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”
2023-09-01 12:00:00 UTC
Headline indicator for 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.
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.
As noted by Hoban et al 2023a, and Hoban et al 2023c, this indicator is also relevant to a number of targets described below and in section 9.
Effective population size (Ne) is a well-accepted metric for measuring the rate of loss of genetic diversity within populations. As explained below (see figure 1), 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 reintroduction of populations and species. Populations with low genetic diversity suffer inbreeding, low viability, and low resilience. Unfortunately, genetic diversity has declined due to habitat loss, fragmentation, overharvest, and other human activities. 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. However, genetic status of species and populations can be assessed via Ne without needing DNA data. This is the fundamental basis of this indicator - to assess genetic status without DNA sequence data. This is very important since relatively few species have DNA-based studies, especially in biodiversity hotspots. As explained in the methodology below, proxies of demographic and geographic data can approximate the Ne of populations.
In 2020, three genetic diversity indicators were proposed, including the Headline Indicator on Ne 500. They have the following important features (see Hoban et al 2023a, and Hoban et al 2023c):
Genetic diversity indicators have multiple practical uses beyond reporting. They will help countries understand and mitigate genetic diversity loss by guiding conservation action, improve allocation of resources, and communicate to the public about genetic threats to flagship species. Also, genetic diversity indicators highlight how local populations provide adaptation and resilience, which facilitates empowerment and leverage for local communities and indigenous peoples. They are useful under other legislation including national level species protections.
What exactly 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. (figure 1)
Ne 500 i 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 will reduce the risk of the loss of genetic diversity within populations to near zero. Much lower and genetic loss becomes rapid.
Ne can be measured with and without DNA data. 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), Hoban et al 2023c and Hoban et al (2020) and as a pilot application (explained below) show, there are many sources of census size data which countries can employ, including 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.
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 a 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 or above 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 genetic scorecard (O’Brien et al. 2022), a contribute to other indicators or initiatives (e.g., Key Biodiversity Areas, spatial planning, assessing protection level of species). Note: the Ne 500 indicator is relevant for genetic diversity within populations and a separate indicator (i.e. complementary indicator for Goal A 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 (Hoban et al 2020, Hoban et al 2023b).
Figure 2. presenting the concept of genetic diversity lost. The Headline Indicator A.4 is shown on the right- small populations lose genetic diversity. Complementary indicator on loss of populations is shown on the right. Legend: Colors represent different genetic compositions
These two indicators are compared below- headline indicator A.4 on the right, indicator on populations maintained on the left.
Indicator definition:
The indicator, “The proportion of populations within species with a genetically effective population size > 500.” 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)and Hoban et al 2023c. As a proportion it ranges from 0 to 1, with 1 as the desired value. 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.).
Other key concepts and definitions:
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 and reliable 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. Some scientists have argued for a more conservative minimum Ne of 1000, though the Ne 500 recommendation remains common and well supported.
To safeguard genetic diversity 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.)
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).
Choosing species to evaluate. Biased selection of species is an important concern for the indicator. For example, selecting only charismatic species (butterflies, orchids, etc.), species of economic value or rare/ endangered species would result in an indicator that represents the genetic condition of species in that subset rather than all species. To avoid misleading results from a biased selection, the indicator could be calculated for
A systematic assessment involves pre-defining certain categories, in particular taxonomic groups, e.g. plants, vertebrates, invertebrates, fungi, algae. Then a number of species within each group should be chosen randomly (see Baille et al 2008). The indicator will be less accurate when small numbers of species are used. At minimum, 100 species should be used, though ideally many more will be used (Baille et al 2008 recommend 900 species with sufficient data; however, to allow for species missing data, the initial list of taxa to evaluate should be 1500). IUCN has published guidelines on selecting species and populations for monitoring of genetic diversity (Hvilsom et al. 2022)
Again, the set of species should be as unbiased as possible. As explained below, analysis of the indicator may wish to disaggregate for particular subsets e.g. harvested species, pollinators, keystone species, but the overall indicator value should represent all species.
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. "Available data" should be considered broadly and it includes citizen science, local knowledge, indigenous knowledge, and informal data held by small NGOs and similar groups. 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 1/10th or 0.1 (thus the minimum Nc would be 5000). 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 (thus the minimum Nc would be 1500). 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
For some organisms, assessment of Nc is fairly straightforward. It is the number of reproductively mature individuals, that is, those which are of sufficient maturity to produce gametes or offspring. A count of mature individuals may mean an actual count of all organisms, an estimate made by counting within given units of area and extrapolating, or an estimate from a model such as a capture-mark-recapture model. The IUCN Red List Guidelines (IUCN Standards and Petitions Committee 2022) contains extensive discussion on consideration of reproductively suppressed individuals, trees, fish, and other cases of interest, and it adhering to this guidance in its entirety, with one exception - clonal organisms, is suggested
Clonal organisms. In assessing Nc for the use of converting to Ne, it is important to use the “genet” (the genetically distinct organism) as opposed to the “ramet” (each distinct part which is capable of surviving on its own). An extreme example is a Populus clone which may have thousands of stems aboveground which are each capable of reproduction, but which are identical in their genotype. This clone formed over thousands of years. The assessor should consider each entire clone as a mature individual when counting Nc, not each stem. This can be done similar to the advice on page 28 of the aforementioned IUCN Red List Guidelines, e.g. “For diffuse, wholly visible organisms in continuous habitats (e.g., reef-forming corals, algal mats) assessors may assume an average area occupied by a genet and estimate the number of genets from the area covered by the taxon. The area covered by the taxon should be estimated at a scale (grid size; e.g. 1 m2) that is as close as practicable to the area assumed to be occupied by a genet.” The typical area covered by a genet can be determined by consulting scientific literature on a similar organism (as above, many estimates are available for corals and Populus), contacting an expert in that species or genus, which may include contacting an IUCN Specialist Group for that taxon or the IUCN Conservation Genetic Specialist Group
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).
What to do if a population goes extinct? Any population that goes extinct after the country’s baseline year (each country is directed by the CBD to choose a baseline, which defaults to 2010-2020 but which may be adjusted to country context) is assigned an Nc and Ne of 0 and are therefore below Ne 500. These populations must be retained in the calculation in order to avoid the perverse incentive to “raise” the indicator value through population extinction
Step 4: Temporal change in the indicator can be calculated using multiple time point values of population size
An important consideration is that calculating temporal change in the indicator requires the use of the same set of species at all time points, similar to the Red List Index (Bubb et al 2009, “IUCN Red List index : guidance for national and regional use. Version 1.1”). As a default guidance, all species used in the first time point should be included in the second
However, the country may wish to change or add to the species lists over time (e.g., owing to taxonomic revisions, additional data sources, etc.). In such cases, countries can do one of the following:
In addition, it is anticipated that biodiversity monitoring capacity within countries will increase over time, and thus countries may wish to increase the number of species included in their indicator calculation, e.g. from 100 to 1000 species. In such cases, the species being newly evaluated can have retrospective indicator calculations made, assuming historic data is available.This highlights a broader opportunity, that such retrospective evaluation could extend indicator calculation into the past
Temporal increases in the proportion of populations with Neabove 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). 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).
Management based on the indicator: The indicator is designed for use in practical biodiversity management – not just for reporting to the CBD. For example, it can be used for: raising alarm in regions or taxonomic groups with low indicator values, prioritizing which species and populations are most in need of management to halt genetic erosion, designing management strategies (e.g. reintroduction, population supplementation), setting achievable goals, tracking the consequences or effectiveness of management (e.g. if the indicator value improves), and communicating to the public about genetic diversity conservation.
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, and Hoban et al 2023c) 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, collaboration with local knowledge holders, citizen science, 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. An online data collection form using Kobotoolbox (www.kobotoolbox.org/) have been created 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.
Parties can directly calculate country-level values of this indicator by leveraging national data, expertise and biodiversity assessments, and by following the published guidance manual. The method has been peer reviewed in several publications (see list of References below, or https://www.coalitionforconservationgenetics.org/p...), and a detailed methodology has been made available (see Supporting Information for Hoban et al. 2023b and Hoban et al 2023c)
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; South Africa- Biodiversity Management Plans; USA- the 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, and the Coalition for Conservation Genetics, 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, citizen science, local knowledge, 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).
Ready for deployment and updated approximately every four years. First draft of the guidance manual is available now and an indicator is being calculated, see Hoban et al (2023b) .
Genetic diversity indicators have been demonstrated as feasible and affordable including in middle income and megadiverse countries. They have been calculated for >900 species and thousands of populations in nine countries: Australia, Belgium, Colombia, France, Japan, Mexico, South Africa, Sweden, and USA(Figure 3). Data are available and can be compiled quickly. Results from the nine-country deployment highlight that most populations are very small and in danger of imminent genetic losses. Early use of these indicators shows we are at a threshold of dramatic genetic diversity decline unless swift action is taken, guided by genetic diversity indicators.
Figure 3. Initial unpublished preliminary results of the first deployment of indicator A.4
The amount of data available:
Overall, >64% of species investigated have enough data to calculate the headline indicator (grey shows species without sufficient data). This is shown in the chart at right. This does vary by country. All countries have approximately 50% or more of species with enough data.
Figure 4 shows the actual indicator values calculated for more than 900 species. It was found that the median across all species for Proportion of populations below Ne500 is 0, i.e. 58% of species assessed have that indicator value. Even more worrying, ~70% of species have an indicator value less than 0.25. This means that the majority of species assessed have less than 25% of their populations large enough to sustain genetic diversity- most species are likely in danger of or are already experiencing significant genetic losses.
There are differences in indicator values among taxonomic groups e.g. indicator values tend to be lower for mammals for example. Data are more available for some groups than others e.g. angiosperms, mammals, birds have more data available than invertebrates, especially clams and mussels. The indicators are not greatly influenced by the method used to define populations meaning that a variety of data are acceptable for defining populations.
Results on the populations maintained indicator are also included which is an important complement to the Headline indicator on Ne 500. The investigation on 900 species showed that the median across all species for Proportion of populations maintained is 1, i.e. 55% of species have that indicator value. This means that most species still maintain all their populations. However, 38% of species have an indicator value less than 0.90, meaning that they have lost at least 10% of their original populations. Number of populations maintained should be reported jointly with the Ne indicator, to ensure that goal A and Target 4 are fully met - maintaining species' adaptive potential and reducing extinction risk. This is a possibility where IPLCs can be included and empowered.
Figure 4. actual indicator values calculated for more than 900 species
Date range is dependent on data availability 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.This is noted above under Step 4 of Method of Computation, 5b.
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.
Example data sources from countries that participated in piloting the indicator from 2021-2023 can be found in Hoban et al (2023b)
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.
Expected (and demonstrated in the pilot application to 900 species) 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.
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).
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.
Scale of application:Global, Regional, National
Scale of data disaggregation/aggregation
Global/ regional scale indicator can be disaggregated to national level: Yes
National data is collated to form global indicator:Yes
Data is applicable at the local, national, regional and global scales.
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.
The guidance document explains national methodology. The global figure is a mean, or weighted mean, of all contributing countries.
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).
The pilot application in 900 species showed that data gaps vary by country, but all countries examined have a large number of species with sufficient data available.
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).
The guidance (documents and videos) will be improved with a new version released by approximately January 2024, and there are a series of online tools (mapping tools, easy data entry) in development that will help make it even easier to calculate the indicator (GEOBON offers BON-in-a-Box to support calculation of the indicator).
No
Species, taxa, rarity categories, habitat type, guilds.
As noted by Hoban et al 2023a, this indicator is also relevant to Targets 1, 2, 3, 5, 9, 10 and 12.
Linked to and is complemented by other important genetic diversity indicators (CBD/COP/15/5), including:
The caretakers of this indicator are also developing guidance and suggestions for NBSAPs and are available to help support capacity as countries develop their NBSAPs. This document will be available in spring 2024.
Group on Earth Observations Biodiversity Observation Network (GEO BON)
The Morton Arboretum
Stockholm University
G-BiKE
Coalition for Conservation Genetics
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)
GEO BON (info@geobon.org)
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
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.
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
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.
Frankham, R. (1995). Effective population size/adult population size ratios in wildlife: a review. Genetic Research, 66, 95–107.
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.
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
Resources and guidance, description of methods for 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
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
Hoban, S., da Silva, J., Hughes, A., Hunter, M., Stroil, B.K., Laikre, L., Yanes, A.M., Millette, K., Paz-Vinas, I., Ruiz, L. et al., (2023c). Too simple, too complex, or just right? Advantages, challenges and resolutions for indicators of genetic diversity. Bioarxiv preprint
Figure 5. 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). Note that the lost population is considered an extirpation (but is not used for calculating the Ne 500 indicator). Three of four 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 6: Pictorial representation of how genetic diversity is found within and among populations (see color variations) and is the foundation 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 7: Pictorial representation of Nerelative to the census size of a population. Neis 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.
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”
2023-09-01 12:00:00 UTC
Headline indicator for 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.
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.
As noted by Hoban et al 2023a, and Hoban et al 2023c, this indicator is also relevant to a number of targets described below and in section 9.
Effective population size (Ne) is a well-accepted metric for measuring the rate of loss of genetic diversity within populations. As explained below (see figure 1), 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 reintroduction of populations and species. Populations with low genetic diversity suffer inbreeding, low viability, and low resilience. Unfortunately, genetic diversity has declined due to habitat loss, fragmentation, overharvest, and other human activities. 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. However, genetic status of species and populations can be assessed via Ne without needing DNA data. This is the fundamental basis of this indicator - to assess genetic status without DNA sequence data. This is very important since relatively few species have DNA-based studies, especially in biodiversity hotspots. As explained in the methodology below, proxies of demographic and geographic data can approximate the Ne of populations.
In 2020, three genetic diversity indicators were proposed, including the Headline Indicator on Ne 500. They have the following important features (see Hoban et al 2023a, and Hoban et al 2023c):
Genetic diversity indicators have multiple practical uses beyond reporting. They will help countries understand and mitigate genetic diversity loss by guiding conservation action, improve allocation of resources, and communicate to the public about genetic threats to flagship species. Also, genetic diversity indicators highlight how local populations provide adaptation and resilience, which facilitates empowerment and leverage for local communities and indigenous peoples. They are useful under other legislation including national level species protections.
What exactly 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. (figure 1)
Ne 500 i 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 will reduce the risk of the loss of genetic diversity within populations to near zero. Much lower and genetic loss becomes rapid.
Ne can be measured with and without DNA data. 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), Hoban et al 2023c and Hoban et al (2020) and as a pilot application (explained below) show, there are many sources of census size data which countries can employ, including 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.
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 a 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 or above 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 genetic scorecard (O’Brien et al. 2022), a contribute to other indicators or initiatives (e.g., Key Biodiversity Areas, spatial planning, assessing protection level of species). Note: the Ne 500 indicator is relevant for genetic diversity within populations and a separate indicator (i.e. complementary indicator for Goal A 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 (Hoban et al 2020, Hoban et al 2023b).
Figure 2. presenting the concept of genetic diversity lost. The Headline Indicator A.4 is shown on the right- small populations lose genetic diversity. Complementary indicator on loss of populations is shown on the right. Legend: Colors represent different genetic compositions
These two indicators are compared below- headline indicator A.4 on the right, indicator on populations maintained on the left.
Indicator definition:
The indicator, “The proportion of populations within species with a genetically effective population size > 500.” 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)and Hoban et al 2023c. As a proportion it ranges from 0 to 1, with 1 as the desired value. 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.).
Other key concepts and definitions:
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 and reliable 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. Some scientists have argued for a more conservative minimum Ne of 1000, though the Ne 500 recommendation remains common and well supported.
To safeguard genetic diversity 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.)
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).
Choosing species to evaluate. Biased selection of species is an important concern for the indicator. For example, selecting only charismatic species (butterflies, orchids, etc.), species of economic value or rare/ endangered species would result in an indicator that represents the genetic condition of species in that subset rather than all species. To avoid misleading results from a biased selection, the indicator could be calculated for
A systematic assessment involves pre-defining certain categories, in particular taxonomic groups, e.g. plants, vertebrates, invertebrates, fungi, algae. Then a number of species within each group should be chosen randomly (see Baille et al 2008). The indicator will be less accurate when small numbers of species are used. At minimum, 100 species should be used, though ideally many more will be used (Baille et al 2008 recommend 900 species with sufficient data; however, to allow for species missing data, the initial list of taxa to evaluate should be 1500). IUCN has published guidelines on selecting species and populations for monitoring of genetic diversity (Hvilsom et al. 2022)
Again, the set of species should be as unbiased as possible. As explained below, analysis of the indicator may wish to disaggregate for particular subsets e.g. harvested species, pollinators, keystone species, but the overall indicator value should represent all species.
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. "Available data" should be considered broadly and it includes citizen science, local knowledge, indigenous knowledge, and informal data held by small NGOs and similar groups. 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 1/10th or 0.1 (thus the minimum Nc would be 5000). 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 (thus the minimum Nc would be 1500). 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
For some organisms, assessment of Nc is fairly straightforward. It is the number of reproductively mature individuals, that is, those which are of sufficient maturity to produce gametes or offspring. A count of mature individuals may mean an actual count of all organisms, an estimate made by counting within given units of area and extrapolating, or an estimate from a model such as a capture-mark-recapture model. The IUCN Red List Guidelines (IUCN Standards and Petitions Committee 2022) contains extensive discussion on consideration of reproductively suppressed individuals, trees, fish, and other cases of interest, and it adhering to this guidance in its entirety, with one exception - clonal organisms, is suggested
Clonal organisms. In assessing Nc for the use of converting to Ne, it is important to use the “genet” (the genetically distinct organism) as opposed to the “ramet” (each distinct part which is capable of surviving on its own). An extreme example is a Populus clone which may have thousands of stems aboveground which are each capable of reproduction, but which are identical in their genotype. This clone formed over thousands of years. The assessor should consider each entire clone as a mature individual when counting Nc, not each stem. This can be done similar to the advice on page 28 of the aforementioned IUCN Red List Guidelines, e.g. “For diffuse, wholly visible organisms in continuous habitats (e.g., reef-forming corals, algal mats) assessors may assume an average area occupied by a genet and estimate the number of genets from the area covered by the taxon. The area covered by the taxon should be estimated at a scale (grid size; e.g. 1 m2) that is as close as practicable to the area assumed to be occupied by a genet.” The typical area covered by a genet can be determined by consulting scientific literature on a similar organism (as above, many estimates are available for corals and Populus), contacting an expert in that species or genus, which may include contacting an IUCN Specialist Group for that taxon or the IUCN Conservation Genetic Specialist Group
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).
What to do if a population goes extinct? Any population that goes extinct after the country’s baseline year (each country is directed by the CBD to choose a baseline, which defaults to 2010-2020 but which may be adjusted to country context) is assigned an Nc and Ne of 0 and are therefore below Ne 500. These populations must be retained in the calculation in order to avoid the perverse incentive to “raise” the indicator value through population extinction
Step 4: Temporal change in the indicator can be calculated using multiple time point values of population size
An important consideration is that calculating temporal change in the indicator requires the use of the same set of species at all time points, similar to the Red List Index (Bubb et al 2009, “IUCN Red List index : guidance for national and regional use. Version 1.1”). As a default guidance, all species used in the first time point should be included in the second
However, the country may wish to change or add to the species lists over time (e.g., owing to taxonomic revisions, additional data sources, etc.). In such cases, countries can do one of the following:
In addition, it is anticipated that biodiversity monitoring capacity within countries will increase over time, and thus countries may wish to increase the number of species included in their indicator calculation, e.g. from 100 to 1000 species. In such cases, the species being newly evaluated can have retrospective indicator calculations made, assuming historic data is available.This highlights a broader opportunity, that such retrospective evaluation could extend indicator calculation into the past
Temporal increases in the proportion of populations with Neabove 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). 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).
Management based on the indicator: The indicator is designed for use in practical biodiversity management – not just for reporting to the CBD. For example, it can be used for: raising alarm in regions or taxonomic groups with low indicator values, prioritizing which species and populations are most in need of management to halt genetic erosion, designing management strategies (e.g. reintroduction, population supplementation), setting achievable goals, tracking the consequences or effectiveness of management (e.g. if the indicator value improves), and communicating to the public about genetic diversity conservation.
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, and Hoban et al 2023c) 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, collaboration with local knowledge holders, citizen science, 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. An online data collection form using Kobotoolbox (www.kobotoolbox.org/) have been created 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.
Parties can directly calculate country-level values of this indicator by leveraging national data, expertise and biodiversity assessments, and by following the published guidance manual. The method has been peer reviewed in several publications (see list of References below, or https://www.coalitionforconservationgenetics.org/p...), and a detailed methodology has been made available (see Supporting Information for Hoban et al. 2023b and Hoban et al 2023c)
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; South Africa- Biodiversity Management Plans; USA- the 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, and the Coalition for Conservation Genetics, 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, citizen science, local knowledge, 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).
Ready for deployment and updated approximately every four years. First draft of the guidance manual is available now and an indicator is being calculated, see Hoban et al (2023b) .
Genetic diversity indicators have been demonstrated as feasible and affordable including in middle income and megadiverse countries. They have been calculated for >900 species and thousands of populations in nine countries: Australia, Belgium, Colombia, France, Japan, Mexico, South Africa, Sweden, and USA(Figure 3). Data are available and can be compiled quickly. Results from the nine-country deployment highlight that most populations are very small and in danger of imminent genetic losses. Early use of these indicators shows we are at a threshold of dramatic genetic diversity decline unless swift action is taken, guided by genetic diversity indicators.
Figure 3. Initial unpublished preliminary results of the first deployment of indicator A.4
The amount of data available:
Overall, >64% of species investigated have enough data to calculate the headline indicator (grey shows species without sufficient data). This is shown in the chart at right. This does vary by country. All countries have approximately 50% or more of species with enough data.
Figure 4 shows the actual indicator values calculated for more than 900 species. It was found that the median across all species for Proportion of populations below Ne500 is 0, i.e. 58% of species assessed have that indicator value. Even more worrying, ~70% of species have an indicator value less than 0.25. This means that the majority of species assessed have less than 25% of their populations large enough to sustain genetic diversity- most species are likely in danger of or are already experiencing significant genetic losses.
There are differences in indicator values among taxonomic groups e.g. indicator values tend to be lower for mammals for example. Data are more available for some groups than others e.g. angiosperms, mammals, birds have more data available than invertebrates, especially clams and mussels. The indicators are not greatly influenced by the method used to define populations meaning that a variety of data are acceptable for defining populations.
Results on the populations maintained indicator are also included which is an important complement to the Headline indicator on Ne 500. The investigation on 900 species showed that the median across all species for Proportion of populations maintained is 1, i.e. 55% of species have that indicator value. This means that most species still maintain all their populations. However, 38% of species have an indicator value less than 0.90, meaning that they have lost at least 10% of their original populations. Number of populations maintained should be reported jointly with the Ne indicator, to ensure that goal A and Target 4 are fully met - maintaining species' adaptive potential and reducing extinction risk. This is a possibility where IPLCs can be included and empowered.
Figure 4. actual indicator values calculated for more than 900 species
Date range is dependent on data availability 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.This is noted above under Step 4 of Method of Computation, 5b.
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.
Example data sources from countries that participated in piloting the indicator from 2021-2023 can be found in Hoban et al (2023b)
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.
Expected (and demonstrated in the pilot application to 900 species) 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.
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).
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.
Scale of application:Global, Regional, National
Scale of data disaggregation/aggregation
Global/ regional scale indicator can be disaggregated to national level: Yes
National data is collated to form global indicator:Yes
Data is applicable at the local, national, regional and global scales.
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.
The guidance document explains national methodology. The global figure is a mean, or weighted mean, of all contributing countries.
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).
The pilot application in 900 species showed that data gaps vary by country, but all countries examined have a large number of species with sufficient data available.
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).
The guidance (documents and videos) will be improved with a new version released by approximately January 2024, and there are a series of online tools (mapping tools, easy data entry) in development that will help make it even easier to calculate the indicator (GEOBON offers BON-in-a-Box to support calculation of the indicator).
No
Species, taxa, rarity categories, habitat type, guilds.
As noted by Hoban et al 2023a, this indicator is also relevant to Targets 1, 2, 3, 5, 9, 10 and 12.
Linked to and is complemented by other important genetic diversity indicators (CBD/COP/15/5), including:
The caretakers of this indicator are also developing guidance and suggestions for NBSAPs and are available to help support capacity as countries develop their NBSAPs. This document will be available in spring 2024.
Group on Earth Observations Biodiversity Observation Network (GEO BON)
The Morton Arboretum
Stockholm University
G-BiKE
Coalition for Conservation Genetics
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)
GEO BON (info@geobon.org)
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
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.
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
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.
Frankham, R. (1995). Effective population size/adult population size ratios in wildlife: a review. Genetic Research, 66, 95–107.
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.
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
Resources and guidance, description of methods for 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
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
Hoban, S., da Silva, J., Hughes, A., Hunter, M., Stroil, B.K., Laikre, L., Yanes, A.M., Millette, K., Paz-Vinas, I., Ruiz, L. et al., (2023c). Too simple, too complex, or just right? Advantages, challenges and resolutions for indicators of genetic diversity. Bioarxiv preprint
Figure 5. 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). Note that the lost population is considered an extirpation (but is not used for calculating the Ne 500 indicator). Three of four 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 6: Pictorial representation of how genetic diversity is found within and among populations (see color variations) and is the foundation 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 7: Pictorial representation of Nerelative to the census size of a population. Neis 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.
Feedback: UNEP-WCMC is keen to ensure that our data is accurate and up to date. We welcome any feedback on the quality, reliability, and accuracy of the information on this site. If you see any errors or missing information, please get in touch.