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March 18th, 2013 by Rachael Martin

Good Reads for Tree Thinking

Spring Break is long over. Of course I had plans to catch up on work, but that never happened.  Another week has flown by. Last week David gave a lecture on methods for dealing with large trees (with datasets much larger than the ones we are using for our projects). Romina explained how to partition and combine (concatenate) our data. On Thursday Romina gave us a tutorial on a program called SATé and then we discussed a paper comparing the program with other methods. It was our first paper discussion, so David brought out his basket filled with tubes containing our names. This method of sampling with replacement to pick the discussion leader filled me with dread last spring in the Biology of Symbiosis course I took with David, but a year later, I’m starting to feel more confident (watch me get picked next week!).

I thought I would mention the textbooks we are using in case anyone is curious. Getting new textbooks is my favorite part of starting a new semester. I’ve always been a book nerd and this part of my life has been completely accepted at Clark. I’ve even convinced a few friends to join goodreads!

So for this course we are using the textbook Tree Thinking: an Introduction to Phylogenetic Biology by David Baum and Stacey Smith. I’m really enjoying this textbook, the writing style is very clear and the examples and quizzes at the end of each chapter are useful. Of course the book can’t cover everything we are discussing in great detail, so supplementary books and articles are used.

The Phylogenetic Handbook provides great detail (often more than you ever wanted to know!) This is a good reference when you need a more comprehensive treatment of a particular topic. One problem is that it is impossible to keep up with rapid advances in the field, so many of the programs we are using are not included in this edition from 2009 and some programs the book mentions are no longer in use.

Phylogenetic Trees Made Easy: A How To Manual provides step by step instruction with screen shots. It doesn’t have much background information, but it is a good reference if you forget how to actually run something with the computer.

Evolutionary Pathways in Nature: A Phylogenetic Approach is an optional text recommended to the class. This is a book I wish I had read three or four years ago. Honestly when I started becoming interested in biology I hated phylogenetic trees. They were annoying to stare at and impossible to decipher. I knew they showed evolutionary relationships, but I had no idea the various applications and questions that could be answered using these methods. Now I can look at a tree without panicking. If you can’t this book would be a great place to start. A variety of topics (although disappointingly only one fungal example) illustrate the many applications of phylogenetic. Diverse examples include aposematic coloration in poison dart frogs, male pregnancy in seahorses, web building in spiders, and coral conservation.

This last book isn’t part of the class, but if you are looking for an introductory textbook on fungi I highly recommend The 21st Century Guidebook to Fungi by David Moore, Geoffrey D. Robson, and Anthony P. Trinci. Published in 2011, it covers a broad range of topics including fungal classification, development, cell biology, and genetics, the role of fungi in ecosystems, as symbionts and pathogens, and in biotechnology.

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