Molecular Evolution and Ecology. Martin Polz

Transcription

1 Molecular Evolution and Ecology Martin Polz

2 Overview I. Molecular evolution 1. History of life on Earth 2. Genes as chronometers 3. Tree of life II. Molecular ecology 1. Prokaryotic abundance and diversity

3 The oldest fossils are ~3,500 Myrs old. History of life on Earth

4 History of life on Earth

5 History of life on Earth

6 How can we study evolution? homologous structures i.e., similar by descent fossil record of intermediate forms but can only study closely related organism, which share significant morphological similarity.

7 Ancestral genes change because of mutations ATCGGCCACTTTCGCGATCA Ancestral sequence ATCGGCCACTTTCGCGATCG ATAGGCCACTTTCGCGATCA ATCGGCCACTTTCGTGATCG ATCGGCCACGTTCGTGATCG ATAGGCCACTTTCGCGATTA ATAGGGCAGTTTCGCGATTA ATCGGCCACGTTCGCGATCG ATAGGGCAGTTTTGCGATTA ATCGGCCACCTTCGCGATCG ATAGGGCAGTTTCGCGATTA ACCGGCCACCTTCGCGATCG ATAGGGCAGTCTCGCGATTA Homologous sequences ACCGGCCACCTTCGCGATCG ATAGGGCAGTCTCGCGATTA

8 can we use this nucleotide change for reconstructing evolutionary relationships? Yes, if mutations accumulate ~ proportional to time since last common ancestor. Neutral theory of evolution: Types of mutations

9 Redundancy of genetic code

10

11 How can estimate evolutionary relationships from sequences? Is the gene present in all organisms of interest? Does it vary sufficiently to resolve the relationships? (Or, does it vary too much?)

12 Bacteria Archaea Ribosomal RNA genes are used as universal chronometers

13 B B A A Bacteria Archaea C A universally conserved B length conserved sequence variable C neither sequence nor length conserved C

14

15 Variable in length Conserved in length but variable in sequence Conserved

16

17

18 Molecular ecology Microbes are small and have few distinguishing features. How can we estimate how many ifferent types (species) are present in the environment? Gene sequences are also fingerprints of organisms

19 Counting: How many microbes are in a sample? 1. Collect environmental sample 2. Concentrate microbes on filter 3. Stain (with fluorescent dyes) 4. View under microscope (with UV light) Filter Stained bacteria 0

20 Global prokaryotic abundance Marine Freshwater Sediments/Soils Subsurface sediments (0-3,000 m) Animal guts Cells/ ml or g x , Total cells x , , (Whitman et al. 1998)

21 B B A A Bacteria Archaea C A universally conserved B length conserved sequence variable C neither sequence nor length conserved C

22 Molecular Diversity of Bacteria and Archaea 2. Lyse cells and purify DNA. DNA PCR 4. Purify rrna genes on a gel, Then separate them by inserting individual rdnas into plasmids. DNA DNA DNA DNA DNA DNA DNA DNA DNA 1. Collect water or soil sample containing bacteria and archaea. 3. Use universal primers to amplify rrna genes in sample by PCR. AGGCTTACCGTAAC Insert plasmids into E.coli cells. The cells grow rapidly to produce millions of copies of each rdna. 6. Purify rdna from plasmids. 7. Sequence rdna; compare to known sequences.

23 Diversity of Coastal Ocean Bacteria ~500 different species in 1 liter seawater

24 Culture collections vs. clones Example: coastal and open Ocean bacterioplankton SAR11 Roseobacter SAR116 SAR86 (gamma) Marine Actinobacteria Picophytoplankton SAR202 (GNS) SAR324 (delta) SAR406 aphotic zone cultured representatives % of Clones Most abundant organisms have eluded cultivation --> need environmental genomics approaches

25 Microbial ecology of the human body Fig. 1. Phylogenetic analysis of bacterial 16S rdna detected in normal skin from six subjects Gao, Zhan et al. (2007) Proc. Natl. Acad. Sci. USA 104, Copyright 2007 by the National Academy of Sciences

26 Fig. 2. Collector's curves of observed and estimated SLOTU richness of pooled forearm skin samples from six healthy subjects Gao, Zhan et al. (2007) Proc. Natl. Acad. Sci. USA 104, Copyright 2007 by the National Academy of Sciences