1. Speciation I. Modes II. Mechanisms A. Progressive Genomic Incompatibility B. Hybrid Incompatibility C. Differential Selection D. Hybridization E. Polyploidy

2. E. Polyploidy Autopolyploidy Allopolyploidy

3. E. Polyploidy Allopolyploidy Spartina Spartina alternifolia, native to US, was found in southern England in late1800's. There is a European species Spartina maritima. Early in the 20th century a sterile hybrid was found and was called Spartina townsendii This went through a process of diploidization (increased ploidy) and became a new sexually reproducing species known as Spartina anglica S. maritima S. alterniflora S. anglica sterile hybrid

4. E. Polyploidy Allopolyploidy

5. Speciation I. Modes II. Mechanisms III. Rates

6. Mark Pagel,* Chris Venditti, Andrew Meade.2006. Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level. Science 314:119.* A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.

7. Origin of Life Hypotheses

8. I. Earth History 4.5 bya: Earth Forms

9. I. Earth History - Earliest Atmosphere - probably of volcanic origin Gases produced were probably similar to those created by modern volcanoes (H2O, CO2, SO2, CO, S2, Cl2, N2, H2) and NH3 and CH4

10. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks

11. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.5 bya: Oldest Fossils

12. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.5 bya: Oldest Fossils Stromatolites - communities of layered 'bacteria'

13. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.4 bya: Oldest Fossils 2.3-2.0 bya: Oxygen in Atmosphere

14. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.4 bya: Oldest Fossils 2.3-2.0 bya: Oxygen 1.8 bya: first eukaryote

15. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.4 bya: Oldest Fossils 2.3-2.0 bya: Oxygen 1.8 bya: first eukaryote 0.9 bya: first animals

16. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.4 bya: Oldest Fossils 2.3-2.0 bya: Oxygen 1.8 bya: first eukaryote 0.9 bya: first animals 0.5 bya: Cambrian

17. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.4 bya: Oldest Fossils 2.3-2.0 bya: Oxygen 1.8 bya: first eukaryote 0.9 bya: first animals 0.5 bya: Cambrian0.24 bya:Mesozoic

18. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.4 bya: Oldest Fossils 2.3-2.0 bya: Oxygen 1.8 bya: first eukaryote 0.9 bya: first animals 0.5 bya: Cambrian0.24 bya:Mesozoic0.065 bya:Cenozoic

19. I. Earth History 4.5 bya: Earth Forms4.0 bya: Oldest Rocks3.4 bya: Oldest Fossils 2.3-2.0 bya: Oxygen 1.8 bya: first eukaryote 0.9 bya: first animals 0.5 bya: Cambrian0.24 bya:Mesozoic0.065 bya:Cenozoic 4.5 million to present (1/1000th of earth history)

20. II. Origin of Life Hypotheses - Oparin-Haldane Hypothesis (1924): - in a reducing atmosphere, biomonomers would form spontaneously Aleksandr Oparin (1894-1980) J.B.S. Haldane (1892-1964)

21. II. Origin of Life Hypotheses - Oparin-Haldane Hypothesis (1924): - in a reducing atmosphere, biomonomers would form spontaneously - Miller-Urey (1953) all biologically important monomers have been produced by these experiments, even while changing gas composition and energy sources

22. II. Origin of Life Hypotheses - Oparin-Haldane Hypothesis (1924): - in a reducing atmosphere, biomonomers would form spontaneously - Miller-Urey (1953) - Sydney Fox - 1970 - polymerized protein microspheres

23. II. Origin of Life Hypotheses - Oparin-Haldane Hypothesis (1924): - in a reducing atmosphere, biomonomers would form spontaneously - Miller-Urey (1953) - Sydney Fox - 1970 - polymerized protein microspheres - Cairns-Smith (1960-70) - clays as templates for non-random polymerization - 1969 - Murcheson meteorite - amino acids present; some not found on Earth. To date, 74 meteoric AA's. - 2004 - Szostak - clays could catalyze formation of RNA's

24. III. Acquiring the Characteristics of Life A. Three Primary Attributes: - Barrier (phospholipid membrane) - Metabolism (reaction pathways) - Genetic System

25. III. Acquiring the Characteristics of Life B. Barrier (phospholipid membrane) - form spontaneously in aqueous solutions

26. III. Acquiring the Characteristics of Life C. Metabolic Pathways - problem: how can pathways with useless intermediates evolve? These represent 'maladaptive valleys', don't they? ABCDE How do you get from A to E, if B, C, and D are non-functional?

27. III. Acquiring the Characteristics of Life C. Metabolic Pathways - Solution - reverse evolution ABCDE

28. III. Acquiring the Characteristics of Life C. Metabolic Pathways - Solution - reverse evolution E suppose E is a useful molecule, initially available in the env.

29. III. Acquiring the Characteristics of Life C. Metabolic Pathways - Solution - reverse evolution E suppose E is a useful molecule, initially available in the env. As protocells gobble it up, the concentration drops.

30. III. Acquiring the Characteristics of Life C. Metabolic Pathways - Solution - reverse evolution E Anything that can absorb something else (D) and MAKE E is at a selective advantage... D

31. III. Acquiring the Characteristics of Life C. Metabolic Pathways - Solution - reverse evolution E Anything that can absorb something else (D) and MAKE E is at a selective advantage... but over time, D may drop in concentration... D

32. III. Acquiring the Characteristics of Life C. Metabolic Pathways - Solution - reverse evolution E So, anything that can absorb C and then make D and E will be selected for... DC

33. III. Acquiring the Characteristics of Life C. Metabolic Pathways - Solution - reverse evolution ABCDE and so on until a complete pathway evolves.

34. III. Acquiring the Characteristics of Life D. Genetic Systems - conundrum... which came first, DNA or the proteins they encode? DNA RNA (m, r, t) protein

35. III. Acquiring the Characteristics of Life D. Genetic Systems - conundrum... which came first, DNA or the proteins they encode? DNA RNA (m, r, t) protein DNA stores info, but proteins are the metabolic catalysts...

36. III. Acquiring the Characteristics of Life D. Genetic Systems - conundrum... which came first, DNA or the proteins they encode? - Ribozymes info storage AND cataylic ability

37. III. Acquiring the Characteristics of Life D. Genetic Systems - conundrum... which came first, DNA or the proteins they encode? - Ribozymes - Self replicating molecules - three stage hypothesis

38. IV. Early Life - the first cells were probably heterotrophs that simply absorbed nutrients and ATP from the environment. - as these substances became rare, there was strong selection for cells that could manufacture their own energy storage molecules. - the most primitive cells are methanogens, but these are NOT the oldest fossils.

39. IV. Early Life - the second type of cells were probably like green-sulphur bacteria, which used H2S as an electron donor, in the presence of sunlight, to photosynthesize.

40. IV. Early Life - the evolution of oxygenic photosynthesis was MAJOR. It allowed life to exploit more habitats, and it produced a powerful oxidating agent! These stromatolites, which date to > 3 bya are microbial communities.

41. IV. Early Life - about 2.3-1.8 bya, the concentration of oxygen began to increase in the ocean and oxidize eroded materials minerals... deposited as 'banded iron formations'.

42. IV. Early Life - 2.0-1.7 bya - evolution of eukaryotes.... endosymbiosis.

43. IV. Early Life Eukaryote Characteristics - membrane bound nucleus - organelles - sexual reproduction

44. IV. Early Life Origins infolding of membrane

45. IV. Early Life B. Origins endosymbiosis - mitochondria and chloroplasts (Margulis - 1970's)

46. IV. Early Life Relationships among life forms - deep ancestry and the last "concestor"

47. IV. Early Life Woese - r-RNA analyses reveal a deep divide within the bacteria

48. IV. Early Life

50. Curiously, the very root of life may be invisible to genetic analysis. Bacteria transfer genes by division (to 'offspring'), but they also transfer genes "laterally" to other living bacteria. This makes reconstructing bacterial phylogenies difficult.

51. IV. Early Life So, reconstructing the patterns of relatedness among these ancient life forms is difficult. Different genes give different patterns of relatedness among domains

52. IV. Early Life C. Domains - "Ring of Life" hypothesis (2004)