Introduction to Evolution I

Question 1

How is evolution achieved by the influenza virus?

Answer 1

Different flu strains infecting the same cell can swap parts of their genetic material, which the goes through reassortment to give rise to different strains.

Question 2

What are the genes being swapped in the influenza virus when different strains are swapping their genetic material?

Answer 2

• H-haemagglutinin: This binds the host cells by recognising specific receptors on their cell and is then able to infect. This specifies its host range.
• N-neuraminidase: Enzymes that allow the viral particles to be released from the cells. The better it is able to release its contents, the more the virus will spread.

Question 3

What is evolution?

Answer 3

Accumulated, heritable changes within a population, over generations, giving rise to new species.
Evolution is an observable fact. The process by which it has most likely occurred is by natural selection, which is a theory.

Question 4

How are we able to observe evolution?

Answer 4

Patience is needed to observe evolution.
Experiment:
1. A group of researcher took 12 colonies of E Coli that had each come from a single clone
(so 1 bacterium)
2. They spilt the culture into bacterial flask (Sub-culture) and every day for the next 27 years
they have taken that culture and they moved it into a fresh flask
3. They Froze the culture samples every 500 generations that approx. Every 75 days
4. Currently there are over 63,500 generations observed
5. One of the things they are testing the bacteria for is their ability to grow in a substrate
called citrate in the presence of oxygen (normally bacteria will not grow in citrate when
there is oxygen in the environment, it is something they use in anaerobic conditions).
6. Some of those bacterial cultures have developed the ability to grow in citrate which
evolved after about 30,000 generations in one group in particular when at the start of the
experiment they couldn’t grow in citrate.
NOTE: Earlier generations from this same ancestral E coli were repeatedly able to evolve the ability
to utilize citrate at about the same time to understand why and how this is happening you can
sequence the DNA of the bacteria.

Question 5

How is citrate utilised in E.Coli?

Answer 5

In the presences of oxygen, the promoter is turned off which mean that bacteria do not make that enzyme and it does not grow in citrate.
However, the citrate gene sits next to another gene called RNK, which is on in the presence of oxygen.
The bacteria that are able to grow in citrate are able to duplicate the piece of DNA- duplication which has turned on a gene that is normally turned off.

Question 6

How do changes in the genotype arise?

Answer 6

• Mutation and recombination of genetic material during reproduction.
• Natural selection: organisms better adapted to the enviroment survive to produce more offspring.
• Genetic drift: variation in relative frequency of different genotypes in small populations due to chance (seen in isolated populations).
• Gene flow: transfer of alleles from one population to another (e.g. viruses).

Question 7

How are applied selection caused by humans?

Answer 7

• plant or animal breeding

- antibiotics (misprescribing, patients not finishing the full course), drugs, pesticide resistance.

Question 8

How are mutations able to act as molecular clocks?

Answer 8

• mistakes can accumulate over times

- species that share a common ancestor will have fewer differences than species that are more distantly related.

Question 9

How do populations evolve?

Answer 9

By changes in gene frequency brought about by random genetic drift, gene flow and especially by natural selection.
Populations contain genetic variation that arises by random mutations (chemical, radiation or by chance) and by recombination.

Question 10

What is microevolution?

Answer 10

Most adaptive variants have individually slight phenotypic effects so that phenotypic changes are gradual- this microevolution.
An example of this is all people are humans but there is minor differences among us.

Question 11

How does diversification come about?

Answer 11

It comes about by speciation (the gradual evolution of reproductive isolation among populations).

Question 12

What will happen if the different processes that lead to evolution continues over a long period of time?

Answer 12

It will give rise to higher taxonomic levels.

Question 13

What are systematics and what are the different types?

Answer 13

Systematics deals with classifying with different things. and includes the following:

• Taxonomy- naming of groups of organisms (taxa)
• Classification- arranging taxa into an ordered, hierarchical system.
• Phylogeny- determination of ancestral relationships of organisms and their evolutionary history.

Question 14

LOOK AT NOTES TO SEE TABLE OF CLASSIFICATION

Answer 14

LOOK AT NOTES TO SEE TABLE OF CLASSIFICATION

Question 15

What is phylogenetics?

Answer 15

Since new species arise from earlier species, they must share relationships. All organisms are derived from a distant, common ancestor. Phylogeny means the history of species and phylogenetic relationships can be represented using phylogenetic trees. The last universal common ancestor is named LUCA but this is not an observed organism.

Question 16

How is a phylogenetic tree created?

Answer 16

A phylogenetic tree can be created using various different traits not necessarily a complete history of everything. Usually a morphological criteria is used.

Question 17

What does monophyletic mean?

Answer 17

All species in a monophyletic group are descended from a common ancestor that is not the ancestor of any other group and no species descended from that ancestor are not in it.

Question 18

What does paraphyletic mean?

Answer 18

An unnatural group that does not contain all the species descended from the most recent common ancestor; some species are outside it (e.g. reptiles- cold blooded where birds are excluded because they are warm blooded).

Question 19

What does polyphyletic mean?

Answer 19

An unnatural group that contains species descended from several ancestors from which members of other groups also descended (e.g. hemotherms - birds, humans; also warm blooded).

Question 20

What is the fossil record?

Answer 20

• To know how organisms have risen and how they interrelate, we could observe part of the evidence which comes from the fossil record.
• Older rocks lie below more recent rocks.
• Rock and organic material can be dated by measuring the decay of naturally occurring radioactive isotopes that are presents in the rock or in the sedimentary material.
• Fossils usually form in sedimentary rock.
• Fossil dates can be bracketed by the age of surrounding igneous rock (forms from earthquakes and volcanoes- it is where the rock becomes molten and then solidifies, surrounding the sedimentary rock).

Question 21

What is the evidence that can be gained from fossil records to prove the theory of evolution?

Answer 21

-If you look in the fossil record, you will find evidence of organisms that are not present on Earth today and things that have characteristics between different species that are live today.
-Intermediate fossils are found:
*Fossils of hybrids between a bird and dinosaur have
been found- Archeopteryx.
-The order and the age of organisms can be determined.
-Only simpler life forms are present in older rock.
-Non-extant fossilised organisms are found.

Question 22

What is radiometric dating?

Answer 22

-Measuring the ratio of parent/daughter nucleotides

Question 23

How does radiometric dating work?

Answer 23

-Radiative material will decay and we measure the decay by half-life (amount of time that it
takes to decrease by 50%).
-At the same time as that radioactive material is decaying its producing a daughter isotope
-As the percentage of parent atoms decrease the percentage of daughter atoms decrease,
and we can use the balance between the 2 to date things like rocks.
-Parent and daughter nuclides cannot leave or enter material after it is formed (forms a closed
system)
-If we know how quickly a radioactive isotope decays we can measure the ratio of the parent to
the daughter and work out how long it has been there.

Question 24

What are the requirements needed for radioactive dating?

Answer 24

There are different kinds of radio isotopes and they have different half-lives (some decays very
rapidly and more slowly) and so we can use the short lived isotopes to date things that have
formed more recently and the long lived isotopes to date things that have formed much longer
ago.
For that to work radioactive decay has to be constant it can’t be affected by temperature,
pressure, chemicals, electrical or magnetic fields. And as far as we know it does have the
following properties.
If you are looking at the ratios of daughter and parent nuclei it is important that they are in a
closed system and that things can’t leave and enter after that has formed
Because rocks fold over time (wavy broken layers of rocks), you have be careful that what you
are looking at is time wise different to the older rock below it. In other words there no intrusion of
other, later rock. It is also important that the rocks are not contaminated by: Other rocks or
sediments nearby, or by you.

Question 25

What is the Cambrian explosion?

Answer 25

It is a point in evolutionary history where you are able to see relatively simple organisms and then there is a sudden amount of much more complex organisms in the fossil records.
By definition it means the rapid appearance (and disappearance) of complex organisms in the fossil records (about 525 mya).

Question 26

What does homologous mean?

Answer 26

Two structures from a common ancestral version. These structures are derived from a common ancestor, they form by a common mechanism.

Question 27

What does analogous mean?

Answer 27

No common ancestor but have similar structures produced by selection to meet similar function (convergent evolution- e.g. insect wing and bird wing).
Although different developmental mechanisms, some molecular components may be the same.

Question 28

What are tetrapods limbs considered as?

Answer 28

Tetrapod limbs are homologous but with great diversification.
All modern tetrapods limbs have evolved from later remodelling of the elements e.g. human, bird, bat, horse whale.

Question 29

What are the different variations of different organisms eyes?

Answer 29

Between the different organisms eyes there are variations in:
-Origin of photoreceptors
-Type of photoreceptor - ciliary or microvillar and what
direction they face (inward/outward)
-Position of retina

Question 30

Are eyes considered to be analogous or homologous?

Answer 30

All those eyes are analogous because they share a similar function but they form in slightly different ways as shown in the list above.

Question 31

What does the diversity of the eye suggest?

Answer 31

The diversity of eyes suggests that they have evolved several times independently (that’s an example of convergent evolution and polyphyletic - because it’s in lots of different groups.

Question 32

What are crystallins?

Answer 32

Crystallins (clear lens proteins in the eye) in different taxa are not related. This means that there is no Crystallins gene that has been used for all animals rather it was that different animals have found different protein that perform that function.

Question 33

What are the similarities between eukaryotes and their eyes?

Answer 33

-ALL eukaryotes use a homologous family of proteins, opsins, to detect light
-Opsins are G-protein coupled receptors that convert light to nerve impulses
-Eukaryotic opsins share sequence homology but have diverged to detect different
wavelengths of light, for example there are opsins that are sensitive to red light or
green light or UV light depending on what kind of animal.

Question 34

What is the difference between eukaryotes and prokaryotes ospin?

Answer 34

Interestingly, Prokaryotes also have GPCR opsins, but with a different molecular origin, so if you sequence the DNA it won’t be related to eukaryotic opsins. It performs the same function so has the same basic structure when it fold as a protein – convergent evolution.

Question 35

What is molecular convergence (molecular analogy)?

Answer 35

Where proteins perform the same function but may not be related (with no structural identity). E.g. the crystallins (clear proteins present in the lens) are needed to be stable a transparent. They have other functions or have been derived from protein that have other functions but are now being used in the eye. There are many different transparent proteins in different species however all have other functions (in addition to being stable, to being stable, transparent and refractive).

Question 36

What is molecular homology?

Answer 36

Molecular homology is determined from amino acid or nucleic acid sequence
-Two genes from same organism (by duplication) – paralogs (a type of homolog)
-Two genes from different organisms (common ancestor) – orthologs (a type of
homolog)
-In evolution not only the coding sequence changes there are also large scale changes like:
Gene duplication.
-Complementary functions of the original gene and duplicated gene: doing the same
thing
-Non-overlapping functions: doing a completely different function
-Partition ancestral activity by regulatory mutation.

Question 37

What is regulatory mutation?

Answer 37

In cases of gene duplication usually the organisms has an extra gene, so if that duplicated gene mutates and has a slightly different function due to that mutation, the organism which it arose from can still survive because t has an original copy. On the other hand, if the duplicated copy does something beneficial to that organism it allows it to survive better than its competition.

Question 38

What is the drosophila eyeless mutation?

Answer 38

It is a mutation in the Pax6 gene called eyeless.

Question 39

How is Pax6 involved in the development of the eye?

Answer 39

• Mutations in the Pax6 gene cause a disease called aniridia (absence of iris) in humans.
• Mutation in the Pax6 gene in the mouse is called small eye
• Eyeless is orthologous to Pax6 in humans (aniridia) and mouse (smalleye)
• If you take the mouse eyeless gene and express it ectopically (not in normal place) in Drosophila you will get eyes forming in those places.
• Therefore we know that the Mouse Pax6 gene functions in fly.
• In fact, Pax6 is involved in eye development throughout the whole animal kingdom
• Is that Convergence evolution or homology evolution? – convergence

Question 40

Are all eyes homologous and is Pax6 a master gene that can form an eye wherever it is expressed?

Answer 40

• Because there are other genes can induce ectopic eyes in the fly and also there are animals without eyes that have the Pax6 gene.
• Pax6 is present in, and required for, other tissues, this means it’s not always associated with just eye formation.
• But it’s more likely it organises a gene network (turns on a group of genes) required for eye formation.

Question 41

Why might eyeloss occur?

Answer 41

-Eyeloss is common feature in animals that are found often underground, and this is due to them not needing to use their eyes (which is probably due to conserve energy). Examples of these animals are worms, moles.

Question 42

What is an example of the evolution of eyeloss?

Answer 42

• An example of an organism that has eyeloss is the Mexican, blind cavefish (Astyanax mexicanus – fish with no eyes)
  -Comparing the Surface-dwelling ancestral form of Astyanax mexicanus and the blind cave fish, we see that the blind fish doesn’t have pigment or eyes.
  -As there name suggests they live in caves and have been derived form a surface dwelling ancestral in recent geological time (last 1 million years)
  -Those distinct populations and other several populations of fish have become geographically
  isolated form on another in caves after water levels receded 0.1-1Mya, this has left the isolated population in caves unable to get out, so they are underground in the caves and its dark, resulting in Eye loss.

Question 43

Is there a way for the blind cavefish to fix the mutation?

Answer 43

The defect in the cavefish is due to the lens but it can be rescued by transplanting a surface dwelling fish lens into their eyes. The cavefish lens is smaller and this is due to apoptosis.

Question 44

Why do the cavefish eyes begin to form but then degenerate?

Answer 44

• The lens is essential for the development of other parts of the eye because it produces signals for other eye bits to form like the Iris, pupil, cornea, photoreceptors.
• Cavefish lens is smaller and undergoes apoptosis (programmed cell death) that will kill it and stop it from sending those signals.
• The Small, apoptotic lens is caused by earlier reduction of Pax6 expression (still there, but turned down in cavefish lens) and subsequent changes to signaling molecules.
• If you look at the different isolated populations of cavefish they have all evolved to loss their eyes but have done that in different ways.
• So cross breeding of different strains (population) from 2 different caves, can result in offspring with better developed eyes - and vision. This means they have got different mutations in different pathways that are responsible for eye loss in different caves.

Question 45

What is drosophila antennapedia?

Answer 45

Drosophila (fruit fly) Antennapedia is a mutant fruit fly which has legs instead of antennae.
The reason for that is a mutation in one of its Hox genes.

Question 46

What is the mutation that causes drosophila antennapedia?

Answer 46

• Mutation that causes the Antennapedia to be mis-expressed in the place where antennae normally form leading got leg formation instead.
• There are homologs of that hox gene in the Drosophila genome. These are arranged in a cluster along the chromosome.
• The order in which these genes are arranged in the chromosomes relates to the position along that cranio-caudal) axis in which those genes are expressed.
• The hox gene contains a homeodomain which is the bit that binds to DNA, that homeodomain has been used in lots of other transcription factors. Sometimes it is partnered by other domains.

Question 47

How are the hox genes expressed in mice and humans?

Answer 47

• Hox genes in humans have the same function where they confer positional identify along the cranial caudal axis.
• Paralogs duplicated within ancestral animals (b1 gene and b2 gene are paralogues within the mouse).
• Example: Labile gene in drosophila is an Orthologue of the hox b1 gene in mouse.
• Present in clusters along chromosome.
• Present in vertebrates.
• Chromosomal organisation and function conserved.

Question 48

How are Hox genes are developmentally important for transcription factors?

Answer 48

• Hox genes bind DNA in a sequence-specific fashion and regulate the expression of adjacent/nearby genes.
• Confer positional identity along the Anterior-Posterior (cranio-caudal) axis (from head to tail).

Question 49

How is evolution occured in the Hox genes?

Answer 49

• The DNA-binding homeodomain is used in other, related transcription factors
• Vertebrates have 4 Hox gene clusters (called A, B, C, D), which have arisen from two duplication events of an ancestral chromosome. But the basic arrangement on each of the gene clusters have stayed the same.
• So the Gene order has stayed the same along the chromosome and correspond to the position of expression within the embryo.
• The hox genes in vertebrates will determine the boundaries or where particular structures form. For example where (not how!) your pancreas will bud from the endoderm when the gut is forming.