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Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to reporting the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socio-economic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of the taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators., (© 2024 The Author(s). Ecology Letters published by John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

A horizon scan was conducted to identify emerging and intensifying issues for biodiversity conservation in South Africa over the next 5-10 years. South African biodiversity experts submitted 63 issues of which ten were identified as priorities using the Delphi method. These priority issues were then plotted along axes of social agreement and scientific certainty, to ascertain whether issues might be "simple" (amenable to solutions from science alone), "complicated" (socially agreed upon but technically complicated), "complex" (scientifically challenging and significant levels of social disagreement) or "chaotic" (high social disagreement and highly scientifically challenging). Only three of the issues were likely to be resolved by improved science alone, while the remainder require engagement with social, economic and political factors. Fortunately, none of the issues were considered chaotic. Nevertheless, strategic communication, education and engagement with the populace and policy makers were considered vital for addressing emerging issues.

Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g. via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size (Ne  < 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting. [ABSTRACT FROM AUTHOR]

Genetic diversity (GD) and phylogenetic diversity (PD) respectively represent species' evolutionary potential and history, and support most of the biodiversity benefits to humanity. Yet, these two biodiversity facets have been overlooked in previous biodiversity policies. As the Parties to the Convention on Biological Diversity (CBD) adopted the Kunming–Montreal Global Biodiversity Framework (GBF) in December 2022, we analyze how GD and PD are considered in this new framework and discuss how their incorporation in the GBF could strengthen their conservation. Although the inclusion of certain indicators could be elevated, both GD and PD are an integral part of the recently adopted GBF. This represents a significant improvement compared to the CBD strategic plan 2011–2020 and an unprecedented opportunity to bring species' evolutionary potential and history to the core of public biodiversity policies. We urge the scientific community to leverage this opportunity to actually improve the conservation of species' evolutionary potential and history. [ABSTRACT FROM AUTHOR]

Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to protect biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA‐based assessment, have been proposed for reporting to the Convention on Biological Diversity and other conservation and policy initiatives. These indicators allow an approximation of the status and trends of genetic diversity to inform policy, using existing demographic and geographic information. Application of these indicators has been initiated and here we describe ongoing efforts in calculating these indicators with examples. We specifically describe a project underway to apply these indicators in nine countries, provide example calculations, address concerns of policy makers and implementation challenges, and describe a roadmap for further development and deployment, incorporating feedback from the broader community. We also present guidance documents and data collection tools for calculating indicators. We demonstrate that Parties can successfully and cost‐effectively report these genetic diversity indicators with existing biodiversity observation data, and, in doing so, better conserve the Earth's biodiversity. [ABSTRACT FROM AUTHOR]

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators. [ABSTRACT FROM AUTHOR]

Given the ever-increasing anthropogenic changes to natural ecosystems, it is imperative that temporal changes in genetic diversity be monitored to help safeguard the future viability of species. Capensibufo rosei is a small, range-restricted bufonid from South Africa, believed to have experienced an enigmatic decline likely due to the suppression of natural fires and the loss of grazing animals from some areas. Without these disturbances, their habitat becomes overgrown, which might affect the characteristics of their breeding pools. Since the 1980s, four breeding sites have been lost, presumably due to loss of breeding habitat through encroachment of vegetation. Currently, there are only two known populations [Cape of Good Hope (CGH) and Silvermine nature reserves] both within Table Mountain National Park. Consequently, this species may be vulnerable to stochastic events and genetic erosion through the loss of metapopulation connectivity. To assess the genetic status of this species, genetic diversity within both populations was quantified for two time periods using 11 microsatellite markers. Despite evidence of severe population bottlenecks, both populations possess levels of diversity similar to other anurans, and Silvermine has greater diversity than CGH. A close examination of the data revealed both populations to be genetically dynamic through time, with the loss and gain of rare alleles. Both populations also experienced a slight increase in overall diversity between sampling periods. While the latter was not statistically significant, the monitoring period was perhaps too short to understand changes in diversity over time. These results will form the baseline for future monitoring to better understand this threatened and declining species and to track genetic erosion or recovery. [ABSTRACT FROM AUTHOR]

Aim To investigate whether morphological variation in a continental radiation of lizards (Chamaeleonidae) was driven by ecological opportunity. Location KwaZulu-Natal, South Africa. Methods Chameleons from all morphotypes were genotyped ( n = 279) using 10 microsatellite and one mitochondrial marker ( n = 130). Genetic spatial structure was examined in a Bayesian framework and compared to ecomorphological forms, to identify distinct chameleon groups using a total evidence approach. Ecological niche modelling projected back to the Last Glacial Maximum and the Last Interglacial was used to make inferences regarding the processes that may have facilitated diversification through ecological opportunity. Results For the three inland groups, genetic and morphological evidence were in agreement suggesting these are candidate species. However, there was discordance in evidence for populations from coastal regions, although the different time-scales of the data allow us to make some inferences regarding this disparity. The microsatellite data suggest at least three independent origins of coastal chameleons, although all three clusters show the same ecomorph, which indicates convergence of phenotype in a similar environment. The species distribution models revealed high niche stability among inland groups, suggesting the presence of refugia for these chameleons; whereas the coastal niche is more dynamic and likely resulted in recent origins of these groups. Main Conclusions A dynamic climatic niche and corresponding vegetation shifts are likely to have shaped contrasting ecomorphological and genetic patterns within this continental radiation by creating ecological opportunity for the coastal chamleons. In contrast, inland groups are in climatically stable regions, and show concordance between lines of evidence, suggesting that niche stability has allowed for these chameleons to diverge genetically and phenotypically. [ABSTRACT FROM AUTHOR]

On the Cape Peninsula,Capensibufo roseiis known from only two isolated breeding populations within Table Mountain National Park. Because of its declining state, there is an urgent need to understand the genetic diversity, population structure and patterns of movement of this species. To do this, 15 microsatellite primer pairs were designed, optimised and tested. Successful loci were screened for null alleles and genotyping errors and then analysed, specifically noting the number of alleles, allelic size range, observed and expected heterozygosities, deviations from Hardy–Weinberg equilibrium (HWE) and linkage disequilibria. Bottleneck tests and analyses of molecular variance (AMOVA) were also conducted to gain insight into each population’s structure. Eleven primer pairs produced unambiguous polymerase chain reactions (PCR) products and scoreable bands, which were found to be polymorphic across both breeding populations. Deviations from HWE were detected owing to the presence of null alleles and inbreeding. Significant bottleneck signatures were detected for both populations and the AMOVA revealed significant differentiation between the two populations, indicating genetic structure at the population level. [ABSTRACT FROM AUTHOR]

For over a decade, molecular short standardised DNA fragments, termed DNA barcodes, have been developed for species discrimination around the world. As of 2010, the vast majority of barcoding research was biased toward particular taxonomic groups and geographic regions largely because researchers in developed countries were the ones with the resources and capacity to carry out such work. To rectify this, the International Barcode of Life Project was launched with the intent to extend the geographic and taxonomic coverage of the barcode reference library. South Africa committed to this mission in an attempt to catalogue all of its known biodiversity and, possibly, help identify new species. To date, approximately 48 000 South African faunal barcodes are housed in the Barcode of Life Data System (BOLD), which represent only 2.3% of all known South African animal species. Although insects are the best represented in absolute terms, with over 37 000 samples recorded, they are still grossly lacking with just over 1% representation. Much like the global trend, there is a general taxonomic bias, with fish, birds and mammals showing the greatest representation. Moreover, geographic bias is also present, with the Free State province particularly under-represented on BOLD, likely owing to limited human capacity. Although few studies have been published with respect to barcoding, the majority reveal that the cytochromecoxidase 1 (CO1) gene, used in isolation or in conjunction with other molecular markers, can greatly benefit South African biodiversity research. Several limitations of DNA barcoding are discussed and recommendations specific to South Africa provided. [ABSTRACT FROM PUBLISHER]

African reptiles are under threat primarily due to habitat loss as a result of agriculture, resource extraction, and urbanisation. Extinction risk of South African reptiles was assessed as of 2018 using IUCN criteria and we 'backcast' these assessments to infer extinction risk circa 1990. A Red List Index (RLI: a measure of the extinction risk for a group of species) for 1990 and 2018 was estimated, and the protection level afforded to South African reptiles was investigated by intersecting reptile distributions with the network of protected areas. Furthermore, phylogenetic diversity of South African reptiles was mapped and intersected with national land cover for 1990 and 2013 to identify areas of high phylogenetic richness that may be impacted by habitat transformation. Level of extinction risk for South African reptiles (ca. 5.4%) is lower than the global average, and most currently threatened species would have already been at risk by 1990. The RLI is slightly lower in 2018 than it was in 1990, and the decrease is more prominent for endemic reptiles than for all reptiles combined. Most South African reptiles fall into the Well Protected category, implying that the protected area network has substantial conservation impact. However, most threatened reptile species are Poorly Protected or Not Protected. The current extent of the protected area network therefore, does not adequately mitigate extinction risk for reptiles. Notably, two South African reptiles are Critically Endangered and in protected areas, two others are already classified as Extinct, and rough estimates of extinction rates are similar to values estimated for other vertebrates. Phylogenetic diversity mapping showed that the greatest historical impacts to phylogenetic richness for reptiles are in the northeast (Limpopo, Mpumalanga, and Gauteng provinces), southwest (Western Cape Province) and the coastal margin of KwaZulu-Natal. By considering additional metrics that are directly guided by our in-depth knowledge of the species, their distributions and the threats, we demonstrate that South African reptiles are under pressure, that risk of extinction is tangible for several species and that phylogenetic richness of reptiles in certain areas of South Africa is imperilled by loss of habitat. [ABSTRACT FROM AUTHOR]

In biodiversity research, the retrieval of genetic material from organisms is a common and essential component for assessing genetic diversity. The welfare of the organism, however, needs to be balanced against the overall goal of the intended research. One sampling technique often applied to retrieve DNA material from small reptiles is the removal of a small portion of the distal end of the tail. While most squamate reptiles have tail autotomy, some species (e.g. many iguanid lizards and snakes) do not regenerate tail tissue. We therefore explored the efficacy of a minimally disruptive technique, buccal swabbing, as an alternative to tissue sampling via tail clipping, particularly for species without tail autotomy, using dwarf chameleons (Bradypodion spp.) as a case study. The two sampling techniques were compared to assess the efficacy of DNA retrieval. We also evaluated the financial implications of each technique. The results indicate that buccal swabs paired with a specialised DNA extraction kit offer a feasible (although expensive), once-off alternative to tissue sampling, but with no material left for biobanking. Deviations in swab type used and the DNA extraction process (i.e. using more affordable extraction procedures) resulted in poor DNA retrieval and unreadable sequences. This finding suggests that buccal swabbing can be a suitable alternative when finances are not constrained, an expensive extraction kit is available, and biobanking is not a concern. For researchers from low- to middle-income economies, this expensive alternative may hamper research progress by placing a financial obstacle in the way, and therefore the next best option is tissue sampling. Significance: This study provides guidance on the efficacy of buccal swabs as a viable alternative to tissue samples collected via tail clipping for DNA retrieval from small reptiles. The results indicate that swabs may be a feasible alternative to tissue samples when finances are not constrained. Deviations in buccal swabbing method (i.e. using more cost-effective alternatives) performed poorly in DNA retrieval and do not offer competitive alternatives to tissue samples. Although buccal swabs were shown to offer an alternative to tissue samples, the financial implications to research in low- to middle-income economies may hinder research goals unnecessarily. [ABSTRACT FROM AUTHOR]

International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on progress. However, the CBD and similar policy agreements have often neglected genetic diversity. This is a critical gap because genetic diversity underlies adaptation to environmental change and ecosystem resilience. Here we aim to inform future policy, monitoring, and reporting efforts focused on limiting biodiversity loss by conducting the largest yet evaluation of how Parties to the CBD report on genetic diversity. A large, globally representative sample of 114 CBD National Reports was examined to assess reported actions, progress, values and indicators related to genetic diversity. Although the importance of genetic diversity is recognized by most Parties to the CBD, genetic diversity targets mainly addressed variation within crops and livestock (a small fraction of all species). Reported actions to conserve genetic diversity primarily concerned ex situ facilities and legislation, rather than monitoring and in situ intervention. The most commonly reported status indicators are not well correlated to maintaining genetic diversity. Lastly, few reports mentioned genetic monitoring using DNA data, indigenous use and knowledge of genetic diversity, or development of strategies to conserve genetic diversity. We make several recommendations for the post-2020 CBD Biodiversity Framework, and similar efforts such as IPBES, to improve awareness, assessment, and monitoring of genetic diversity, and facilitate consistent and complete reporting in the future. • We assessed genetic diversity in reports to the Convention on Biological Diversity • Countries recognize diverse values of, and threats to, genetic diversity • Most countries neglect to monitor or develop strategies for genetic diversity • Many countries focus on ex situ genetic conservation, neglecting in situ actions • Many countries use insufficient indicators and focus strongly on domesticated species [ABSTRACT FROM AUTHOR]

Compared to the global average, extinction risk for mainland African reptiles, particularly for South Africa, appears to be relatively low. Despite this, African reptiles are under threat primarily due to habitat loss as a result of agriculture, resource extraction, and urbanisation, and these pressures are expected to increase into the future. South Africa's reptile fauna is relatively well-studied, allowing an investigation of whether threat status assessment limitations are driving the comparably low threat status for the country, a large component of Africa's reptile fauna (ca. 25% of mainland African reptiles are found in South Africa). Extinction risk of South African reptiles was assessed as of 2018 using IUCN criteria and we 'backcast' these assessments to infer extinction risk circa 1990. A Red List Index (RLI: a measure of the extinction risk for a group of species) for 1990 and 2018 was estimated, and the protection level afforded to South African reptiles was investigated by intersecting reptile distributions with the network of protected areas. Finally, a coarse estimate of extinction rate was made. Level of extinction risk for South African reptiles (ca. 5.4%) is lower than the global average, and most currently threatened species would have already been at risk by 1990. The RLI was slightly lower for 2018 than for 1990, and the decrease was more prominent for endemic reptiles than for all reptiles combined. Most South African reptiles fall into the Well Protected category, implying that the protected area network has substantial conservation impact. However, many threatened reptile species are Poorly Protected or Not Protected. The current extent of the protected area network therefore, does not adequately mitigate extinction risk for reptiles. Furthermore, the protected area expansion plan for South Africa would not capture any additional threatened species within its boundaries. Despite the lower level of extinction risk indicated by IUCN assessments, it would be premature to assume that South African reptiles are faring better than reptiles globally based only on this one measure. Notably, two South African reptiles are Critically Endangered and theses are not found in protected areas, two others are already classified as Extinct, and rough estimates of extinction rates are similar to values estimated for other vertebrates. By considering additional metrics that are directly guided by our in-depth knowledge of the species, their distributions and the threats, we demonstrate that South African reptiles are under pressure and that risk of extinction is tangible for several species. [ABSTRACT FROM AUTHOR]