Old School vs. New School

I’m going to try something different for this post. I usually write about one SRMP lab at a time, but sometimes you can’t ignore the way that individual research projects “speak” to one another. So this is a story about poop and dirt and the people that study them.

Let’s jump right into the poop, or more properly feces or scat. Your choice. It can tell you so much about the source animal including sex, identity, stress levels, pathogen loads, and of course diet. Joshua and Catherine - joined by SRMP alumna, Olivia - are working alongside Neil Duncan and I on a study to describe the diet of NYC coyotes. Olivia and others describe in detail how, but suffice to say, the key is identifying hard, undigested remains of prey (e.g. hair, bone, and teeth) that make it through the gut into the scat.

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But there is the assumption that all prey are equally likely to be detected in scat. This is clearly violated, no? Take an easy example. Do urban coyotes eat human foods like Big Macs? Most research says, not often. The problem is that unless the coyote ate the foil wrapper there are no parts in a Big Mac to make it through the gut undigested. So, it is possible to underestimate the contribution of certain prey groups using traditional scat analysis.

Enter Claudia Wultsch, Tatyana and Alejandro. They are taking advantage of innovative next-generation sequencing (NGS for short) technologies to amplify and sequence prey DNA found in scat using a metabarcoding approach. At least some prey will make it through the gut even if hard parts aren’t ingested or there are no hard parts to the prey. In other words, if a NYC coyote ate a hamburger and the resulting scat found its way to Claudia’s lab, DNA of cow (assuming Big Macs are beef) would be amplified.

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I saw the amount of data Claudia’s team was generating and it was astounding. They are focused mostly on jaguar diet (disclaimer, I’m a big fan of the jaguars, a study animal of my youth). For a test run of 24 scats, they generated over 28 million strands of DNA which they are now identifying to taxa. One jaguar sample even amplified mouse DNA, species that rarely--if ever--are listed as jaguar prey.

Do jaguars catch mice, a prey item overlooked by earlier studies? Or, as Claudia posited, did a mouse run over the scat? RUN OVER THE SCAT. This genetic technique is so sensitive that the poop might have been contaminated (can poop be contaminated?) by exogenic mouse DNA. So, while Neil and his team are worried that they are missing prey items, Claudia and her team are worried about counting animals as prey that maybe aren't!

Let’s get back to the mouse. If Claudia’s hypothesis is right, modern genomics can detect a small mouse using DNA it left behind on the course of its travels (e.g, urine, hair, skin cells). That is exactly what Anthony Caragiulo, Saimon and Chris are hoping. They are using modern genomic techniques to extract and amplify trace mammalian DNA found in soil. The idea is that they can accurately survey the biodiversity of an area simply by looking at DNA found in dirt. They are testing this in our hometown and comparing animals caught on camera traps to animals “caught” via their DNA in the dirt. Saimon and Chris are hoping the genomic method will be more sensitive by detecting animals that evade camera traps (e.g. small rodents). Saimon and Chris’s project is the first to use this metabarcoding technique in the field and could revolutionize mammalian survey methods. My mind is sufficiently blow and this blog post is already way too long