Genetic diversity loss and causes

Domestication of plants, animals and other organisms can be thought of as a process whereby populations adapt to artificial environments.  The more artificial the environment, the more likely the population will be less resilient when disruptions occur or when the population has to survive in a different environment. Domestication is a long standing process, but conventional farming and food processing environments have become increasingly artificial. Lecocq (2019) describes domestication as "... the process in which populations are bred in man-controlled environment and modified across succeeding generations from their wild ancestors in ways making them more useful to humans who control, increasingly during the process, their reproduction and food supply".  He identifies 5 levels of domestication: 1) acclimatization of a wild population to man-controlled environments begins, often a captive environment where living conditions and diet are controlled; 2) seed materials are collected from the wild to maintain the captive population; 3) the full lifecycle of the organism is controlled, but wild genes are introduced by various means; 4) full control but without wild inputs; 5) selective breeding or engineering for traits humans deem desirable.

The challenge is to balance genetic improvements that help with food system function without unduly compromising genetic diversity.  But we have largely failed to create the right balance. The genetic base of the plants, animals, insects and micro-organisms on which we depend for survival has been dramatically narrowed and we are not doing enough to maintain biodiversity and resilience.  The consequence is on-going species, breed and variety extinction, and for the survivors, plants, animals and other organisms that are more subject to disease pressures, less adaptable in the face of a changing climate and other environmental disruptions, less responsive to local environments and food cultures, and more expensive to manage.

Seeds and plants

According to Seeds of Diversity, "Today, only a tiny fraction of Canada's crop genetic diversity is available to farmers. Most varieties are forgotten and all but abandoned in seed banks. Of the 7,098 apple varieties documented as having been in use between 1804 and 1904, for instance, about 86% have been lost. Similarly, 95% of the cabbage, 91% of the field corn, 94% of the pea, and 81% of the tomato varieties no longer exist."

As well, by some accounts

  • Only 200 of the over 300,000 species of edible plants in the world are significantly consumed by humans
  • "75% of global food biodiversity has become extinct in the past 100 years.
  • 60% of the remaining gene pool of crop plants is inadequately conserved and studied.
  • 90% of the remaining gene pool of crop plants is not being used commercially." (Seeds of Diversity)

Although seeds receive much of the attention, similar problems are recorded in plant propagation (asexual or vegetative reproduction).


The FAO has produced 2 reports to date on the state of animal genetic resources.  The first report (FAO, 2007) found that 49 mammalian breeds in North America were already extinct (sheep and pigs experiencing the highest losses).  Extinctions on a global basis were occurring at the rate of one / month.

The second report, FAO (2015), concluded that globally 17% of livestock breeds were at risk of extinction and this is an underestimate because some 58% of breeds do not have sufficient population data for an assessment. Conservation programs have slowly been increasing and  64 countries had in vitro gene banks and 41 more were planning to establish them.  However, because these collections are in early stages of development, there are many gaps. Unfortunately, the forces creating genetic erosion and extinction continue to grow.

Fish (and other organisms used in aquaculture)

The FAO has also identified genetic erosion, inbreeding depression and loss of fitness as risks in the aquaculture sector.  The range of species used in aquaculture is dramatically less than the capture fishery. According to Fisheries and Oceans Canada, the aquaculture sector in Canada uses about 45 different species of finfish, shellfish and marine algae but finfish comprise 90% of the production volume and salmon (Atlantic, Coho and Chinook) are dominant within that category (Nyugen and Williams, 2013).  For shellfish, mussels and oysters are the largest volume production, with some clams and scallops. For marine algae, kelp, moss and seaweed are cultivated in small but increasing volumes in the Atlantic provinces.  In each category, a limited number of species are involved (see Canadian Aquaculture Industry Alliance). Farmed species may also be contributing to wild population declines (Waples et al., 2012; Nyugen and Williams, 2013).  Other species being researched for aquaculture in Canada include: cod, eels, halibut, wolffish, abalone, haddock, blackcod, quahaugs, geoducks, sea urchins and striped bass (DFO).

Although farmed aquatic organisms are based on wild species, the FAO (2019) reports that some 60% on a global basis have undergone some type of genetic manipulation, sometimes using advanced genetic techniques. Genetic tools are being applied in Canada (including genetic engineering, see Goal 4) to these farmed species in ways that parallel what has happened to animal production, not a surprising development since aquaculture generally follows an industrial production and distribution model.


Because insect species are so numerous and diverse (the highest of any other animal or plant taxon), there is a tendency to dismiss human activity as cause for concern.  But some 40% of insect species are thought to be at risk of extinction with dramatically plummeting numbers being reported in many parts of the world.  Most at risk are Leptidoptera, Hymenoptera and dung beetles and 4 major aquatic taxa (Sánchez-Bayo and Wyckhuys, 2019).  It is widely established that farm landscape simplification and associated pesticide and fertilizer use are significantly reducing the biodiversity of insect populations (and species that depend upon them like bats and insectivorous birds) (Raven and Wagner, 2020).  Less than 1% of these insects are pest problems, most are beneficial providing numerous ecosystem functions including suppressing pest populations (Jankielsohn, 2018).

Some insect populations have been directly manipulated by humans, either to reduce their pestilence (e.g., sterile insect techniques), or for beneficials to enhance their capacity to manage pests (e.g., improving the fecundity and survival rates of insects that feed on weeds). There have also been many exotic introductions to regions for pest management purposes, not all of which have been successful, and several of which have created secondary problems.  These approaches have frequently been very helpful for reducing pesticide use, which since the 1960s has had numerous negative impacts on target and non-target insects.

But at this stage we know little about innumerable insect species and  the broader implications of our direct  manipulation of insect genetic diversity, which calls into question our regulatory approach.


As with insects, we know little about most of the micro-organisms on the planet and how humans have negatively affected soil micro-organisms through farming practices. We have manipulated certain microbial populations (e.g, trying to improve the efficacy of nitrogen fixing rhizobia or myccorhizae) to positive agricultural effect, though not necessarily wider ecosystem function. Genetic engineering contributes to this with crop (eg., Bt corn) and processing applications (see Hanlon and Sewalt, 2020) that run counter to ecological theory supporting biodiversity (see Goal 4).

Micro-organisms play numerous roles in food and beverage processing, including direct food source (eg., mushrooms and spirulina),  fermentation (some 3500 products worldwide) and other transformations, for enzyme production (e.g., amylase in bread making), for ripening (e.g., molds in cheese), for analytical purposes to indicate problems, and to compete with bacteria that can cause food safety problems. They are taken as supplements to assist with digestion. Many of these have been manipulated for uniformity, specific conditions and improved performance.

They are also used in the production of some animal feed, as direct food, as feed additives to deliver certain nutrients, for animal gut health, and as protection from organisms causing spoilage.

Domestication  processes are thus also in play for microorganisms, although somewhat different than plants and animals because of the sheer volume of organisms involved. Certainly for food processing, the organisms best studied for genomic changes (cf. Douglas and Klaenhammer, 2010), a limited number of very important microbes have been artificially selected and isolated from wild relatives to serve processing needs, particularly those involved in making bread, cheese, beer, wine, saké, yoghurt, soy sauce or spirits.  The domestication process has significantly altered microbial behaviour, sufficiently so that many processors are turning to wild relatives to capture new flavours and characteristics in foods and beverages (Steensels et al., 2019).

Increasingly, genomics are being applied to other areas of potential human benefit, including biological control and soil nutrient uptake.

How did we get into this situation?

As with many other sustainability challenges, our current circumstance is tied to the failure to use agroecology to guide farming system research, design and implementation.

Privatization of genetic resources

Farmers and their communities were the original breeders and protectors of biodiversity because their ability to produce depended on their interaction with the ecosystem of their farm and region. In these earlier periods, breeding science and agricultural extension were not yet professionalized, and industrial approaches to farming based on new ideas of capital accumulation were just emerging (mid-19th century in Britain, see Albury and Schwartz, 1982).  Farmers were early versions of what we now refer to as  "citizen scientists" and "barefoot agronomists".  However, the professionalization of breeding and the post WWII emergence of large and transnational firms with a commercial interest in agricultural inputs (including seeds, plants, animal breeds) has shifted control of genetic resources to private firms, facilitated in part by the abandonment or curtailing of many public sector programs.

Narrow focus on traits with commercialization potential within conventional production and distribution systems

The drive to increase yields has focused breeding attention on a narrow range of traits that support the industrial model of food production.  The food industry's perceptions of consumer demand and how to meet it in a profitable way has also shifted the kinds of traits deemed important.  Supply chain logistics also create pressure for certain characteristics that facilitate low cost movement along supply chains and look appealing to consumers in grocery stores. The CGIAR (2014) concluded that global diets are being homogenized, becoming 36% more similar over the last 5 decades, with significant dependence on genetically homogenous wheat, rice, maize, potato, soybean, sunflower oil, and palm oil.  Related processes are occuring in animals and it appears that the modern aquaculture sector has not learned the lessons of plants and animals to avoid following similar trajectories.

Simplification of farm environments

As farm ecosystems have been simplified, so too are the organisms that populate the farm.  A farm that specializes in a limited number of crops in short rotations does not, for example, look for plant varieties that do well in more complex rotations with intercropping.  A beef feedlot operation wants breeds that gain weight quickly on grain diets and does not want cattle breeds that digest well pasture grasses and thrive in all year outdoor environments on the range.

In contrast, farmers trying to practice ecological  sustainability are typically interested in a wider set of traits in plants and animals than high yield, processing characteristics and resistance against the dominant diseases.  Many ecological producers are looking for plants and animals that yield well, but not necessarily "highly", and have other features including: minimal environmental impacts, minimal resource and maintenance requirements for the yield obtained, and climate resilience (Entz et al., 2015), multiple uses (e.g., long-stemmed grains that provide bedding and compostable material, in addition to grain), multiple products (e.g., wool and meat for sheep), and multiple services (e.g., hogs for pasture renovation, weed control, nutrient cycling and meat) (MacRae et al., 1989).  Ecological vegetable producers are concerned about pest and disease tolerance in non-chemical environments, early vigour, weed competitiveness, and flavour (Dey et al., 2018).

Ecological illiteracy among breeders, companies and decision makers

The community of breeders does not have significant training in ecology.  This is an inherent flaw of the genetic and molecular sciences that now dominate breeding work (see Goal 3 Public Research). Fundamentally, agroecology and molecular biology/genetics are different paradigms (see Table)

Table: Contrasting characteristics of agroecology and molecular biology as they relate to the food system

Agrecology Molecular biology
Contextual Acontextual Place is important in agroecological investigation
Self-reliance Dependence Agroecological investigations are often designed to better understand knowledge and management rather than imported to the farm products
Scientific, open ended inquiry Teleological Teleological, meaning that the endpoint is determined in certain ways when the investigation begins
Normative Positivist
Holistic Reductionist
Ecological design Genetic design Very different biological scales
Multiple causes and effects Limited cause and effect
Evolutionary Time truncated There is a field of evolutionary genetics, but it isn't necessarily part of molecular level inquiry
Science, practice and movement Science, commercialized product


As a result different kinds of questions are asked and answered.  When, for example, looking at a weed problem,

An agroecologist asks:

  • How do conditions favour the weed?
  • What is weed telling us about the soil?
  • Are tillage and crop rotation part of a design problem?
  • How can weed be prevented by altering conditions with socio-economic circumstance of the farm?

A molecular biologist (and a farm input company) asks:

  • What gene sequences give this weed its competitiveness?
  • What changes to its genetic structure might make it more susceptible to chemical control?
  • How can we make the crop resistant to the most effective chemical controls and widen the window of their application?
  • Can we develop a process to make these genetic manipulations commercially viable?

Because most decision makers have limited training in ecology, their capacity to appreciate the processes and products that emerge from these different paradigms is also very constrained.  Because the molecular approaches are currently dominant, and agroecological ones, marginal, there is a strong inclination to support the dominant.

The drive to lower costs in food and feed processing

Since many processors are squeezed financially by the economic power of retailers, there is constant pressure to lower production costs.  Similarly, animal feed manufacturers try to provide low cost products, especially given the thin margins for farmers on many animal products. Creating a uniform product is also central to production and marketing strategies.  Natural occurring micro-organisms are variable in efficacy and consistency and this is typically eliminated to create more uniform, lower-cost products.

The anti-fraud regulatory paradigm

The legislative architecture of Canada's system for managing plants, animals and other organisms emerged primarily within an anti-fraud period in the early 20th century, driven by the criminal law powers of the Constitution (see Constitutional Provisions). Today's legislation still carries the residues of those early preoccupations and although there have been improvements over the years, the legal frameworks are not about assuring diverse genetic resources in perpetuity.