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The Archaeology of the Genome
• Haemophilus influenzae, a small Gram-negative
bacterium. In July 1995 when the entire 1830137
DNA base pairs of its genome was published－the
first of a free-living organism. A new era in
biological science had begun.
Yeast: Saccharomyces cerevisiae
Archaea: Methanococcus jannaschii
• The 3.3 billion bases that make up the genome of
Homo sapiens.
• Gene sequences are now recognized as an invaluable
document of the history of life on earth.
• 1970 when Carl Woese and colleagues, using the
highly conserve 16S ribosomal RNA (rRNA) gene,
showed that there were in fact two very different
groups of prokaryotes-the Eubacteria like
Haemophilus influenzae, now simply referred to as
the Bacteria, and the Archaebacteria whose
members include Methanococcus jannaschii, now
known as the Archaea.
• Lives on deep-sea hydrothermal chimneys, at
pressures of 200 atmospheres and temperatures of
85℃.
• In 1990 the Centers for Disease Control
(CDC) in Atlanta received reports of AIDS
in a young woman in Florida whose only
risk of HIV infection was seemingly that
she had previously been treated by a dentist
suffering from AIDS.
The HIV genome
had therefore stored
evolutionary
information, in the
form of the
mutations which
had accumulated.
• The commonly held view was that humans
were phylogenetically distinct from the
great apes, being placed in different
taxonomic families, and that this split
occurred at least 15 million years ago.
The split between apes and Old World
monkeys some 30 nillion years ago.
Fig. 34.38
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Two alternative hypotheses have been proposed
• In the multiregional
hypothesis, fully modern
humans evolved in parallel
from the local populations
of H. erectus.
– In this view, the great
genetic similarity of all
modern people is the
product of occasional
interbreeding between
neighboring populations.
Fig. 34.41a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The other hypothesis, the “Out of Africa” or
replacement hypothesis, argues that all Homo
sapiens throughout the world evolved from a
second major migration out
of Africa that occurred
about 100,000 years ago.
– This migration completely
replaced all the regional
populations of Homo
derived from the first
hominid migrations.
Fig. 34.41b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Using changes in mitochondrial DNA (mtDNA)
among human populations as a molecular clock,
research have reported a time of genetic
divergence of about 100,000 years ago.
• The mtDNA extracted from Neanderthal bones
fall completely outside the range of mtDNA for
modern Europeans.
• By comparing the Y chromosomes of males
from various geographic regions, researchers
were able to infer divergence from a common
African ancestor less than 100,000 years ago.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Nucleotide (DNA) sequences have now
replaces proteins as the main source of data,
particularly since the invention of the
polymerase chain reaction (PCR) in the mid1980s
• It is now apparent that DNA sequences not
only contain a record of their phylogenetic
relationship and times of divergence, but also
the signatures of what evolutionary processes
have shaped their history and even the size of
past populations.
Trees
• All of life is related by common ancestry.
• Interpreting them eventually becomes
second nature.
Trees
• All of life is related by common ancestry.
• Interpreting them eventually becomes
second nature.
請別依老賣老
Since we come from a
common 老祖宗
•Endeavour to reconstruct the characters of each
hypothetical ancestor.
If a node has a degree greater than three then
that node is a polytomy
Typically
polytomies
are treated
as ‘soft’
That multiple lineages would diverge at exactly the
same time; however, if lineages diverge rapidly in time
relative to the rate of character evolution.
This format makes it easy to describe a tree in
the body of some text without having to draw it.
The most basic tree is the cladogram
which simply was shows relative
recency of common ancestry.
In the biomathematical literature
cladograms are often called ‘n-tree’.
Additive trees sometimes also called
‘dendrograms’.
Ultrametric (Dendrogram) In which
the tips of the trees are all equidistant
from the root of the tree.
1
24
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
3 1
24
3 1
34
2
Fig. 25.15
A rooted tree has a node identified as
the root from which ultimately all
other nodes descend.
The node closest to the root is the
ancestor of the node.
Unrooted trees lack a root, and hence
do not specify evolutionary
relationships in quite the same way.
Herpes-I-alpha
Herpes-II-alpha
HHV-2
HHV-1
(WNBE71)
(NP_044482)
HHV-1
(TVBE17)
0.2
BoHV-1
100
(S61242)
0.2
GaHV-2
GaHV-1
(NP_057771)
(F48552)
100
HHV-2
(B43674)
93
(WZBEN3)
(NP_073306)
BoHV-1
(S35782)
100
SuHV-1
MeHV-1
100
79
MeHV-1
SuHV-1
(JQ2350)
(D10451)
100
100
EHV-4
HHV-3
(WZBE47)
(T42592)
EHV-1
(WZBEE2)
HHV-3
(TVBE66)
EHV-4
(NP_045286)
EHV-1
(NP_041708)
Pox-I
Pox-II
Pox-Ib
●
Chordopoxvirinae
(Copenhagen)
TVVZ9Z
VACV (Copenhagen) F42507
TVVZVW (WR)
U32589
Pox-Ia
VACV (WR)
(Ankara)
T37440
T30787
VACV (Ankara)
(India)
(India)
A36855
E36840
VARV
AAA60910 (Banbladesh)
T28472
VARV
T28600
H72154
VARV (Garcia)
NP_039189
FWPV MYXV NP_051734
MOCV T30619
NP_039175
FWPV
NP_039074
AF063866-1
0.5
Entomopoxvirinae
TVVZB2 (Copenhagen) VACV
(Ankara)
T37448
VACV
TVVZBW (WR)
VACV
AAC99565
ECTV
MSEV
Chordopoxvirinae
AF063866-2
0.5
0.5
5.0Entomopoxvirinae
Reconstruct the history
Given a tree, we can distinguish between ancestral
(‘primitive’) and derived character states.
These ancestors are hypothetical, but some methods of
phylogenetic reconstruction allow us to infer what they
(or their sequence) may have looked like.
sister taxa or anscestor
何者較古老
A
A
A
B
A
B
C
A
Species disappear in a different sense when their
lineage is transformed over evolutionary time or
when they divide into two or more separate
lineage (called pseudoextinction).
Tree and Distance
The two largest distances are equal
Paraphyletic groupings are based on shared
primitive characters (plesiomorphies) and hence
typically exclude one or more taxa that have
autapomorphies.
Polyphyletic groups are typically assemblages of
taxa that have been erroneously grouped on the
basis of convergent characters, such as ‘vultures’.
Fig. 34.20
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Gene tree and species tree
基因的分化與物種種化一致 ?????
This is the point at which the two gene lineages coalesce
and the time at which this occurs is the coalescence time.
Alleles 1 and 2 are both found in the same species, they
are not each other’s closest relative.
Hypothetical example illustrates the problem of lineage
sorting. If the alleles present in a lineage prior to that lineage
speciation are not monophyletic then the distribution and
relationships of these alleles need not accurately reflect the
phylogeny of the organisms themselves.
基
因
的
分
離
與
支
系
的
分
離
不
一
致
Gene tree and species tree
基因的分化與物種種化一致 好玩
Nature 2003, 421:31
Nature 2003, 421:63
• Independent origin of PK gene in large
double-strand DNA viruses: horizontal
transfer in situ or gene duplication in
vivo
Wen-Bin Yeh and Hong-Hwa Chen
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(TVBE17)
0.2
BoHV-1
100
(S61242)
0.2
GaHV-2
GaHV-1
(NP_057771)
(F48552)
100
HHV-2
(B43674)
93
(WZBEN3)
(NP_073306)
BoHV-1
(S35782)
100
SuHV-1
MeHV-1
100
79
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SuHV-1
(JQ2350)
(D10451)
100
100
EHV-4
HHV-3
(WZBE47)
(T42592)
EHV-1
(WZBEE2)
HHV-3
(TVBE66)
EHV-4
(NP_045286)
EHV-1
(NP_041708)
Pox-I
Pox-II
Pox-Ib
●
TVVZB2 (Copenhagen) VACV
(Ankara)
T37448
VACV
TVVZBW (WR)
VACV
AAC99565
ECTV
(Copenhagen)
TVVZ9Z
VACV (Copenhagen) F42507
TVVZVW (WR)
U32589
VACV (WR)
(Ankara)
(Ankara)
T37440
T30787
VACV
(India)
A36855
E36840
VARV (India)
AAA60910 (Banbladesh)
T28472
VARV
T28600
H72154
VARV (Garcia)
NP_039189
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MOCV T30619
NP_039175
FWPV
NP_039074
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AF063866-1
0.5
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MSEV
Chordopoxvirinae
AF063866-2
0.5
0.5
5.0Entomopoxvirinae
Consensus tree
Compare trees derived from different
sequences, or from the same sequence using
different methods.
Actual evolutionary history may not be
particularly tree-like.
Mitochondria and chloroplasts
• Non-coding DNA is rare in mitochondria and
chloroplasts.
• Mitochondria originated more than a billion years
ago when a free-living bacterium, the closest
living relatives of which are the α-proteobacteria,
entered a eukaryotic cell.
• Bacterial endosymbiosis is also thought to be the
origin of chloroplasts, with the cyanobacteria
(blue-gree algae) as the most likely ancestors.
• Mitochondrial genome (mtDNA) sizes range from
only 6kb (kilobases) up to more than 2000kb, with
the human version being some 16kb in length. In
animals and plants, mitochondria are maternally
inherited through the egg cytoplasm.
• mtDNA does not appear to undergo recombination
and in mammals evolves about tenfold faster than
nuclear DNA, make it an extremely important
study tool in molecular population genetics and
systematics.
• In many plant and fungal mtDNAs, self-splicing
introns.
• The chloroplast genome (cpDNA) is ranging in size
from 120 to 220kb.
• Two inverted repeat (IR) regions which separate a
large single copy (LSC) region and a small single
copy (SSC) region.
• Sometimes because genes have migrated to the
nuclear genome and been lost from the chloroplast
genome.
• Consists of about 1000 protein-coding genes, about
30 tRNA genes and four rRNA genes.
• Plant chloroplast genes evolve some four- to fivefold
more slowly than those the nucleus, but about
threefold faster than plant mtDNA genes.
•Multigene families are located in a specific region of a single
chromosome and can be repeated many times, whilst others are
dispersed throughout the genome.
• Some have acquired mutations, such as those that
block the initiation of transcription, prevent correct
RNA splicing or introduce premature stop codons,
which inactivate them. These dead genes are called
pseudogenes.
• These processed pseudogenes have probably been
produced by the reverse transcription of the mature
mRNA transcript of a gene (which will itself lack
introns and promoter sequences.
• Pseudogenes are sometimes found on a different
chromosome from their functional ancestor, it is
clear that they can be transmitted throughout the
genome.
 globin family
A
A
B A
B
B
B
A
• This may act as a ‘hot-spot’ for gene conversion
because the DNA here forms a structure that increases
the rate of recombination.
• In bacteria recombination can also occur between
genes from different species. This interspecific
recombination (or horizontal gene transfer).
• The large-scale exchange of genes between bacterial
species also means that the evolutionary relationships
between them cannot always be represented as simple
bifurcating trees, and are better described by an
interconnecting network.
Genome organization and evolution
• The vast majority of DNA in the genomes of
Bacteria and Archaea produces protein (88% in
the case of E. coli), yet 97% of the vertebrate
genome is composed of non-coding DNA and may
therefore have no function.
• Most of the eukaryote genome is made up of DNA
sequences that are repeated very many times and
many genes are arranged into multigene families.
One of the first
indications that
genomes are highly
flexible entities was
the finding that their
sizes can very greatly
between species. The
amount of DNA per
haploid genome,
called the C-value.
• Only a twofold variation in genome size
among mammalian species (the largest
known genome is found in the aardvark, the
smallest in a Muntjak deer), there is tenfold
variation within anuran amphibians (frogs
and toads), at least a hundredfold variation
between insects, and an enormous 350-fold
variation among bony fish.
• Why are genomes so large if most DNA is
redundant?
• The number of
genes found in
different species
also varies
considerably.
• These differences
in gene number
cannot explain the
huge variation in Cvalues.
The evolution of multigene families
• Gene number can change between species is through
gene duplication.
• Unequal crossing-over.
• Can take place is through polyploidy. Polyploidy is
much more common in plants. Occurred fairly
regularly in amphibians like the toad Xenopus laevis.
Other species in the genus Xenopus verying from 20
to 108.
• Gene duplication can occur is through transposition.
The transposable elements, which are a major
component of eukaryotic genomes.
Polyploidy may also be important in speciation.
The new copy is automatically redundant.
• Becoming a pseudogene, or even being deleted from
the genome.
• With a slightly altered function.
• With new functions can arise.
Crystallins, proteins that play a structure role in the
eye lenses of animals.
ε-crystallin, found in the eye lenses of some birds
and crocodiles, is also the enzyme lactate
dehydrogenase (LDH).
The protein’s original function was as an enzyme
but it was then recruited into a new structural role
through changes.
• In vertebrates are those in the Hox family. For invertebrates,
like Drosophila.
• The homeotic gene complex (HOM).
• Mutations in the HOM/Hox genes can drastically affect the
organisation of body parts.
• The antennapedia mutation in Drosophila causes leg-like
structures to grow in place of the antennae.
• In some of the HOM clusters, genes at the 3’ end control
development of the anterior body part of the embryo, while
those positioned at the 5’ end control the posterior sections.
• Conservation of genes in vertebrates and invertebrates.
• Mutations in the eyeless gene of Drosophila and the
homologous Pax6 gene of humans both affect the pattern of
eye development.
• In the mouse, each of its four clusters is located on
a different chromosome and extends for over
100kb.
• There are two clusters of HOM gene in D.
melanogaster, Bithorax and Antennapedia, which
are found on the same chromosome.
• Amphioxus has a single cluster of at least 10 Hox
gene (spanning 270 kb), each of which is
homologous to a different Hox gene in vertebrates,
so that the origin of the vertebrates coincided with
s series of gene duplications.
• The vertebrate Hox genes, the family members are also
dispersed over number of chromosomes. Other
multigene families however are repeated side by side
many times, so that they contain multiple copies of
genes with the same function. These are known as
tandem arrays.
• Because the host cell required large amounts of the
protein they produce.
• The rDNA array which codes for ribosomal RNA
(rRNA), part of the ribosome.
• Three types of rRNA: 18S, also known as the small
subunit (~1800 bp), 28S, the large subunit (＞4000 bp),
and 5.8S rRNA (~160 bp).
• Three types of rRNA: 18S, also known as the small
subunit (~1800 bp), 28S, the large subunit (＞4000 bp),
and 5.8S rRNA (~160 bp).
• In bacteria, the equivalent rRNA types are 16S, 23S
and 5S.
• An external transcribed spacer (ETS) and two internal
transcribed spacers (ITS-1 and ITS-2).
• From a single copy in the protist Tetrahymena to
• 19300 copies in the lizard Amphiuma means.
• About 200 tandemly repeated copies are found
on the X and Y chromosomes of D.
melanogaster,
• while in humans there are approximately 300
copies on five chromosomes.
• rDNA sequences have been used frequently in
molecular systematics because they include both
highly conserved (18S) and highly variable
sequences (NTS), and so can reconstruct the
phylogenetic relationships between both distant
and very closely related species.
• Unequal crossing-over and gene conversion, which
transfer DNA sequences between genes so that they
evolve together.
• Concerted evolution and is one of the most
important acting on multigene families because it
means that mutations can spread to all members, even
if they reside on different chromosomes.
• It becomes difficult to discern which genes are really
homologous, so that orthologous and paralogous gene
can be mixed.
• They are often composed of ‘mosaics’ of sequences,
each with a different phylogenetic history, rather than
strictly homologous gene.
Noncoding repetitive DNA sequence
• Other types of repetitive DNA, do not encode
products used by the cell.
• Does not mean they are without interest: by some
of these sequences spread solely for their own
benefit, a tendency which has earned them the
nickname of selfish DNA.
• ‘ultra-selfish’ because they can interfere with the
function of other gene to increase their own copy
number.
• Species-specific differences in the type and amount
of non-coding repetitive DNA is a major reason
why genome sizes differ between species.
Tandemly repeated DNA
• Short sequence motifs tandemly repeated many
hundreds or thousands of times; termed satellite DNA,
is located mainly in regions of heterochromatin and
consists of motifs from 2 bp up to 40 kb in length.
• The α-satellite of primates is based on a 171 bp
sequence; for hundreds of kilobases.
• For example, 60% of the genome of Drosophila
nasutoides is made up to satellite DNA. Although it is
usually assumed to be ‘junk DNA’, it is possible that
satellite DNA is involved in the structure and function
of centromeres.
• Minisatellites and microsatellites.
• Although less frequently than satellite
DNA. These short repetitive motifs are
thought to be produced by
mutation
unequal crossing-over
DNA slippage.
Minisatellites, or VNTR loci (‘variable
number of tandem tepeats’), are found in the
euchromatic regions of vertebrates, fungi and
plants. Each repeat unit contains a short Grich ‘core’ sequence, ranging in size from 11
to 60 bp.
New variants arise on average at a frequency
of 1-2% per gamete, per generation (although
this can be as high as 15%) whereas most
gene loci have a mutation rate 10-5 to 10-6 per
generation.
• With a simple pattern of Mendelian inheritance.
• They are extremely powerful molecular
markers. More precisely, because of variation in
allele size, can be used to distinguish different
individuals within a population. This is known as
DNA profiling (or DNA fingerprinting).
• DNA profiling has been used with great success
in both population biology and forensic science.
In behavioural ecology, can be used to determine
which male in a population is the father of a set
of offspring.
• Microsatellites, or STRs (‘short tandem repeat
polymorphisms’), are sequences composed of
runs of repeat units 2-5 bp in length; again
mostly in regions of euchromatin and in the
plant chloroplast genome.
• In the human genome there are perhaps 35000
microsatellite loci, with allele lengths of
usually between 2 and 50 repeats per locus.
FI2a
FI2b
5’-AGGCGAAGCCTTCTCCCCTCT-3’ STR
5’-ACCCCCTCCTCGCACTCCCCT-3’
FI5a
FI5b
5’-CTGGGCACGATCTGGCTTATT-3’
5’-GCATGGGTAAAGGTTTTGATGA-3’
STR
FI8a
FI8b
5’-GAGGGTCTCAAAATTGGCATGTC-3’
5’-GTAAGGTTTCTATGGTTGGACA-3’
STR
FI9a
FI9b
5’-CAATACCCCCTCCTCGCACT-3’
5’-CCCACGATGGTCCGCGTAC-3’
STR
FI10a
FI10b
5’-TGGCGGCAACCAAAGTGGGT-3’ STR
5’-TGGGCTGTCCATGTGCTGGCGT-3’
FI11a
FI11b
5’-ACGCCAGCACATGGACAGCCCA-3’
STR
5’-CCTTTCGGGCTTTGTTAGCA-3’
FI12a
FI12b
5’-CCACAGAGTCTTAACATACACA-3’
5’-GTGTTTGTTTCTCTGAAGCCT-3’
STR
FI14a
FI14b
5’-CATCACCCAAAGTGAAAGCCA-3’
5’-CCTGGCTACCAATCTCATCA-3’
STR
• High mutation rates, between 10-2 and 10-5 per
gamete, per generation.
• Such high levels of genetic diversity coupled
with neutral evolution, codominance and simple
Mendelian inheritance mean that they are also
an ideal, and currently extremely popular, set of
molecular markers.
• Most endangered species of canid, the Ethiopian
wolf.
• Microsatellites have also been use in forensic
cases.
Male
Female
M
F 子代
Male
Female
M
F
子代有 2 種可能性
• Microsatellites may also be of medical
importance as a number of human genetic
diseases, such as fragile X syndrome,
Huntingdon’s disease, myotonic dystrophy and
spino-bulbo-muscilar dystrophy are associated
with a dramatic increase in the copy number of
trinucleotide microsatellite repeats.
• Fragile X syndrome, appears to be caused by
expansion of a GGG repeat in exon 1 of the
FMR1 gene. Normal alleles contain between 6
and 50 repeat units whereas clinically affected
individuals have more than 200 repeats, and
frequently more than 1000.
DNA Exclusions
孩子的老爸是誰
The Wanted
• The transposable elements (TEs)－increase their
copy number by jumping around the genome
making additional copies of themselves as they do
so. If one group of DNA sequences deserve the
title of ‘selfish’, it is these.
• More than 50%of the maize genome is made up of
transposable elements and a similar figure may yet
be uncovered in humans
• 10-20% of the genome of Drosophila
melanogaster is already known to be composed of
DNA of this type.
• Transposable elements can be divided into three
groups based on their mechanism of transposition.
Class I transposable elements, or retroelements,
transpose through an intermediate RNA stage (i.e.
DNA→RNA→DNA) using the enzyme reverse
transcriptase. This process is called
retrotransposition.
• In contrast, Class II or DNA elements, transpose
directly from DNA to DNA.
• The miniature inverted-repeat transposable
elements or MITEs.
Retroposon
• Long Interspersed Nuclear Elements (LINEs)
which are a major component of the G-banded
regions of mammalian chromosomes.
• 6-8 kb in length and are present in many
thousands of copies.
• L1 (Line 1) family have a consensus length of 6 kb
(although most are truncated) and are present in a
staggering 590000 copies in the human genome,
so that they make up almost 17% of all our
genomic DNA.
Retroposon
• Short Interspersed Nuclear Elements (SINEs),
or Alu-like sequences, which are frequently found
in the R-banded regions of mammalian
chromosomes.
• Are not considered true retroelements (no RT).
• 130 to 300 bp and have copy numbers ranging
from 50000to over 1000000 per genome.
• Alu sequences are approximately 300 bp in length
and are present in about 1100000 copies in the
human genome (almost 12% of four total DNA
content).
• Both LINEsand SINEs appear to be originally
derived from RNA transcripts: LINEs from RNA
polymerase II and SINEs from RNA polymerase
III (tRNA) transcripts.
• Also related to retroelements are the endogenous
retroviruses.
• These are copies of retroviruses which have
integrated as their DNA form (known as the
provirus) into the germ-line of eukaryotes and
which are now inherited along with the host
genomic DNA.
• Class II (DNA) elements also possess terminal
repeat sequences, less than 100 bp in length－and
frequently inverted.
• Some 1.6% of the human genome is composed of
elements of this kind, the P and hobo elements of
Drosophilia, the mariner elements of animals, the
Tcl elements of nematodes and the Ac/Ds
(‘Activator/Dissociation’) elements of maize.
• Between 0 and 60 copies of this 2907 bp element are
found in the genome of D. melanogaster. P elements
illustrate two of the most important aspects;
Jumping around genomes, sometimes able to move
between species and that they can affect the
phenotype of their host organism.
• Hybrid dysgenesis－an increase infertility due to
chromosome breakage. However, P elements are
only a recent introduction into wild populations of D.
melanogaster and flies maintained in laboratory
stocks established in the early part of this century do
not carry them.
• P elements are not found in the fly species mostly
closely related to D. melanogaster－D. simulans, D.
sechellia, D. mauritiana－but are present in more
distantly releated species, such as those from the D.
willistoni species group. This means that P elements
in D. melanogaster must have been transferred from
the D. willistoni group (perhaps by viruses or
parasitic mites) after D. melanogaster splitfrom its
sibling species about two million years ago.
• Inserted into host gene often inactivate them
• Leads to a number of chromosomal rearrangements;
Recombination between elements of the same family that
occupy different (non-homologous) sites on
chromosomes－a process known as ectopic exchange－
will also cause mutations.
• When transposable elements are cut, with sections of
indigenous DNA also being removed.
• Studies in Drosophila have shown that transposable
elements are very rare in coding regions, yet occur at high
frequency in regions of heterochromatin where fewer
genes are found and where the rate of meiotic
recombination.
• However, despite their deleterious effects, transposable
elements may be used to beneficial effect in genetic
engineering, where they can act as vectors for carrying
genes to new location.