Goals: The goals of this lecture are to introduce the concept and tree representation of phylogeny.
Related Textbook Material: Freeman and Herron (2001) Chapter 2 has a good introduction to reading phylogenetic trees; the main chapter on phylogenetic trees is Freeman and Herron Chapter 13.
Lab Manual Questions in Lab Manual Chapter XI (and most of the chapters after it) require the background material in this lecture; there are also practice questions over this material at the end of this lecture.
Other Assignments The material in this section also provides the basic background necessary for conducting your second outside assignment, on phylogenetic analysis of toucans.
Phylogeny refers to the evolutionary relationships among
species. The following paragraph illustrates what this means. Species have
evolved through speciation which refers to the process through which
one species becomes divided into more than one new species. We can think
of all species as being part of a family tree which traces back to the
ancestor to all life. That ancestral species (which your textbook calls
the cenancestor) then evolved through speciation into two new species;
these descendent species evolved into more new species, and so on. The
result is the great diversity of life currently present on earth. The history
of speciation tells us how these species are related to each other; if
they evolved to be separate species relatively recently, then they are
close relatives; if they evolved to be separate species long ago, then
they are distant relatives. So the pattern of evolutionary relationships,
or history of speciation, among species is what we call their phylogeny.
Because species evolve as ancestral species split into more than one new species, it is convenient to represent phylogeny as a tree in which lines represent species and places where lines split into two represent points where ancestral species speciated (evolved through speciation) into two new species. A tree representing phylogenies is often simply called a phylogeny. Consider for example the following phylogeny of some species belonging to some of the main land-dwelling vertebrate groups:
Let's consider in detail what this tree means. First, the species listed at the top, the salamander, frog, mouse, bird, lizard, and snake, are all currently existing species. What the tree tells us is how they are related to one another. Remember that none of these species is an ancestor to any other, since no modern species is an ancestor to another modern species. These modern species have from common ancestral species that existed in the past. The tree tells us the pattern of evolution from these ancestral species, as follows:
The line marked "A" at the base of the tree is the ancestor to all the modern species (the salamander, the frog, the mouse, the bird, the lizard, and the snake all trace back to this ancestor.)
This ancestral species, "A", speciated into two species, indicated by the lines labeled "B" and "C". Species "B" is the ancestor to the salamander and the frog. Species "C" is the ancestor to the mouse, bird, lizard, and snake.
Ancestral species "B" speciated into two species, one of which evolved into the frog and the other of which evolved into the salamander.
Ancestral species "C" speciated into two species. One evolved into the mouse. The other is species "D", the ancestor to the bird, lizard, and snake.
Ancestral species "D" speciated into two species. One evolved into the bird. The other is species "E", the ancestor to the lizard and snake, which then speciated into two species, one of which evolved into the lizard and the other of which evolved into the snake.
Note that the species I1ve called A,B,C,D, and E are all species that existed in the past, but are not considered to exist any more since the species that are descended from them have evolved to be different from those species. We also don't typically worry about naming those species. Sometimes, from fossils, we may have a good idea of what they were and what their characteristics were like; other times we do not have a good fossil record for a group so we do not know. Later, we'll see that we may be able to determine what some of their characteristics were, just by knowing about the modern species. For now, note that we would not give a species like "A" a name, we'd just refer to it as "the ancestor to the salamander, frog, mouse, bird, lizard, and snake."
Now, let's consider how we describe the relationships among the modern species, based on the phylogeny (the tree.) Based on this tree, the frog and the salamander are each other's closest relatives -- they are more related to each other than to any other species on the tree since they evolved from ancestor "B" and "B" was not an ancestor to any other species on the tree. The frog and salamander are equally related to the mouse, bird, lizard, and snake. That is, the frog is just as related to the mouse as it is to the lizard, or the snake, or the bird. This is true because the most recent ancestor the frog and salamander share with the other species on the tree is "A".
Using this kind of reasoning, you should work out from this tree that the lizard and snake are each others' closest relatives, that the bird is equally related to the lizard as it is to the snake, and more related to the lizard and snake than it is to the mouse, frog, or salamander. The mouse is equally related to the bird, lizard, and snake, and more related to the bird, lizard, and snake than it is to the salamander or frog.
IMPORTANT NOTE: for the rest of this lecture and for much of what we do in the rest of this course it is crucial that you can read and understand a phylogenetic tree such as this one! If you have questions on how to read this tree, e-mail me now! Ask them!
Now we'll look at different ways people draw phylogenetic trees. First,
note that the horizontal order of species on the tree doesn't tell you
anything about how they are related -- what tells you how they are related
is whether or not they trace back (vertically, on a tree drawn like the
one above) to recent or distant common ancestral species. So the phylogeny
drawn above could also be drawn in several different ways; for example,
the following two phylogenies MEAN EXACTLY THE SAME THING as each other,
and as the phylogeny drawn above. To convince yourself of this, take some
time now and find the same ancestral species (A,B,C,D, and E) as are shown
in the tree above and see that exactly the same modern species have evolved
from each of these ancestral species as were shown in the tree above.
Now, consider one more convention in drawing trees. Trees can be drawn in different formats (these are introduced in the introductory lecture to this course) that mean the same thing. One of the most common ways of drawing trees is to use a "slanted" format; it is easier to draw than the format above but is sometimes confusing. Here's the first tree shown from above, with the same ancestors (A,B,C,D, and E) on it, drawn in slanted format:
In this format, every time a line branches into two the species above the branch point are two new species that have arisen by speciation from the species below the branch point.
Here are the other two trees from above drawn in slanted format. As before, you should take some time, identify the ancestral species, and convince yourself that all these trees mean exactly the same thing (they are different ways of drawing the same phylogeny.)
Study Tip:
Before you continue to the next lecture, be SURE that you can read and interpret phylogenies in both of these formats. For phylogenies in lecture and the textbook, you should describe in words all relationships in the phylogeny. To do this, you should make sure you have a statement about relationship for each ancestral species present in the tree. For the tree above, you would need to say:
