What would we tell Darwin

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What would we tell Darwin?
H. John Newbury
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David Attenborough
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Linnaeus and species
This Swedish biologist established conventions
for the naming of living organisms.
Implicit in his organisation of species into
classes, orders, genera etc was the concept that
some species are more closely related to each
other than others.
1707 1778
Scientists at this time were treating species as
fixed entities and there was not yet a suggestion
that one species could evolve into another (or
that more closely related species had more recent
common ancestors).
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Darwins Theory of Evolution
During Darwin lifetime, some biologists were
thinking about existing species being able to
change into new species by a process of
evolution.
(12 February 1809 - 19 April 1882)

• Darwins real claim to fame is his explanation of
  the forces that drive evolution and,
  critically, of powerful role of Natural
  Selection.

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Darwins Theory of Evolution

• Evolution can be summarised as the inevitable
  result of two processes

1. Random changes in individuals that are passed
on to their offspring.
2. Natural Selection acting on individuals
resulting in the survival of the fittest.
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Darwins Theory of Evolution

• The result of these processes is that a species
  can change its characteristics (evolve) over
  time.

If some members of a species change and others do
not then this diversification can lead to the
development of two different species
(speciation).
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What have we found out about this since Darwin
was alive?
The first part of Darwins process of evolution
involved random changes in individuals that are
passed on to their offspring.
It is in this area that there have been enormous
advances.
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Important initial discoveries during Darwins
lifetime
Mendel and patterns of inheritance
Discovery of chromosomes in eukaryotes
Pasteur and the discovery of bacteria
Eukaryotic genetics
Recognition that DNA is the genetic material and
elucidation of the genetic code
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Gregor Mendel
Gregor Mendel was an Augustinian monk working in
a monastery in Austria. He is commonly referred
to as the Father of Genetics.
1822 - 1884
He used peas as his model system and looked at
the inheritance of seven different characters.
This involved crossing and selfing and then
examining some 29,000 pea plants.
He developed generalisations which later became
known as Mendels Laws of Inheritance.
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An example of Mendelian inheritance
Mendel proposed that invisible internal units of
information account for observable traits, and
that these "factors" are passed from one
generation to the next.

• The character here seed shape. This can be
  round or wrinkled.

Round X Wrinkled
RR
rr
F1 seeds all round
Rr
selfed
F2 seeds ¾ round, ¼ wrinkled
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Discovery of chromosomes
1882 Discovery of chromosomes and mitosis.
1887 Each species has a fixed number of
chromosomes discovery of meiosis during egg and
sperm production.
1900 Pairing of homologous chromosomes during
meiosis
1902/3 Egg and sperm receive one chromosome from
each pair from each parent.
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Chromosomes
These discoveries were possible because of
improvements in technology in microscopy and in
stains.
Note that the stains bind to the bases (A, G, C
and T) in the DNA in the chromosomes.
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Chromosomes
The discovery that the pattern of inheritance of
Mendelian traits was mirrored by the pattern of
inheritance of chromosomes led to the proposal
that chromosomes are the carriers of heredity.
i.e. that Mendel's "factors" are located on
chromosomes.
Took some time to become accepted. Some, like
Bateson, rejected the idea.
1861 1926
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DNA, inheritance and Louis Pasteur
Much later, it was shown that the genes (as
Mendels factors had become known) were regions
of DNA within chromosomes.
1822 1895
Some of the seminal work that led to the
discoveries about DNA involved bacteria.
Louis Pasteur was responsible for the
demonstration that micro-organisms actually
exist.
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Pasteur and micro-organisms
He showed that a clear broth would start to
ferment if one left it open to the air.
If one boiled it and left it sealed, it did not
ferment.
He proposed that micro-organisms were all around
us and that they were responsible for the
fermentation.
This become known as the germ theory (of
disease) cf the spontaneous generation
theory.
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Bacteria and the DNA story
DNA is the genetic material
Oswald Avery showed that DNA is the genetic
material by demonstrating that it was transfer of
DNA from a virulent to an avirulent strain of
Streptococcus that transferred the virulence.
1877 - 1955
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Bacteria and the DNA story
The genetic code

• The sequence of three nucleotide bases (a codon)
  that tell the cell which of the 20 amino acids to
  put into a protein was initially determined by
  using E. coli cell extracts and synthetic mRNAs.

BUT the genetic code is UNIVERSAL
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Model organisms in Genetics
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But what examples could we give that are relevant
to the theory of evolution through natural
selection?
So, if Darwin was here today, we could explain
all this new information about genetics and DNA.
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Let us consider one of Darwins classic examples
of evolution

• Darwins finches.

Time line
These birds were collected by Darwin when HMS
Beagle visited the Galapagos islands in 1835.
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The value of islands in evolutionary studies
Islands represent an isolated environment where
there may originally have been only a few species
and there is a low rate of invasion of new
species.
In the Galapagos, the proposal is that one
species of finch arrived at the islands and
subsequently adapted into many different species.
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Adaptive radiation
The major changes in the Galapagos finches have
been in the beak structure and this has been
associated with the ease with which different
food can be accessed.
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But has anything been discovered about the
inheritance of beak characters?

• Work in various laboratories has attempted to
  identify genes controlling beak shape.

The Grant group from Harvard are able to spend
part of their time in the field and part in the
molecular genetics laboratory
One of the Grant research group in the Galapagos
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A beak development gene
There is experimental evidence that some genes
are involved in controlling craniofacial
development in vertebrates i.e. the development
of the structures in the area in which birds
produce beaks.
One of these is called Bmp4 and there is evidence
that it controls beak width and depth in birds.
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Genetic engineering experiment
Chicken embryos were genetically engineered so
that they expressed Bmp4 more strongly.
At a stage before the structure of the beak can
be seen, an extra copy of the Bmp4 gene was
introduced and strongly expressed in the
mesenchyme tissue that will eventually form the
base of the beak.
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Result
Embryos with the extra Bmp4 later produced wider
and deeper beaks.
The conclusion of the authors is that, while
other genes may also contribute to the control of
beak development, Bmp4 is a key gene in the
evolution of beak shapes in Galapagos finches.
Control
Extra Bmp4
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Another gene controls beak length
In a set of parallel experiments, a gene
controlling beak length (a Calmodulin gene) has
been found.
Genetically engineering chick embryos expressing
the Calmodulin gene more strongly during beak
development produced longer beaks.
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What other contributions has molecular genetics
made to evolutionary study?
The new missing links
... A P G X I V C C K R L E D .
1... A P G M I V C C K R L E D .
2... A P G M I V C C K R L E D .
4... A P G K I V C C K R L E D .
3... A P G M I V C C K R L E D .
5... A P G K I V C C K R L H D .
6... A P G K I V C C K R L E D .
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Application of sequence analysis to Darwins
finches?
Using sequence data from a couple of proteins,
one can propose the evolutionary process that led
to todays surviving species. One can also
suggest the timescales over which these processes
occurred.
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What could we tell Darwin about recent work on
fossils?
Hell Creek is in Montana and very well-preserved
fossils have been found in the sandstone rock.
One of these is the 68 million year old
Tyrannosaurus rex specimen MOR1125.
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Collagen found in fossil bones
If samples of the bones are demineralised and
then examined using a specialised electron
microscope, fibrous structures can be seen.
This looks like collagen, which is the most
abundant class of protein found in bones (gt90).
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Analysis of T. rex collagen
The collagen is present at very low
concentrations, but it is possible to obtain
fragments of the protein and identify the amino
acids in these fragments.
An example of one of the amino acid content of
one of the fragments Gly Leu Pro Gly Glu Ser Gly
Ala Val Gly Pro Ala Gly Pro Ile Gly Ser Arg
Note that collagen has a high glycine content
(about 33) and this it is at the gly residues
that it bends to produce its helical shape.
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What living organism has a protein that is most
similar to that in the T. rex bone?
If we go to the BLAST software, we can search the
international databases of DNA and protein
sequence to find out.
BLAST website http//www.ncbi.nlm.nih.gov/BLAST/B
last.cgi
Amino acid sequence of protein fragment from T.
rex. grpgapgpagargndgatgaagppgptgpagppgfpgavgakxx
xxxxxxxgsegpqgvrgepgppgpagaagpagnpgadgqpgakgangapg
iagapgfpgargapgpqgpggapgpkxxxxxxxxxxxxgdgakgepgpvg
iqgppgpageegkrxxxgepgptglpgppgerxxxxxxgfpgadgvagpk
gapgergsvgpagpkgspgeagrpgeaglpgakgltgspgspg
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Result

• The results show that several modern vertebrates
  have collagen sequences quite closely related to
  dinosaurs.