BIOL 1010 Introduction to Biology: The Evolution and Diversity of Life. Spring 2011 Sections A & B

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1 BIOL 1010 Introduction to Biology: The Evolution and Diversity of Life. Spring 2011 Sections A & B Steve Thompson: 1

2 ʻTree of Life,ʼ ʻprimitive,ʼ ʻprogressʼ & ʻcontingencyʼ... or... getting used to treethinking. Nothing in evolutionary biology makes sense except in the light of a phylogeny. J. M. Savage (1997) 2

3 Phylogenetics! from the Greek phyllon for leaf. It... Is the study of the branching patterns of the tree of life, i.e. how all organisms (the leaves of the tree) are related, one to another. The focus can be on individuals within a population, a genealogy of paternity; on species within any larger category, such as within a Phylum or even all the way up to all of life, a species tree of speciation events; or it can even be of genes or genomes, a gene tree, which reflects DNA duplications and/or speciation events. 3

4 The text very briefly touches on this. We ll go way further. Let s start with what the text says: Tree diagrams are known as evolutionary trees or phylogenies. So far, so good. They... Depict a species (or molecule s) relationships based on descent from common ancestors (OK); where the... Branching indicates divergence (OK); and... Discontinuation is extinction (still OK). (However,... ) The angle of a branch point indicates gradualism versus punctuated equilibrium (not a standard convention, at all!) Originally derived from fossil data (and living species morphological characters, i.e. the way things look!), but... Newer molecular data is based on all sorts of different DNA sequences [not just mitochondrial DNA (mtdna)]! 4

5 A couple of examples are shown: OK, with the caveats I just made. 5

6 But let s talk about where these come from, what good they are, and their historical context. Perhaps the very first use of the tree metaphor was by Lamark in 1809 (remember inherited acquired characters ). But trees were clearly on Darwin s mind in

7 By the time Haeckel came around, he was clearly treethinking (in 1879). It s surprisingly insightful, albeit overly progressive with MAN at the top! 7

8 And by the time I was in school everybody knew their were five kingdoms of life. This became dogma, as proposed by Whittaker (1969) and endlessly expounded upon, e.g. Margulis (1998). 8

9 However, as we ve seen, this is bogus. Carl Woes was the first to suggest it Archaea. 9

10 The three domains of life... And there s WAY more diversity (number of critters) in the Bacteria and Archaea, than the Eukarya! Plus, Bacteria and Archaea are just as advanced as we are they work great in the environments in which they live. 10

11 But lateral gene transfer and primordial endosymbiosis considerably confounds the picture... e.g. as portrayed by W. Ford Doolittle (1999), and popularized by Lynn Margulis. 11

12 Here s a nice, albeit still too darn progressive and overly simplistic, video from the Wellcome Trust fund: 12

13 There are lots of Web resources for exploring the tree of life Here s a few of them: atol.sdsc.edu/ tellapallet.com/ tree_of_life.htm node/

14 OK, so what? What good are trees? Lots of interesting practical applications beyond just scientific curiosity. 14

15 How about upcoming flu seasons? 15

16 And discovering the origin of HIV... HIV in North America came from Haiti! 16

17 Plus, phylogenomics helps us predict the function of unknown genes. 17

18 Still more applications... Drug Discovery predicting natural ligands for cell surface receptors that are potential drug targets (e.g., G- protein coupled receptors). Vaccine development engineer vaccines to confer immunity against multiple virus populations by targeting their inferred common ancestors. Protein structure prediction. OK! I m convinced. How are they built? 18

19 To begin at the beginning Organisms have a history. 2 Parental strain 0 diverged into two different strains over time, strain 1 and strain 2. 19

20 Many trees show evolutionary distance A s 1 s 4 C Branch lengths represent this. s 3 They re additive... B s 2 s 5 D The distance from A to D is S1 + S3 + S5, etc. 20

21 Common Phylogenetic Tree Terminology 21

22 Rooting a tree establishes the direction of evolution Evolution is now proceeding from an ancestor midway between everybody. And now I need six volunteers from the audience! 22

23 How are trees rooted? The best way is with other evidence. 23

24 The goal of phylogeny inference is to resolve the branching orders of lineages in evolutionary trees. 24

25 There are three possible unrooted trees for four taxa (A, B, C, D) 25

26 This is tough because... the number of unrooted trees increases in a greater than exponential manner with the number of taxa. 26

27 But, HOW are trees estimated? This falls way outside the realm of this course, but I encourage you to pursue the knowledge if you are interested. I can help! The principles are similarity (shared common features) and parsimony (Occam s razor), though they extend way beyond these most similar is not necessarily most related. Suffice it to say, that we now have REALLY good methodology that works REALLY well for reconstructing phylogenies based on molecular (DNA, RNA, or protein) data. These trees are real! The conclusions are valid. 27

28 That s plenty for now. Next time we ll start to survey examples of evolution at work... Seeing evolution... First in morphologies, i.e. how things look, and... Second in molecules, i.e. DNA and the products it encodes. 28

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