Human phylogenetics and evolution

Question 1

who produced the first reconstruction of the entire ‘Tree of Life’ in (1866)?

Answer 1

Ernst Haeckel

Question 2

Who Coined the term ‘phylogeny’ (Ancient Greek: phyle = tribe, race; genesis = birth) for the evolutionary relationships between organisms?

Answer 2

Ernst Haeckel

Question 3

Why is phylogenetics important?

Answer 3

To understand ‘our place in Nature’, and that of every other organism

Question 4

What are the medical uses of phylogenetics?

Answer 4

Medical uses, e.g. origins of diseases
Multiple origins of HIV
Origin of MERS

Question 5

What are Networks?

Answer 5

If organisms are able to exchange genes with each
other, their relationships can be represented as a network

Question 6

What are Trees?

Answer 6

If organisms are not able to exchange genes with each other their relationships can be represented as a branching tree

Question 7

What are trees made up of?

Answer 7

Nodes and Branches

Question 8

What is an internal node?

Answer 8

an internal node represents the most recent
common ancestor (MRCA) of the descendant branches

Question 9

What is an outgroup taxa?

Answer 9

taxa that we already know are definitely more distantly related than the other taxa (= the ingroup)

Usually, a tree is rooted with an outgroup (or multiple outgroups)

root is between the outgroup taxon (or taxa) and the remaining ingroup taxa

Question 10

What is the Definition of relatedness?

Answer 10

Two taxa (species, families etc.) are more closely related to each other than either is to another taxon if they share a more recent common ancestor

Question 11

What are the different types of data for producing phylogenies?

Answer 11

Morphological or other phenotypic data:
* only kind of data available for fossils (if ancient DNA or proteins not preserved)

Molecular data:
* Today, the most commonly used form of molecular data is sequence data –
either nucleotide sequence data (DNA or RNA) or protein sequence data
(amino acids)

Question 12

How many different types of amino acids are sequences of proteins comprised of?

Answer 12

20-22

Question 13

What are the sequences of amino acids in a protein specified by?

Answer 13

Sequence of amino acids in a protein is
specified by DNA sequence of the gene
coding for that protein, e.g. BRCA1 gene
codes for BRCA1 protein

Question 14

What are the types of DNA mutations?

Answer 14

• Substitution = replacement of one base by another e.g. G by C
• Insertion = addition of a new base somewhere in the sequence
• Deletion = loss of an existing base somewhere in the sequence

Question 15

How do protein sequences evolve?

Answer 15

Amino acid sequence of a protein is specified by the DNA sequence of the gene that codes that protein

• each amino acid is specified by a triplet of nucleotides (= codon)
• AAA = lysine (Lys or K)
• GCT/GCU = alanine (Ala or A)
• GTG = valine (Val or V)
  …
• TAA/UAA = STOP

Question 16

How do protein sequences evolve cont…?

Answer 16

Changes (substitutions, insertions, deletions) in the DNA sequence of a protein-coding gene can alter the amino acid sequence of the protein

But…genetic code is “degenerate”

• multiple codons code for same amino acid
  → change in DNA sequence doesn’t always
  result in a change in amino acid sequence
• Leucine coded for by 6 different codons
• Alanine coded for by 4 different codons
• STOP coded for by 3 different codons
• Methionine coded for by 1 codon only

Question 17

What is a synonymous mutation?

Answer 17

DNA mutation in protein-coding gene that does not change amino acid sequence of protein

Question 18

What is a non-synonymous mutation?

Answer 18

DNA mutation in protein-coding gene that does change amino acid sequence of protein

Question 19

which evolves faster? A DNA sequence coding for a protein, or the amino acid sequence of that protein?

Answer 19

Amino acid sequence of that protein