So, this week\u00e2\u20ac\u2122s question was:<\/p>\n
What inferences can you draw from a phylogenetic tree? Why is knowing phylogeny important?<\/p>\n
Answer below the fold.<\/p>\n
A phylogenetic tree is a bushy network mapping the relationships of species living and long extinct. It\u00e2\u20ac\u2122s a lot like a personal family tree you might construct to find out who your descendents are, but the phylogenetic tree doesn\u00e2\u20ac\u2122t worry about individuals. It deals in relationships at a species level. Looking at any large-scale phylogenetic tree can be daunting. The branches and twigs seem innumerable. It can also be off-putting to learn that the tree is ever shifting. As new discoveries are made, hypotheses about species\u00e2\u20ac\u2122 lineages can change. But that is the very nature of science: fluid based on the facts as they are revealed.<\/p>\n
In Dr. Joel Cracraft\u00e2\u20ac\u2122s essay Building the Tree of Life, he relates how piecing together this tree floundered for a while. With little more than comparative anatomy to go off of, scientists had trouble making clear sense of life\u00e2\u20ac\u2122s interrelatedness. In the 1960\u00e2\u20ac\u2122s, Cracraft writes, the field found its direction with the introduction of cladisitics. This fresh look focused on derived characteristics shared among species rather than the longer view of primitive characteristics. Sure, vertebrates have backbones, but does that really help sort the vertebrates themselves? Derived characteristics are those traits shared by the smaller branches of the tree. Cracraft uses the example: \u00e2\u20ac\u0153early horse relatives had five toes, some of which were successively lost along later lineages, to result in the single-toed lineage we see today.\u00e2\u20ac\u009d These derived characteristics, whether they are physical or genetic, thus determine the forks and clumps on the tree.<\/p>\n
Cracraft\u00e2\u20ac\u2122s next essay, What Is the History of Life on Earth?, goes on to state something that is truly staggering about life on Earth. First of all, right now there are tens of millions of species alive today. Mapping all of them on a tree seems downright impossible. But then it is thought that all of those millions are but a drop in the bucket. They\u00e2\u20ac\u2122re only about 5 percent of all living things that have arisen and died off since the first spark of life nearly 4 billion years ago. That would make one heck of a big family tree!<\/p>\n
Based on the known branches of the tree, we can make all sorts of fascinating inferences about life on this ball of rock over the ages. We can see when the species count exploded and when mass extinctions turned right around and wiped them out. This overlaps with other fields of exploration into deep time, helping to pinpoint atmospheric changes (such as increasing oxygen levels) and catastrophic events.<\/p>\n
Connections can be made on the tree that surprise even the experts. Dr. Maureen O’Leary\u00e2\u20ac\u2122s essay about whale evolution shows how a combination of research methods pinned whales closer to the hippopotamus than originally thought. No fossils had previously made that connection, but DNA analysis did. There was a lot of resistance to this revelation at first. But eventually the appropriate fossil was found and the tree branches were correctly shifted. What was aptly illustrated here was that: \u00e2\u20ac\u0153Both the fossil and the molecular record have their advantages and disadvantages, but each records the same story.\u00e2\u20ac\u009d<\/p>\n
Knowing and using phylogeny is important because it helps make sense of life on Earth. It provides a road map we can follow and shows us just how connected we all are. Cracraft notes in his essay An Overview of the Tree of Life (in the book Evolutionary Science and Society: Educating a New Generation) that it would seem to be obvious that fungi are more closely related to plants than to animals, but the reality is just the opposite. The case for an understanding of phylogeny is even better made by Michael J. Donoghue in his essay Comparisons, Phylogeny, and Teaching Evolution (in the book Evolutionary Science and Society: Educating a New Generation) when he asks: \u00e2\u20ac\u0153Which of the following organisms would you want to know the most about in predicting how humans might respond to a particular disease treatment: a mushroom, a chimp, a corn plant, or a fruit fly?\u00e2\u20ac\u009d Even though the answer seems like a no-brainer, it nonetheless points directly at phylogeny. Donoghue goes on to argue that fully comprehending phylogeny would not only help biology students better grasp biology overall, but also stand a good chance of capturing their attention and engaging them in critical thinking.<\/p>\n
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Most of the referenced essays are part of the course materials, so I can\u00e2\u20ac\u2122t link to them from here. But the Evolutionary Science and Society book can be downloaded free here<\/a>.<\/p>\n The phylogenetic research project we had to do involved skipping around to a handful of different websites. The first task was to select at least eight species, one of them being in some way obviously \u00e2\u20ac\u0153less related\u00e2\u20ac\u009d to the others to serve as an outgroup. I chose to stick with carnivores such as the wolf, coyote, red panda, wolverine, sea otter, red fox and black bear. My outgroup was a non-carnivore, the aardvark. To make the next step easier, I looked up each critter\u00e2\u20ac\u2122s binomial nomenclature here<\/a>.<\/p>\n The next step was to find the gene sequence of a specific gene <\/a>in each species: the cytochrome oxidase 1 (COX1) gene. It\u00e2\u20ac\u2122s a mitochondrial gene involved in respiration that is commonly sequenced. Once those chunks of code are compiled from each critter, they are all copied into one text file and saved. Next, the codes are then fed into the ClustalX program <\/a>where they are all sorted and lined up properly. A new file is produced which is then fed into the Phylowin program<\/a>. Some fiddling around in there then produces a final tree. Cool beans!<\/p>\n I\u00e2\u20ac\u2122m chugging along through my college work. I\u00e2\u20ac\u2122m reviewing photosynthesis in Biology and making my way through anions and cations in Chemistry. Let me tell you, those \u00e2\u20ac\u0153for Dummies\u00e2\u20ac\u009d books are great for getting your feet wet before diving into … Continue reading ![\"\"](\"https:\/\/i0.wp.com\/www.flascience.org\/wp\/wp-content\/uploads\/2008\/04\/bhaught_tree-282x300.jpg?resize=282%2C300\" "\\"bhaught_tree\\"")
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