bio engineering

Assignment 4: Tree of Life (270 pts)

Goals: learn about the origins and diversity of life on Earth and the relationships between organisms

Preface

Darwinian “Tree of Life”

In his book the “Origin of Species,” Darwin, very poetically, proposed a representation of a tree to map the phylogeny of living and extinct organisms:

“The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”

— Darwin, 1859.

Figure 1: The tree of life image that appeared in Darwin's On the Origin of Species, 1859. It was the book's only illustration.

After Darwin’s book, many scientists were inspired to make a Tree of Life based on their own observations of the species they studied.

Mivart’s Tree of Life

One of the first Darwinian Trees to be published was by St. George Mivart in 1865. He analyzed the similarities and differences of primate spinal columns to create his Tree of Life. Mivart’s tree generally follows the form of placing the order Primate as the trunk and giving each branch a genus name (exception is nycticebinae [slow loris]).

Figure 2: Mivart’s Tree of Life

1. Discovery: Look up one of the primates on Mivart’s Tree of Life (except Nycticebinae and its branches). Enter its name as found on the Tree of Life, it’s common name, it’s geographic location and one thing you find interesting about them. (30 pts)

Haeckel’s Tree of Life

Around the same time that Mivart’s book was being published, other scientists were publishing their own interpretations of Darwin’s Tree of Life. These drawings varied depending on the scientists’ interpretation of Darwin’s theory of evolution as well as their own studies of animal biology. Ernst Haeckel published his Tree of Life in 1866 using comparative morphology and embryology in his design.

Figure 3: Haeckel’s Tree of Life

2. Compare and Contrast: Describe two similarities and two differences in the structure, content, or labeling between Haeckel’s Tree of Life and Mivart’s Tree of Life. (30 pts)

One Zoom

The study of the biology of living species combined with the information gained via the fossil record enabled scientists to construct an idea of relationships between species and determine the time period of their last common ancestor. We can combine this past knowledge with modern genetic sequencing to create a more informative Tree of Life. One such open source project that uses genetic information to create their tree is One Zoom. (Information about the data One Zoom uses can be found in the About section http://www.onezoom.org/about.html)

Warning: One Zoom requires a lot of computer resources. If the browser is running slowly, please close all other tabs, windows and programs. Also scroll slowly through the One Zoom tree or use the navigation buttons in the bottom right.

Navigate to One Zoom (http://www.onezoom.org/), click on the Explore button and select “All complex life”:

3. Application: Clicking on “All complex life” or searching on “complex life” will take you to Eukaryotes. Zoom out to All Life (Hint: You can also use the navigation toolbar in the bottom left to determine where in One Zoom you are. Hovering over the compass icon will show your current location as well the last common ancestors up to All Life. Click the “-” button to zoom out or the “^” button to go back one ancestor”). You should see two branches coming from All Life. What are the two major types of life according to One Zoom, i.e. the two it splits into at the base of its tree of life? (10 pts)

4. Explore: On one of the branches coming from the root of all life, One Zoom claims “2125 million years ago during the Rhyacian Period, lived the most recent common ancestor of today’s Archaea and Eukaryotes” Give two reasons why some scientists doubt this. (20 pts)

5. Application: Navigate back to Eukaryotes. According to One Zoom, approximately how long ago did the last common ancestor of Eukaryotes live? During what eon was this? (Note, not the period, but the eon.) According to One Zoom how many Eukaryotic species evolved from this last common Eukaryotic ancestor? (20 pts)

6. Application: The tallest tree in the world is Hyperion, a coast redwood (Sequoia sempervirens) found in California’s Redwood National Park. It has a height of 115 meters (~380 feet), making it taller than the Statue of Liberty. Name the two closest living relative species of the species Sequoia sempervirens. Give both the common name and the scientific name for these two other species. (Hint: You can search for a specific species using the search bar in the top left corner) (20 pts)

7. Application: California’s state trees are the coastal redwood and giant sequoia. California’s state flower is the California poppy. Using the advanced search (tracer mode) by clicking the branch icon left of the search bar you can search for the last common ancestor between two or more species. (Hints: You have to confirm the scientific name of the species name that you type in. If the colors for the trace disappear, you may need to reload your web browser page). What group did the last common ancestor of the California poppy and the coast redwood belong to? What is the scientific name of this group? (20 pts)

8. Application: Find Homo Sapiens (Hint: You can search for species in the search bar in the top right. Scientific as well as common names can be entered). According to One Zoom, what species are most closely related to Homo Sapiens? Approximately how many millions of years ago did the last common ancestor of Homo Sapiens and these species live? (20 pts)

9. Application: What group contains gibbons and gorillas but not langurs? (Hint: You can click the button next to the search bar to do a trace search. This will color the path to your species of interest)? How many million years ago was the last common ancestor between gibbons and gorillas? (20 pts)

10. Application: Of the Great Apes, which species are not considered endangered? (10 pts)

11. Application: Let’s trace our common ancestors back to the first Animals. Starting from humans (Homo sapiens) keep tracing backward through time. Replace the “<>” with the major groups and how long ago the last common ancestor for this group existed. Some groups have been filled out for you. (40 pts)

Human (Homo sapiens) - Current <> <> <> Old World Monkeys and Apes (Catarrhini) - 25 Ma <> <> <> <> Rodents, primates and more (Euarchontoglires) - 75 Ma <> <> <> <> <> Tetrapods (Tetrapoda) - 340 Ma <> <> <> <> Vertebrates (Vertebrata) - 525 Ma <> <> <> <> Animals (Metazoa) - 650 Ma

12. Application: Approximately how many millions of years did it take for the first Eukaryotes to develop into the first proper Animal (i.e. Metazoan)? (10 pts)

13. Application: Find the banana slugs, Ariolimax. What other genus shares the most recent common ancestor with banana slugs? Name a species (scientific and common name) from that other genus. (20 pts)

More Information:

http://phylonetworks.blogspot.com/2012/08/who-published-first-phylogenetic-tree.html

Blog question: (30 pts)

1. How could One Zoom be extended to include genetic information?

Full 30 points are earned by participating in answering this Blog or commenting 5 times on other student’s responses.