Charlotte E. Hacker Science Reviews - Biology, 2023, 2(3), 1-7

Decoding the DNA of scat and the application of ge-

netic methodologies to understanding carnivore diet

Charlotte E. Hacker, PhD

The Snow Leopard Conservancy; Sonoma, California, USA; charlotte.hacker00@gmail.com

https://orcid.org/0000-0002-4641-3631

https://www.ScienceReviews.info/getfile.php?file=2748&orig_file=2748.pdf

Received July 17, 2023. Revised July 25, 2023. Published online August 28, 2023.

Abstract: Carnivore species are vital to ecosystem function and maintenance. One key component to

understanding carnivore ecology and the most effective means of management is knowledge of dietary resource

use. Traditional methods used to study carnivore diet, such as microhistology, have several technical and

logistical shortcomings. These have hindered the quality and quantity of data that shape understanding of how

carnivores exploit prey. Advances in genetic methodologies and their application to wildlife biology has

transformed the manner in which information about species can be gained. DNA metabarcoding is one such

example. With this approach, genetic sequences present in scat can be determined via next-generation

sequencing and matched to reference databases, revealing the carnivore that deposited the scat and the prey it

consumed. DNA metabarcoding has the ability to overcome many of the previous challenges associated with

dietary analysis and works to advance and inform current knowledge surrounding carnivore ecology, predator-

prey relationships, conflicts between carnivores and humans, and potential adaptability to large-scale landscape

shifts. Its use has provided novel insights on numerous carnivore species to help inform research priorities and

wildlife policies, including those living in unique fragile environments such as the Qinghai-Tibetan Plateau of

China. The continued development and increased capacity of molecular dietary analysis via DNA

metabarcoding has the promise to grossly improve carnivore conservation management strategies on a global

scale.

Keywords: Carnivore, Conservation Genetics, DNA Metabarcoding, Molecular Dietary Analysis, Next-

Generation Sequencing, Predator

Introduction

Carnivores play key roles in the functional

maintenance of the ecosystems they occupy. They

influence herbivore populations which in turn con-

trols vegetation (Ripple et al., 2014), impact disease

dynamics and parasite transmission (Terborgh &

Estes, 2010), and provide carrion for scavengers

(Wilmers et al., 2003). Successful habitat conserva-

tion and management may hinge on the holistic un-

derstanding of carnivore species in a given area,

and necessitates the obtainment of information on

their ecology, natural history, and diet.

The importance of understanding carnivore diet

Knowledge of carnivore diet can inform the

accessibility and availability of prey, the degree of

competition between different carnivore species

and how resources are partitioned, the extent of

livestock loss and its potential economic impact on

human livelihoods, as well as the adaptive potential

of a species and how it may respond to large-scale

environmental changes (Symondson et al. 2002;

Foster et al., 2013; Hacker et al., 2022).

Traditional methods used for carnivore diet

analysis

The dominant method for understanding car-

nivore diet has historically been microhistology.

With this approach, a sample, typically scat, is non-

invasively collected in the habitat where the carni-

vore of interest is found. The scat sample is then

dried, and digested hairs or bones are extracted for

Charlotte E. Hacker Science Reviews - Biology, 2023, 2(3), 1-7

comparison to the reference material of already-

known species (Pompanon et al., 2012). Another

method, albeit most commonly used to assess live-

stock predation rather than native prey, is the inter-

viewing of local community members sharing land-

scapes with carnivores (Meena et al., 2011; Oli et al.,

1994). Carnivores outfitted with global positioning

systems (GPS) have also been used as a way to find

kill sites and subsequently identify prey species (Ba-

con et al., 2011; Johansson et al., 2015), as has the ex-

amination of carnivore stomach contents (Balesrieri

et al., 2011).

Limitations and disadvantages of traditional

methods of analysis

Each of the above methods has drawbacks

that limit the ability to accumulate large amounts of

accurate data. Microhistology is a tedious process

that can be time intensive and subject to misidenti-

fication errors and inter-observer bias (Pompanon

et al. 2012). Biological reference material may not be

available and the host carnivore thought to have de-

posited the scat may be erroneously identified

(Weiskopf et al., 2016). With interviews, respond-

ents may incorrectly recall predation events, misi-

dentify the carnivore responsible, are subject to so-

cial pressure and bias, and may experience fatigue

or disinterest if the interview is too long (De Vaus &

De Vaus, 2013; Fisher 1993; Oli et al., 2014). Use of

GPS coordinates to identify kill sites requires the

carnivore to be GPS collared and the kill site to be

physically accessible to researchers (Johansson et al.,

2015). Lastly, the analysis of stomach contents re-

quires either euthanasia of the animal, or depend-

ence on fresh carcasses resulting from natural and

non-natural mortality events, such as roadkill.

Novel approaches to dietary analysis

Advancements in genetic methodologies have

resulted in the application of novel approaches to

replace the methods described above. Next-genera-

tion sequencing (NGS) platforms, such as Illumina,

now allow scientists to quickly and accurately de-

termine the order of nucleotides that comprise

DNA (A, C, T, G), resulting in terabytes of data in

the form sequencing reads. Online databases such

as NCBI GenBank

(https://www.ncbi.nlm.nih.gov/genbank/) and

BOLD (http://www.boldsystems.org/) have be-

come reservoirs of uploaded genetic sequences for

species genes and genomes. These known se-

quences serve as references by which sequencing

reads obtained by NGS can be uploaded, matched,

and compared for identification purposes.

The method of DNA metabarcoding

NGS technology is leveraged to study carni-

vore diet via DNA metabarcoding (Figure 1). With

this method, researchers collect scat in the field and

then bring it to a laboratory. The DNA present in

the scat is then non-specifically extracted from the

sample and subjected to PCR (polymerase chain re-

action) with a pair of universal primers. Universal

primers are less-specific and smaller stretches of

pre-made genetic sequences that attach to target ar-

eas of the animal’s DNA. These primers then “run”

across the DNA to make copies of a specific gene

segment of interest via a series of pre-programmed

cycles in a thermocycler. The selection of the seg-

ment of DNA to be amplified and sequenced is im-

portant. It must be conserved enough so that all

possible species possess it, but different enough in

its nucleotide sequence to tell them apart (Valentini

et al., 2009). For example, mitochondrially encoded

12S ribosomal RNA (MT-RNR1) is found in all ver-

tebrate species, but may not be different, or differ-

ent enough, between all vertebrate species (Shehzad

et al., 2012).

The resulting genetic material undergoes an-

other round of PCR to attach index tags to each in-

dividual sample so that they can be multiplexed

into one tube and later “pulled out” of the mix for

analysis. The final product of pooled samples with

index tags is pipetted onto a flow cell and placed on

the sequencer. Once finished, data files of returned

sequences and other documents, such as a quality

control report, are available for retrieval and analy-

sis using bioinformatics.

Bioinformatic tools allow researchers to ana-

lyze and process complex and voluminous genetic

data in a streamlined, collaborative, and efficient

manner (Gauthier et al., 2018). Researchers load re-

turned sequences onto a computer, and use bioin-

formatic pipelines and software programs to match

returned sequences to reference sequences. Param-

eters and other predetermined metrics are used to

help ensure confidence in the determination of the

host species as well as the prey item.

There are a number of key benefits to DNA

metabarcoding, many of which overcome the limi-

tations associated with more traditional dietary

analysis approaches. DNA metabarcoding allows

for multiple samples to be processed rapidly in tan-

dem, resulting in large amounts of data in a

Science Reviews - Biology, 2023, 2(3), 1-7 Charlotte E. Hacker

relatively short period of time (Shokralla et al., 2012).

It also eliminates issues surrounding human-ob-

server bias and produces more accurate infor-

mation (Pompanon et al., 2012; Valentini et al., 2009).

Further, DNA metabarcoding requires only a small

amount of scat as starting material. Alternatively,

microhistology may necessitate collection of the en-

tire sample, which takes up more space, challenges

transportation logistics and costs, and fully re-

moves potentially important chemosensory infor-

mation from the environment.

Figure 1:

A workflow example showing the application of DNA metabarcoding to determining carnivore diet.

Using DNA metabarcoding to study carnivore diet

in China

One area where DNA metabarcoding has

been heavily leveraged to understand carnivore

diet is the Qinghai-Tibetan Plateau (QTP) of China.

The QTP is a 2.5 million km

landscape with an av-

erage altitude of 4,500 m above sea level (Zhang et

al., 2002). The relatively recent and rapid uplift of

the plateau has led to numerous ecosystems and en-

demic species found nowhere else in the world

(Chang, 1981). Carnivores on the QTP include the

Tibetan wolf (Canis lupus), Tibetan brown bear (Ur-

sus arctos pruinosus), snow leopard (Panthera uncia),

Eurasian lynx (Lynx lynx) (Xu et al., 2008), Tibetan

fox (Vulpes ferrilata), red fox (V. vulpes), Pallas’s cat

(Otocolobus manul), and Asian badger (Meles

leucurus), among others. Native prey species in-

clude blue sheep (Pseudois nayaur), Tibetan gazelle

(Procapra picticaudata), argali (Ovis ammon), white-

lipped deer (Cervus albirostris), marmot (Marmota

spp.), chukar partridge (Alectoris chukar), and pika

(Ochotona spp.), among others (Jackson, 2012; Schal-

ler et al., 1988). Pastoralism remains heavily prac-

ticed in the area by local Tibetans and a number of

livestock that may serve as food for wild carnivores

are also present. These include domestic yak (Bos

grunniens), goat (Capra aegagrus hircus), sheep (Ovis

aries), and horse (Equus caballus).

Livestock depredation causes financial bur-

dens on herders, their families, and the local econ-

omy, promotes negative attitudes towards carni-

vores, is emotionally traumatizing, can create ten-

sion between residents and agencies seeking to pro-

tect at-risk species, and can lead to retaliatory kill-

ings . Herders who retaliate may also sell body parts

to recuperate their financial losses depending on the

carnivore killed, which can contribute to the illegal

wildlife trade . Understanding the use of livestock

as a food source is needed for carnivore conserva-

tion in areas dominated by pastoralism, as it is nec-

essary for constructing tailored mitigation strate-

gies, validating herder knowledge to outside

Charlotte E. Hacker Science Reviews - Biology, 2023, 2(3), 1-7

entities, and designing assistance programs such as

livestock insurance .

In an effort to better understand the role that

different carnivore species play in livestock loss on

the QTP, DNA metabarcoding was used to deter-

mine the livestock species in 147 red fox, 25 Tibetan

fox, 153 Tibetan wolf, 191 snow leopard, and 72 Eur-

asian lynx scats collected from September 2017 to

July 2018 in Qinghai and Gansu Provinces (Hacker

et al., 2022). As expected via previous interviews

with local herders (Hacker et al., 2020), the Tibetan

wolf had the highest percentage of livestock in their

diet at 21.7% of total prey counts, followed by red

fox at 5%, snow leopard at 4.9%, Tibetan fox at 4%,

and Eurasian lynx at 3.6%. Domestic yak were most

often identified, followed by sheep, and then goat.

Interestingly, two isolated occurrences of horse and

pig (Sus scrofa) were identified as being consumed

by snow leopard, a species that is often described as

a near-specialist (Lyngdoh et al., 2014). The degree

of livestock present in the diets of smaller carni-

vores such as the red and Tibetan fox was unex-

pected, but may be attributable to scavenging or the

depredation of newborns. Unfortunately, DNA

metabarcoding is unable to reveal the life stage of

the prey identified and cannot confirm if the host

carnivore killed the species it ultimately consumed.

From these findings, mitigation measures that

work in the interest of local herders and at-risk car-

nivore species could be recommended. For example,

the dominance of yak in Tibetan wolf diet helped to

validate herder knowledge, and assisted in leverag-

ing support for yak protection practices specifically

tailored to wolf ecology. In addition, the diversity

of livestock in snow leopard diet provided insight

into the potentially opportunistic and adaptable na-

ture of the species. All herders may want to take

protective measures if a snow leopard is in the area

regardless of livestock species kept. However, the

overall low percentage of livestock in snow leopard

diet suggests that losses caused by this carnivore

are relatively uncommon.

Continued dietary work on the QTP will be

imperative given the fragile nature of its unique

ecosystems and endemic species present. Climate

change, rapid urban development, and shifts in tra-

ditional practices will continue to impact the region,

including the human livelihoods and wildlife that

reside there. Carnivores in shifting landscapes may

find themselves overlapping with previously

unencountered species that outcompete them, caus-

ing an increased pursuit of livestock. Dietary infor-

mation can be a helpful indicator of ecosystem mod-

ifications that alter the distribution and abundance

of species as well as predicting how carnivores and

prey may adapt to future changes.

Application of DNA metabarcoding for species in

other parts of the world

DNA metabarcoding has also elucidated the

feeding habits of mammalian carnivores in other ar-

eas of the world. The analysis of 96 scat samples be-

longing to Tasmanian devils (Sarcophilus harrisii) in-

troduced to Maria Island, Tasmania revealed the

first instance of domestic cat (Felis catus) (McLennan

et al., 2022). It also confirmed that the drastic de-

creases in short-tailed shearwater (Puffinus tenuiros-

tris) and little penguin (Eudyptula minor) popula-

tions were likely due to Tasmanian devils (McLen-

nan et al., 2022). Eurasian otters (Lutra lutra) were

found to have a potentially much more flexible

feeding strategy than previously known in western

China (Wang et al., 2022). The examination of red

fox scats in Scotland found a curiously high per-

centage of domestic dog (C. l. familiaris) DNA. Re-

searchers linked this finding to coprophagia, which

may help to sustain red fox populations when their

natural prey base fluctuates (Waggershauser et al.,

2022). Coyotes (C. latrans) in New York City were

expected to have human food in their diet, but DNA

metabarcoding showed that domestic chicken (Gal-

lus gallus), presumably intended for human con-

sumption, comprised nearly half of dietary counts

(Henger et al., 2022).

An evaluation of DNA metabarcoding

Despite the vast information and novel find-

ings generated by DNA metabarcoding, it remains

an intensive and sensitive procedure that is expen-

sive, requires access to advanced laboratory equip-

ment and computers, and demands rigorous train-

ing in molecular techniques and bioinformatics.

Even minor changes in laboratory practices or pro-

tocols can cause differences in data when compared

between labs. Contamination risk is also high

(Hacker et al., 2021; Pompanon et al., 2012). The mo-

lecular marker, or genetic segment, selected must be

one that can differentiate carnivores and prey down

to a level appropriate for the research question to be

answered (Hacker et al. 2021). Further, scientists

Science Reviews - Biology, 2023, 2(3), 1-7                                                                                                       Charlotte E. Hacker                      
5 
 
must ensure that uploaded sequences to be used as 
references are available and accurate . 
 
Conclusion
 
 
  Advancements in the molecular dietary anal-
ysis of carnivores will continue to move forward as 
genetic methodologies improve and become more 
accessible. Recent notable insights into the ecology 
and  behavior  of  various  species  demonstrates  the 
ability  of  such  technology  to  shift  understanding 
and  apply  novel  information  to  wildlife  manage-
ment plans. Continued capacity in DNA metabar-
coding  has  the  potential  to  improve  our  under-
standing  of  many  more  traditionally  difficult-to-
study carnivores, ultimately enhancing the conser-
vation outcomes that impact them and the humans 
they share landscapes with. 
 
 
 
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Conflict of Interest

No conflicts of interest to declare.