13 - Big cat phylogenies, consensus trees, and computational thinking

Summary

Phylogenetics seeks to deduce the pattern of relatedness between organisms by using a phylogeny or evolutionary tree. For a given set of organisms or taxa, there may be many evolutionary trees depicting how these organisms evolved from a common ancestor. As a result, consensus trees are a popular approach for summarizing the shared evolutionary relationships in a group of trees. We examine these consensus techniques by studying how the pantherine lineage of cats (clouded leopard, jaguar, leopard, lion, snow leopard, and tiger) evolved, which is hotly debated. While there are many phylogenetic resources that describe consensus trees, there is very little information regarding the underlying computational techniques (such as sorting numbers, hashing functions, and traversing trees) for building them written for biologists. The pantherine cats provide us with a small, relevant example for exploring these techniques. Our hope is that life scientists enjoy peeking under the computational hood of consensus tree construction and share their positive experiences with others in their community.

Introduction

For millennia, scholars have attempted to understand the diversity of life, scrutinizing the behavioral and anatomical form of organisms (or taxa) in search of the links between them. These links (or evolutionary relationships) among a set of organisms form a phylogeny, which served as the only illustration for Charles Darwin's landmark publication The Origin of Species. Phylogenetic trees most commonly depict lines of evolutionary descent and show historical relationships, not similarities [1].