1. The diversity of genomes and the tree of life
Chapter 1
The diversity of genomes and the tree of life

2. Living organisms obtain energy in different ways
- Organotrophic
- Phototrophic
- Lithotrophic
- aerobic
- anaerobic

4. Some Cells Fix Nitrogen and Carbon Dioxide for others

5. The greatest biochemical diversity is seen among procaryotic cells

7. The phototrophic bacterium Anabaena cylindrica

8. A lithotrophic bacterium, Beggiatoa, gets its energy by oxidizing H2S
and can fix carbon even in the dark

9. The tree of life has three primary branches: Bacteria, Archaea, and Eucaryotes

10. The three - kingdom classification of
organisms as proposed by Haeckel in
1866

11. Classification of organisms into five kingdoms first
proposed by Whitaker in
1959.
The five kingdoms were:
Animalia, Planta, Fungi,
Protista, and Monera

12. Since molecular structures and sequences (of bases in DNA/RNA and of
amino acids in proteins) are more revealing of evolutionary relationships
than classical phenotypes (particularly among microorganisms), beginning
in the 1950s, the basis for the definition of taxa shifted from the organismal
to the cellular to the molecular level

13. Universal phylogenetic tree in rooted form showing the three domains –
Bacteria, Archaea, and Eucarya

15. Some genes evolve rapidly; others are highly conserved

16. Most Bacteria and Archaea have 1000 - 4000 genes

19. Aug 31, 2004

20. Microbial Genomes – August 30, 2005

21. Microbial Genomes – complete; August 30, 2005

23. As of September 5, 2007

24. Eukaryotic Genomes – August 30, 2005

26. As of September 5, 2007

27. As of September 5, 2007

28. New genes are generated from preexisting genes

30. 47% of the genes in this bacterium have one or more obvious relatives
Gene duplications give rise to families of related genes within a single cell
Families of evolutionarily related genes in the genome of Bacillus subtilis
47% of the genes in this bacterium have one or more obvious relatives

31. different evolutionary pathways
Paralogous genes and orthologous genes: two types of gene homology based on
different evolutionary pathways
Orthologs - genes in two separate species that derive from the same
ancestral gene in the last common ancestor of those two species
Paralogs - related genes that have resulted from a gene duplication event
within a single genome, and are likely to have diverged in their
function
Homologs - genes that are related by descent in either way

32. different evolutionary pathways
Paralogous genes and orthologous genes: two types of gene homology based on
different evolutionary pathways

34. Genes can be transferred between
organisms, both in the laboratory
and in nature

35. Horizontal gene transfers in early evolution

36. The function of a gene can often be deduced from its sequence

37. More than 200 gene families are common to all three primary
branches of the tree of life

39. Mutations reveal the functions of genes

40. Spotlight on E. coli
We have a more thorough knowledge of the working of E. coli than of any other
living organism, yet we hardly understand everything about this bacterium

41. The major features of eucaryotic cells

42. Eucaryotic cells may have originated as predators

43. Eucaryotic cells evolved from a symbiosis

46. Eucaryotes have hybrid genomes

47. Eucaryotic genomes are big