phylogeny

read the instructions and read a research paper the is in the instructions , and answer the questions carefully and correctly please This assignment must be completed individually. Name as on OneCard: ________________________ TA name: ______________________ Section: ________________ BIOL 111 Phylogenetics homework (10 points) Due in lab week 14 (30 Nov – 3 Dec) Using the skills you learned in the library session in Week 1, locate and download the following paper (this will work best from an on-campus location): Berenbrink, M., Koldkjaer, P., Kepp, O. and Cossins, A. R. (2005). Evolution of oxygen secretion in fishes and the emergence of a complex physiological system. Science 307, 1752-1757. This paper is an excellent and very well-reasoned example of how phylogenetic trees can be used to test evolutionary hypotheses (in particular, see the text near the bottom of page 1756). Although you certainly may not understand all of the physiological details and figures, you should be able to interpret some of the key findings in the data, particularly in the phylogenetic trees themselves. Background information: This very interesting paper was published in one of the two premier scientific journals in the world (the other being Nature). The paper describes a hypothesis for the evolutionary patterns of development of a major physiological innovation in fishes, namely the ability to secrete oxygen gas from the circulating blood into an organ called the swimbladder. A swimbladder is a gas-filled structure that can be used by a fish to regulate its buoyancy. (As you will learn, the swimbladder is homologous to our lungs.) At a certain depth, the buoyant force of the swimbladder equals the force of gravity pulling the fish toward the bottom of the sea; at this depth the fish no longer needs to expend energy staying at a constant depth. Prior to this evolutionary innovation, fishes possessing a swimbladder could only inflate the swimbladder by gulping air at the surface of the water, and those species without a swimbladder (such as sharks) must swim continuously – and continuously expend energy – to generate lift to stay at a constant depth. The Root effect is a property of the hemoglobin of certain fish species. Hemoglobin is the respiratory pigment produced by humans and fishes in their red blood cells that carries oxygen to the tissues. Essentially, the Root effect is a significant decrease in the ability of hemoglobin molecules to bind to oxygen molecules when the pH of the blood decreases (in other words, when there are more H+ ions floating around in the blood). A rete mirabile (“wonderful net”) is a bundle of very small veins and arteries flowing in opposite directions to each other. The physiological “beauty” of a rete mirabile is that it can be used to recycle or otherwise retain something in a particular region of the body. In this case, dissolved oxygen – released from hemoglobin due to the Root effect – is retained near the swimbladder. Fish take advantage of this arrangement of blood vessels to increase their ability to inflate the swimbladder with oxygen gas. In the eye of some fishes, another rete mirabile (the choroid rete) helps to supply oxygen to the retina, which does not have a dense network of capillaries and is thus not well-oxygenated. Instructions for reading scientific papers: Read through the paper once without stopping. Focus on the main points and don’t worry about terms you don’t understand. Then read the paper a second time, stopping to make notes, to look up terms that are unfamiliar to you, and to look closely at the data presented in the figures and tables. Questions to answer: After reading the paper, answer the following questions, referring especially to the phylogenetic tree on p. 1753 (Figure 1): 1. How many times did the swimbladder rete mirabile originate? ________ 2. How many times did the choroid rete mirabile originate? ______________ 3. How many times was the swimbladder rete mirabile secondarily lost? __________ 4. The blue pattern of evolution of the swimbladder rete mirabile in the figure is an example of evolutionary: a. Diversification b. Copying c. Convergence d. Homology 5. What advantages do fishes that possess the oxygen-inflation mechanism for the swimbladder enjoy over other fishes lacking this mechanism? _________________________________________________________ _________________________________________________________ _________________________________________________________ 6. Which originated later: the Root effect or the rete mirabile? _______________ 7. Did the most recent common ancestor of Brycinus and Pelteobagrus possess a swimbladder rete mirabile? ____________ Did it possess a choroid rete mirabile? ___________ 8. In what way is the MRCA of the clade containing Gnathonemus and its sister taxon unusual relative to other clades, specifically with reference to the presence/absence of retes? ___________________________________ ____________________________________________________________ 9. The Platichthys are a group of flatfishes (such as flounders) that have secondarily lost the swimbladder rete mirabile and, in many cases, the swimbladder structure itself. Knowing this and the benefits of having a swimbladder, where would you be most likely to find this group of animals in the ocean? a. On the bottom b. Swimming near the surface c. Hovering in the midwater 10. To which group are humans (in the group Homo) most closely related: a. Sharks (the clade containing Scyliorhinus, Mustelus, and Squalus) b. Salmon and trout (Oncorhynchus) c. Xenopus 11. Sharks do not contain a swimbladder, and we mentioned above that the swimbladder is homologous to our lungs. Draw a simplified version of the tree from the paper below, and indicate on the tree where the swimbladder/lung must have originated. (+1 if correct)