line and somatic cell

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48
Q

how often do transposable elements transpose

A

NOT every cell generation

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49
Q

name some types of transposable elements

A

DNA transposons
RNA elements :
NON-LTR retrotransposons -LINEs&SINEs
LTR retroelements:endogenous retroviruses-in humans

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50
Q

what are RNA elements divided into

A

NON-LTR retrotransposons

LOT retroelements inc.LTR retrotransposons (not in humans) and Endogenous Retroviruses (in humans)

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51
Q

how much of human genome % is made of DNA transposons

A

3%

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52
Q

how much of humans DNA is made of selfish genetic elements

A

46%`

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53
Q

what constitute Non-LTR retrotransposons

A

LINEs

SINEs

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54
Q

what are LINEs/SINEs

A

Long Interspersed Nuclear Elements

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55
Q

in what form in DNA do transposable elements generally exist

A

epigenetically silenced form
eg. through DNA methylation
histone modification
RNA directed DNA methylation

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56
Q

name some ways of epigenetically silencing

A

DNA methylation
histone modification
RNA directed DNA methylation

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57
Q

what are DNA transposons

A

transposable elements:

DNA sequences that are able to move from one location to another via copy paste mechanisms

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58
Q

how long are DNA transposon sequences

A

1-19kb long

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59
Q

what mechanism do DNA transposons use

A

cut and paste mechanism

60
Q

how many gene products do DNA transposons produce

A

a single transposase product

61
Q

outline the mechanism for DNA transposons

A
  1. transposase binds to donor DNA
  2. formation of a paired end complex with a monomer of Tn10 transposase bound to each end
  3. Transposase cuts donor and target DNA
  4. Dbl stranded cleavage of donor DNA at both ends of transposase DNA complex (DNA remains supercoiled)
  5. Staggered cuts in target DNA
  6. Each strand of donor DNA is covalently joined to target DNA
  7. Staggered cuts are filled in by DNAP1, this explains the target site duplication
62
Q

what can transposable element mobilization promote

A

gene inactivation
gene expression
induce illegitimate recombination

63
Q

how can TEs inactivate/alter the expression of genes

A

insertion with introns, exons or regulatory genes

64
Q

give examples of Non-LTR retrotransposons

A

LINEs

SINEs

65
Q

give examples of LTR retroelements

A 
LTR Retrotransposons -not in humans
Endogenous Retroviruses (in humans)
66
Q

which LTR retroelemenrs are in humans

A

endogenous retroviruses

67
Q

which LTR retroelements are not in humans

A

LTR retrotransposons

68
Q

what forms when a DNA transposase binds to donor DNA

A

formation of a “paired end” complex with a monomer of Tn10 transposase bound to each end

69
Q

what is a “paired end complex”

A

forms when DNA transposase binds to donor DNA, with a monomer of Tn10 transposase bound to each end

70
Q

what is Tn10 involved in

A

paired end complex - one is bound to each end

71
Q

how are staggered cuts in supercoiled DNA that has been bound to transposase filled

A

with DNAP1

72
Q

what are retrotransposons

A

transposons via RNA intermediates

genetic elements that can amplify themselves in the genome

73
Q

where are retrotransposons particularly abundant

A

in plants - principle component of nuclear DNA

in maize, 49-78% genome made up of retrotransposons

74
Q

how much of genome in maize is made up of retrotransposons

75
Q

how much of human genome is made up of retrotransposons

76
Q

how do retrotransposons induce mutations

A

by inserting near/within genes, copying themselves to RNA, then back to DNA that may integrate back into the genome

77
Q

what do retrotransposons encode to enable encoding of DNA

A

reverse transcriptase

78
Q

what subdivisions of retrotransposons are there

A

LTR and Non-LTR

79
Q

what does LTR stand for

what is it

A

Long Terminal Repeats

it is a retrotransposon

80
Q

what are the structural domains present in retrotransposons

A 
gag - core particle components
en-endonuclease
rt-reverse transcriptase
LTR-Long Terminal Repeat
int-integrase
env-envelope gylcoprotein
81
Q

what is gag

A

a structural domain in retrotransposons that encodes core particle components

82
Q

what is int

A

structural domain in retrotransposons that encodes integrase

83
Q

what subdivisions of LTR retroelements (of retrotransposons) are there

A

Ty1-copia
gypsy
retrovirus

84
Q

what is Ty1-copia

A

a non LTR retrotransposon retrotransposable element

85
Q

what is gypsy group

A

LTR retrotransposon

86
Q

what is retrovirus

A

an LTR retrotransposon

87
Q

what structural domains are present in non-LTR retrotransposons

A

gag - en - rt

88
Q

what structural domains are present in Ty1-copia LTR retrotransposons

A

LTR - gag - int - rt - LTR

89
Q

what structural domains are present in gypsy LTR retrotransposons

A

LTR - gag - rt - int - LTR

90
Q

what structural domains are present in retroviruses LTR retroelements

A

LTR - gag - rt - int - env - LTR

91
Q

what is the following the structure of

LTR - gag - int - rt - LTR

A

Ty1-copia LTR Retrotransposon

92
Q

what is the following the structure of

gag - int - rt

A

Non - LTR retrotransposons eg. LINEs

93
Q

what is the following the structure of

LTR - gag - int -rt - LTR

A

gypsy group retrotransposon

94
Q

what is the following the structure of

LTR - gag - rt - int - env - LTR

A

retrovirus

95
Q

what are LTR Retroelements

A

RNA elements which use reverse transcriptase to make cDNA

96
Q

how many bp long are LTR retroelements

A

~100bp to >5kb long

97
Q

what are the effects of transposable elements on the host

A

few are beneficial besides RAG1 and RAG2 genes in immune system

98
Q

outline some beneficial effects of transposable elements on the host

A

RAG1 and RAG2 immune system

99
Q

outline some neutral effects of transposable elements on the host

A

variegation in morning glory

100
Q

outline some deleterious effects of transposable elements on the host

A

P elements in Drosophila cause chromosome breaks

0.1-0.2% human disease causing mutations are due to insertion of transposable elements

101
Q

what is RAG1 and RAG2

A

transposable elements that are beneficial to immune system

102
Q

what are P elements

A

found in Drosophila and cause chromosome breakage

103
Q

what is the effect of P elements

A

cause chromosome breaks in drosophila

104
Q

what are 0.1-0.2% of human disease causing mutations due to

A

insertion of transposable elements

105
Q

discuss the fate of tranposable elements in humans

A

63 families of extinct DNA transposons (no movement in 50MYRS)
20 families of endogenous retrovirus all invaded in the last 100MYR and almost all inactive

106
Q

how many active transposable elements are in a single individual`

107
Q

how many families of extinct DNA transposons are there in humans

108
Q

how many families of endogenous retrovius have invaded humans in last 100MYRs, what has happened to them

A

20 families of endogenous retroviruses have invaded humans in last 100MYRS, all now inative

109
Q

give some examples of adaptive traits

A

melanic form of peppered moth

beak size and shape of Darwin’s finches

110
Q

what is parallel evoln

A

the indep evoln of similar traits, starting from a similar ancestral codon

111
Q

give an example of widespread parallel evoln

A

in sticklebacks - repeateed fixation of Ectodysplasin alleles

112
Q

what allele is involved in stickleback parallel evoln

A

Ectodysplasin alleles - secreted signalling molecule known to affect scale growth

113
Q

what is Ectodysplasin

A

allele involved in scale growth - affects sticklebacks in parallel evoln

114
Q

what two types of stickleback forms are there

A

marine forms: heavily armored

freshwater forms: lightly armored

115
Q

how are freshwater forms of sticklebacks armored

A

lightly armored freshwater forms

116
Q

how are marine forms of sticklebacks armored

A

heavily armored marine forms

117
Q

how many aa changes between the two alleles for heavy/light armor of sticklebacks

A

marine - heavy Armoured
freshwater - lightly armored
4 aa changes between the 2 alleles

118
Q

how has parallel evoln of stickleback low plated phenotypes @ freshater locations around the world occured

A

by repeated selection of Ectodysplasin alleles derived from an ancestral low plated haplotype that first appeared >2MYA

119
Q

what methods were used to identify the major chrom locus controlling armor plate patterns in sticklebacks

A

positional cloning methods

  • mapping
  • sequencing
  • transgenic studies
120
Q

how did EDA trait evolve

A

EDA low-plated allele evolved once and then spread globally

121
Q

what types of sequencing technologies exist

A

sanger
454
illumina

122
Q

which sequencing has a readlength of 700BP

A

pyrosequencing 454

123
Q 
PYROSEQUENCING 454
Read length
Accuracy
Reads and time per run
\+ves
-ves
A

-700BP
-99.9%
1 MILL, 24HRS
long read size, fast
expensive, homopolymer errors

124
Q 
SEQUENCING MY SYNTHESIS - ILLUMINA
Read length
Accuracy
Reads and time per run
\+ves
-ves
A 
50-300BP
98%
3BILL, 1-10DAYS
Potential high sequence yield
v. expensive, require high [DNA]
125
Q 
CHAIN TERMINATION SANGER
Read length
Accuracy
Reads and time per run
\+ves
-ves
A 
400-900BP
99.9%
NA
20min-3HRS
long individual reads
v useful
more expensive/impractical for larger projects
requires time consuming plasmid cloning
126
Q

what are pros&cons of illumina sequencing

A

potential high sequence yield as 3BILL reads in 1-10days

BUT v. expensive and require high [DNA]

127
Q

what are pros and cons of 454 Sequencing

A

99.9% accurate, can read 1 mill in 24hrs

long read size but expensive and homopolymer errors

128
Q

which type of sequencing can lead to homopolymer errors

129
Q

which type of sequencing requires the time consuming plasmid cloning

130
Q

what are the genes behind beak shape and sinze in finchers

A

BMP4 bone growing protein: wider heavier

and Calmodulin:longer and thinner

131
Q

what is the BMP4 gene involved in

A

bone growing protein; allowing wider and heavier beak size in finches

132
Q

what is Calmodulin gene involved in

A

longer and thinner beak size in finches

133
Q

what lovus is involved in th e pepered moth

A

Carbonaria locus

134
Q

what makes us human

A

bipedal
language
hypoid bone: horseshoe shaped bone -midline neck and chin

135
Q

what is FOXP2 gene

A

language gene forkhead box protein

136
Q

what do FOXP2 mutations cause

A

speech and language disorder

137
Q

what happened when FOXp2 mutation was induced in mice

A

less vocalisation, less exploratory, increased dendrite growth and synaptic plasticity in basal ganglia
better learning ability

138
Q

what happened when FOXp2 mutation was induced in songbirds

A

inaccurate song

139
Q

which gene is involved in language in humans

A

FOXP2 forkhead box protein gene

140
Q

who do humans share FOXP2 gene with

A

NEanderthals

141
Q

who do humans share hyoid bone with

A

Neanderthals

142
Q

what positively selected genes exist in humans

A 
FOXP2
Hyoid bone genes
THADA
genes associated with cognitive ability -schizophrenia, autism
RUNX2
143
Q

what is THADA gene associated with

A

diabetes

energy metabolism

144
Q

what is RUNX2 associated with

A

delayed closure of cranial sutures- frontal bone protrusion

145
Q

which positively selected gene is associated diabetes and energy metabolism

146
Q

what have been the revelations of gene sequencing

A

1st rev: PCR and DNA sequencing

2nd: next gene whole genome, pop genetics, epigenetics
3rd: make sense of emerging data

HELENP EE Evolution and Natural Selection (14 decks)

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