What would we tell Darwin?

H. John Newbury

David Attenborough

Linnaeus and ‘species’

1707 – 1778

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.

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).

Darwin’s Theory of Evolution

Darwin’s real claim to fame is his explanation of the forces that drive evolution – and, critically, of powerful role of Natural Selection.

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)

Darwin’s 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’.

Darwin’s 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).

What have we found out about this since Darwin was alive?

The first part of Darwin’s 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.

Important initial discoveries during Darwin’s 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

Gregor Mendel

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.

Gregor Mendel was an Augustinian monk working in a monastery in Austria. He is commonly referred to as the Father of Genetics.

He developed generalisations which later became known as Mendel’s Laws of Inheritance.

1822 - 1884

An example of ‘Mendelian inheritance’

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

Round X Wrinkled

RR

selfed

F1 seeds all round

F2 seeds ¾ round, ¼ wrinkled

rr

Rr

Mendel proposed that invisible internal units of information account for observable traits, and that these "factors" are passed from one generation to the next.

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.

Discovery of chromosomes

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.

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

DNA, inheritance and Louis Pasteur

1822 –1895

Much later, it was shown that the ‘genes’ (as Mendel’s ‘factors’ had become known) were regions of DNA within chromosomes.

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.

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.

Bacteria and the DNA story

1877 - 1955

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.

DNA is the genetic material

Bacteria and the DNA story

The genetic codeThe 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

Model organisms in Genetics

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.

Let us consider one of Darwin’s classic

examples of evolution

‘Darwin’s finches’.

These birds were collected by Darwin when HMS Beagle visited the Galapagos islands in 1835.

Time line:

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.

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.

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

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.

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.

Result

Embryos with the extra Bmp4 later produced wider and deeper beaks.

Control

Extra Bmp4

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.

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.

Control Extra CaM

What other contributions has molecular genetics made to evolutionary study?

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 ….

3... 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 ….

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 ….

... A P G X I V C C K R L E D ….The new ‘missing links’

Application of sequence analysis to Darwin’s finches?

Using sequence data from a couple of proteins, one can propose the evolutionary process that led to today’s surviving species. One can also suggest the timescales over which these processes occurred.

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.

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 (>90%).

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.

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/Blast.cgi

Amino acid sequence of protein fragment from T. rex.

grpgapgpagargndgatgaagppgptgpagppgfpgavgakxxxxxxxxxgsegpqgvrgepgppgpagaagpagnpgadgqpgakgangapgiagapgfpgargapgpqgpggapgpkxxxxxxxxxxxxgdgakgepgpvgiqgppgpageegkrxxxgepgptglpgppgerxxxxxxgfpgadgvagpkgapgergsvgpagpkgspgeagrpgeaglpgakgltgspgspg

Result

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