Research Methods



There are several methods commonly used to figure out how species are related to one another: maximum parsimony, maximum likelihood, and Bayesian inference.

Parsimony is basically Occam’s Razor–the simplest answer is the most likely. This is standard in analysis of morphological data. Maximum likelihood and Bayesian inference are both model-based methods. They work great if you’re able to model the chances that one thing will evolve into another, which makes them standard for molecular data since scientists have actually determined the rates at which one base pair changes to another. But for morphological data?….not so much.

Phenotype doesn’t follow mathematical models of which molecule fits best to another or what amino acid they’ll code for. It’s completely dependent on interactions with the environment, which is complicated and changes all the time. This is far from being a perfect analogy, but using model-based methods for morphological data is almost like trying to set up a model for whether a horn will become shorter or longer, only to have it turn blue.

That’s not to say that they can’t be used for morphological data at all, but they do have a very strong tendency to overestimate confidence levels, which is worse than underestimating because it means the people using your phylogenetic hypotheses may very well be making incorrect a priori assumptions. Better to say “we aren’t sure what happened in this part of the tree”, which is what parsimony is more likely to give.


I’ll be using several different morphometric methods. There’s traditional morphometrics, which is the use of linear measurements, angles, and ratios; then there’s geometric morphometrics, which uses landmarks, semi-landmarks, and outlines. In most studies, geometric morphometrics is preferred because it removes size (except for allometry, which can be tested for and informative in its own right), which leaves shape as the only thing being analyzed.

I’m quantifying the evolution of snout length relative to body size. Since this is a size variable more than shape, I’m using traditional morphometrics for it. I’ve already presented results of this at two meetings, and will add more data this summer and fall.

I have an undergraduate assistant using my photographs to digitize outlines of the back teeth and/or their alveoli. We’ll be doing Fourier transform to quantify these data.

I’ll also be looking at the morphological evolution of other aspects of alligatorine skeletons, and this will be through landmarks and semi-landmarks, which are point data that capture shape.

Biogeographic methods

There are two camps of biogeographic methods: pattern-based (e.g., TreeFitter), and process-based (e.g., dispersal-extinction cladogenesis). I’ll be using both to study alligatorines in the context of phylogeny.

Diversity measures

There are a lot of different ways to illustrate diversity through time. You can look at how many originations (speciation events) there are in a set period of time, how many extinctions, presence/abscence counts of lineages, etc… I’ll be doing a variety of these and comparing them to climate throughout the Cenozoic.

Why Study Alligatorine Evolution?


Many people think of alligators and other crocodylians as “living fossils”, which is completely untrue (The phrase “living fossil” really just needs to die in a fire because it’s completely useless, misleading, and damaging, but that’s a discussion in and of itself). They have changed quite a lot in the course of their evolution and that’s what I’m studying. My research is on quite a few evolutionary concepts: phylogeny & taxonomy, ecomorphology, biogeography, and diversity in relation to climate change.

Phylogeny & Taxonomy

All of the “big picture” questions I’m looking should be approached in a phylogenetic context (how species are related to one another). Taxonomy (what species and higher units are named) goes hand in hand with that because taxonomy can change if our understanding of phylogeny does. Phylogeny is the documentation of how lineages split and gives scientists a framework to ask other questions.


One of these other questions is how shape and size change, and what that has to do with ecology. Modern American alligators are really weird–if you look at basal alligatorines and other species just outside the alligator-caiman split, they’re all these short-snouted, small (~6ft) animals with big, bulbous, crushing back teeth. I’m quantifying how shape and size change over time and through lineages and how this relates to changes in ecological niche.


Modern alligators have a disjunct distribution, with one species in the southeastern US and the other in southeastern China. Crocodiles have disjunct distributions too, but they also have physiological attributes that make them tolerant of saltwater which alligators lack. Alligators are mostly restricted to freshwater. They can enter saltwater for small periods of time and will be fine if they can make it back to freshwater before dehydrating, and often do (there’s a set of studies on Georgia island gators on this). But these are mostly adult or large juvenile individuals–and remember that most extinct gator species were small as adults. Small individuals lose water through their skin at a much quicker rate because of the surface area to volume ratio.

This all means that dispersing across continents is hard for gators. They need land bridges or island chains with freshwater supplies. But these would only be present in high latitudes during alligators’ existence, so climate is an additional limiting factor. I’m trying to figure out what routes they may have taken and when.

Diversity & Climate Change

As “cold-blooded” animals, alligators are geographically restricted by ambient air temperature. As crocodylians go, they’re actually pretty cold-tolerant, and can survive freezing temperatures by staying underwater with only their noses above the surface, but this can only last for so long. They need warmer temperatures to feed, breed, and hatch.

This means that they’ve been used as “paleothermometers”–indications that the climate in the place and time their fossils are found fell above certain climatic parameters. They’ve been around for all or nearly all of the Cenozoic, and the climate has changed substantially since it began. The early Cenozoic, the Paleogene, was much warmer and wetter. At this time, alligatorines ranged as far north as Ellesmere Island. But when it cooled off and dried out in the Neogene, their range became much more restricted and their number of species fell. It’s been a while since anyone examined how their diversity changed over time and they used simple species counts rather than considering phylogeny (which accounts for unsampled lineages that had to of been around based on who’s most closely related to whom). The taxonomy has also been revised quite a lot since this was last done. I’ll be updating it and analyzing how closely alligatorine diversity matches climate change through time.