Holbrook Lab @ Rowan

Phylogeny and evolution of perissodactyls:

What I am doing:
Much of my work has concerned the evolutionary relationships among the members of the Perissodactyla, the order of mammals including horses, rhinos, tapirs, and their fossil relatives.  Perissodactyls have a rich fossil record extending back at least 56 million years on North America, Europe, and Asia. Perissodactyls later extended their ranges into South America and Africa. My work has focused on the early evolution of the group, including the relationships among the various fossil lineages from the first 20 million or so years of perissodactyl history. The primary goal of this research is to determine the phylogenetic relationships among these lineages, typically represented as a branching "tree", or cladogram.

How I do it:
Because it is largely based on fossils, this research requires me to travel to various museums around the world in order to examine numerous specimens of fossil (as well as living) perissodactyls.  Because fossils are so prominent in this work, my data consist largely of scoring different perissodactyl taxa (as well as some non-perissodactyl "outgroups") for a variety of characters based on their skeletal anatomy. I analyze these data using computer algorithms that determine which tree best fits the data.

Why it is interesting to me:
Phylogenies are a critical component of evolutionary studies, because they allow us to consider ancestry when trying to explain patterns in biodiversity. The excellent fossil record of perissodactyls makes them attractive as the subject of evolutionary studies. Phylogenies allow us to use that fossil record to answer questions about where, when, and how perissodactyls evolved.

The early radiation of mammals:

What I am doing:
One of my long-term interests has been the diversity of mammals and how they radiated into so many forms. In addition to the approximately 4000 living species of mammals, there are a great many fossil taxa of mammals, known as far back as the Jurassic. The greatest diversity of mammals is known from the Cenozoic Era, which followed the mass extinction at the end of the Cretaceous. During the first epochs of the Cenozoic, namely the Paleocene and Eocene, we find the earliest members of many extant mammal lineages, but we also find fossil mammals whose relationships to living forms are not so clear. My current main project is looking at the relationships among some of these enigmatic fossils, particularly a hodgepodge of groups that look vaguely like primitive "hoofed" mammals and are referred to as "condylarths".

How I do it:
Examining the phylogeny of mammals is similar in its essence to how I study the phylogeny perissodactyls. Again, because many of these taxa are known only from fossils, I study morphology, largely from teeth and skeletons, in search of evidence for relationships among different mammal groups. Besides simply examining museum specimens, in our lab we have also started analyzing data from microCT scans of specimens. This gives us a chance to look inside of specimens, and gives us virtual access to the morphology without having to travel back and forth to museums.

I also need to compare fossils to a wide variety of extant mammals, for which we also have data on DNA sequences. In recent years, new methods have been developed that allow me to do two important things. One is that I can use computer algorithms that use both the morphology and the gene data determine the phylogeny of both extant and extinct taxa. Second, these same algorithms combine information on the ages of fossils with "molecular clocks" based on the DNA sequences to determine when different mammal lineages split from their common ancestor.

Why it is interesting to me:
Mammal phylogeny is interesting because it tells us something about our own ancestry. In addition, understanding the shape and timing of the branching of the mammalian tree allows us to address the possible causes of that diversification. What role, if any, did the extinction of dinosaurs play in the diversification of mammals? Was the diversification triggered by other causes, such as tectonic movement of the continents?

Convergent evolution of complex traits in perissodactyls:

What I am doing:
Convergence is one of the most interesting phenomena in evolutionary biology. An interesting phenomenon in the evolution of perissodactyls is the repeated evolution of certain traits. Even our incomplete knowledge of perissodactyl phylogeny allows us to recognize that many traits have evolved independently in different perissodactyl lineages. For instance, all three families of living perissodactyls are large in comparison to their earlier relatives, but it is clear that large body size has evolved in each of these three living lineages--as well as a number of extinct ones--independently. Body size increase is a complex trait with many consequences for an organism's biology. Other complex traits have also evolved independently in different perissodactyl lineages, such as the tendency for the surface of cheek teeth to be composed of crests (lophodonty) rather than of bumps (bunodonty), and the tendency for premolars to resemble molars in their morphology (premolar molarization). The question this raises is why these traits evolve so many times. I am interested in tracing the evolution of these complex traits and looking at possible causes for these interesting cases of convergent evolution.

How I do it:
My work on perissodactyl phylogeny equips me with one of the tools I need for this project, namely a phylogeny of perissodactyls. A phylogeny is necessary for tracing the evolution of these traits and determining how often they evolved. I also need a way to measure these traits. This is relatively straightforward for body size, but much less so for assessing lophodonty and premolar molarization. In my lab we are using three-dimensional geometric morphometrics to quantify tooth shape. What this means in essence is that we use tools for plotting the position of various landmarks on teeth in three-dimensional space, and then, with help of special software, we compare the positions of these landmarks on teeth from different individuals. This allows us to come up with a quantitative description of the variation in tooth shape among our individuals.

Why it is interesting to me:
Once we can describe the variation in tooth shape and relate it to lophodonty and premolar molarization, we can use these data to address questions about why convergence is happening. For instance, do evolutionary changes in body size, lophodonty, or premolar molarization coincide with environmental change? Or are changes in one of these traits (e.g., body size) driving changes in the others?