1. Genetics and Evolutionary Biology
What are the major questions
How do we measure genetic variation in natural populations?
What do we mean by a biological species.?
How can we use DNA to define species relationships.?
Why do proteins evolve at different rates?
Why does the mutation rate differ in different parts of the the eukaryotic genome ?introns exons pseudogenes.

3. Modes of speciation Allopatric separation Sympatric separation
Genome Duplication events.

7. Segmental duplication of Chromosomes in the Arabidopsis genome

14. Comparative Genomic Highlights

15. Hedges, Nat Rev Genet 2003

16. Why Are Some Genomes So Large?
There is no clear correlation between genome size and genetic complexity.
C-value – The total amount
of DNA in the genome (per
haploid set of chromosomes)
C-value paradox – The
lack of relationship
between the DNA content
(C-value) of an organism
and its coding potential.
Haploid Genome Size (log scale)

17. The amount of TE correlate positively with genome sizeMb
Genomic DNA
3000
2500
TE DNA
2000
Protein-coding
DNA
1500
1000
500
Slime mold
Brassica
Rice
Plasmodium
Maize
Mosquito
Neurospora
Arabidopsis
Sea squirt
Budding yeast
Fission yeast
Nematode
Drosophila
Zebrafish
Fugu
Mouse
Human
Feschotte & Pritham 2006

18. Transposable Elements Gone Wild!
High Turnover in TEs despite gene conservation

19. Transposable Elements…
Variation in gene numbers cannot explain variation in genome size among eukaryotes
Most of variation in genome size is due to variation in the amount of repetitive DNA (mostly derived from TEs)
TEs accumulate in intergenic and intronic regions
CONCLUSIONS…
TEs have played an important role in genome evolution and diversification
Facilitate expansion and contraction of genomes AND gene families

20. Comparative Genomics – Synetny Human Chrom.1 vs. Chimp

21. Comparative Genomics – Synetny Human Chrom.1 vs. Mouse

22. Comparative Genomics – Synetny Human Chrom.1 vs. Cow

23. Comparative Genomics – Synetny Human Chrom.1 vs. Opossum

24. Comparative Genomics – Synetny Human Chrom.1 vs. Platypus

25. Comparative Genomics – Synetny Human Chrom.1 vs. Chicken

26. Synteny
Large blocks of synteny exist even at great phylogenetic distance
Also substantial scrambling, even at short distance…

27. Whole Genome Alignments
Functional sequences often evolve more slowly than non-functional sequences, therefore sequences that remain conserved may perform a biological function.
Comparing genomic sequences from species at different evolutionary distances allows us to identify:
Coding genes
Non-coding genes
Non-coding regulatory sequences

28. The Rate of Evolution Depends on Constraints
Human vs. Rodent Comparison
Highest substitution rates:
pseudogenes
introns
3’ flanking (not transcribed
to mature mRNA)
4-fold degenerate sites
Intermediate substitution rates:
5’ flanking (contains promoter)
3’, 5’ untranslated (transcribed
to mRNA)
2-fold degenerate sites
Lowest substitution rates:
Nondegenerate sites
Differences in rate of molecular evolution are consistent with Neutral Theory

29. Selection of Species for DNA comparisons
Both coding and non-coding sequences
~70-75%
~150 MYA
4.2
Opossum
0.4
2.5
3.0
Size (Gbp)
~65%
~80%
>99%
Sequence conservation (in coding regions)
Primarily coding sequences
Recently changed sequences and genomic rearrangements
Aids identification of…
~450 MYA
~ 65 MYA
~5 MYA
Time since divergence
Pufferfish
Mouse
Chimpanzee
Human vs..

30. ENCODE Project
Cross-reference existing with new data on human genome function
Identify the functional relevance of as many bases of human genome as possible.