Biodiversity Informatics, 18, 2024, pp. 24-27 24 GUIDELINE MATERIALS AND DOCUMENTATION FOR THE GENETIC DIVERSITY INDICATORS OF THE MONITORING FRAMEWORK FOR THE KUNMING-MONTREAL GLOBAL BIODIVERSITY FRAMEWORK Alicia Mastretta-Yanes1,2, Sofía Suárez3, Rebecca Jordan4, Sean Hoban5,6, Jessica M. Da Silva7,8, Luis Castillo-Reina9, Myriam Heuertz10, Fumiko Ishihama11, Viktoria Köppä12, Linda Laikre12, Anna J. Macdonald13, Joachim Mergeay14,15, Ivan Paz-Vinas16, Gernot Segelbacher17, Alicia Knapps17, Henry Rakoczy17, Amelie Weiler17, Angelica Atsaves17, Kira Cullmann17, Simone Bagnato17, Brenna R. Forester18 1 Consejo Nacional de Humanidades Ciencias y Tecnología (CONAHCYT), Avenida Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México. C.P. 03940. Mexico.* 2 Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México. Av. Ciudad Universitaria 3000, 04510, Coyoacán, Ciudad de México, Mexico 3 Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacion- al Autónoma de México. Ciudad de México, Mexico 4 CSIRO Environment, 15 College Rd, Sandy Bay 7005, Tasmania, Australia 5 Center for Tree Science, The Morton Arboretum, Lisle, USA 6 Committee on Evolutionary Biology, The University of Chicago, Chicago, USA 7 South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7 Claremont 7735, Cape Town, South Africa 8 Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johan- nesburg, Auckland Park 2006, Johannesburg, South Africa 9 Department of Biology, Faculty of Science,KU Leuven, Leuven, Belgium 10 Univ. Bordeaux, INRAE, BIOGECO, F-33610 Cestas, France 11 National Institute for Environmental Studies, Onogawa16-2, Tsukuba, Ibaraki, Japan 12 Department of Zoology, Stockholm University, SE10691 Stockholm, Sweden 13 Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kings- ton, Tasmania 7050, Australia 14 Research Institute for Nature and Forest, Gaverstraat 4, 9500 Geraardsbergen, Belgium 15 Ecology, Evolution and Biodiversity Conservation, KU Leuven, Charles Deberiotstraat 32, Box 2439, Leuven, Belgium 16 Universite Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, F-69622, Villeurbanne, France 17 University of Freiburg, Wildlife Ecology and Management, 79106 Freiburg im Breisgau, Germany 18 U.S. Fish and Wildlife Service, Fort Collins, CO, USA *Corresponding author: Alicia Mastretta-Yanes, Email: amastretta@iecologia.unam.mx Abstract. Genetic diversity is fundamental to biological diversity, vital for species’ health and adaptation to environmental change. Under the recently adopted Kunming-Montreal Global Biodiversity Framework (GBF), 196 Parties committed to report the status of genetic diversity for both wild and domesticated species. For this, three genetic diversity indicators were developed, two of which focus on processes contributing to ge- netic diversity conservation: ensuring that populations are large enough to maintain genetic diversity (effec- tive population size Ne 500 indicator) and maintaining genetically distinct populations (populations main- tained, PM indicator). A third indicator focuses on the number of species being monitored using DNA-based methods. Adopted by 196 CBD Parties in December 2022, GBF integrated Ne 500 and PM as headline and complementary indicators, respectively. To aid nations in quantifying these indicators, a detailed set of guide- line materials was developed, encompassing species selection, data compilation, and indicator computation. These guidelines draw from the collaborative efforts of the first multinational assessment of genetic diver- Mastretta-Yanes et al. – Guidelines for Genetic Diversity Indicators for the Kunming-Montreal Framework 25 sity indicators that was recently completed and that will be refined continually through a versioning system, as more experience is gained and shared. The materials aim to support the global monitoring framework es- tablished by the CBD and are accessible online for utilization and updates. The guidelines are available at https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/ Key words: biodiversity indicators, Kunming Montreal Global Biodiversity Framework, biodiversity monitor- ing, COP15, effective population size, population maintained, populations. Genetic diversity is the foundation of all biolog- ical diversity. It is necessary for populations of both wild and domesticated species to remain healthy and be able to adapt to environmental change, and for conserving nature’s contributions to people (Des Roches et al., 2021). Starting in 2020, during prepa- ration of what would become the Kunming Mon- treal Global Biodiversity Framework (GBF), three genetic diversity indicators were developed (Hoban et al., 2020, 2021; Laikre et al., 2020): (1) effective population size (Ne) 500 indicator, which measures the proportion of populations within a species that are of sufficient size (Ne > 500) to maintain genetic diversity and adaptive potential within that species; (2) populations maintained (PM) indicator, which measures the proportion of populations that still ex- ists compared to the total number of populations that used to occur; and (3) a DNA-based monitoring in- dicator, which is a count of the number of species in which genetic diversity has been or is being moni- tored using DNA-based methods. The first two in- dicators focus on processes contributing to genetic diversity conservation: ensuring that populations are large enough to maintain genetic diversity (Ne 500 indicator) and maintaining genetically distinct pop- ulations (PM indicator). These two indicators were adopted in 2022 by GBF as headline A4 and com- plementary indicators, respectively, which means that GBF parties will use these indicators to report on their progress over the next decade (CBD, 2022b, 2022a). They also cover two key aspects of the GBF: conserving genetic diversity both within populations and between populations. The GBF commitment to monitoring genetic di- versity for all species, instead of only socioeconom- ically and culturally valuable taxa (as was required in 2010-2020), represents a significant milestone for conservation genetics, but comes with new challeng- es. By focusing on processes underlying the genera- tion and maintenance of genetic diversity, the PM and Ne 500 indicators alleviate some of these challenges because they can be estimated using both genetic and non-genetic data (Hoban et al., 2020; Laikre et al., 2020). Genetic data include DNA-based molecular markers to estimate Ne or delimit population bound- aries, whereas non-genetic data include census pop- ulation size (Nc), which could be transformed to Ne using a Ne/Nc ratio, as well as occurrence data and knowledge of the species’ biology, history and dis- persal to define populations geographically (Hoban et al., 2023, 2024). Integrating data from these di- verse sources, formats and disciplines, from global databases to local knowledge, would make it possible to monitor genetic diversity across the world, much faster than is possible with genetic studies alone (Mastretta-Yanes et al., 2024). Gathering and shar- ing biodiversity data has its own difficulties (Blair et al., 2020; Enke et al., 2012). However, integrating the diverse data needed to estimate genetic diversity indicators also requires capacity building to integrate genetic principles to new fields, designing new data collection protocols, and mobilizing data for indica- tor calculation in a reliable, transparent, and inclu- sive way, without stretching the personnel, time, and financial resources of the agencies in charge of re- porting them. To contribute to meeting these challenges, with colleagues, we co-developed the following guide- line materials, as part of the first multinational as- sessment of the genetic diversity indicators (Mas- tretta-Yanes et al., 2024). Part of the guidelines were described previously in Hoban et al. (2023), but after implementing them across nine countries (Australia, Belgium, Colombia, France, Japan, Mexico, South Africa, Sweden, and the United States of America), several improvements were made. These improve- ments incorporate feedback from around 80 partic- ipants (students, practitioners and researchers) who gathered data for the indicators, as well as feedback from 13 international webinars & seminars with hundreds of participants. This publication leverag- es our shared experience, with more detailed guide- lines in an online documentation format, that will be kept updated through a versioning system as more teams share insights. The materials are intended to assist nations in quantifying genetic indicator values https://ccgenetics.github.io/guidelines-genetic-diversity-indicators/ https://www.zotero.org/google-docs/?kKvP8A https://www.zotero.org/google-docs/?kKvP8A https://www.zotero.org/google-docs/?XCO5ok https://www.zotero.org/google-docs/?XCO5ok https://www.zotero.org/google-docs/?jf50bO https://www.zotero.org/google-docs/?jf50bO https://www.zotero.org/google-docs/?KVVcC2 https://www.zotero.org/google-docs/?KVVcC2 https://www.zotero.org/google-docs/?dcHu3i https://www.zotero.org/google-docs/?dcHu3i https://www.zotero.org/google-docs/?Qq8JdQ https://www.zotero.org/google-docs/?NoVdxv https://www.zotero.org/google-docs/?NoVdxv https://www.zotero.org/google-docs/?TOSgNj https://www.zotero.org/google-docs/?TOSgNj https://www.zotero.org/google-docs/?07BfcZ Mastretta-Yanes et al. – Guidelines for Genetic Diversity Indicators for the Kunming-Montreal Framework 26 at every stage of the process: from species selection to data compilation to indicator calculation. We hope they become useful as a reference point, from which countries can adjust their protocols to their own needs and preferences. The guidelines are available as an online docu- mentation at https://ccgenetics.github.io/guidelines-genetic- diversity-indicators/ The online documentation consists of eight con- tent sections, as follows: (1) Background on the pop- ulation genetics rationale behind the genetic diversity indicators, (2) Quickstart guide summarizing steps needed to estimate the indicators, (3) Discussion on how many and which species to include in the spe- cies list to evaluate the indicators, (4) How-to guides with practical examples showing how to perform the most common tasks involved in assessing the genet- ic diversity indicators, (5) Example assessments of real-life species, (6) Data collection advice with a ready-to-use template for a web tool for data collec- tion using KoboToolBox, (7) Equations, scripts and examples for calculations and reporting of the indi- cators, and (8) Glossary. Acknowledgments These materials are based on the co-creation ex- perience of the first pilot multinational assessment of the genetic diversity indicators, and on interactions with practitioners, researchers and students of sev- eral institutions across the world. We are particular- ly grateful to the Swedish Environmental Protection Agency, the Ad Hoc Technical Expert Group on In- dicators for the Kunming-Montreal Global Biodi- versity Framework, and to the following people for providing feedback and ideas: Akio Takenaka, Ale- jandra Domínguez Álvarez, Alexander Llanes-Que- vedo, Alice Hughes, Ana Wegier, Ashley Hamilton, Atsaves Angelica, Austin Koontz, Bastian Silva, Belma Kalamujić Stroil, Caitlin Miller, Catherine E Grueber, W Chris Funk, Emma Suzuki Spence, Er- ica Robertson, Eugenia Zarza, Fleur Visser, Gaëlle Brahy, Georgina Wood, Glenn M Shea, Henrik Thurfjell, Hesiquio Benitez, Irene Ramos, Iris Lang, Isa-Rita Russo, Juan Francisco Ornelas, Katie Mil- lette, Keiichi Fukaya, Kira Cullmann, Libertad Arre- dondo-Amezcua, Lily Durkee, Lucía Ruíz, Luke Dedecke, Malte Julius Benedikt Lehmann, Malte Lehmann, Margaret E. Hunter, Maria Alejandra Ro- driguez-Morales, María Camila Latorre, Marlien van der Merwe, Matt DeSaix, Meg Mahoney, Metztli Arcila Santiago, Mónica Alegre, Paulette Bloomer, Per Sjögren-Gulve, Philipp Ungar, Robyn E. Shaw, Santiago Ramírez-Barahona, Sheela Turbek, Simone Bagnato, Sofía Treviño, Tanya Latty, Taylor Stack, and Victor Julio Rincon-Parra. Author Contributions AM-Y developed the Github repository and coordi- nated the overall project with BRF. SS and AM-Y loaded the content into the Github repository and programmed the Kobo-form. AM-Y, SS, RJ, SH, JMDS and BRF wrote most of the updated version of the guidelines and made figures. AM-Y, RJ, SH, JMDS, BRF, LC-R, MH, FI, VK, LL, AJM, JM, IP-V wrote the initial version of the guidelines and made figures. GS coordinated the testing of the guidelines and contributed to the test. AK, HR, AW, AA, KC and SG tested the guidelines and provided step-by- step examples following them. 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