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What’s In A Wolf Scat? New DNA-Based Method To Detect Prey From Carnivore Scats

Posted on September 15, 2021 by Sam Perrin Leave a comment

This is a guest post by Cecilia di Bernardi.

Image Credit: Rick Heeres, CC BY 2.0, Image Cropped

Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats (2021) Di Bernardi et al., Ecology & Evolution. https://doi.org/10.1002/ece3.7918

The Crux

Studying carnivore diet can be a crucial tool to inform both management and conservation of predators and their prey. If we’re going to ensure a carnivore’s survival, we need to know which species it relies on for food, and in what quantities.

Digging into an animal’s stomach isn’t the nicest way to get the crucial data we’re looking for, so non-invasive sampling of scats (that’s science for poop) has for been a more ideal approach to collecting valuable information on the occurrence, genetics, and diet of animals, especially when dealing with elusive and threatened species. Nowadays, DNA-based analyses of scats are allowing researchers to get more and more high-resolution data on predators’ food habits.

What We Did

We developed a DNA-based method to detect prey from wolf scats, taking advantage of the huge leaps the DNA analysis has been through in recent years. We also made use of nanotechnology (specifically Nanofluidic array technology fromFluidigm Inc.), which has been useful for detecting pathogen species in ticks, or traces of herbivores on browsed twigs, but has never applied to detect prey from predator scats!

Starting from the big bank of DNA sequences available online (GenBank, NCBI), we looked at specific areas of the genome, (the mitochondrial genome), in order to tell apart the different target prey species present in the wolf scat. We developed species-specific molecular markers (see Did You Know?) and tested them with reference tissue samples, kindly provided by the Swedish Museum of Natural History. After the protocol development and optimization, we ended up with a set of 80 markers for our 18 target species. We then applied the newly developed molecular method on a pilot sample of wolf scats collected in the field.

Did You Know: Molecular Markers

Since any species’ genome is an incredibly long sequence, scientists have developed more efficient ways of defining what DNA belongs to which species. The motivation is simple – if you’re trying to tell whether a genome belongs to a human or to a chimpanzee, you don’t want to be looking through the 99% of DNA we have in common, you want to go straight to that 1%. That’s why scientists develop ‘markers’. It helps them narrow down their search and identify species much more quickly.

What We Found

The molecular markers we developed did their job well, correctly detecting the 18 prey species, showing an overall good distinction between the tissue samples of the target and non-target species. In other words, this means that a tissue sample taken from a moose was detected by the moose markers but not by the reindeer markers, which is the sign of a successful marker!

When applied to the pilot of wolf scats collected in the wild, the method detected a total of 16 species, comprising wild ungulates (moose, roe deer, red deer, fallow deer, wild boar), domestic and semi-domestic animals (reindeer, cattle, sheep), small prey species (European badger, European hare, mountain hare, Western capercaillie, black grouse), and other carnivores (Eurasian lynx, wolverine, red fox).

Just because fox DNA turns up in a wolf scat, it doesn’t mean that a wolf has eaten a fox – it could simply mean tha a fox has urinated on the scat! (Image Credit: Joanne Redwood, CC0 1.0)

Problems?

While the method detects the target species as we’d like, it cannot distinguish whether predation, scavenging, or territorial marking has occurred. Detection of fox DNA in wolf scats can mean a wolf predating on a fox, a wolf scavenging on a fox, but also a fox marking with its urine on a wolf scat! To partly disentangle this aspect, we are investigating the contribution of scavenging to wolves diet in Scandinavia, with data from GPS-collared wolves.

So What?

This molecular method, with its high-resolution prey detection, can help better understanding under what circumstances wolves eat certain prey and how that can affect ungulate populations, serving as a valuable complement to the current GPS technology used to investigate wolf predation. Wolf natural expansion is an ongoing and controversial phenomena in the Northern hemisphere, and any technique that tells us more about their impact is a welcome addition to our knowledge base.

Cecilia Di Bernardi is an ecologist who is currently investigating wolf predation ecology within her PhD at the University of Rome La Sapienza in collaboration with SLU Swedish University of Agricultural Sciences. You can follow her on Twitter @c_dibernardi.

Paper of the Week

Environmental DNA Provides Lessons On Life

Posted on September 24, 2020 by Krista Bonfantine One comment

Using eDNA, we can figure out where shy animals like this platypus live without disturbing them (Image credit: Amber Noseda, Great Ocean Photography, CC BY 2.0)

As an undergraduate student, more than twenty years ago, discussions of species often referenced ‘lumpers’ and ‘splitters’. Some biologists were more likely to ‘lump’ all variation within a single species while others attributed variation to distinct subspecies, and ‘split’ organisms as such. Back then, we talked about biomes such as forests and grasslands but the term ‘microbiome’ barely existed. Now, even the concept of an organism is questioned as some scientists argue that the individual cannot be separated from the microbiome it hosts. Thanks to advances in molecular biology, every organism is now an ecosystem.

Opinions

Surprises From the Past: The Revelations of Ancient DNA

Posted on May 7, 2020 by Sabhrina Gita Aninta 2 comments

Forest Tundra on the Taymyr Peninsula between Dudinka and Norilsk near Kayerkan, Russia, taken in 2016. Was it always look like this? Should it look like this?
Image Credit: Ninaras, CC BY 4.0, Image Cropped

Although obtaining ancient DNA can be quite a headache, it is a very rewarding headache. After all the work that goes into obtaining DNA from a bone, fur, hair, or Viking’s leftover meal, researchers have to make sense of the apparent random sequence of nucleotide bases. But once that’s taken care of, there are a series of really interesting questions we can start to answer. Were DNA strands that are present in the modern times inherited from the past? How similar are today’s species to their forebears? Where is my pet velociraptor?

Opinions

Using eDNA to Avoid Being Eaten on the Job

Posted on May 6, 2020 by Sam Perrin One comment

Image Credit: pxfuel, CC0 1.0, Image Cropped

Monitoring the silver carp invasion in Africa: a case study using environmental DNA (eDNA) in dangerous watersheds (2020) Crookes et al., NeoBiota, http://doi.org/10.3897/neobiota.56.47475

The Crux

One thing the last two months have taught us all is that testing for a problem is crucial. The earlier you catch a problem, the more of a chance you have to stop that problem spreading. Coronavirus is one example, invasive species is another. Detecting an invader arriving early on means you can potentially remove it before it has become properly established, saving millions of dollars down the line.

But often testing isn’t practical. Take freshwater environments. Sometimes a river may be hard to get to. Sometimes it may be infested with crocodiles and hippos. Makes regular testing methods like electrofishing or gillnetting a bit tricky.

Paper of the Week

The Revolutionary Headache of Ancient DNA

Posted on March 16, 2020 by Vanessa Bieker 4 comments

Ancient DNA can teach us a great deal about prehistoric life. So why is it so troublesome? (Image Credit: Flying Puffin, CC BY-SA 2.0)

When we’ve talked about type specimens on Ecology for the Masses, we‘ve spent a lot of time emphasising how important it is to preserve them. Bottom line is, if they get destroyed, there are a lot of really important biological questions that become very difficult to answer.

Thankfully, landmark leaps in technology have made it possible to extract DNA from those specimens and store them in a public repository (e.g. the NCBI nucleotide database). So then even if a specimen is lost, the DNA would still be there and could be compared to that of other specimens to figure out if it’s the same species. Sounds like a clever and straightforward thing to do, but as always, it’s more complicated in reality.

Opinions

The Why and How of Genetic Diversity

Posted on January 13, 2020 by Sabhrina Gita Aninta 2 comments

Whilst cichlid fish might look incredibly diverse, they are actually all relatively genetically similar. So how do we define genetic diversity, and how do we conserve it? (Image Credit: Emir Kaan Okutan, Pexels Licence, Image Cropped)

Biodiversity has become an immensely popular buzzword over the last few decades. Yet the concept of genetic diversity has been less present in everyday ecological conversations. So today I want to go through why genetic diversity is important, how we define it, and why there is often controversy about its application in conservation science. Read more

Opinions

Donald Hobern: Cataloguing the Planet’s DNA

Posted on July 8, 2019 by Sam Perrin 2 comments

I spoke with GBIF’s executive secretary and amateur lepidopterist Donald Hobern about how DNA barcoding fits into modern conservation and ecology (Image Credit: Donald Hobern, CC BY-2.0, Image Cropped)