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Biological Diversity: a molecular re-analysis
• Phylogenetic refresher• History of kingdom conceptions• Molecular re-analysis of organism
Enter on the Scene: Molecular phylogenyPace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html
* By comparing macromolecular sequences, we can calculate evolutionary distances between organisms
Organism A is 70% identical to organism B,Fractional identity is 0.70,30% different.
* You can't compare sequences unless they are homologous - of common ancestry. Homologous sequences are not necessarily identical and identical sequences are not necessarily homologous
HOMOPLASY
Which molecules should be used?Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html
Need to: a) Be homologous and occur in all organisms consideredb) Have enough nucleotides or amino acids to be statistically robustc) Changes have to exist across the evolutionary distance—i.e. not be
randomized
• originated with protein sequences, since 1980s easier to isolate and sequence genes
• most common choice - ribosomal RNAs• Effect protein synthesis• Present in all organisms (& major organelles)• Large enough for reasonable statistics
d) No lateral transfer – genes have to be related by decent rather than jumping
How is a tree made from sequence data?Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html
1. Align sequences in pairs & count the number of changes2. Correct for multiple back mutations at any given site3. Computer fit overall tree to best fit pair wise dist.
Close to 3000 sequences available as of 1999
And they immediately began to indicated that major tree re-arrangement was necessary
Brooker et al 2011
Pace Science 2 May 1997:Vol. 276. no. 5313, pp. 734 - 740
What are the differences?
Key differences in the diagramsMorphological Phylogeny Molecular Phylogeny
Subjective & Qualitative Objective & quantitative
Branch length is meaningless Branch length indicates evolutionary dist.
Higher (superior) & lower (inferior) positions are suggestive of hierarchy
No (less?) hierarchy is suggested
Fungi, plnts & animals 3/5 of total diversity Multicellular Eukarya just tip of 1 branch
Eukaryotes evolve from prokaryotes Eukaryotes as ancient as and separate from prokaryotes
Prokaryotes 1/5 or 2/6 of Tree Prokaryotes fill 2/3 of tree (2 of 3 domains)
No comparison between kingdoms All organisms can be compared
Includes mitochondria & chloroplasts(support endosymbiont theory of origin)
Published by AAAS
S. L. Baldauf et al., Science 290, 972 -977 (2000)
kingdom-level phylogeny of eukaryotes, based on combined protein sequences
Drilling (back) down one level…Focus on the Eukaryotes
Published by AAAS
S. L. Baldauf et al., Science 290, 972 -977 (2000)
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Your textbook (Brooker 2011)
* So, in conclusion, molecular phylogeny is leading to drastic changes in our understanding of evolutionary history between and among “kingdoms”
*Understanding all of the underlying mechanisms you will learn about in Bio43 informs our understanding of the relatedness, sameness and differentness which is the stuff of organismal biology (Bio 44)
*Where will your textbook need major revision?
Main sources: http://tinyurl.com/jameswbrown http://tinyurl.com/normpace