Annotated Bibliography part 2

Here's part 2 of my annotated bibliography:

Jarvis, Erich, and Siavash Mirarab. "Whole-genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds." Science 346, no. 6215 (2015): 1320.

I discussed this article earlier in my blog. The paper summarizes the findings of a research project in which scientists performed a genome-scale phylogenetic analysis of 48 bird species. It outlines the various programs the scientists used to perform the analysis, and explains the research methods quite thoroughly. This article will serve as a great resource for explaining some of the current phylogenetic research, and the paper's explanation of this team's analysis will likely help my mentor and me as we perform our own phylogenetic analysis on the San Diego zoo data. 

Huelsenbeck, John, Bruce Rannala, and John Masly. "An Introduction to Bayesian Inference of Phylogeny." Science.

My mentor shared this article with me. It's a very in-depth explanation of Bayesian Inference, which is a statistical method used to analyze evolutionary trees. The paper gives several examples of how to apply BI to evolutionary problems, and I think it will help me as I use BI to analyze the San Diego Zoo data. 
Drummond, Alexei J, and Andrew Rambaut. "BEAST: Bayesian Evolutionary Analysis by Sampling Trees." BMC Evolutionary Biology: 214.

My mentor and I will be using the BEAST program to perform our analysis, which uses Bayesian Inference to create the phylogenetic trees (as opposed to Maximum Likelihood or Parsimony). This article uses statistical and evolutionary principles to explain how the program works, and compares it to other existing programs that use Bayesian Inference. It will help me understand how to use BEAST, and will also help me understand the principles and assumptions that the program is built on.

"Analysing BEAST Output." Analysing BEAST Output. Accessed January 30, 2015. http://beast.bio.ed.ac.uk/analysing-beast-output.

This is a simple tutorial for BEAST. It actually takes you step-by-step through the BEAST program, providing helpful screenshots and including lots of detail about how the program works. This particular tutorial teaches you how to analyze BEAST output. 

Week of January 14th

This week, Dr. Miller and I discussed an article that I read over break, "Whole-genome analyses resolve early branches in the tree of life of modern birds" (published in Science, December 2014). We could only meet for 45 minutes because Dr. Miller had to catch his plane, but I still got a pretty thorough understanding of recent evolutionary biology research.

This paper discusses the findings of a mammoth research project in which scientists performed a genome-scale phylogenetic analysis of 48 bird species. These 48 genomes were computationally aligned and evaluated to create the most reliable avian evolutionary tree yet produced. Previous research efforts only analyzed selected genes, but this project analyzed whole genomes, which is why it is so accurate.

Most bird species became extinct soon after dinosaurs underwent their large-scale extinction, and as a result, the branches of the avian evolutionary tree were extremely muddled. By choosing species that represented the broadest possible diversity of birds, and by using whole-genome data, these scientists created an accurate picture of avian "family history." The paper also reveals why avian genomes tend to be small compared to those of other vertebrates: because they have lost a lot of genes and have far fewer repeat sequences. 

Here is an example of one of the several figures in the paper:

Reading and discussing this paper gave me a good understanding of the current evolutionary biology research occurring. The researchers who led this project applied the same techniques that I've been learning this year, and I think learning about this research and the methods they used will help me when I start the project with the San Diego Zoo this semester.