9. From genes to species

Question 1

What is horizontal gene transfer (where is this most common and what is another way genes can be transferred)?

Answer 1

The process by which an organism obtains a new gene directly from another organism, or even from another species, rather than by mutation or inheritance from a parent.

• More common in prokaryotes, where it is thought to be the reason for the emergence of multi-drug resistant strains of bacteria that have evolved
• Conjugation is another way genes can be transferred from one bacteria to another

Question 2

Why do proteins not accumulate randomly?

Answer 2

• Protein function is determined by its primary structure
• Mutations can change amino acids and so can potentially change the structure of a protein
• Some sections of a protein are more sensitive to amino acid changes for function than others (these sections or amino acids are said to be conserved)

Question 3

Give 2 examples of what conserved amino acids may be due to:

Answer 3

1. A particular R group being essential to bind the substrate
2. An amino acid may be semi-conserved, where as long as ‘like is swapped with like’, such as a hydrophilic amino acid with another hydrophilic, there is no consequence to the protein function.
   - The more essential the gene, the more important sequences will be conserved

Question 4

Describe why molecular homology is evidence of evolution:

Answer 4

• Looks at the similarity of patterns in DNA sequences or amino acid sequences.
• The more similar a comparable sequence is between organisms, the more closely related they are.
• Useful to use as technology has made sequencing proteins or DNA relatively easy.
• Both DNA and protein sequences are linear molecules with a limited number of possible building blocks.
• Changes tend to be random over time (outside of conserved sequences).

Question 5

What does bioinformatics use and what is it used for? Give an example:

Answer 5

The science of bioinformatics uses mathematics, computer science, engineering, chemistry and biology with the application of computer storage and retrieval to analyse large volumes of biological data (Eg. To determine the closeness of the relationship between different species)

Question 6

Where is mitochondrial DNA (mtDNA) found and how is it inherited?

Answer 6

Found in all eukaryotes and are inherited maternally.

Question 7

Describe 4 reasons why studies of mtDNA are useful in evolutional studies:

Answer 7

• Each cell has many copies of mtDNA (unlike the single copy of nuclear DNA), making it more likely to survive for long periods (mtDNA samples from Neanderthals have been sequenced).
• There is no crossing over and recombination in mtDNA, so there is no mixing of alleles from two parents.
• Mitochondrial DNA has a higher mutation rate than nuclear DNA, especially in a variable region of the genome known as the D-loop. This makes it useful in tracing divergence between populations over relatively short time periods.
• Variation in human mtDNA can indicate waves of migration and provide info on our early origins. Among modern human populations, various patterns of mutations in mtDNA can indicate where their ancestors came from, and how long ago they separated from other human populations.

Question 8

What does the molecular clock refer to? How does it provide evidence of relatedness between species?

Answer 8

The number of substitutions that have accumulated in the amino acid sequence over time.
-Not all genes mutate at the same rate
-The more essential the gene, the slower the mutation rate
-Differences can also change from species to species
• Eg. Large animals tend to have longer generation times than small animals
• Higher metabolic rates can lead to more mutations

Question 9

List the 2 types of phylogenetic trees:

Answer 9

• Rooted

- Unrooted

Question 10

What are rooted phylogenetic trees?

Answer 10

Do not show a common ancestor, just how different two or more species are from each other (the longer the arm, the more differences from the others).

Question 11

What are unrooted phylogenetic trees?

Answer 11

Show the history of ancestor (each node represents the last common ancestor).

Question 12

List the 2 types of rooted trees:

Answer 12

• Cladograms

- Phylograms

Question 13

What are cladogram rooted trees?

Answer 13

Just show evolutionary relationships (who evolved from who).

Question 14

What are phylogram rooted trees?

Answer 14

A scaled or quantified version that shows a time frame of when branches occurred.

Question 15

What is taxonomy?

Answer 15

The process or system of classification.

Question 16

What is systematics?

Answer 16

The branch of biology that categorises organisms based on their phylogeny.

• The goal in systematics is to define taxonomic groups as a clad (line) within a cladogram
• For a given classification name (Eg. Order) to be correct, all the species within that order should be descended from the same common ancestor (monophyletic)
• If a species in a group are paraphyletic, the group is invalid or misnamed

Question 17

How can master control genes lead to the evolution of species?

Answer 17

• Some genes initiate the developmental program for a particular body plan or tissue type during embryonic development
• Act by regulating the whole set of other genes for cell development either directly or indirectly (turning on/off the expression of another regulatory gene)
• Changes in expression of developmental changes can lead to big changes
• If these changes are beneficial to the organism, then new species can evolve

Question 18

What is the bone morphogenic protein 4 (Bmp4)?

Answer 18

Is a type of transforming growth factor (a secreted signalling factor) that tells cells to divide and differentiate.

Question 19

Describe how the master control gene Bmp4 is an example of adaptive radiation in Darwin’s finches:

Answer 19

• Is a major factor as to why the finches described by Charles Darwin have different shaped beaks
• Darwin collected 14 songbird finches from the Galapagos and Cocos islands in 1835
• Different finches on each island specialised in different food sources but each beak would match the food, despite the species
• Beak shape is determined genetically and is evident at hatching (so the phenotypes are only genetic, not environmental)
• Timing and amount of Bmp4 expression in the embryo determines the shape and size of the bird beak
• The earlier or greater the expression, the bigger the beak
• Mutations in the common ancestor of the finch meant there were different alleles for beak shape and so alternative phenotypes
• Each island had different main food sources meaning some birds were better suited for the conditions (food type) and survived and reproduced more than others
• Over time, these versions became more prevalent and over many generations, different species evolved from each population.

Question 20

Describe how the master control gene Bmp4 is an example of adaptive radiation in cichlid fish:

Answer 20

• The regulatory gene, Bmp4, is also essential in the jaws of cichlid fish
• 7 days after fertilisation, Bmp4 expression can be measured and differences in expression account for the different mouth types.
• More robust-jawed cichlids express more Bmp4 during development than those with more delicate jaws

Question 21

What is DNA hybridisation and what does it rely on?

Answer 21

• The DNA of different species can be compared by producing single strands of their DNA molecules
• Relies on the complementary DNA base pairing pattern

Question 22

Describe the process of DNA hybridisation:

Answer 22

1. DNA from two different species are cut to manageable sizes by restriction enzymes
2. DNA is heated to above 95˚C to break the hydrogen bonds (‘melts’ the DNA) between the two strands and the exact temperature each species’ DNA melts is noted
3. Two different pools of DNA are mixed and allowed to cool to hybridise (cool)
4. The temperature to melt the hybrid DNA is then measured
   - The higher the temperature, the more related the species are
   - The lower the temperature, the less related the species are

Question 23

What does the term conserved refer to?

Answer 23

When amino acids are retained during the course of evolution, while other amino acids of the protein may become substituted.