Why phylogeny is important

Now, it is important to understand that two speciation events and two ancestors is the minimum number of speciation events and ancestors needed to account for these three species.

It does not mean that these are all the ancestors in this part of the Tree of Life. In fact, as we add fossil chimps and fossil humans to our tree, we will add additional ancestors. To assert that ancestors are hypothetical is to assert that evolutionary descent itself is hypothetical.

And, the monophyletic groups to which chimp and human are parts extend back to the split between the common ancestor of all chimps and humans which occurred after the split of the common ancestor of chimps, humans and gorillas.

Finally, the common ancestor of chimps and humans is neither a chimp nor a human. A hypothesis of relationships among gorillas, chimpanzees, and humans shown as two different, but complementary, tree graphs. In a , each lineage is traced back to a speciation event shown at each node. In a , the ancestors X and Y are unsampled, encompass the entire lineage between speciation events, and represent only the minimum number of ancestors needed to account for descendant lineages.

In b , each ancestral lineage and descendant group is folded into a single node and the arrow lines represent statements of parent—child relationships, not lineages. In b , speciation events are not shown but implied by the parent—child relationships. Two hypothetical synapomorphies uniting chimps and humans are placed on each tree graph.

A similar mapping is shown in Hennig The tree on the right shows exactly the same kind of relationship ancestors and descendants have, but it is organized differently. It is much more like a human genealogy, turned upside down, with ancestors at nodes connected to descendants children at the tips. The edges are, symbolically, explicit statements of genealogical relationship, the equivalent of parent—child statements, just like a family tree of a human family except that there is usually only one parent.

So, in Fig. I have garnished both trees with two hypothetical characters that are synapomorphies shared by humans and chimps, but not gorillas.

In Fig. Just because one is lower than two does not mean that we know that one arose before two. We do not even know if both characters arose in one ancestor or in two ancestors. The only sense of the plotting of these characters on Fig. I use the terms node-based and stem-based trees as usefully neutral terms. But do not be misled; they are both phylogenetic trees, and one can be converted into the other.

However, one can get in trouble if they are mixed. Nodes must either be taxa or speciation events and internodes must be either taxa or statement of relationships over the entire tree.

There is another way of thinking of these trees. Stem-based trees such as Fig. Node-based trees Fig. Figure 1a is probably the natural way that people think about phylogenetic trees but Fig.

If there were only two kinds of trees in the world, then interpretation of trees would be easy and straightforward. Alas, graph theory is much richer. Stem-based and node-based trees of the sorts discussed by Hennig are simply two kinds of acyclic graphs and acyclic graphs are simply graphs with no loops.

Gene trees are acyclic graphs and gene trees do not always portray the descent of the species of which the genes are a part. Phenetic trees phenograms are acyclic graphs. Cladograms are acyclic graphs usually thought of as common ancestry trees. Figures drawn by Louis Agassiz in the s look very much like those drawn later by Romer. Yet, they are not meant to represent evolutionary descent Agassiz rejected evolution. Imposing an evolutionary interpretation on an acyclic graph that is not meant to portray evolutionary descent is a category mistake; yet, the graphs may take exactly the same form.

Thus, we must exercise caution: we must know the intention of the graph, what it is meant to portray; we cannot divine it purely from the form. There are other problems, relatively minor but vexing in our quest for full understanding of the diagrams we draw and the evolutionary biology they are meant to document. For example, when Baum et al. Surely this must be so, for in a stem-based tree, a node branch point is an event speciation and not a thing ancestral species.

Fortunately, this should not cause major problems in interpretation of the relationships of descendants, but they are relevant to meaning. Ancestral species do not exist on a stem-based tree at nodes; they exist between nodes Hennig Descent species may or may not exist only at tips on a phylogenetic tree, but the lineage to which they belong has existed since the speciation event that founded the edge that connects them to their closest analyzed relative.

And, we have no idea how many other species join that edge until we have a full account of the diversity represented by that edge. In the chimp—human case, there are a number of other lineages that join along both edges. Such graphs may be accurate in a relative sense without having to be accurate in an absolute sense.

The analogy to a highway map is apt. Highway maps may not show all the intersections, but the intersection they do show must be accurately drawn.

Robustness in phylogenetic inference refers to how well methods work in the face of violations of the assumption of the method or model used in an analysis. A robust tree would be one that is relatively immune to violations of the assumptions used to generate the tree hypothesis and might be expected to stand the test of new data, perhaps analyzed using different methods.

Hopefully, a robust tree is an accurate tree. Phylogeneticists have put a great deal of effort in exploring how violations of assumption affect the results of an analysis for example, Holder et al.

Suffice to say, how robust a phylogenetic tree needs to be depends on the use to which it is put. If the goal is to convict a physician of second-degree murder, then we require a very robust tree that is likely to closely estimate the actual descent of HIV strains. If the goal is to estimate rates of speciation, then not only must the tree be a robust estimate of the Tree of Life but it must also be populated by a significant number of species of the group.

Every missing species represents an underestimation of speciation events. If the goal is to use the tree to forecast the potential distribution of an invasive species based on the ecological niche of it and its nearest relatives, then the result could influence policy decision on a national or international level. The major point is that before using a tree, one should access the relative strength of the hypothesis, and the greater the consequences, the more closely we should question the strength of the tree hypothesis.

We must remind ourselves that tree hypotheses, like all scientific hypotheses, are conjectures, not facts. Phyloproteomics: What phylogenetic analysis reveals about serum proteomics. J Proteome Res. Baum DA, Offner S. Phylogenies and tree thinking. Am Biol Teach. Google Scholar. The tree thinking challenge.

Applied evolution. The evidence that all life descends from a single common ancestor includes such things as the unity of the genetic code.

Organisms use a simple code to determine how to make proteins from DNA sequences, and all organisms use the same code although some minor exceptions exist; go to Chapter 15 for details. To find out more about the genetic code and its importance to evolution, refer to Chapter 3. Beyond enabling scientists to trace genetic connections back through time, phylogenetics lets scientists better predict what's to come.

Being able to anticipate future mutations is an especially important function in areas like health care; virologists and epidemiologists use info gleaned from phylogenetics to stay one step ahead of the bugs that are trying to stay one step ahead of the human immune system.

You can read more about viruses and the race for vaccines in Chapter Related Posts Phylogenetics Reconstructing the Tree of Life Reconstructing the history of hominid evolution Flour beetles A group selection example Your fitness your relatives fitness inclusive fitness Selecting for nicer chickens Applications of group selection Chicken Coop Plans.

Responses Calimero Why do biologist care about phylogenies? Usually, the context of such trees makes it clear that the branch lengths have meaning. However, when this is not the case, it is important to avoid reading in any temporal information that is not shown. For example, Figure 8 may appear to suggest that the node marking the last split leading to tips A and B marked x occurred after the node separating tip C from tips D and E marked y. However, this should not be read into the tree; in reality, node x could have occurred either before or after node y.

Given the increasing use of phylogenies across the biological sciences, it is now essential that biology students learn what tree diagrams do and do not communicate. Developing "tree thinking" skills also has other benefits. Most importantly, trees provide an efficient structure for organizing knowledge of biodiversity and allow one to develop an accurate, nonprogressive conception of the totality of evolutionary history.

It is therefore important for all aspiring biologists to develop the skills and knowledge needed to understand phylogenetic trees and their place in modern evolutionary theory. Figure 8: Trees contain information on the relative timing of nodes only when the nodes are on the same path from the root i.

In this tree, nodes x and y are not on the same path, so we cannot tell whether the ancestral organisms in node x lived before or after those in node y.

Avise, J. Baum, D. The tree thinking challenge. Science , — Phylogenies and tree thinking. American Biology Teacher 70 , — Dawkins, R. O'Hara, R. Homage to Clio: Toward an historical philosophy for evolutionary biology.

Systematic Zoology 37 , — Population thinking and tree thinking in systematics. Zoologica Scripta 26 , — Maddison, W. Origins of New Genes and Pseudogenes. Evolutionary Adaptation in the Human Lineage. Genetic Mutation. Negative Selection. Sexual Reproduction and the Evolution of Sex.

Haldane's Rule: the Heterogametic Sex. Hybrid Incompatibility and Speciation. Hybridization and Gene Flow. Why Should We Care about Species? Citation: Baum, D. Nature Education 1 1 Phylogenies are a fundamental tool for organizing our knowledge of the biological diversity we observe on our planet. But how exactly do we understand and use these devices? Aa Aa Aa. What an Evolutionary Tree Represents. Figure 1. Figure Detail. The Lexicon of Phylogenetic Inference.

A node represents a branching point from the ancestral population. Terminals occur at the topmost part of each branch, and they are labeled by the taxa of the population represented by that branch. Figure 4: A monophyletic group, sometimes called a clade, includes an ancestral taxon and all of its descendants. A monophyletic group can be separated from the root with a single cut, whereas a non-monophyletic group needs two or more cuts.

How to Read an Evolutionary Tree. Figure 6: Types of phylogenetic trees. Bioinformatics and computing : Many of the algorithms developed for phylogenetics have been used to develop software in other fields.

Coming soon…? With the advent of newer, faster sequencing technologies, it is now possible to take a sequencing machine out to the field and sequence species of interest in situ.

Phylogenetics is needed to add biological meaning to the data. Phylogenetics An introduction.