1. Evolution at the Molecular Level

2. Outline Evolution of genomes Based on DNA alterations and selection
Genomes grow in size by repeated duplications, which can arise by recombination and transposition
Duplication, diversification, and selection results in genome evolution
Genetic drift, selection, duplication of exons,
globin gene family: an example of molecular evolution

3. Earliest cells evolved into three kingdoms of living organisms
Archaea and bacteria now contain no introns
Introns late evolutionary elaboration
Figure 21.3
Fig. 21.3

4. Many species resulting from metazoan explosion have disappeared
Basic body plans of some Burgess shale organisms
Figure 21.4
Many species resulting from metazoan explosion have disappeared
Fig. 21.4

5. Evolution of humans 35 mya – primates
6 mya – humans diverged from chimpanzees
Figure 21.5
Fig. 21.5

6. Evolution of Humans Human and chimpanzee genomes 99% similar
Karyotypes almost same
No significant difference in gene function
Divergence may be due to a few thousand isolated genetic changes not yet identified
Probably regulatory sequences

7. DNA alterations form the basis of genomic evolution
Mutations arise in several ways
Replacement of individual nucleotides
Deletions / Insertions: 1bp to several Mb
Single base substitutions
Missense mutations: replace one amino acid codon with another
Nonsense mutations: replace amino acid codon with stop codon
Splice site mutations: create or remove exon-intron boundaries
Frameshift mutations: alter the ORF due to base substitutions
Dynamic mutations: changes in the length of tandem repeat elements

8. Effect of mutations on population
Neutral mutations are unaffected by agents of selection
Deleterious mutations will disappear from a population by selection against the allele
Rare mutations increase fitness

9. Genomes grow in size through repeated duplications
Some duplications result from transposition
Other duplications arise from unequal crossing over during recombination

10. Transposable elements move from place to place in the genome
1930s Marcus Rhoades and 1950s Barbara McClintock – transposable elements in corn
1983 Nobel Prize - McClintock
Found in all organisms
Most 50 – 10,000 bp
May be present hundreds of times in a genome
TEs can generate mutations in adjacent genes

11. Common mechanism of transposition
Catalysed by transposases
Regulation of transposase expression controls transposition
Catalytic domain of transposase involved in transphosphorylation step that initiates DNA cleavage & strand transfer.

12. Common mechanism of transposition
2 sequential steps
  Site specific cleavage of DNA at the end of TE
Complex of transposase-element ends brought to DNA target where strand transfer is carried out by covalent joining of 3’end of TE to target DNA

13. Figure b

14. Transposons are now classified into 5 families
On the basis of their transposase proteins
1)      DDE-transposases
2)      RT/En transposases
(reverse transcriptase/endonuclease)
3)  Tyrosine (Y) transposases
4)      Serine (S) transposases
5) Rolling circle (RC) or Y2 transposases
Transposons move in different ways. Five protein families dictate different transposition pathways: DDE-transposases,
reverse transcriptase/endonucleases (RT/En), tyrosine (Y)-transposases, serine (S)-transposases and rolling-circle (RC)- or
Y2-transposases. Transposons (blue) can be either ‘cut-out’ or ‘copied-out’ of the flanking donor DNA (green). a | Most DDEtransposons
excise from the flanking DNA to generate an excised linear transposon, which is the substrate for integration into a
target (orange). b | Retrotransposons copy-out by reverse-transcribing (RT) a full-length copy of their RNA (purple) that is generated
by transcription (Txn). Long-terminal repeat (LTR)-retrotransposons make a full-length cDNA copy (pink represents newly replicated
DNA) from their RNA and integrate this into a target using a DDE-transposase. c | TP-retrotransposons use reverse transcriptase
(RT) to copy their RNA directly into a target that has been nicked by a transposon-encoded nuclease (En). d | Y-retrotransposons are
thought to generate a circular cDNA intermediate by reverse transcription. A Y-transposase integrates the element into the target.
e | and f | Y- and S-transposons encode either a tyrosine or serine transposase, which mediates excision of the transposon to form
a circular intermediate. A reversal of the catalytic steps results in transposon insertion. g | Y2-transposons ‘paste’ one strand of the
transposon into a target and use it as a template for DNA replication. Two models have been proposed for Y2-transposition.
Representatives of each type of transposon are listed below each pathway.
Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

15. Recombination Homologous recombination
exchange between homologous DNA sequences; accomplished by a set of enzymes
function: meiosis I of eukaryotic cell division, double-strand break repair, telomere maintenance
replication is an integral part of the reaction, allowing reformation of functional replication forks after any fork blocking event

18. Genetic drift and mutations can turn duplications into pseudogenes
Diversification of a duplicated gene followed by selection can produce a new gene

19. Genome size increases through duplication of exons, genes, gene families and entire genomes
Figure 21.10
Fig

20. Basic structure of a gene
Figure 21.11
Fig

21. Exon duplication
Genes may elongate by exon duplication to generate tandem exons that determine tandem functional domains e.g. antibody molecule
Figure 21.12a
Fig a

22. Exon shuffling may give rise to new genes e. g
Exon shuffling may give rise to new genes e.g., tissue plasminogen activator (TPA)
Figure 21.12b
Fig b

23. Duplications of entire genes can create multigene families
Figure 21.13a
Fig a

24. Unequal crossing over can expand and contract gene numbers in multigene families
Figure 21.13b
Fig b

25. One gene is changed, the other is not
Intergenic gene conversion can increase variation among members of a multigene family
One gene is changed, the other is not
Fig a
Figure 21.14a

26. Concerted evolution can lead to gene homogeneity
Figure 21.15
Fig
Unequal crossing over
Gene conversion

27. Evolution of gene superfamilies
Large set of genes divisible into smaller sets, or families
Genes in each family more closely rated to each other than to other members of the family
Arise by duplication and divergence

28. Evolution of globin superfamily
Fig
Figure 21.16

29. Organisation of globin genes
Fig
Figure 21.16

30. Developmental variation in gene expression
a-like chains - z & a
b-like chains - e, g, d, b
Fig
Adult human made of
a2b2 – 97%;
a2d2 - ~2%;
a2g2-~1% (fetal persistence)
Figure 21.16

31. Gene expression controlled by location
e – embryonic yolk sac
g – yolk sac & fetal liver
b & d – adult bone marrow
Fig
Figure 21.16

32. Evolution of mouse globin superfamily
Fig
Figure 21.16

33. Evolution of mouse globin superfamily
Fig
Figure 21.16

34. The Haemoglobinopathies
Thalassemias
Anaemias associated with impaired synthesis of Hb subunits
Thalassaemias can arise from different mutations causing a disease of varying severity.
a0/b0 thalassaemias – globin chain absent
a+/b+ thalassaemias – normal globin chain in reduced amounts
Figure 21.16

35. a- thalassemias
Figure 21.16

36. a- thalassemias deletion of one or both a globins in an a gene cluster
Severity depends on whether the individual has 1,2,3, or 4 missing a globin genes.
GENOTYPE PHENOTYPE
a+ a+ a+a+ Normal
a+a a+a+ Silent carrier asymptomatic condition a-thalassaemia – 2
a+ a a+a a-thalassaemia trait minor anaemic conditions
a+a+ a a
a+a a a HbH mild – moderate anaemia
a a a a Hydrops foetalis foetus survives until around birth
Figure 21.16

37. b- thalassemias
Figure 21.16

38. b- thalassemias Mutations in b globin cluster are of different types
Non coding regulatory regions Exons Introns (InterVening Sequences) 3’ cleavage mutant deletion RNA splicing mutant transcription mutant nonsense mutation frameshift insertion frameshift deletion
Mutations in b globin cluster are of different types
gene deletion
transcriptional mutation
RNA processing mutations
RNA cleavage signal mutations
Nonsense & frameshift mutations
Figure 21.16

39. b- thalassemias
Figure 21.16

40. Main genetic mechanisms that contribute to the phenotypic diversity of the b-thalassaemias.
Figure 21.16