The Genetics of Fossils?

But where are all the fossils?  This, I found myself wondering on occasion as I listened to talks at the 75th Annual Meeting of the Society of Vertebrate Paleontology.  This year, perhaps because I haven’t been in a couple, one thing stood out above all others—the methods for studying vertebrate paleontology have exponentially advanced in complexity since I got my start back in the mid-1990s.  Gone are the days of simply collecting specimens, describing them, and doing a simple cladistic analysis to figure out their relationships.  Now, paleontologists include developmental biology, Bayesian statistics, changes in three-dimensional morphology over extremely long periods of time, and supertrees in their quest to explain the history of life on earth.

Although Brian K. Hall referred only to paleontology and evolutionary developmental biology1, I would argue that all of vertebrate paleontology represents a marriage of the “19th and 21st Centuries”.   The original vertebrate paleontologists of the 1800s such as Edward Drinker Cope and Othniel Charles Marsh (of the infamous “Bone Wars”), represent the historical perspective on paleontology.  These earlier paleontologists collected specimens, named them, and described them with qualitative evaluations.  Indeed, until the onset of cladistics in the mid-to-late 20th Century, paleontology was almost as much art as it was science.  The classic Osteology of the Reptiles by A.S. Romer is both an invaluable scientific reference as well as a collection of meticulous illustrations and prose that is rich with imagery.  Of course, we still rely heavily on more “traditional” practices of paleontology today.  We would be lost without new specimens collected regularly, and descriptions, drawings, and photographs of those illustrations published for all of us to use.  Functional morphology, based simply on visual comparisons of fossil bones to those of living taxa (groups of organisms) is still a valuable way of formulating hypotheses about how extinct taxa may have functioned in their environments.  Indeed, even examining the histology of fossil bones gives insights into the biology of extinct taxa based on qualitative and simpler quantitative comparisons with living organisms.


Figure by A. Goswami from Goswami Lab website at UCL.
When I started my graduate work, unbeknownst to me, paleontology was entering a new era of interdisciplinary inquiry.  It started with a trickle, such as quantitative analyses of the skull shapes of fossils in comparison with extant (living) taxa.  Then a discovery of preserved dinosaur soft tissue2 pushed the envelope of what was theoretically possible to learn from a fossil.  As we began to see the publication of genome after genome, we also began to adopt those data for analyses of extinct taxa.  For example, if we understand that Gene X is responsible for the formation of structure Y, we can infer when and how that gene was turned on in evolutionary history by looking for the structure in fossil taxa.  Many studies now combine genetics in the phylogenetic context of fossil taxa.  Measurements (2-D or 3-D) of fossil taxa can be examined for correlations in change between skeletal elements, which allow us to map more completely the way that morphology (shape) in vertebrates has changed over time.  If some parts of the skeleton typically evolve together, it suggests that paleontologists should take that into account when looking into relationships among taxa.

Figure 1 from Boisvert et al.  EvoDevo 2013, 4:3  doi:10.1186/2041-9139-4-3.


Cladistic analyses have become increasingly complex as both computing power has improved and our understanding of evolution has embraced the idea that nature is an often-messy interaction of genes, environment, and a million other factors.  A phylogeny is no longer a simple hypothesis of relationships, rather, it is the most likely hypothesis based upon discrete and continuous characters, whose evolution itself is modeled with maximum likelihood and the posterior probability thereof taken into account.

At the SVP meeting I found myself noting that these days results are not just reported with p-values, but Akaike Information Criterion scores, temporal scaling parameters, and edge exclusion deviance values (in addition to significance).  A few times, I wasn’t even sure what the statistics were even summarizing.   In time, I will come to understand these newer techniques, probably just as the field of vertebrate paleontology takes another huge leap forward.  I mentioned my observations to a slightly older colleague while at the meeting.  His response perfectly summed things up: “That’s why I work with younger collaborators.”  Time for me to hit the books again.

-Allison L. Beck

1 Hall BK. 2003.  Palaeontology and Evolutionary Developmental Biology:  A Science of the Nineteenth and Twenty-First Centuries.  Palaeontology 45(4): 647-669.

2 Schweitzer MH, Wittmeyer JL, Horner JR, Toporski JK. 2005. Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rexScience 307(5717): 1952-1955. doi:10.1126/science.1108397.
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