Phylogeny Reconstruction

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Name: _______________________ Lab Instructor: ________________

PHYLOGENY RECONSTRUCTION

Objectives
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To understand the theoretical basis of phylogeny reconstruction, and to gain an understanding of how phylogenetic trees are constructed in practice 2) To gain an appreciation of the value of phylogenetic reconstruction for understanding evolutionary patterns and processes 3) To construct your own phylogenetic hypotheses

Introduction
The Tree of Life Perhaps the most important implication of the theory of evolution is that all species of organisms, including humans, are related to each other in a genealogical sense. Even organisms as distinct as fungi, humans, and bacteria have ancestors in common. Some species, such as chimps and humans, share a fairly recent common ancestor (less than 10 million years ago), while for others you have to go way back to find a common ancestor (e.g., the common ancestor of humans and jelly fish lived at least 600 million years ago). A very useful way of thinking about relationships among organisms is as a tree of life. Imagine that at the base of the tree is the original population of organisms. As they evolve through time, two things can happen: 1) This lineage of organisms can acquire new characteristics, and 2) the lineage of organisms can split into two separate lineages (speciation). These processes, repeated over and over, result in a “tree of life” that represents the relationship among organisms (see Figure 1). This tree of life is also referred to as a phylogeny or phylogenetic 1 tree.

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The situation isn’t always this simple. In some cases genes are shared across species (e.g., bacteria), or hybridization is common (e.g., oaks), and sometimes even very distantly related organisms merge to form a composite (e.g., eukaryotes). Each of these cases would cause the branches to rejoin. Fortunately, this doesn’t appear to be a major problem for higher organisms.

Copyright © Dr. Jeffrey S. Jensen BBIO180, Fall 12 - University of Washington, Bothell.

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Phylogeny Reconstruction

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Today we will investigate the theory and practice of reconstructing the phylogeny of organisms. As you can imagine, reconstructing events that occurred millions, or even billions, of years ago is not an easy task. Fortunately, the last 30 years have produced astounding theoretical and technical breakthroughs in phylogenetic reconstruction. Phylogeny reconstruction (and the related field of systematics) now plays a central role in all of comparative and historical biology, and advances in systematic knowledge and theory have led to tremendous progress in understanding the patterns and processes of evolution.

Figure 1. Simplified cladogram of vertebrates Phylogenies—Why Are They Useful? Before we discuss how phylogenies are reconstructed, it’s worth asking the always relevant question “why bother?” Creating a non-arbitrary classification— Systematics has traditionally been concerned with the identification and naming of species, and the grouping of these species into a classification. Carolinus Linnaeus (1707–1778), an early and very influential taxonomist, developed the hierarchical classification system used today in which species are arranged into ever more inclusive groups. The complete Linnean classification for humans is at right ->

While this seems very straightforward, confusion can arise about which groups of species to put together. For example, should we put insects, birds and bats in the same phylum because they all have wings (despite the fact that they are only very distantly related and their wings clearly have separate
Copyright © Dr. Jeffrey S. Jensen BBIO180, Fall 12 - University of Washington, Bothell. 2

Phylogeny Reconstruction

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origins)? Should all warm-blooded vertebrates be