Shitty research: Value of faeces in conservation and evolution

“Disgusting”, “Useless”, “Waste”

These are often synonymous to “faeces”, or poop. However, in conservation research, scientists have overturned the above common perception. In fact, the study of faecal samples is also useful in evolutionary studies. It is no surprise that while scientists are looking deeper into faecal samples for genetic and evolutionary studies, they are also tracking poop from space!

Video of poop tracking from space to study penguin populations: https://www.youtube.com/watch?v=49_W6i9aWVM

INTRODUCTION TO SCATOLOGY

In conservation research, faecal analysis, also known as scatology, is a non-invasive method to study animals. This allows researchers to collect faeces, or scat, without coming into direct contact with animals.

Invasive methods involve the collection of blood and tissue samples directly from animals. On the other hand, non-invasive methods collect hair, saliva or faecal samples.

This method is increasingly preferred over traditional live capture methods in specific studies of endangered or elusive animals and complements camera trap methods1. Applications of faecal analysis have since been carried out on penguin colonies (like above), felids, whales, primates and bears. Recent development has also shown that scatology can be used to study species distribution, abundance and evolutionary studies using fossilised faeces1. But before we discuss about the benefits of faecal analysis, it is important to first recognise the advancement of molecular techniques.

STUDYING FAECAL SAMPLES IN LABORATORIES

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Figure 1. Molecular workflow of faecal analysis (Figure by me)

Faecal samples were once very difficult to work with due to low DNA concentration, low DNA quality due to rapid degradation and high level of contamination2. However, improvement of molecular techniques helped scientists to overcome many of the above problems in the workflow (Figure 1). These include DNA extraction kits for faecal samples, design of specific primers to amplify molecular markers and metabarcoding approaches1,2.  Introduction of Next-Generation Sequencing (NGS) also allows high throughput sequencing at lower cost and higher efficiency in large-scale studies.

WHAT GOES IN, MUST COME OUT

So, what can scientists infer from poop? The most commonly seen application is in diet analysis and habitat requirement, for instance on primates.

Primates like tree-dwelling monkeys are difficult to capture. Instead, researchers are able to collect their faecal samples from the ground.

From their faecal samples, scientists are able to isolate genetic materials of prey or vegetation to monitor their diet and health3. Scientists can then study the presence and distribution of vegetation and prey to establish the animals’ foraging range. This informs about their habitat requirements to aid conservation and reserve management policies. Other studies which have adopted this approach include research on the elusive leopard cat (Prionailurus bengalensis) by Shehzad et al. in 2012, various whale species by Hunt et al. in 2013 and the endangered Pyrenean desman (Galemys pyrenaicus) by Gillet et al. in 2015.

Yet the research does not just stop here. Diet analysis can also help understand foraging behaviours, fruit dispersal and digestive physiology. In 2012, Pickett et al. carried out diet analysis from faecal samples of on six primate genus and revealed a huge insect diversity in their consumption (Figure 2)3.

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Figure 2. Pickett et al. 2012 study on diet analysis of monkeys using faecal samples

Coupled with observational studies, scientists are able to affirm foraging behaviours of woolly monkeys (which consume more fruits than insects hence lower diversity of insects observed). Saki monkeys were also inferred to be good insect foragers with a higher than expected insect diversity from their faecal samples.

FOLLOWING POOP TRAIL OF POPULATIONS

As seen in the above video, tracking of penguin poop from space allows scientists to infer locations of populations. Similarly, scientists are able to track species distribution from faecal samples and account for population numbers.

Some endangered species are difficult to track or capture by scientists due to their elusive nature. They may also be in extremely low numbers or live in low densities.

One example includes the Iberian lynx (Lynx pardinus) which was recorded by the IUCN Red List of Threatened Species to have less than 200 mature individuals in remaining wild subpopulations (Critically Endangered) yet little was known about the habitat area of the species. Hence in a study by Palomares and teamthey systematically surveyed potential lynx habitats for faecal samples to estimate its species distribution (Figure 3)4.

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Figure 3. Left: Map shows location of faecal samples found within the Iberian Peninsula. Circles denote records from systematic surveys with positive (black) and negative (open) locations of faeces. Squares denote records from non-systematic surveys. Star denotes location of Donana National Park. Shaded areas denote patches previously identified to be probable habitat areas of Iberian lynx. Right: The Iberian lynx

From the presence records of affirmed lynx’s scats, researchers were able to estimate the broad distribution area where the lynx could be found. In fact, tracking of faecal samples was continually applied in following studies like Simón et al. study in 2012 to infer population counts. Janečka and team’s research in 2011 also found that faecal studies were more efficient in tracking snow leopards in the wild than camera-trapping methods.

NEW WORD OF THE DAY: COPROLITE

Coprolite is the scientific term for fossilised faeces of animals.

Coprolite comes from the Greek words Kopros, meaning “dung”, and Lithos, meaning “stone”. Together, “dung stone” which refers to preserved and fossilised faeces. Coprolites allow study of diets of extinct organisms (Figure 4)5.

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Figure 4. Coprolite and its preservation

Most studies of coprolites focus on extinct carnivores. This is because diets of carnivores contain higher levels of phosphate content which preserves faeces in better condition than those from herbivores5. However, apart from diet, what else can coprolites tell about extinct animals? Here is a hint:

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Figure 5. Grooming observed in chimpanzees

Yes, hair (or feathers too) can be found in coprolites! Hair from extinct animals with self-grooming behaviours can be preserved in coprolites5. Scientists have also found soft-tissue parasites preserved to study ancient parasitism and understanding of coevolution of host and parasite5. And the list of possible discoveries continues with arthropods, bacteria, microfossils or macrofossils of plants and fungi5.

What’s more, the study of coprolites is not restricted within the biological field. Check out this short introductory talk by Dr Fiona Gill on Coprolite Chemistry, the study of organic compounds in coprolites!

Video by The Royal Society during its Summer Science Exhibition 2012: https://www.youtube.com/watch?v=vQL8elYXurI

NEVER JUDGE A POOP BY ITS COVER

“Valuable”, “Informative” and “Potential”

Now, doesn’t one begin to think of “faeces” with the above words instead? Faeces may be commonly perceived as waste yet it unlocks a whole new field of scientific study to better understand the diet, habitat requirement, species distribution and even evolutionary histories of various organisms. “One man’s trash is another man’s treasure”. At times, a shitty research may just in fact be a golden opportunity!

LITERATURE CITED:

  1. Rodgers, T. W. & Janečka, J. E. Applications and techniques for non-invasive faecal genetics research in felid conservation. Eur. J. Wildl. Res. 59, 1–16 (2013).
  2. Broquet, T., Ménard, N. & Petit, E. Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates. Conserv. Genet. 8, 249–260 (2007).
  3. Pickett, S. B., Bergey, C. M. & Di Fiore, A. A Metagenomic Study of Primate Insect Diet Diversity. Am. J. Primatol. 74, 622–631 (2012).
  4. Palomares, F., Godoy, J. A., Piriz, A. & O’Brien, S. J. Faecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian lynx. Mol. Ecol. 11, 2171–2182 (2002).
  5. Qvarnström, M., Niedźwiedzki, G. & Žigaitė, Ž. Vertebrate coprolites (fossil faeces): An underexplored Konservat-Lagerstätte. Earth-Sci. Rev. 162, 44–57 (2016).
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