EBP Position Paper - Genomics in Conservation

version 1.0-April 2025

Authors: Carolyn Hogg, Ann Mc Cartney, Anne Muigai, Eduardo Eizirik, Guojie Zhang, Camila Mazzoni, Linda Wong, Andrew J. Crawford, Federica Di Palma

Intent

This position paper is for those EBP Members who wish to engage with their local governmental authorities, NGOs and industry on the benefits and limitations of using genomics to inform conservation management actions, particularly in light of Goal A under the new Kunming-Montreal Global Biodiversity Framework (KM-GBF) that aims to maintain wild and domesticated species’ genetic diversity to safeguard their adaptive potential.

Why is Genetic Diversity Important?

Genetic diversity is a fundamental pillar of biodiversity and refers to variation in DNA within and between individuals and populations of the same species. Genetic diversity plays a critical role in shaping the traits and survival of organisms, and is essential for species to adapt to changing environments, including shifts in climate, emerging diseases, and habitat changes. Beyond its role in species survival, genetic diversity also contributes to the overall stability and resilience of ecosystems, enabling them to recover from disturbances and maintaining their main ecological functions. Genetic diversity is critical for successful ecological restoration efforts. The genetic diversity of many species is declining primarily due to human-induced changes of the environment, including but not limited to, habitat fragmentation, habitat loss, and over-harvesting. Summarised from Hoban et al. 2023 (https://doi.org/10.1111/conl.12953).

Genetic Indicators

Indicators are measurable values that track progress toward a specific goal. Under the Kunming-Montreal Global Biodiversity Framework (KM-GBF), the Convention on Biological Diversity (CBD) has adopted SMART indicators, Specific, Measurable, Achievable, Relevant, and Time-bound, for each goal and target. For Goal A, which focuses on preserving genetic diversity. Starting in 2020, several genetic diversity indicators were proposed to monitor progress in a scalable manner. The proposed indicators estimate genetic status primarily using proxies because we do not yet have DNA-based data for large numbers of species in all countries in the world:

  1. The proportion of populations within species with a genetically effective size (Ne) > 500. Adopted as Headline Indicator A.4 of the KM-GBF (required for CBD Parties to report)

  2. The proportion of populations maintained within a species, i.e. the number of different populations a species has retained. Adopted as a Complementary Indicator of the KM-GBF

  3. The number of species (and populations) monitored using DNA-based methods. Not a part of the GBF but encouraged for reporting

While these indicators are valuable for guiding biodiversity conservation, EBP emphasizes that these current (proxy) indicators should not replace, the ongoing efforts to develop genomic resources and empirical genetic datasets. Instead, these proxies should complement the current approaches by integrating more robust genomic data to enhance biodiversity conservation outcomes. Numerous genetic scientists including those who developed the proxy based genetic indicators concur with this viewpoint (Hoban et al 2024).

Benefits of Biodiversity Genomics

Genomics is a powerful tool for conservation, with high-quality reference genomes providing a starting point, for increasing the accuracy and utility of further DNA-based datasets. However, generating a single reference genome per species is insufficient to fully inform conservation efforts. The impact lies in the integration of the reference genomes with other conservation genomics data (e.g., population-level whole-genome resequencing, reduced-representation genomic data, genome-enabled marker panels). This integration enables more informed decisions driving significant advancements in biodiversity conservation.

Over the last decade, the fields of biodiversity and conservation genomics have provided valuable insights into species management across landscapes (see table 1 in Translating genomic advances into biodiversity conservation for detailed global examples). Genomic data can inform population management by identifying populations with low genetic diversity or inbreeding risk, guide conservation actions such as gene flow or translocation efforts, or identify genes associated with climate adaptation or disease resistance, enabling targeted restoration efforts, especially in regions facing rapid climate change.

Costs, access to infrastructure, quality samples, and unequal capacity across regions have limited the use of whole-genome data for conservation actions. As of 2024, although sequencing costs have decreased in some nations, obtaining genomic DNA data remains prohibitively expensive for most species, except for those few high-profile, charismatic ones. Recent examples of successful use of whole genome data for conservation applications include koalas, jaguars, kākāpō, vaquita, giant pandas, crest ibis, corals, American chestnut, Eucalyptus, Galapagos tortoises, and pangolins, in addition to indigenous farm animal and domesticated plant genetic resources. However, addressing these capacity challenges remains pivotal as sequencing costs continue to decline and it requires scalable solutions, such as shared regional sequencing facilities, innovative funding models, and investment in local capacity-building.

Current Challenges/Limitations

We have identified several key challenges/limitations impacting our ability to use genomics in global conservation applications. This is not an exhaustive list but a reflection of the working group’s experience and local knowledge, and the scientific literature (Hogg 2024, Leigh et al 2024, Klütsch et al 2021, Pärli et al 2021, Taft et al 2020).

  • Understanding genomic diversity. More research is needed to determine how genomic diversity reflects species’ conservation status and its implications for survival. Assessing genomic diversity as both a measure of past stressors, and predictors of traits such as disease resistance and reproductive success, will be crucial for forward looking conservation strategies.

  • Scalability and cost. The trade-off between cost versus the sample sizes required to generate meaningful data from different ecosystems and across a species’ range remains a significant barrier. We need to investigate cost effective and scalable solutions to realise the impact of genomics data.

  • Comparing data types. It is essential to compare the different types of genomic data (e.g. whole genomes vs. other DNA-based methods) to assess how they inform conservation actions/decision-making, and to evaluate the conservation benefits relative to the cost of data generation. This evaluation should include an assessment of reproducibility and the transfer of methods among stakeholders.

  • Unequal access. We acknowledge that access to sequencing methods is unequal across regions and countries within regions. The expectation of the scientific community to always use the “latest & greatest” is unrealistic in conservation applications, particularly for developing or poor nations, and the territories of Indigenous Peoples or local communities. However, such limitations should not prevent the use of simpler yet informative and accurate DNA-based approaches, which can still yield impactful conservation insights when supported by foundational genomic research.

  • Insufficient synergies. The lack of synergies between scientific research, infrastructure development, and conservation practitioners hinders the effective application of genomic tools in biodiversity protection. Strengthening diverse/multidisciplinary collaborations and communication across these sectors is essential to maximize the impact of genomic data on conservation outcomes.

  • Standards for genomic data (information related to structure and function of a species’ genome). Clear standards are needed to ensure the genomic data are interoperable and represent conservation metrics. These standards should include guidelines for the generation of empirical data and the conversion of genetic information into actionable indicators, in addition to protocols for quality control on data collection, sequencing, and analysis to ensure reliability in decision-making.

  • Data transparency and sharing. Improved transparency and minimum standards for sharing aggregated data, rather than raw data, are necessary. It is important to clarify that sharing all raw data with practitioners, governmental decision makers and society is often not required, and that aggregated data are sufficient to inform decision making. We need to establish ethical data-sharing frameworks for conservation management, to provide confidence to those sharing sensitive information, for example Indigenous communities. Currently, biodiversity monitoring data are difficult to access, and data duplication issues are further depleting needed resources.

  • Building in-country capacity. Funds must be dedicated to build ‘in-country’ capacity, to alleviate reliance on sending samples for sequencing elsewhere, unless it is justifiable in terms of cost, conceptual necessity, or time efficiency. Investment in ‘in-country’ infrastructure is essential to ensure sustainability. Sharing and testing different models across countries can help make technologies more widely available.

  • Monitoring approaches. Both species-based and ecosystem-based genetic diversity monitoring approaches need to be developed, with species-based monitoring approaches building off successful application in countries like Sweden, USA, Australia, and others. These approaches might involve using different species either opportunistically or according to a strategic plan, while exploring how the integration of genomic data and genetic indicators can complement biodiversity protection efforts.