What examples can you think of? Geocentrism Heliocentrism: Copernicus, Kepler,

Newton, Galileo

Alchemy Nature of the chemical bond (Rutherford, Pauling…)

Aristotelian  view  of  the  biosphere   Woese/Pace (subject of today!)

This is a dynamic process!���- Some of these ideas were known and lost, then found again. ���- We are not done. We can only work with what we understand at the time.

Can you think of others?���

Woese and Fox, 1977 •  All cellular life falls into one of 3 large groups:

-Eukaryotes, Eubacteria, Archeabacteria

•  Used 16S rRNA sequencing to classify life. This choice of a molecular chronometer was very thoughtful. Why?

•  All life is phylogenetically related on the molecular level!

•  Evolutionary and microbiology connected, microbes are central to studying biosphere

Pace,  PNAS  2012  

________  

Technology has changed the way we ask questions in science

16S rRNA sequencing in 1977 vs. now are very different.

Ribosome: 50% RNA, 50% protein. ���Small subunit 16S rRNA is in all organisms because it’s involved in essential function inside cell.

It is a marker for relating organisms through evolutionary history, and has changed how evolutionary trees were viewed.

What  is  “S”?    Answer    =  a  unit  for  sedimentaAon  rate      

Discuss: 1. Why is 16S a good molecule to use for relating organisms? What other molecules can be used for this purpose?

2. Claim: fundamental  concepts  in  biology  are  rapidly  evolving,  unlike  in  physics  and  chemistry.    Do  you  agree?     3. How to root the tree of life? Universal common ancestor? What do you think of the progenote?

Introducing David and Alm paper  

Summary:

The authors analyze distribution of gene families in modern species

• Gene family: a set of genes which arose from duplication of one gene. Usually code for similar functions.

To do this, the authors developed a mathematical/computational model that uses modern genomes to mimic evolution of ancient organisms.  

Introducing David and Alm paper  

Conclusions: ���

• Ancient environmental change 3.3-2.8 billion years ago caused huge expansion in diversity of genes: 27% of genes today are a result of the evolution that happened during the Archaean expansion.

• Those genes allowed microbes to make energy from photosynthesis through electron transport. They released a lot of oxygen into the atmosphere, an event for which there is evidence today.

• Horizontal gene transfer played a big role… let’s talk about that.

Video  

•  hHp://glencoe.mcgraw-­‐hill.com/sites/9834092339/student_view0/chapter24/horizontal_gene_transfer.html  

Conceptual tree of life ���with and without extinct lineages

Through  HORIZONTAL  GENE  TRANSFER  (HGT),  molecules  from  now-­‐exAnct  lineages  might  have  survived  in  today's  organism.    

Zhaxybayeva  and  Gogarten  (2004)  Trends  in  GeneAcs  20  (4)  

Does  this  mean  anything  for  16S  RNA  sequencing-­‐based  tree-­‐making?  

Let’s  put  geological  history    into  perspecAve  

More  detailed  Ameline:  hHp://exploringorigins.org/Ameline.html  

4.5   4.0   3.5   3.0   2.5   2.0   0.5   0.0  

Earth  forms  

~4.6  bya  

Oldest  evidence  for  

life  

Evidence  for  oxygen  in  atmosphere  

PhotosyntheAc  microbial  mats  

First  Eukaryotes  

1.0  1.5  

Cambrian  radiaAon  

[Time  (bya)]  

0.5   0.4   0.3   0.2   0.1   0.0  0.6  

Paleozoic   Mesozoic   Cenozoic  

oldest  definite  mulAcellular  life  

Ediacaran  

PHANEROZOIC  

Sketch a geological timeline on a clock���

Include  the  Following:  1.  FormaAon  of  Earth  2.  Oldest  Evidence  for  Life  3.  PhotosyntheAc  Microbial  Mats  4.  Oxygen  in  the  Atmosphere  5.  First  Eukaryotes  6.  Cambrian  RadiaAon  

Approximate  Time:    1.  4.6  bya  2.  3.8  bya  3.  3.4  bya  4.  2.4  bya  5.  1.6  bya  6.  0.6  bya  

4.6  bya  +  Today  

Final questions •  The difference between two strains of microorganisms is

superficially much more subtle than the obvious difference between a person and a flower, but the evolutionary distance between two microbes is often much larger than the distance between humans and plants. What do you think about this?

•  Many questions remain about the “best” way in which living things can be classified according to their relationships with one another. For example, should the molecular diversity exhibited by microbes be compared on an equal plane with the much more apparent morphological differences found in eukaryotes? What type of classification system do you think makes sense?

Pace,  PNAS  2012  

Video and Website •  Summary of Woese and Pace contributions on

the creation of the phylogenetic tree of life ���http://www.microbeworld.org/index.php?option=com_content&view=category&layout=blog&id=54&Itemid=195���http://getmadcat.com/video/49797/Solving-the-Puzzle.html

•  Tree of life with extinct lineages—some sequences survive through HGT���http://gogarten.uconn.edu/