1. BIOLOGY 2 Chapter 20 PHYLOGENIES AND THE HISTORY OF LIFE 20.1 Organizing Life on Earth 20.2 Determining the Evolutionary Relationships 20.3 Perspectives on the Phylogenetic Tree WHAT SHOULD I KNOW BY THE END: Why do we need a comprehensive classification system? What is the point of science again? What are the different levels of this system? How do systematics and taxonomy relate to phylogeny? What do you find in a phylogenetic tree and why?

2. FIGURE 20.1 The life of a bee is very different from the life of a flower, but the two organisms are related. Both are members the domain Eukarya and have cells containing many similar organelles, genes, and proteins. (credit: modification of work by John Beetham)

3. FIGURE 20.2 Both of these phylogenetic trees shows the relationship of the three domains of life— Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba) PHYLOGENY: relationships among organisms and their evolutionary history, provides shared ancestry but NOT similarities & differences

4. FIGURE 20.3 The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy. Important point: while the sister taxa have common ancestor, they did not evolve from each other, neither taxa gives rise to the other. Note: Length of time is not indicated by the branches! But does indicate the order of appearance

5. FIGURE 20.4 This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share. SYSTEMATICS: data-based organizing and classifying organisms based on evolutionary relationships, e.g, DNA analysis (genetic) and fossils, (morphologic) Consider that relationships do not imply similar appearances! You can look like something else but not be closely related to them Interactive Tree of Life: http://openstaxcollege.org/l/tree_of_lifehttp://openstaxcollege.org/l/tree_of_life

6. FIGURE 20.5 The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo. (credit “dog”: modification of work by Janneke Vreugdenhil) TAXONOMY: Science of classifying organisms Recall chapter 15: Carl Linnaeus So we become more specific and selective the “deeper” we go with organisms appearing more SIMILAR….. NOTE that there are also “super” and “sub” when need to make some distinctions. Think of this as an agreed upon “sorting process” What is binomial nomenclature?

7. FIGURE 20.6 At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. (credit “plant”: modification of work by “berduchwal”/Flickr; credit “insect”: modification of work by Jon Sullivan; credit “fish”: modification of work by Christian Mehlfu ̈ hrer; credit “rabbit”: modification of work by Aidan Wojtas; credit “cat”: modification of work by Jonathan Lidbeck; credit “fox”: modification of work by Kevin Bacher, NPS; credit “jackal”: modification of work by Thomas A. Hermann, NBII, USGS; credit “wolf”: modification of work by Robert Dewar; credit “dog”: modification of work by “digital_image_fan”/Flickr) AT WHAT LEVEL ARE DOGS & CATS THE SAME? http://www.pbs.org/wgbh/nova/nature/c lassifying-life.html

8. 20.2 DETERMINING EVOLUTIONARY RELATIONSHIPS So did you figure out basic language and purpose? NOW What are homologous and analogous traits, recall chapter 15 What is maximum parsimony? What does cladistics accomplish?

9. FIGURE 20.7 Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM) Overlap in form and genetics will render you homologous

10. FIGURE 20.8 The (c) wing of a honeybee is similar in shape to a (b) bird wing and (a) bat wing, and it serves the same function. However, the honeybee wing is not composed of bones and has a distinctly different structure and embryonic origin. These wing types (insect versus bat and bird) illustrate an analogy—similar structures that do not share an evolutionary history. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM; credit c: modification of work by Jon Sullivan) Analogous: similar characteristics due to environmental factors not an evolutionary relationship http://peabody.yale.edu/exhibits/tree-of-life/what-phylogenetic-relationship

11. FIGURE 20.10 Lizards, rabbits, and humans all descend from a common ancestor that had an amniotic egg. Thus, lizards, rabbits, and humans all belong to the clade Amniota. Vertebrata is a larger clade that also includes fish and lamprey. How to build a Phylogenetic Tree: organize the homologous traits using cladistics Okay, so what are clades (aka monophyletic)? Groups of organisms from SINGLE ancestor, includes all the descendants from a branch point Which animals belong to a clade which includes animals with hair?

12. FIGURE 20.11 All the organisms within a clade stem from a single point on the tree. A clade may contain multiple groups, as in the case of animals, fungi and plants, or a single group, as in the case of flagellates. Groups that diverge at a different branch point, or that do not include all groups in a single branch point, are not considered clades.

13. SO HOW DOES THIS HAPPEN? 1)Change in genetic makeup = new trait (how does this happen again?) 2)New trait becomes prevalent (how does that happen?) 3)Many organisms descend from this and trait is retained 4)New variations arise and are adaptive and persist (WHAT!) 5)A branch point occurs 6)Repeat and pretty soon there are millions

14. BEFORE WE MOVE ON….. What is maximum parsimony and how does this help? This task of organizing based on homologous characteristics and DNA is NOT straight forward and HOW do you decide the order and importance of connections? When in doubt assume the simplest and most obvious. Look for the most simple order and obvious evolutionary events to cause the traits to appear and diverge http://evolution.berkeley.edu/evolibrary/article/usingparsimony_01

15. SECTION 20.3 PERSPECTIVES ON THE PHYLOGENETIC TREE The (a) concept of the “tree of life” goes back to an 1837 sketch by Charles Darwin. Like an (b) oak tree, the “tree of life” has a single trunk and many branches. (credit b: modification of work by “Amada44”/Wikimedia Commons) Okay….so you now can define homologous and analogous structures, what a clade is, and what maximum parsimony NOW Describe horizontal gene transfer How this transfer occurs in prokaryotes and eukaryotes What are the other models of phylogenetic relationships

16. DYNAMIC FIELD & NEW TECHNOLOGIES, NEW DISCOVERIES (a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi, and scientists speculate that aphids acquired these genes through HGT after consuming fungi for food. If genes for making carotenoids are inactivated by mutation, the aphids revert back to (b) their green color. Red coloration makes the aphids a lot more conspicuous to predators, but evidence suggests that red aphids are more resistant to insecticides than green ones. Thus, red aphids may be more fit to survive in some environments than green ones. (credit a: modification of work by Benny Mazur; credit b: modification of work by Mick Talbot) HORIZONTAL (Lateral) GENE TRANSFER: Genes transferred between unrelated species? WHAT and HOW? Note what is vertical gene transfer?

17. HGT IN PROKARYOTES So you are probably most familiar with the transfer of antibiotic resistance ….So HOW does this happen? See table 20.1 1)Transformation (naked DNA) 2)Transduction (virus) 3)Conjugation (recall from chapter 4) 4)Gene transfer agents (virus-like)

18. WHAT ABOUT THE EUKARYOTES? This group has multicellular organisms and sex cells are sequestered in protected areas. In plants we have transposons (Dr. Barbara McClintok) Fungal species feeding on the yew tree have acquired taxol making abilities Example of the aphids and the fungus, fig 20.13

19. THE ULTIMATE IN HGT = GENOMIC FUSION The theory that mitochondria and chloroplasts are endosymbiotic in origin is now widely accepted. BUT Try this one on: More controversial is the proposal that (a) the eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes, and that (b) Gram-negative bacteria, which have two membranes, resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane. Note that due to DNA analysis, we have discovered that eukaryotes probably did not evolve from Archaea and in fact we are closer to bacteria in SOME ways

20. SO THE ORIGIN OF EUKARYOTES Three alternate hypotheses of eukaryotic and prokaryotic evolution are (a) the nucleus first hypothesis, (b) the mitochondrion-first hypothesis, and (c) the eukaryote-first hypothesis. Remember that the nucleus and organelles with membranes are the BIG dividing points Some bacteria have chromosome in a membrane but it is not a nucleus And some bacteria have DNA enclosed by 2 membranes

21. WEB AND NETWORK MODELS In the (a) phylogenetic model proposed by W. Ford Doolittle, the “tree of life” arose from a community of ancestral cells, not a single ancestor and has multiple trunks, and has connections between branches where horizontal gene transfer has occurred. Visually, this concept is better represented by (b) the multi-trunked Ficus than by the single trunk of the oak similar to the tree drawn by Darwin Figure 20.12. (credit b: modification of work by “psyberartist”/Flickr)

22. OK, HOW ABOUT THIS: RING OF LIFE According to the “ring of life” phylogenetic model, the three domains of life evolved from a pool of primitive prokaryotes. Make no concessions for this “tree-thing” AND acknowledge the importance of “genetic exchange” in the evolution of life

23. SO WE DO HAVE TO MODIFY THE TREE BUT HOW MUCH DEPENDS ON THE DATA Driven on by discovery reshaping the tree is essential This chapter begins our look at taxonomy and systematics to help us understand life on this planet by relationships and change through time