Thursday, March 10, 2016

Break It Down!: Taphonomic Factors Affecting Parasite Preservation

Greetings Fellow Parasitophiles!

Today, is an exciting day for's the day that I sent my dissertation manuscript off to my supervisory committee for approval before I defend my dissertation here in a few weeks! (Things are getting very, very real!) In celebration of this occasion, I decided to allow myself more writing! (I really am a bit of a nerd sometimes...well, most of the time...and more than a bit...) In trying to decide what to share with all of you, I realized that I had not yet posted about my most recent paper. So, here it is! My first paper of 2016 and the story behind it!

I remember sitting at coffee one Friday, as I do with my advisor for our weekly lab meetings, and discussing some of the various factors that affect the preservation of parasite eggs in archaeological materials. We talked about both the abiotic (non-living) factors, like soil pH and climate, and some of the biotic (living) factors, like the actions of decomposer species. My advisor turned to me and said something along the lines of, "you should write a paper on that sometime".

I found the idea intriguing and thought about it a lot over the next few months. I started working on a manuscript without a clear idea of where I would go with the paper. I thought about how to categorize the major contributing factors that affect the preservation of parasite eggs in both positive and negative ways. I eventually came up with five broad categories of taphonomic (taphonomy is the study of decomposition and preservation) factors that affect parasite eggs existing in archaeological contexts. Those five broad categories were as follows:

[From Morrow et al., 2016]

1) Abiotic Factors--Those non-living things that influence preservation, such as temperature, soil conditions, and the chemical environment in which archaeological materials are found.

2) Contextual Factors--Those reflecting the archaeological context from which we collect parasite data. (i.e. parasite eggs in mummies preserve differently than those in coprolites or latrines)

3) Anthropogenic Factors--Those arising from the interactions humans have with the deposition, manipulations, excavation, transportation, and analyses of archaeological materials.

4) Organismal Factors--Those inherent in the biology of the organisms you are studying, such as the features of an egg that make them more susceptible to degradation or the natural history of a parasite that makes it more likely to be recovered from human feces.

5) Ecological Factors--Those involving the interactions of parasite evidence with other organisms, like decomposers, predators that my ingest parasite eggs, or vectors than can transport the eggs from one fecal deposit to another.

Each of these broad categories could be further subdivided into other categories and can affect the preservation of parasites in both positive and in negative ways. To provide examples of how these factors affect parasite egg preservation, we presented three case studies and discussed these five categories of taphonomic agents for each case.

I won't go into case-by-case detail (you are more than welcome to read the paper if you are interested in that bit), but I will tell you a bit about the three cases. These sites were each near and dear to my heart as they were the first three things that I published about. (One in a special historical journal that hasn't come out yet and two peer-reviewed articles that I talked about in previous posts here and here.)

Case 1: The recovery of intestinal parasites from historic mummies in Vilnius, Lithuania. In the first paper about these parasites, we highlighted a taphonomic issue that only arises with the analysis of mummies.

Case 2: The recovery of intestinal parasites from coprolites recovered from medieval skeletonized burials in Nivelles, Belgium. In the original publication of this material, we discussed an instance of extreme parasitism revealed by the analysis of coprolites from one one of the burials.

Case 3: The lack of parasites recovered during the analysis of embalming jar contents from crypts containing members of the famed Medici family of Florence, Italy. The potential reasoning for the lack of parasite evidence was discussed at great length in the original paper (which is still "in press" after several years). These reasons ranged from taphonomic to cultural in nature and included a discussion of how Medici affluence likely played a role in reducing the risk of parasite infections and in providing the most effective treatments of the time to control for infections had they occurred.

Each of these studies demonstrated a range of taphonomic considerations for the interpretation of archaeoparasitological data. This paper concludes with a discussion of how important it is for researchers to consider taphonomic factors when they discuss their findings. It urges future studies to discuss the five broad categories of taphonomic factors that may have positively or negatively affected the preservation of their parasite eggs.

I have to say that this is probably my favorite paper to have ever published. I love how it turned out. I was happy to have run with a simple suggestion (which my advisor may or may not have expected me to actually follow through with so quickly) and to have created an article that is actually really important for the advancement of the field. I got to work with an undergraduate as a mentor and I got to publish with an international colleague. I feel that this experience has helped me to grow in many ways professionally and I am proud to have such an elegant paper to show for it.

The Moral of the Story
When your advisor gives one of those small comments like, "you should do...." don't brush it off and put it on your list of things to do after you graduate. Take a little time to assess whether or not you could actually gain a lot from working on something might end up with something that is much bigger than you had originally thought it would be! Also, don't let your dissertation be the only thing that you leave with when you graduate. You are much more marketable if you can show that you have the ability to do other things!

Title Shot!

Saturday, February 27, 2016

Sharing Poop and Parasites

I've missed writing to you guys...dissertation and general life has been a little OP lately. (OP = "over powered"'s a slang term used often in the gaming world and I've been married to a gamer for too long to not use it.) I won't waste time saying that this is me starting up regular posts again, the dissertation is still not finished (though I'm getting close!) and I have a pretty busy few months ahead of me. I'm hoping to start back up this summer, after I (FINALLY) graduate, but I'm not making any promises just yet.

Today, I'm writing to you for a different reason. I recently competed in an Elevator Speech Competition hosted by my school. I had a bit of a rough time with delivery, but in the end it wasn't all bad. For this competition, I was given 1 slide (with no moving animations) and three minutes to tell a general audience about my research. For those interested, I've included the slide and a transcript of my speech below. Happy reading!

My Elevator Speech

Poop and parasites; two things that I love despite what other people think. Though not always appropriate dinner conversation, poop provides a wealth of data regarding diet and disease. This is as true for what many of you made earlier today as it was for humans thousands of years ago.

My dissertation focuses on retrieving data from 1,300-year-old paleo-poops known as “coprolites”, like the one in the middle of this slide. By analyzing coprolites, we are able to reconstruct diets and patterns of parasite infections that occurred in pre-history. This allows us to better understand the origins of human-parasite associations that still affect people in the modern world.

The coprolites that I work with come from a cave in Mexico known as “La Cueva de los Muertos Chiquitos”. This cave held hundreds of coprolites that were sealed beneath two adobe floors, making for some of the best-preserved parasite evidence in the world…now that’s the kind of high-quality crap that we archaeoparasitologists dream about!

The diversity of parasites recovered from this site is amazing. Starting at 12 o’clock, we see a Physaloptera egg, which is associated with dogs. Moving clockwise we see a human whipworm egg, then at 4 o’clock we see Toxascaris, another dog parasite that infects humans from time to time. At 6 o’clock are the results of a molecular test used to look for parasites that don’t leave behind eggs. Ignoring the control wells on the top left, every place that you see yellow represents a positive sample for a diarrhea-inducing parasite called Cryptosporidium parvum. Moving along, the egg you see at about 7 o’clock belongs to a tapeworm and the green egg is that of a human pinworm. Finally, the one up there at about 10 o’clock is a fluke egg. Each of these parasites has a distinct life cycle involving different hosts and modes of transmission.

By recovering parasite data, we are able to infer patterns of human behavior, for example, the dog parasites I mentioned tell us that the people using this cave had close associations with dogs and the molecular test at 6 o’clock tells us that lots of people had diarrhea. The pinworm eggs were so prevalent among the coprolites that we know the vast majority of people at this site were infected.
At night, the female pinworm crawls out of the anus to lay her itchy little eggs on the perianal folds, so you know that as soon as the sun set on La Cueva de los Muertos Chiquitos, everyone was either scratching or dealing with diarrhea.  It doesn’t sound like much of a party for them, but it does provide us with lots of information 1,300 years later!

As we continue collecting parasite data from this site, we will gain a picture of the daily lives of people who left no written record, only ancient nuggets of information reflecting what they ate and what was eating them.