Lecture 2: Describing Microbial Diversity: the ... - MCD Biology

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24 C. Highly conserved throughout evolution; e.g., ca. 50% identity between E. coli and human SSU rRNAs over alignable nt 1. Length variation between molecules may cause problems; must consider only “homologous” nt (the alignment problem - more later). 2. Note that rRNA, while useful for distantly related organisms, is not good for establishing (resolving) close relationships: it is too conservative. Consequently, close relatives have too few differences to be reliable. e.g. human/apes/mice have the same rRNA seqs. e.g. E. coli and Yersinia pestis (causes Black Plague) have essentially the same rRNA seqs. D. The rRNA genes are large enough for reasonable statistics (more later on this). E. First used for all-life phylogenetic trees by Carl Woese (University of Illinois). For historical overview; Pace et al. “Phylogeny and beyond: scientific, historical and conceptual significance of the first tree of life.” Proc. Natl. Acad. Sci. 109:1011-1018, 2012. 9. Given sequences of multiple organisms (>2 million now available, but spotty representation of diverse phyla – MMBR reference): $Align seqs., count number of differences -- is some measure of evolutionary change/distance
25 $”Correct” for multiple and back mutations – the number of changes you count is always less than the number of mutations that have occurred. $Computer-fit pairwise “evolutionary distances” to best-fit overall tree topology. (More detail on all this below) 10. The “Big Tree” emerges: Outlines first seen by Woese in 1977. A. Note that Woese did not have tree-building methods now available. In fact, he did not have full sequences, only short “signature” oligonucleotides (more on “signatures” later.
Page 1 and 2: Lecture 2: Describing Microbial Div
Page 3 and 4: 3 A. Slowly evolving molecules (e.g
Page 5 and 6: 5 B. Phylogenetic perspective allow
Page 7 and 8: 7 Indeed, the lexicon of biology st
Page 9 and 10: 9 A. Still, “monera” (mostly te
Page 11 and 12: 11 4) Supposition that the eucaryot
Page 13 and 14: 13 3) You cannot meaningfully compa
Page 15 and 16: Note that organism-to-node “dista
Page 17: 17 Vignette - Tree-reading - Baum,
Page 20 and 21: 20 A. Doesn’t really matter so lo
Page 22 and 23: 22 3. Changes must span the evoluti
Page 26 and 27: B. In essence, the tree is a quanti
Page 28 and 29: 28 Bacteria C. The eucaryote nuclea
Page 30 and 31: 30 H. Note how deeply divergent are
Page 32 and 33: 32 You can download trees, carry ou
Page 34 and 35: 34 C. Most of what we know about ba
Page 36 and 37: 36 B. Environmental sequences have
Page 38 and 39: 38 A. Note that the microbial eucs
Page 40 and 41: 19. The three-domain tree is seen f
Page 42: 42 D. Even enzymes in the same bios
Page 45: Gary Olsen edits the Doolittle tree

Lecture 2: Describing Microbial Diversity: the ... - MCD Biology

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