Tag Archives: genomics

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

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.

How You Can Help Ancient Ungulate Conservation Using Ancient DNA

We write so much here on Ecology for the Masses about the danger that countless species face in today’s world. So every now and then we need to give tangible solutions and talk about how to actually save an endangered species. It’s not an easy task, and every one comes at it from a different angle. But right now, I want to talk about the fate of two amazing species, the work my colleagues and I have been doing to try and save them using DNA from museum collections, and how you can help. Yes, you. Our awesome readers. Here is a story about my research.

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A Beginner’s Guide to Endangered Species Reintroduction

Tasmanian Devil at the Zoo Duisburg.

Tasmanian Devil at the Zoo Duisburg, in 2017. The only zoo in Germany that keeps them. (Credit: Mathias Appel / CC0)

With the seemingly endless stream of bad news relating to the environment we’re often faced with these days, hearing ecosystem restoration or conservation success stories are always a welcome relief. With the number of species that have been displaced from their native habitats, the news of an endangered species being successfully introduced to a new area should be shouted out. So you cannot blame a conservation geneticist like me for jumping happily when I heard news of the release of the European bison and Tasmanian devil back to their native habitat. 

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The Changing Face of Ecology: Part Six

Image Credit: Lahiru Prabudda Fernando, CC BY-SA 4.0, Image Cropped

In a year like 2020, when everything short-term seems disastrous, it’s hard to focus on long-term change. How everything from ecology’s relationship with the public, to the health of freshwater ecosystems, to just our general sanity seems to be in flux at the moment.

But we’ve been reading about that ad nauseam recently, and I’m sure there will be plenty more to come. So instead, let’s return to an ongoing segment, and have a look at some of the ways that ecology has changed over the last few decades, according to some of the intriguing and prominent researchers we’ve had the chance to speak to over the last few months.

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Surprises From the Past: The Revelations of Ancient DNA

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?

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Preserving Biological Heritage: The Importance of Type Specimens

Museum collections may seem like they’re just for display, but they often house important biological information (Image Credit: Andrew Moore, CC BY-SA 2.0, Image Cropped)

Last September, the devastating news of a fire in Brazil’s National Museum in Rio de Janeiro hit the world. The fire destroyed most of the collection, including about 5 million insect specimens. Many of the samples were holotypes, a subset of type specimens which are particularly valuable to the scientific world. If you want an indication of just how valuable, some researchers even charged back into the building while it was on fire to rescue these specimens, saving about 80 % of the mollusc holotypes.

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Does Invading Change You?

The red lionfish, an aggressive, fecund, and competitive species invasive to the Atlantic Ocean (Image Credit: Alexander Vasenin, CC BY-SA 3.0, Image Cropped).

The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges (2019) Burford Reiskind et al., Biological Invasions, https://doi.org/10.1007/s10530-019-01992-0(0123456789

The Crux

Invasive species are one of the most destructive forces and largest threats to native ecosystems, second only to habitat loss. The “how” and “when” of a species invading new habitats is obviously important, and as such many studies focus on if invasive species are present and if they are spreading. Yet these studies often disregard the mechanisms behind why a species is spreading or succeeding in these new environments. The mechanisms are important here, because by and large most invasive organisms will have very small populations sizes, leaving them vulnerable to stochastic events like environmental flux, disease, and inbreeding depression.

Two key paradoxes of invasive species are that these small groups of invasive organisms tend to not only have more genetic diversity than the native species (making them more adaptable to environmental change), but they are also able to outcompete the native organisms, despite having evolved in and adapted to what may be a completely different environment. The authors of this study used genomic approaches to address and try to understand these paradoxes.  Read more

Changing with the Climate

An immature female blue-tailed damselfly (Ischnura elegans)

An immature female blue-tailed damselfly (Ischnura elegans) (Image Credit: Charles J Sharp, CC BY-SA 4.0, Image Cropped)

Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans) (2018) Dudaniec et al., Molecular Ecology http://doi:10.1111/mec.14709

The Crux

Terrestrial organisms aren’t always stationary entities, they often move around the landscape searching for food, potential mates, or more ideal environments. Over time, these movements may introduce the species into new environments, as some change allows the species to expand their historical range.

An interesting aspect of this shifting of the species range is how the organisms at the edge of the distribution are maladapted to the novel environments, as most of the species will be adapted to conditions at the core of the species range. To overcome this, they must adapt to the new conditions. Successful adaptation is dependent on changes in gene frequencies away from the historical genotypes, with an increase in genes that promote survival in the new habitats. The authors in this study used molecular techniques to identify genes that new environments might select for.

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