Reading the history of caribou decline using their DNA

For caribou populations across Western Canada, declining numbers and shrinking habitat are visible signs of a species under pressure. But there is another story unfolding beneath the surface, one written into the animals’ DNA.

Charlotte Bourbon, a PhD candidate at the University of Calgary Faculty of Veterinary Medicine (UCVM), is looking to that genetic record to understand how caribou populations have changed over time and what their genetics can tell us about their ability to survive into the future.

Working under UCVM supervisors Dr. Jocelyn Poissant, PhD, and Dr. Marco Musiani, PhD’03, Bourbon examined the genetic diversity of 759 caribou from 45 populations in Western Canada. Her research provides a detailed genomic assessment of inbreeding and effective population size in caribou, offering new information that could help guide conservation efforts for some of the country's most threatened populations.

Their DNA carries a record of population changes stretching back generations, revealing both the pressures caribou have faced and the genetic challenges they now carry forward.

“We want to know how we can reduce the risk of inbreeding and maintain genetic diversity,” says Bourbon. “If we can understand what has happened to these populations, we have a better chance of helping them persist into the future.”

“What is truly remarkable about this study is the scale and resolution of the sampling. This was only made possible through long-term collaboration with many partners, including the Government of British Columbia, Parks Canada, the Canadian Wildlife Service and multiple First Nations,” says Poissant.

For Bourbon, one of the central concerns is the size an location of these herds of caribou. 

 “When populations get smaller and more isolated, there’s an increased risk of inbreeding,” says Bourbon. “And higher levels of this can have an impact on growth, reproductive success and survival. 

When closely related animals reproduce, it increases the chance that offspring inherit identical copies of genes from both parents, which over time can affect an animal’s ability to thrive and reproduce. Inbreeding is difficult to measure in wild animals as it’s not as simple as counting how many animals remain on the landscape.

That is where genomics comes in.

Reading the genetic fingerprints of inbreeding

Bourbon and her collaborators analyzed more than 33,000 genetic markers, known as single nucleotide polymorphisms (SNPs), across hundreds of caribou.

One of the things they were looking for was runs of homozygosity (ROHs), stretches of DNA where an individual has inherited the same genetic sequence from both parents.

“We’re looking at these stretches of DNA that are identical,” says Bourbon. “The longer those stretches are, themore they can tell us about recent inbreeding.”

For caribou populations already struggling to survive, that genetic information matters.

Several southern caribou populations in British Columbia and the Rocky Mountains have experienced severe declines and, in some areas, have become functionally extinct, locally. Conservationists have responded with increasingly intensive efforts to support remaining populations, including capturing females and assisting reproduction, predator management and translocation to stronger populations.

Bourbon's research adds another tool to that conservation toolbox.

A population is more than a head count

Another important measure in the study is effective population size.

While census population size is essentially the number of animals that can be counted in a population, effective population size provides an estimate of the number of individuals contributing genes to the next generation.

That distinction can be crucial.

“You can have a population that looks relatively large when you count the animals, but genetically, it can be much smaller,” says Bourbon. “Effective population size gives us a different snapshot of what is happening genetically within that population.”

The results were concerning, with many populations showing effective population sizes that could increase their susceptibility to inbreeding and limit their ability to adapt to future environmental change. Even when researchers accounted for connections between populations and the potential for gene flow, the genetic picture remained concerning, underscoring the challenges facing increasingly isolated caribou herds.

Those thresholds are important because very small effective populations can face greater risks to their short-term viability and their ability to retain the genetic diversity needed to adapt over the long term.

The study found census population size was associated with inbreeding, but contemporary effective population size was not, suggesting the genetic story of these populations is more complicated than simply asking how many caribou remain today.

A genetic window into the past

Perhaps the most revealing part of the research is that effective population size can tell researchers more than what is happening now. It can also provide a window into the past.

By reconstructing historical effective population sizes, Bourbon and her collaborators were able to identify a striking north-to-south pattern of when caribou populations experienced major declines.

Northern populations showed evidence of possible decline beginning roughly between 1700 and 1780. In central B.C., the decline appeared later, around 1780 to 1860. Southern populations experienced their decline later still, around 1860 to 1940.

The timing broadly coincides with documented periods of environmental change and increasing human disturbance across the region.

“We can use the genetics to look back in time,” says Bourbon. “It gives us information about what these populations looked like many generations ago and can help us understand when their declines happened.”

The result reveals a historical pattern that would be difficult to see by looking only at present-day population numbers.

Protecting more than the animals we have today

If a population becomes too small and isolated, it can lose genetic diversity over generations, leaving fewer options to respond to changing environmental conditions. 

“We’re trying a lot of different approaches to save these populations,” says Bourbon. “The genetic information can help us understand where those interventions are most needed and how we might support the remaining populations.”