Conservation genomics is a new and emerging field of research that harnesses the power of genomic technology to preserve species, habitats and ecosystems.
From genetically engineering heat-resistant coral reefs, to bringing a critically endangered mammal back from the brink of extinction, genomic technology is on a fast track to becoming a commonplace tool in the world of conservation. In this feature we dive into the applications, advancements and ethics of conservation genomics.
From Genetics to Genomics
Conservation genomics studies an organism’s genome in its entirety, the interaction of genes within it and how this information can help conservation efforts. The transition from conservation genetics to conservation genomics is recent, only occurring in the last few decades. Genome-scale data offer insights that are completely unachievable through traditional genetic techniques, made possible by technological advancements such as CRISPR-Cas9 gene editing and cloud-based data management.
Both genetic and genomic approaches are used to inform decision-makers, guiding conservation efforts and natural resource management. Additionally, whole genome sequencing gives us an idea of the genetic diversity within a population that can be applied in many aspects of conservation.
Why is Genetic Diversity Important?
Genetic diversity is essential for the long-term survival of a species.
A population with high genetic diversity contains many different alleles. Alleles are different forms of a gene that exist at the same locus on a chromosome, determining traits that are specific to individuals. When a species experiences environmental change such as warmer temperatures, some individuals will have a natural advantage over others because they have the right alleles to cope with that change – this is the basis of natural selection.
For example, two birds of the same species may nest in the same forest. Some individuals prefer to build their nests high up in the canopy whereas others choose to nest on the ground. This preference has some inherent genetic basis. When faced with deforestation, the ground-nesting birds will have a survival advantage; they will reproduce faster and pass their genes to their offspring, increasing the prevalence of ground-nesting related alleles in the population. In contrast, if an invasive species that hunts on the ground populates their habitat, the tree-nesting birds will have a selective advantage over the ground-nesting birds.
The same is true for disease. If a new disease emerges, some individuals will have alleles that make them genetically immune. This is, of course, random but genetic diversity ensures that the likelihood of at least some individuals resisting the disease is high.
Figure 1 | Darwin’s Finches are often used as an example of evolution. The size and shape of their beaks are adapted to different food sources. This evolution arose from genetic diversity in the original finch population. Source: Journal of Researcher, 1845.
A genetic bottleneck can pose a serious threat to a species survival. These are characterised by a rapid reduction in the size of a population, leaving only a fraction of the original population remaining and severely reducing genetic diversity. Genetic bottlenecks are difficult to recover from because they often result in inbreeding, which negatively impacts the fitness of offspring. In nature, bottlenecks can be caused by catastrophic events such as volcanic eruptions or wildfires. Unfortunately, human activity amplifies the risk of a genetic bottleneck occurring through land-use change, climate change and many other factors.
In essence, genetic diversity within a species maintains biodiversity across species. Genomic conservation presents a way to preserve endangered species and maintain both genetic and biodiversity.
Ecosystem services describe the wide range of benefits that humans receive from the natural environment (Fig. 2). These include but are not limited to:
- Food, water and raw materials
- Climate regulation and oxygen production
- Cultural, spiritual and aesthetic value
- Sources of medicine
Figure 2 | Overview of ecosystem services. Source: Metro Vancouver Regional Planning 2018.
All ecosystem services are underpinned by what is known as supporting services, which are fundamental to ecosystem function. These include nutrient cycling, soil formation and biodiversity.
Tackling a Sixth Mass Extinction
We are living through a mass extinction event, the sixth in Earth’s history. The last one occurred around 65 million years ago and is famed for the extinction of the dinosaurs. Today, up to 1 million plant and animal species are threatened with extinction due to human activity, and organisms are going extinct 22 times faster than the historical baseline rate.
The number of different species in an ecosystem (biodiversity) underpins its functioning; a wide range of organisms completing their roles within their ecological niche. Biodiversity loss has dire consequences for the functioning of our planet as we know it.
The loss of biodiversity and genetic diversity go hand in hand.
Adding Genomics to the Conservation Toolkit
Obtaining a clear picture of the entire genome allows researchers to begin to identify significant genes and their function, building up a reference genome. Reference genomes allow researchers to compare their own data and identify non-reference alleles in a population or species. They can use this information to make more informed decisions about conservation actions.
This has only become possible in recent years; low-cost Next Generation Sequencing has made such data readily available to conservation managers.
Next-Gen Sequencing: Easier, Cheaper and Faster Than Ever
NGS became available in the early 2000s, offering the ability to produce a huge amount of data in a rapid and efficient manner, unlike traditional Sanger sequencing methods. However, NGS technology really kicked off in 2014 following the launch of Illumina’s HiSeq X Ten Sequencer, driving the cost down from around $1 million per genome to just $1000. Advances from the past year see whole genome sequencing costing as little as $100, which is sure to drop even further in the future.
Population decline is a vicious cycle. When a population size drops the risk of inbreeding rises because there is less choice when selecting a sexual partner. Inbreeding dampens genetic diversity within a population, reducing the population’s ability to adapt to environmental change or survive novel diseases.
In comes genetic rescue – the reintroduction of genetic diversity into an endangered species. The outcomes of this technique can be difficult to predict so it is not often used. However, whole genome sequencing provides the potential to analyse the genetic diversity and amount of inbreeding within a population.
Genetic rescue was successfully implemented in the Florida panther, a subspecies of mountain lion that had only 20-25 individuals in the wild during the late 1990’s. High levels of inbreeding rendered the remaining population unlikely to successfully reproduce. Eight wild mountain lions from the Texas subspecies were introduced in combination with other conservation efforts, and today up to 230 Florida panthers exist in the wild.
Gene drives are genetically engineered to significantly increase the likelihood of the inheritance of a specific allele from parent to offspring, aiming to spread it through the entire population. A 2020 study used CRISPR-based gene drives in the lab to suppress the reproductive ability of mosquitoes, aiming to reduce the spread of malaria. Furthermore, Hammond et al., observed no functional resistant alleles in the mosquito population despite a strong selection for resistant alleles. These results are promising but further study is needed to identify whether applying this technology to wild mosquito populations would be effective and safe.
Case Study 1: Heat-resistant Coral Reefs
Coral reefs are of vital importance to the healthy function of our planet, supporting spectacular biodiversity that provides a wealth of ecosystem services to coastal populations. This includes fisheries, coastal protection, tourism and medicine, which collectively generate billions of dollars annually. Corals are described as “ecosystem engineers”, meaning they build a habitat for other organisms. In fact, many species rely on coral reefs for their survival; more than 25% of marine fishes are associated with coral reefs at some point during their lives.
However, more than 60% of our coral reefs are threatened by human activity, including climate change. In recent years the phrase “coral bleaching” has become more prevalent in the public eye. Coral bleaching describes the stress response of these animals when they lose the endosymbiotic algae that live in their stomach lining. The algal cells contain a chlorophyll pigment that give corals their colour. When they are lost, only the white calcium carbonate exoskeleton remains, hence the name “bleaching”.
Environmental changes such as warmer water, increased solar radiation (visible and UV) and extreme salinity changes are all triggers of coral bleaching, often resulting in the death of the animal which can have a cascading effect on the whole ecosystem.
Figure 3 | Coral exhibiting fluorescence under ultra-violet light. Source: Canva.
Genomics offers a modern avenue of conservation by exploiting the genetic diversity of algal symbionts. Coral symbionts exhibit a range of responses when exposed to elevated temperatures (influencing the coral’s reaction to the same conditions) and some types of symbiont are more resilient than others to heat stress. Unfortunately, the most thermally tolerant type is also the rarest amongst coral species. Selective breeding programs of coral are already underway to increase the prevalence of heat-resistant genes. Synthetic biology techniques could aid current efforts by identifying and introducing specific heat-resistant genes to corals under threat.
In 2018 the CRISPR-Cas9 gene editing system was successfully used to genetically modify coral zygotes for the first time. Researchers targeted specific proteins that cause corals to fluoresce under UV light. These proteins act like a sunscreen, preventing DNA damage by reflecting high frequency radiation, making it easy to spot when the protein has been deactivated (Fig. 3 & 4). The generation of said mutations was demonstrated using RFLP analysis, Sanger sequencing and high-throughput Illumina sequencing.
Figure 4 | Visualisation of coral larvae with and without fluorescence. GFP (green) and RFP (red) fluorescence in larvae that had been injected with RFP sgRNA/Cas9 complexes. Most injected larvae showed normal fluorescence patterns indistinguishable from those of wild type. Some injected larvae showed neither GFP nor RFP fluorescence, suggesting that multiple genes control GFP and RFP expression. Adapted from Cleves et al., 2018.
An Australian-French collaborative project called CORALCARE was launched in 2021 in an effort to study the genes and pathways involved in thermal tolerance of corals. This project is an exciting step forward, using CRISPR/Cas9 and CRISPR/dCas9 techniques to disrupt gene function and turn genes on/off, to identify thermotolerance-related functions in corals. Due to be completed at the end of October 2024, this is a prime example of researchers working at the front line of conservation genomics.
Case Study 2: Plague-immune Black-footed Ferrets
Once thought to be extinct, the black-footed ferret (Mustela nigripes) is North America’s most endangered mammal (Fig. 4). A successful captive breeding program brought the animal back from the brink of extinction but introducing it back to the wild has been a challenge. The black-footed ferret is particularly susceptible to sylvatic plague, no doubt a consequence of low genetic diversity within its small population. Infection has a nearly 100% mortality rate in the animal.
A proposal was submitted to the United States Fish and Wildlife Service in 2016 to use genetic engineering to establish immunity in a self-sustaining wild population. The CRISPR/Cas9 system presents a possible method to achieve this. The Cas9 enzyme can be directed to a target DNA sequence; in this case, a sequence that codes for plague immunity.
Figure 4 | Black-footed ferret (Mustela nigripes). Credit: Great Falls Tribune
This can be achieved by sourcing immune-resistant alleles from the domestic ferret and using CRISPR/Cas9 mediated genome editing to integrate the selected allele into the black-footed ferret genome. Successful integration can be verified using PCR techniques. A 2023 study produced the first chromosome-length, annotated reference genome of the black-footed ferret. This provides an exceptionally precise genetic resource that will support future in-depth studies in conservation genomics. This assembly serves as a reference for analysing genetic data from different individuals, allowing researchers to identify deleterious mutations related to inbreeding, and investigate the species’ vulnerability to plague compared to related Eurasian species. In the future, further long-read sequencing data can be integrated into the reference genome to improve its accuracy.
Genome technology is novel and requires careful consideration before being used in a real-life setting. Risks, benefits, cost, who gets to make decisions, public engagement and acceptance are often mentioned when considering the ethics of genome technology.
A 2021 study assessed the Australian public’s perception on introducing genetically engineered coral to the Great Barrier Reef, which has great cultural and economic significance to Australia. The results were overall positive but hesitant, with the 1148 participants “moderately strongly supportive” of the proposal, but only if 50-70% of the Great Barrier Reef was left intact. Many participants expressed concern over the unpredictable, long-term consequences of introducing genetically modified corals to the ecosystem. However, if a species is successfully preserved using genomic technology, specifically genetic engineering, this could pave the way for future use.
An interesting article published in 2019 provides a good presentation of the other side of the argument. Addressing the ethics of genetic engineering and gene drives from a conservation perspective, the author cautions that altering the biological world at the genomic level in line with human desires warrants special attention from those who wish to see it implemented.
We should address the source
We need to ask ourselves, why this is necessary? The primary reason is accelerated climate change. The Paris Climate Agreement established the target of limiting global warming levels to 1.5℃, but it is sadly unlikely that this will be met.
The IPCC Fifth Assessment Report from 2014 included several Representative Concentration Pathways (RCP), which describe different scenarios of future warming, with RCP2.6 used as a low impact scenario and RCP8.5 used as a high impact scenario. This increase is extremely likely to be driven by greenhouse gas emissions. By the end of the century, the global surface temperature is expected to increase by at least 1.5℃ (RCP4.5), but studies conducted since the publishing of the IPCC 2014 have suggested that current greenhouse gas emissions are tracking closest to RCP8.5.
Human-induced changes to the natural world are the primary driver for the biodiversity loss we’ve observed so far. The ability to use genomic technology to conserve species is brilliant, but should not be treated as the only solution. By reducing carbon emissions alongside this, the hope for the future is brighter.
The Future of Conservation Genomics
Conservation genomics is still in its infancy, but its potential is certainly being explored. The research currently underway to conserve coral reefs and the black-footed ferret are powerful indicators of the success that is already underway. Genomic technology can give us a detailed understanding of genetic diversity across the genome and help inform conservation efforts.
Genome technology has the potential to transform the planet we live on. Can you imagine a world where nobody dies from malaria, where 600,000 people every year continue with their lives?
Allendorf, F.W., Hohenlohe, P.A. and Luikart, G. (2010). Genomics and the Future of Conservation Genetics. Nature Reviews Genetics, 11(10), pp.697–709. doi:https://doi.org/10.1038/nrg2844.
Anon (2023). Where to See the Florida Panther | Florida State Parks. [online] Florida State Parks. Available at: https://www.floridastateparks.org/learn/where-see-florida-panther#:~:text=It%20is%20estimated%20that%20there%20are%20approximately [Accessed 18 Aug. 2023].
Armitage, H. (2018). CRISPR Used to Genetically Edit Coral. [online] News Center. Available at: https://med.stanford.edu/news/all-news/2018/04/crispr-used-to-genetically-edit-coral.html [Accessed 18 Aug. 2023].
Britannica (2023). Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services | International Organization. [online] Encyclopedia Britannica. Available at: https://www.britannica.com/topic/Intergovernmental-Science-Policy-Platform-on-Biodiversity-and-Ecosystem-Services [Accessed 18 Aug. 2023].
Cleves, P.A., Strader, M.E., Bay, L.K., Pringle, J.R. and Matz, M.V. (2018). CRISPR/Cas9-mediated Genome Editing in a reef-building Coral. Proceedings of the National Academy of Sciences, 115(20), pp.5235–5240. doi:https://doi.org/10.1073/pnas.1722151115.
European Commission (2020). CORDIS | European Commission. [online] Europa.eu. Available at: https://cordis.europa.eu/project/id/894412 [Accessed 18 Aug. 2023].
Hammond, A., Pollegioni, P., Persampieri, T., North, A., Minuz, R., Trusso, A., Bucci, A., Kyrou, K., Morianou, I., Simoni, A., Nolan, T., Müller, R. and Crisanti, A. (2021). Gene-drive Suppression of Mosquito Populations in Large Cages as a Bridge between Lab and Field. Nature Communications, 12(1), p.4589. doi:https://doi.org/10.1038/s41467-021-24790-6.
IPCC, 2014: Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Core Writing Team, R.K. Pachauri and L.A. Meyer (eds.)]. IPCC, Geneva, Switzerland, 151 pp.
Kliver, S., Houck, M.L., Perelman, P.L., Totikov, A., Tomarovsky, A., Dudchenko, O., Omer, A.D., Colaric, Z., Weisz, D., Aiden, E.L. and Chan, S., 2023. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). Journal of Heredity, p.esad035.
Mankad, A., Hobman, E.V. and Carter, L. (2021). Genetically Engineering Coral for Conservation: Psychological Correlates of Public Acceptability. Frontiers in Marine Science, 8(21). doi:https://doi.org/10.3389/fmars.2021.710641.
Marx, V. (2022). Conservation Genomics in Practice. Nature Methods, 19(5), pp.522–525. doi:https://doi.org/10.1038/s41592-022-01477-4.
Patch, A.-M., Nones, K., Kazakoff, S.H., Newell, F., Wood, S., Leonard, C., Holmes, O., Xu, Q., Addala, V., Creaney, J., Robinson, B.W., Fu, S., Geng, C., Li, T., Zhang, W., Liang, X., Rao, J., Wang, J., Tian, M. and Zhao, Y. (2018). Germline and Somatic Variant Identification Using BGISEQ-500 and HiSeq X Ten Whole Genome Sequencing. PLOS ONE, 13(1), p.e0190264. doi:https://doi.org/10.1371/journal.pone.0190264.
Ryder, O., Phelan, R., Hay, B., Rocke, T., Church, G. and Camacho, A. (2016). A Proposal for Genomically Adapting Black-footed Ferrets for Disease Immunity. [online] Revive & Restore in Partnership with San Diego Zoo Global. Available at: https://graphics8.nytimes.com/packages/pdf/opinion/greenhouse/BFFUSFWSproposal2.pdf.pdf [Accessed 18 Aug. 2023].
Sandler, R. (2019). The Ethics of Genetic Engineering and Gene Drives in Conservation. Conservation Biology, 34(2). doi:https://doi.org/10.1111/cobi.13407.
Supple, M.A. and Shapiro, B. (2018). Conservation of Biodiversity in the Genomics Era. Genome Biology, 19(1). doi:https://doi.org/10.1186/s13059-018-1520-3.
UNFCCC (2015). The Paris Agreement. [online] United Nations Climate Change. Available at: https://unfccc.int/process-and-meetings/the-paris-agreement [Accessed 18 Aug. 2023].
WHO (2022). World Malaria Report 2022. [online] www.who.int. Available at: https://www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2022 [Accessed 18 Aug. 2023].