Biological Diversity: a molecular re-analysis<br /><ul><li>Phylogenetic refresher
History of kingdom conceptions
Molecular re-analysis of organism grouping</li></ul>Jason Price, PhD<br />Science Librarian<br />Jason.price@cuc.claremont...
The fundamental question in evolutionary biology<br />Why are some biological traits the same and others different among a...
One aspect of the answer: phylogeny<br />Why are some biological traits the same and others different among a given group ...
Morphology alone<br />Bill Sellers: http://homepage.mac.com/wis/Personal/lectures/human-evol/2.html<br />
2 types of similarity <br />Homology: (agreement)  <br />similar traits from a shared ancestor<br />e.g. Forelimb skeletal...
Why does tree accuracy matter?<br />To predict the properties of organisms based on their relatives <br />To prevent inacc...
What has this got to do with Bio43?<br />You’ll study other types of “morphology” far richer than external characters….<br...
History of kingdom conceptions…<br />
http://www.mbio.ncsu.edu/MB451/lecture/evolutionaryConcepts/lecture.html James W. Brown<br />1. Ladder of life<br />2. Dar...
Time  (and Superiority?)<br />Eukaryotes from prokaryotes<br />
Purves, Orians, Heller 1995<br />
Enter on the Scene: Molecular phylogeny<br />Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.h...
Which molecules should be used?<br />Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html<br /...
 most common choice - ribosomal RNAs
Effect protein synthesis
Present in all organisms (& major organelles)
Large enough for reasonable statistics</li></li></ul><li>How is a tree made from sequence data?<br />Pace 1999 http://plan...
Brooker et al 2011<br />
Pace Science 2 May 1997:Vol. 276. no. 5313, pp. 734 - 740<br />
What are the differences?<br />
Key differences in the diagrams<br />
Drilling (back) down one level…Focus on the Eukaryotes<br />kingdom-level phylogeny of eukaryotes, based on combined prote...
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Biological Diversity: a molecular re-analysis

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  • We’ll look into more detail about this last example a bit later.
  • And where small biology meets big biology cool things are bound to happen…
  • -Organize living and non-living things-Great chain of being, rungs or links, -pre-evolutionary, no scientific basis, yet embedded on modern biological unconscious thought-e.g. evolutionary ladder, higher &amp; lower eukaryotes and ‘missing links’-------------Darwin: species originate by divergence-Do species A &amp; I exist at the end? No or at least major change from original(redraw splits)-species evolve from diversification, not progression; eukaryotes did not evolve from bacteria, animals not from ciliates, humans NOT from chimps—each of these pair of organisms share a common ancestor from which BOTH diverged--simple vs primitive, all current orgs products of 4 billion yrs of evolution----------1866 Haeckel’s divergent evolutionary tree– darwin’s structure with detail3 divisions of life-plants, protists, animals, Major improvement—species not ranked, modern species not ancestors of other modern orgs, plants and animals not thought of as evolved from prok/moneransHow are Darwins &amp; Haeckel’s tree different?
  • “5 kingdom scheme”, reintroduces some chain of being ideas, prokaryotes replaced by eukaryotes?!?
  • 1969 Whitaker –relationships among microbes, prokary &amp; eukary speculative at best; no criteria to relate orgs BETWEEN kingdoms1995 – 4th edition of your text book, still see strong ladder of life influence, based on morphology-one step in the right direction– addition of archaebacteria
  • Unrooted – cant be inferred from rRNA – no outgroupTwo domains of prokaryotes as diff from each other as from eukLines not all the same length different rates of evolutionSeem to characterize domainsPhylogenetic region of multicellular euk shallow/limited despite extreme diversity of phenotype
  • Model not hypothesis, map based on discrete data
  • This highly simplified evolutionary tree shows the traditional phyla — Ascomycota, Basidiomycota, Glomeromycota, Zygomycota and Chytridiomycota. The Ascomycota and Basidiomycota are united as the dikarya, fungi in which part of the life cycle is characterized by cells with paired nuclei. Their closest relatives seem to be the Glomeromycota, a group that was previously included within the Zygomycota. Neither the Zygomycota nor the Chytridiomycota are monophyletic groups; instead they seem to be &apos;paraphyletic grades&apos; that are grouped only by shared primitive morphologies. Also shown are the microsporidia and Rozella branches, which seem to be basal to the all other fungi. (Note that all of these branches are still in need of stronger statistical support James and colleagues&apos; much more detailed tree1 appears on page 820.)
  • Fig 1 Monophyletic based on juvenile &amp; adult morphologyFig 2 Polyphyletic based on primary structures of macromoleculesSolves prob of homology, assessment independent of morph, biochemMultiple origins of muscle and nervous tissue (move of cnidarians)Red lines- Radiations 1- precamb, diverse new niches protist radiation, some of which gave rise to animals2- bilateral symmetry – locomotion/sensory3-coelom –larger body sizes etc
  • Biological Diversity: a molecular re-analysis

    1. 1. Biological Diversity: a molecular re-analysis<br /><ul><li>Phylogenetic refresher
    2. 2. History of kingdom conceptions
    3. 3. Molecular re-analysis of organism grouping</li></ul>Jason Price, PhD<br />Science Librarian<br />Jason.price@cuc.claremont.edu<br />Main sources: http://tinyurl.com/jameswbrown<br />http://tinyurl.com/normpace<br />
    4. 4. The fundamental question in evolutionary biology<br />Why are some biological traits the same and others different among a group of organisms?<br />e.g. Why are most plants green? vs Why is there such variation in flower color? <br />e.g. Why are prokaryotes all single-celled while eukaryotes vary so much in body size?<br />These types of questions, asked at every level of organization are fundamental to scientific questions about why things are the way they are.<br />
    5. 5. One aspect of the answer: phylogeny<br />Why are some biological traits the same and others different among a given group of organisms?<br />Phylogeny: Phylon = race/class –geny = born<br /> The history of the descent of a group of organisms [from their common ancestor]<br />We construct these groups (and their histories) based on estimates of similarity between organisms<br />
    6. 6.
    7. 7. Morphology alone<br />Bill Sellers: http://homepage.mac.com/wis/Personal/lectures/human-evol/2.html<br />
    8. 8. 2 types of similarity <br />Homology: (agreement) <br />similar traits from a shared ancestor<br />e.g. Forelimb skeletal anatomy of birds and bats<br />Homoplasy: (-plasia molding) similar traits not from shared ancestry<br />Convergent evolution: e.g. Wings in birds and bats<br />Evolutionary ‘reversals’ e.g. <br />http://thelifewire.com Chapter 25; interactive quizzes #2<br />
    9. 9. Why does tree accuracy matter?<br />To predict the properties of organisms based on their relatives <br />To prevent inaccurate comparisons<br />E.g. euglena for study of photosynthesis in plants<br />Between not-so-distantly-related outgroups<br />C. elegans& D. melanogaster<br />
    10. 10. What has this got to do with Bio43?<br />You’ll study other types of “morphology” far richer than external characters….<br />Biochemistry<br />Cell Biology<br />DNA -> Protein<br />Genetics<br />Anatomy & Physiology<br />
    11. 11. History of kingdom conceptions…<br />
    12. 12. http://www.mbio.ncsu.edu/MB451/lecture/evolutionaryConcepts/lecture.html James W. Brown<br />1. Ladder of life<br />2. Darwin: species originate by divergence<br />3.<br />
    13. 13. Time (and Superiority?)<br />Eukaryotes from prokaryotes<br />
    14. 14. Purves, Orians, Heller 1995<br />
    15. 15. Enter on the Scene: Molecular phylogeny<br />Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html<br />* By comparing macromolecular sequences, <br />we can calculate evolutionary distances between organisms<br />Organism A is 70% identical to organism B,Fractional identity is 0.70,30% different.<br />HOMOPLASY<br />* 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<br />
    16. 16. Which molecules should be used?<br />Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html<br />Need to: <br /> Be homologous and occur in all organisms considered<br /> Have enough nucleotides or amino acids to be statistically robust<br /> Changes have to exist across the evolutionary distance—i.e. not be randomized<br />d) No lateral transfer – genes have to be related by decent rather than jumping<br /><ul><li> originated with protein sequences, since 1980s easier to isolate and sequence genes
    17. 17. most common choice - ribosomal RNAs
    18. 18. Effect protein synthesis
    19. 19. Present in all organisms (& major organelles)
    20. 20. Large enough for reasonable statistics</li></li></ul><li>How is a tree made from sequence data?<br />Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html<br />Align sequences in pairs & count the number of changes<br />Correct for multiple back mutations at any given site<br />Computer fit overall tree to best fit pair wise dist.<br />Close to 3000 sequences available as of 1999<br />And they immediately began to indicated that major tree re-arrangement was necessary<br />
    21. 21. Brooker et al 2011<br />
    22. 22. Pace Science 2 May 1997:Vol. 276. no. 5313, pp. 734 - 740<br />
    23. 23.
    24. 24. What are the differences?<br />
    25. 25. Key differences in the diagrams<br />
    26. 26. Drilling (back) down one level…Focus on the Eukaryotes<br />kingdom-level phylogeny of eukaryotes, based on combined protein sequences<br /> S. L. Baldauf et al., Science 290, 972 -977 (2000) <br />Published by AAAS<br />
    27. 27. No Caption Found<br /> S. L. Baldauf et al., Science 290, 972 -977 (2000) <br />Published by AAAS<br />
    28. 28. Your textbook (Brooker 2011)<br />
    29. 29. * So, in conclusion, molecular phylogeny is leading to drastic changes in our understanding of evolutionary history between and among “kingdoms”<br />*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)<br />*Where will your textbook need major revision?<br />Main sources: http://tinyurl.com/jameswbrown<br />http://tinyurl.com/normpace<br />
    30. 30. The next great revolution?<br />Doolittle 2000<br />Scientific American<br />282(2):90-95<br />
    31. 31. Fmi: http://www.talkingsquid.net/archives/663<br />
    32. 32. Evolutionary biology: A kingdom revised<br />Tom Bruns Nature 443, 758-761(19 October 2006) doi:10.1038/443758a<br />
    33. 33. Drilling down one more level…to multicellular animals<br /><ul><li>Molecular Phylogeny of the Animal Kingdom
    34. 34. Katharine G. Field, Gary J. Olsen, David J. Lane, Stephen J. Giovannoni, Michael T. Ghiselin, Elizabeth C. Raff, Norman R. Pace and Rudolf A. Raff
    35. 35. Science, New Series, Vol. 239, No. 4841 (Feb. 12, 1988), pp. 748-753 </li></li></ul><li>http://www.mbio.ncsu.edu/MB451/lecture/evolutionaryConcepts/lecture.html<br />
    36. 36. Review: Eukaryotes vs Prokaryote<br />
    37. 37.
    38. 38. Which is false? <br />A. The positions of branches on the x axis indicates the order in which lineages split. <br />B. The x axis of the phylogenetic tree represents time. <br />C. The y axis of the phylogenetic tree shows degree of similarity between contemporaneous species. <br />D. A split in the tree indicates the formation of two new species. <br />E. The break points of the tree are determined by the appearance of particular derived traits.<br />
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