Metadata Factsheet

1. Indicator Name

The proportion of populations within species with an effective population size > 500

This is sometimes referred to as “the Ne 500 indicator” or “genetic diversity within populations indicator” or “Effective population size 500 indicator”

2. Date Of Metadata Update

2023-06-01 12:00:00 UTC

3. Goals And Targets Addressed

3a. Goal

Goal A The integrity, connectivity and resilience of all ecosystems are maintained, enhanced, or restored, substantially increasing the area of natural ecosystems by 2050; Human induced extinction of known threatened species is halted, and, by 2050, the extinction rate and risk of all species are reduced tenfold and the abundance of native wild species is increased to healthy and resilient levels; The genetic diversity within populations of wild and domesticated species, is maintained, safeguarding their adaptive potential.

3b. Target

Headline indicator for Target 4.Ensure urgent management actions to halt human induced extinction of known threatened species and for the recovery and conservation of species, in particular threatened species, to significantly reduce extinction risk, as well as to maintain and restore the genetic diversity within and between populations of native, wild and domesticated species to maintain their adaptive potential, including through in situ and ex situ conservation and sustainable management practices, and effectively manage human-wildlife interactions to minimize human-wildlife conflict for coexistence.

That being said, as noted by Hoban et al 2023a, and explained below, it is also relevant to Targets 1, 3, 5, 9, and 12.

4. Rationale

Effective population size (Ne) is a well-accepted metric for measuring the rate of loss of genetic diversity within populations. As explained below, an Ne above 500 (usually a census population size of 5000) will maintain genetic diversity within populations. Genetic diversity is necessary for species’ populations to remain healthy and adapt to environmental change, such as climate change, pollution, changing habitats, and pests and disease. Genetic diversity is also vital for resilience of all ecosystems, such as recovery from heat waves and ocean pollution or acidification. It is also vital for the success of ecosystem restoration and the (re)introduction of populations and species. Populations with low genetic diversity suffer inbreeding, low viability, and low resilience. Therefore, an Ne indicator is necessary to measure the conservation and sustainable use of genetic diversity.

Genetic diversity is variation at the DNA level, including differences among individuals within populations of species and differences among populations of each species. However, assessing DNA with genetic sequencing technology can be time consuming, and requires substantial funds, skills and technology, making it challenging for large-scale evaluation, particularly in species-rich nations.

Fortunately, we can assess genetic status of species and populations via Ne without needing DNA data. This is important since relatively few species have DNA-based studies, especially in biodiversity hotspots.

In 2020, three genetic diversity indicators were proposed, including the Ne 500 indicator. They have the following important features:

  • are scientifically valid, based in core conservation and genetic concepts
  • are affordable and feasible with existing data
  • require a moderate to low time and resource investment
  • leverage diverse data and multiple ways of knowing including local knowledge holders
  • can often align with other biodiversity assessments
  • allow for easy translation into policy and management of species
  • are applicable and relevant in all countries, taxonomic groups, and ecosystems.
  • use concepts that are intuitive or accessible to non-geneticists (e.g. genetic losses due to small populations and loss of populations).
  • are ‘forward compatible’, meaning they can incorporate new methods that arise

What is the Effective Population Size (Ne) 500 indicator?This indicator is based on the knowledge that populations that are small in size (effective population size (Ne) < 500) are highly susceptible to rapid loss of genetic diversity and are at high risk of extinction due to genetic threats. As shown in the figure, Ne 500 is widely recognized by scientists and conservation practitioners as a “sufficient” size to prevent loss of genetic diversity within populations (in this case, a statistic called ‘heterozygosity’) – Ne much higher than Ne 500 and genetic loss within populations is near zero. Much lower and genetic loss becomes rapid.

And Ne can be measured without DNA data. Ne can be approximated from population census size. Typically, Ne is about 0.1 of the census size. As Hoban et al (2023b) and Hoban et al (2020) show, there are many sources of census size data which countries can employ, and indeed can leverage existing in-country data, expertise, and biodiversity infrastructure.

The Ne 500 indicator is likely the best evidence of genetic status and risk of genetic erosion when DNA sequencing is not available (the case for most species globally). This indicator provides a measure of the loss or maintenance of genetic diversity within populations and is feasible and scalable for many species per country. Maintaining effective sizes above 500 will protect the genetic diversity within populations for many generations.


Illustration of loss of genetic diversity when Ne <500. Adapted from Willi et al, Dec 2021 PNAS.

Thus, this indicator is directly relevant to Goal A, as it informs the health and resilience of species’ populations, their genetic diversity, and the threat of species extinction. Knowledge of species population’s effective size is relevant to Target 4 as it facilitates active management of species, ex situ breeding programs and informs the conservation efforts and recovery process of species populations following environmental disruption. The Ne 500 indicator is Headline indicator for Goal A and Target 4. As noted by Hoban et al (2023a), the Ne 500 indicator is relevant to other targets such as sustainable harvest Targets 5 and 9 because harvested populations should be maintained at Ne 500. To ensure all genetically distinct populations are represented at sufficient sizes to maintain their persistence, it is relevant for Targets 1 and 3 on biodiversity inclusive spatial planning and representative protected areas, respectively, and Target 12 for increasing area and connectivity of green and blue spaces in urban environments to promote gene flow and species recovery.

The indicator is complementary to, and can be reported in, a wider genetic scorecard (O’Brien et al. 2022), as well as contribute to the refinement of other indicators or initiatives (e.g., identifying Key Biodiversity Areas to inform spatial planning, assessing protection level of species).Note that the Ne 500 indicator is relevant for genetic diversity within populations and a separate indicator (i.e. complementary indicator for Goal A on the “proportion of populations maintained”) is necessary for maintaining genetic diversity among populations. Experts agree that both indicators are critical for assessing and monitoring the genetic health of species.

5. Definitions Concepts And Classifications

5a. Definition

The indicator definition is exemplified in the full name, “The proportion of populations within species with a genetically effective population size > 500.”The indicator should be reported for 100+ representative species per country.It is calculated by taking each population of a species, determining if each population is above the threshold of Ne 500, calculating a proportion of populations above the threshold for each species, and then taking a mean of these proportions across all species examined, as explained in Hoban et al (2023b).As explained in that publication which contains the basic equations for calculation, the indicator can be weighted by taxonomic groups or other categories to offset any biases in the species selected (e.g. due to having more birds, more rare species etc.). IUCN has published guidance on selecting species and populations for monitoring of genetic diversity (Hvilsom et al. 2022).

Other important definitions:

The effective population size (Ne) is a way to quantify the rate of genetic change, or genetic erosion. Effective population size of a population is related to the number of adult/ breeding individuals in a population that contribute offspring to the next generation, the relative evenness of their offspring production, sex ratio, and other factors. The current state of Ne has important meaning for genetic biodiversity as it represents ongoing genetic erosion. Any population with Ne below 500 is likely losing genetic diversity fairly quickly, and signals ongoing loss of genetic diversity.

The effective population size may be a fraction (e.g., 10%) of the species census population size (Nc), which is the number of adult individuals present in a discrete area. As noted below, a fraction of 1/10th is widely recognized as a slightly conservative ratio between Ne:Nc. When knowledge exists for a certain taxonomic group, an alternate fraction may be used.

To maintain genetic diversity typically means that the amount of genetic diversity (alleles, heterozygosity) does not decrease, and there is no loss of within-population genetic diversity or among population genetic diversity; the precise genetic composition may shift for adapting to environmental change. The Ne 500 indicator ensures maintenance of within-population genetic diversity. We note that some scientists have argued for a more conservative minimum Ne of 1000, though the Ne 500 recommendation remains common.

To safeguard genetic diversity typically means to protect genetic diversity e.g. with in situ and ex situ protective measures (e.g. seed banks and botanic gardens, well managed protected areas, translocations, etc.)

5b. Method Of Computation

Effective population size (Ne) can be calculated for most species through a simple mathematical transformation of the population's census size (Nc). Following the widely accepted rule of thumb of 1:10 effective-to-census size ratio, the default is multiplication of Nc by 0.1 (Hoban et al. 2020). For example, this would equate to a census size of 5000 having an effective size of 500. However, for some taxonomic groups, a more refined ratio could be employed (see Step 2 below).

Step 1: Define population boundaries and compile data on census size (Nc). For each focal species it is first necessary to define ‘populations’ and to collect data on census population sizes. Many local and national biodiversity monitoring programs (e.g. at species or ecosystem level) have already defined populations based on geographic isolation, occupying distinct habitats or ecoregions, association with a geographic feature like a mountain range or lake, etc. Full guidance on defining populations for a wide variety of organisms are provided in the guidance manual for this indicator (Hoban et al (2023b) and Supporting Information therein). After defining populations, it is necessary to collect data on census population sizes (or to use genetic data). Again, many biodiversity monitoring programs for priority species will have this data available - in some cases in a centralized national database, while in other cases, it may be scattered among different national reports and assessments.A recent webinar hosted by the CBD Secretariat and GEO BON showcased the different resources available to countries, emphasizing the flexibility of this indicator.

Step 2: Calculate each population’s Ne. This entails first choosing a ratio of effective-to-census size and multiplying the population’s census size by this ratio to obtain the population’s effective size. As mentioned above, the default ratio, which is slightly conservative, is 1:10 or 0.1. Alternatively, a taxon-specific ratio can be obtained in one of several ways: (a) from recent reviews of the literature that have compiled average values for groups such as mammals, bony fish, annual plants, trees, etc. (see Hoban et al 2021), (b) from formulas that take into account a species’ biological characteristics (especially the male-female sex ratio and the variance in offspring production), or (c) from published literature on the species or even populations that are the focus of study. For instance, the ratio in large-bodied mammals and in some trees is often closer to 0.3. These are all valid ways of obtaining the ratio. To incorporate uncertainty in calculations, the calculation can be repeated using multiple Ne/Nc ratios.But it is entirely acceptable and useful to use the well-recognized 0.1 ratio.

Step 3: Calculate the proportion of populations above the 500 Ne threshold. For each species, count the number of populations with Ne above 500 and the number with Ne below 500; these two added together should equal the total number of populations. The indicator can be reported as a proportion (from 0 to 1) of all populations that are above 500, or in the form of a ratio ‘number of populations above 500’:‘total number of populations.’ (Recently extinct populations would have a size of 0 to avoid an increase in the indicator value when populations are lost). To combine across species in a given country or geographic location, a simple average of the proportion from Step 3 for all the relevant species should be performed. If taxonomic groups are not represented evenly, the indicator value is the mean of each taxonomic group’s means, which down-weights overly represented taxonomic groups, e.g. mammals. Additionally, each species can be weighted by the proportion of its geographic range in the country, from 0 to 1, to reflect national responsibility, with full weight for endemic species. Transboundary/ transnational populations can be weighted similarly (e.g. by the proportion of that population falling within the Parties borders). The indicator would range between 0 and 1 (with 1 being the desired state - all populations above an effective size of 500).

Equations for indicator calculation are given in Hoban et al (2023b).

Step 4: Temporal change in the indicator can be calculated using multiple time point values of population size. Temporal increases in the proportion of populations with Ne above 500 would indicate improvement in the maintenance of genetic diversity (on average slowing the rate of genetic erosion and eventually ‘bending the curve’ such that genetic diversity is restored via natural processes of mutation, migration, etc.). Decreases would indicate worsening (accelerating rate of genetic erosion), and static values would indicate a stable state of the indicator (stable rate of genetic erosion - though not necessarily a halting of genetic erosion - it is only halted when Ne >500).The indicator is designed to be recalculated as new data are compiled, which in many species is a timescale of 2 to 5 years, thus the indicator would be calculated and reported on typically once every 4 years (fitting the timespan of CBD reporting).

5c. Data Collection Method

In most cases, the indicator will be calculated using a transformation of census size (Nc), though analysis of DNA data can also be used to obtain Ne and assess if Ne >500. The draft guidance manual (see Hoban et al (2023b) and Supporting Information therein) details other methods of calculating the indicator when other data are available. The census size of local populations of target species can be obtained from a variety of sources, including national biodiversity monitoring databases and programs, endangered species management and recovery plans, detailed population information contained in some Red List assessments, and expert consultation. Detailed guidance on these calculations and a variety of example calculations is available now and will be revised following input from Parties as more Parties undertake this indicator.Demonstrations of the data collection can also be seen in a recent CBD webinar.

The full data collection form can be found online here: https://ee.kobotoolbox.org/preview/2KDHEWrb. We have created an online data collection form using Kobotoolbox (www.kobotoolbox.org/) and a guidance document (Supporting Information) for anyone to use. Kobo is a free and flexible data collection tool commonly used in social, environmental and epidemiological research.The data form adapts to the type of fundamental source data available and can accommodate qualitative and quantitative data and different levels of certainty.By sharing these on github we are promoting interactive engagement with stakeholders who can offer suggestions or ask questions, and removing paywalls that might otherwise limit participation globally.

5d. Accessibility Of Methodology

Parties can directly calculate country-level values of this indicator by leveraging national data, expertise and biodiversity assessments, and by following the guidance manual that is being developed by the GEO BON Genetic Composition Working Group, in collaboration with conservationists globally. The method has been peer reviewed in several publications (see list of References below, or https://www.coalitionforconservationgenetics.org/publications), and a detailed methodology has been made available (see Supporting Information for Hoban et al. 2023b)

5e. Data Sources

As explained in Hoban et al (2023b) the indicator is flexible and adaptable to the data sources already existing in each country.Examples from different countries illustrate the diverse options available. Recovery plans for dozens to thousands of threatened species are mandated by national legislation (Australia- the Environment Protection and Biodiversity Conservation Act, https://www.dcceew.gov.au/environment/epbc; South Africa- Biodiversity Management Plans, https://www.dffe.gov.za/content/management_plans/biodiversity; USA- the Endangered Species Act, https://www.fws.gov/law/endangered-species-act). These documents typically detail species biology and demographic status. In Japan, many threatened vascular plants have been surveyed for census size for over two decades by the Japanese Society for Plant Taxonomy, while for common trees, statistical estimates for population size were estimated from vegetation survey data. In Mexico, taxonomic experts who recently helped validate distribution models for crop wild relatives will be consulted for indicator values. In France, Belgium, UK and Sweden, much biodiversity data from experts, local knowledge holders, and diverse sources are collected in easy to access web-based portals (France- INPN, Belgium - www.observations.be, UK- https://nbnatlas.org/, Sweden- Swedish Species Information Centre, Artdatabanken). In Colombia, the Biodiversity Information System (SIB) repository compiles species surveys from throughout the country (https://biodiversidad.co/), which is mandated by many public and private organizations. These data are reviewed by national experts for validation and used to create freely available species distribution models (http://biomodelos.humboldt.org.co/), and for conservation prioritization.

GEO BON, through its working groups, and national and thematic Biodiversity Observation Networks, is able to provide capacity support, training and consultation. Considering that currently the workflow is manual rather than fully automated, the indicator would be calculated for a relatively small number of representative species per country. This may range from dozens on the low end to 1000 or more on the high end, but for many countries will be on the scale of 100 species. As noted above, data sources include national biodiversity monitoring databases and programs, endangered species management and recovery plans, detailed population information contained in some Red List assessments, and expert consultation. Detailed guidance on these calculations and a variety of example calculations is now available (see References).

5f. Availability And Release Calendar

Ready for deployment and updated every approximately four years.First draft of the guidance manual is available now and an indicator is being calculated, see Hoban et al (2023b) .

5g. Time Series

Dependent on data quality at the national scale. Typically Nc will be obtained from the past decade e.g. post 2010.Going forward it will be reported every 2 to 5 years, typically every 4 years, making it suited to the CBD reporting schedule. As the indicator is increasingly deployed, indicator calculation can be made in temporal windows, including through the use of older biodiversity observation data, reports and consultation with knowledge holders, likely extending indicator assessment at least back to the 1990s.

5h. Data Providers

The data are sourced from in-country existing biodiversity and environment agencies, thus leveraging in-country resources and ongoing programs. Other data may be obtained from conservation organizations, scientific societies, national and public repositories (e.g., Global Biodiversity Information Facility, GBIF, Red List assessments), citizen scientists, and the contributions of local and indigenous peoples and traditional knowledge holders.

5i. Data Compilers

The following organizations are responsible for maintenance of the methodology and tools for use: GEO BON, The Morton Arboretum, Stockholm University, GBIKE, Coalition for Conservation Genetics. Actual compilation of data is performed by in-country agencies

5j. Gaps In Data Coverage

Expected taxonomic gaps include cryptic (e.g. elusive, located underground, etc.) species, micro-organisms, fungi, invertebrates. However, current projects deploying the indicator have shown it can be calculated for cryptic species and invertebrates. Expected thematic and geographic gaps include species from understudied realms and areas (e.g., deep sea, mountains, and islands). These gaps are unfortunately typical for other biodiversity indicators such as the Red List Index.

However, the indicator can be calculated at the population level or species level in any species, and thus has no theoretical gaps, and (weighted) averages can be calculated across populations or species taking into account range sizes.

Note that the Ne 500 indicator should be complemented with the “proportion of populations maintained” indicator , and with expert and local knowledge including as compiled in the “genetic scorecard for wild species” indicator , the “comprehensiveness indicator” (all three suggested as complementary indicators for Goal A: CBD/COP/15/L.26), and the proposed indicator “number of species and populations in which DNA based monitoring is used” (Hoban et al. 2020).

5k. Treatment Of Missing Values

Species with missing data may be aggregated with taxonomically-related species, or species with similar characteristics and life history traits.Populations with missing data can be treated as NAs in the dataset.

6. Scale

6a. Scale Of Use

Scale of application (please check all relevant boxes): Global, Regional, National

Scale of data disaggregation/aggregation:

Global/ regional scale indicator can be disaggregated to national level:

National data is collated to form global indicator: Yes

6b. National Regional Indicator Production

The guidance documents currently developed explain national methodology. Underlying data will be accessible and usable by countries. The existing data collection tool allows easy organization and storage of data and thus tracking across time.

Countries can collaborate on transnational calculations if desired, and the same is true for regions, including the European Union, for example.Otherwise regional calculation is a mean or weighted mean of component countries.

6c. Sources Of Differences Between Global And National Figures

The guidance document explains national methodology. The global figure is a mean, or weighted mean, of all contributing countries.

6d. Regional And Global Estimates And Data Collection For Global Monitoring

6d.1 Description Of The Methodology

Methods and mathematical formulas for aggregating at these scales, and for weighting countries are described in Hoban et al (2023b).

6d.2 Additional Methodological Details

See previous answer

6d.3 Description Of The Mechanism For Collecting Data From Countries

As noted above, national agencies, or conservation organizations can compile the indicator at national levels using the resources provided in Hoban et al (2023b; see Supporting Information).Consultation and questions about data validation can be made to the custodians of the indicator (GEO BON, Morton Arboretum, Stockholm University, GBIKE, and Coalition for Conservation Genetics).

7. Other MEA And Processes And Organisations

7a. Other MEA And Processes

The indicator is currently being deployed in pilot form in several countries.

7b. Biodiversity Indicator Partnership

Yes

8. Disaggregation

Species, taxa, rarity categories, habitat type, guilds.

9. Related Goals Targets And Indicators

Goal A. The genetic diversity within populations of wild and domesticated species, is maintained, safeguarding their adaptive potential.

Target 4. Ensure urgent management actions to halt human induced extinction of known threatened species and for the recovery and conservation of species, in particular threatened species, to significantly reduce extinction risk, as well as to maintain and restore the genetic diversity within and between populations of native, wild and domesticated species to maintain their adaptive potential, including through in situ and ex situ conservation and sustainable management practices, and effectively manage human-wildlife interactions to minimize human-wildlife conflict for coexistence.

That being said, as noted by Hoban et al 2023a, it is also relevant to Targets 1, 3, 5, 9, and 12.

Linked to and is complemented by other important genetic diversity indicators (CBD/COP/15/5), including:

  • Proportion of populations maintained within species
  • Genetic diversity scorecard for wild species (O’Brien et al. 2022)
  • Comprehensiveness of conservation of socioeconomically as well as culturally valuable species(Khoury et al 2019),
  • Proportion of local breeds classified as being at risk, extinction
  • Number of plant and animal genetic resources for food and agriculture secured in either medium- or long-term conservation facilities

10. Data Reporter

10a. Organisation

GEO BON, The Morton Arboretum, Stockholm University, GBIKE, Coalition for Conservation Genetics.

10b. Contact Person

Sean Hoban (shoban@mortonarb.org)

Linda Laikre (linda.laikre@popgen.su.se)

Alicia Mastretta-Yanes (amastretta@conabio.gob.mx)

Jessica da Silva (J.DaSilva@sanbi.org.za)

GEOBON (info@geobon.org)

11. References

Relevant background. Hoban et al (2023a). Genetic diversity Goals and Targets have improved, but remain insufficient. Conservation Genetics 24, 181–191.. https://doi.org/10.1007/s10592-022-01492-0

Description of indicator deployment. Hoban et al (2023b). Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: an ongoing assessment of genetic indicators in nine countries. Conservation Letters 00, e12953. https://doi.org/10.1111/conl.12953

Relevant background. Frankham, R. (1995). Effective population size/adult population size ratios in wildlife: a review. Genetic Research, 66, 95–107.

Resources and guidance, description of methods for indicator deployment. Supporting Information for:Hoban et al. (2023b) Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: an ongoing assessment of genetic indicators in nine countries. Conservation Letters 00, e12953. https://doi.org/10.1111/conl.12953

Description of the indicator. Hoban, S., Bruford, M., D’Urban Jackson, J., Lopes-Fernandes, M., Heuertz, M., Hohenlohe, P.A., et al. (2020). Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved. Biological Conservation, 248, 108654. https://doi.org/10.1016/j.biocon.2020.108654

Description of the indicator. Hoban, S., Paz-Vinas, I., Aitken, S., Bertola, L., Breed, M.F., Bruford, M., Funk, C., Grueber, C., Heuertz, M., Hohenlohe, P., Hunter, M., et al. (2021). Effective population size remains a suitable, pragmatic indicator of genetic diversity for all species, including forest trees. Biological Conservation, 253, 108906.

Relevant background. Hoban, S., Bruford, M., Funk, W.C., Galbusera, P., Griffith, M.P., Grueber, C.E., Heuertz, M., Hunter, M.E., Hvilsom, C., Kalamujic, S.B., Kershaw, F., et al. (2021). Global commitments to conserving and monitoring genetic diversity are now necessary and feasible. BioScience, 71, 964–976.

Relevant background. Laikre, L., Hohenlohe, P.A., Allendorf, F.W., Bertola, L.D., Breed, M.F., Bruford, M.W., Funk, W.C., Gajardo, G., González-Rodríguez, A., Grueber, C.E., Hedrick, P.W., et al. (2021). Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD. Conservation Genetics,22, 533–536. https://doi.org/10.1007/s10592-021-01359-w

Relevant background. Laikre, L., Nilsson, T., Primmer, C.R., Ryman, N. and Allendorf, F.W. (2009). Importance of genetics in the interpretation of favourable conservation status. Conservation Biology, 23, 1378-1381.

12. Graphs And Diagrams

Figure 1. Example of the three genetic diversity indicators, for four hypothetical populations in Illinois, USA. One tree = 1,000 plants (five trees = 5,000 plants). Colors illustrate genetic variation within and among populations. In 2020, 2 of 3 extant populations are Nc<5,000 (Ne<500 considering an effective to census size ratio of Ne/Nc = 0.1) and thus too small to maintain genetic diversity (indicator 1). Three of four historic populations are maintained (indicator 2). DNA-based methods have been used to monitor genetic diversity in two populations (indicator 3 - a value of 1 means that one or more populations of the species is monitored with DNA-based methods).


Figure 2: Pictorial representation of how genetic diversity is found within and among populations (see color variations) and is the foundations for species adaptability and for entire ecosystems. Genetic diversity ultimately is seen at the DNA level, and can be conserved with large (Ne ⩾500) populations and by making sure distinct populations are not lost.


Figure 3: Pictorial representation of Ne relative to the census size of a population. Ne is smaller than Nc, but it is the Ne which determines the rate of loss of genetic diversity within populations, and thus whether they can maintain adaptive capacity.

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