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Effective population size (Ne) is a key concept in biology and conservation. Stripped to its bare essentials, it reflects how much genetic drift a population experiences, expressed as a number of individuals of an ideal theoretical population. Superficially, Ne seems like a fairly simple concept, but the more layers of the onion you peel, the more you feel like crying. Really understanding Ne in all its facets is daunting, as there are various temporal, spatial, biological, and mathematical ways in which Ne can be defined and approached, many of which are erroneously interchanged and often not distinguished. If that is not enough, understanding the intricacies and the assumptions of the many ways in which Ne can be calculated is required to make sense of the concept. This is why a special issue on this topic, especially in relation to biodiversity monitoring, is timely. We assembled 19 original papers, perspectives, and reviews on effective population size estimation in relation to conservation to help practitioners in conservation research and practical management see the forest for the trees with regards to Ne.

(Arabica) and (robusta) almost entirely dominate global coffee production. Various challenges at the production (farm) level, including the increasing prevalence and severity of disease and pests and climate change, indicate that the coffee crop portfolio needs to be substantially diversified in order to ensure resilience and sustainability. In this study, we use a multidisciplinary approach (herbarium and literature review, fieldwork and DNA sequencing) to elucidate the identity, whereabouts, and potential attributes, of two poorly known coffee crop species: and . We show that despite widespread (albeit small-scale) use as a coffee crop species across Upper West Africa and further afield more than 100 years ago, these species are now extremely rare in the wild and are not being farmed. Fieldwork enabled us to rediscover in Sierra Leone, which previously had not been recorded in the wild there since 1954. We confirm that is an indigenous species in Guinea, Sierra Leone, and Ivory Coast. was discovered in the wild in Sierra Leone for the first time, having previously been found only in Guinea and Ivory Coast. Prior to our rediscovery, was last seen in the wild in 1941, although sampling of an unidentified herbarium specimen reveals that it was collected in Guinea-Conakry in 2015. DNA sequencing using plastid and ITS markers was used to: (1) confirm the identity of museum and field collected samples of ; (2) identify new accessions of ; (3) refute hybrid status for ; (4) identify accessions confused with ; (5) show that and are closely related, and possibly a single species; (6) substantiate the hybrid × ; (7) demonstrate the use of plastid and nuclear markers as a simple means of identifying F1 and early-generation interspecific hybrids in ; (8) infer that is not monophyletic; and (9) show that hybridization is possible across all the major groups of key Africa species (Coffee Crop Wild Relative Priority Groups I and II). and may possess useful traits for coffee crop plant development, including taste differentiation, disease resistance, and climate resilience. These attributes would be best accessed via breeding programs, although the species may have niche-market potential via minimal domestication.

Conservation success depends on translating theory into practical guidance and tools that are relevant and useful for non‐scientists. While the complexity of population genetics has challenged the usage of straightforward metrics for conservation, several practical guidelines have been advanced, such as those regarding effective population size (Ne). Allendorf et al. highlight limitations of Ne as a metric for practical use. Specifically, they demonstrate that while Ne is sufficient for predicting heterozygosity, it is not predictive of the number of alleles, another key variable in conservation genetics. This has important implications for Ne‐based metrics, such as the Ne 500 indicator recently adopted in the Convention on Biological Diversity's Kunming–Montreal Global Biodiversity Framework. As developers and advocates of the Ne 500 indicator, we agree with this assessment, and acknowledge that Ne does not comprehensively predict changes in allelic variation. In this article we briefly summarize several major points in Allendorf et al. and provide practical suggestions to better account for allelic variation during indicator assessments. These suggestions include reporting major declines in Nc as part of genetic assessments, clearly articulating the intention and caveats of the Ne 500 indicator, integrating simulations into genetic assessments, and assessing the number of genetically distinct populations. We conclude that the Ne 500 indicator remains a valuable metric uniquely capable of capturing critical aspects of a species' genetic status while remaining accessible and interpretable to policymakers and other non‐geneticists. By acknowledging the limitations of focusing solely on Ne and providing options for more thorough and nuanced understandings of genetic diversity, we hope to guide future usage of the Ne 500 indicator and help bridge the gap between conservation genetics theory and practice.

Estimating effective population size (Ne) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life‐history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to Ne. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected Ne. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary Ne with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower Ne. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on Ne confidence intervals. The magnitude of Ne/Nramets and Ne/Ngenets ratios we provide may be used as reference points for other species with similar life‐history traits. Our findings demonstrate that Ne in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence Ne. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.

Climate change poses a considerable challenge for coffee farming, due to increasing temperatures, worsening weather perturbations, and shifts in the quantity and timing of precipitation. Of the actions required for ensuring climate resilience for coffee, changing the crop itself is paramount, and this may have to include using alternative coffee crop species. In this study we use a multidisciplinary approach to elucidate the identity, distribution, and attributes, of two minor coffee crop species from East Africa: Coffea racemosa and C. zanguebariae . Using DNA sequencing and morphology, we elucidate their phylogenetic relationships and confirm that they represent two distinct but closely related species. Climate profiling is used to understand their basic climatic requirements, which are compared to those of Arabica ( C. arabica ) and robusta ( C. canephora ) coffee. Basic agronomic data (including yield) and sensory information are provided and evaluated. Coffea racemosa and C. zanguebariae possess useful traits for coffee crop plant development, particularly heat tolerance, low precipitation requirement, high precipitation seasonality (dry season tolerance) and rapid fruit development (c. 4 months flowering to mature fruit). These attributes would be best accessed via breeding programs, although these species also have niche-market potential, particularly after further pre-farm selection and post-harvest optimization.

Societal Impact Statement Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as “Digital Sequence Information” (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals. Summary Substantial advances in DNA sequencing over the last decades hold great potential to enhance food security and sustainable use of global biodiversity, benefiting the world's poorest people. Digital Sequence Information (DSI) plays a crucial role in catalyzing research applications that can contribute to international societal and biodiversity conservation targets. However, benefit sharing relating to DSI is difficult to identify and hindered by the lack of clear international governance and legislation, which in turn has led to a reluctance to make DSI publicly and freely available. Critically, no precise definition exists under the Convention on Biological Diversity (CBD), the Nagoya Protocol (NP), or the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The key difference between DSI and biological resources, for which access and use are highly regulated under those frameworks, is that information is nonphysical. Information can be replicated and used without movement of, or access to, physical specimens. Thus, regulating the use of DSI is extremely challenging and remains controversial. Here, we review the regulation of DSI and the possible future steps by the international community, in the context of the benefit‐sharing obligations of the CBD, NP, and ITPGRFA. We highlight how multilateral agreements work in practice and are a solution to this impasse. We provide case studies demonstrating how the Royal Botanic Gardens, Kew, and its collaborators address the uncertainty surrounding the use of DSI, illustrating tangible and equitable benefits that have arisen from such use. We conclude that open access to DSI is needed for scientific research and international policy. Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as “Digital Sequence Information” (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals.

The split between conservation science and real‐world application is an ongoing issue despite several calls for unification. Researchers are empowered to partially bridge the research‐implementation gap by making their findings more accessible. Cypripedium calceolus is the most recognizable orchid of the European flora, and is currently facing habitat change and fragmentation, in addition to threats from collectors and illegal traders. Although several studies have focused on the ecological and genetic features of the species, a comprehensive account of how such aspects can be translated into concrete conservation recommendations is still missing. In this study, we describe microsatellite genetic variation in 188 individuals from different Italian populations of C. calceolus. Our results indicate the need for immediate conservation action for the most isolated populations in the Central Apennines and north‐western Italy. Although our genetic findings are specific to the Italian populations, our aim is to review ecological and population genetic aspects in C. calceolus and their implications for conservation against the existing threats. Therefore, our detailed guidelines for translocation, habitat management and post‐translocation monitoring can be used to inform conservation strategies in threatened populations of C. calceolus across its range.

Analysis of the seed morphology is a widely used approach in ecological and taxonomic studies. In this context, intraspecific variability with respect to seed morphology (size, weight, and density) was assessed in two close Epipactis tremolsii Pau. populations sharing the same ecological conditions, except for the soil pollution distinguishing one of them. Larger and heavier seeds were found in plants growing on the heavy metal polluted site, while no differences in seed density were detected between seeds produced by plants growing on the contaminated and the control site. Moreover, seed coats and embryos varying together in their dimensions were described in the control population, while coats varying in their size independently from embryos were described in plants growing on the polluted site. Seeds from the two studied populations significantly differed in several parameters suggesting that intraspecific seed variability occurred in the case study.

Cyperus esculentus is widespread in tropical and temperate zones and is also present in cooler regions. It is used as a crop plant, but it also occurs in the wild and as a weed. As a consequence of its ecological plasticity, C. esculentus has remarkable variability, with several morphotypes. Four wild-type varieties are presently recognized, in addition to the cultivated form. This study investigates the phylogenetic position and biogeography of C. esculentus with the objective of contributing new data to increase the understanding of its evolutionary history. Genealogical relationships among genotypes were inferred by using plastid DNA haplotype and nuclear ribosomal (nr) DNA ribotype sequences for 70 specimens either collected in the field or obtained from herbaria. Statistical dispersal-vicariance (S-DIVA) and Bayesian binary method (BBM) analyses were used to reconstruct the possible ancestral ranges of C. esculentus. In order to determine the age of C. esculentus, a time-measured phylogenetic analysis was performed. Considerable variation between the chosen nuclear and plastid markers was detected (27 ribotypes vs. six haplotypes). No geographical structure was displayed among the haplotypes, but information on the dispersal pattern may be deduced. Two types of ribotypes were detected in nrDNA, with an evident geographical segregation into an Old World group and a polymorphic New World group. Both S-DIVA and BBM analyses suggested a biogeographical history in which dispersal from the African region has been crucial in shaping the current distribution pattern of C. esculentus. The most recent common ancestor between C. esculentus races has an age of 5.1 million years (95 % highest posterior density 2.5-10.2). The molecular analysis provides novel insights into the evolutionary history of C. esculentus. The results have various taxonomic and phylogenetic implications, including a hypothesis on the origin and phylogeography of this species, which probably originated in the late Cenozoic in Africa, and reached the Americas repeatedly, independently of Columbian exchanges.

Conservation success depends on translating theory into practical guidance and tools that are relevant and useful for non‐scientists. While the complexity of population genetics has challenged the usage of straightforward metrics for conservation, several practical guidelines have been advanced, such as those regarding effective population size ( N e ). Allendorf et al. highlight limitations of N e as a metric for practical use. Specifically, they demonstrate that while N e is sufficient for predicting heterozygosity, it is not predictive of the number of alleles, another key variable in conservation genetics. This has important implications for N e ‐based metrics, such as the N e 500 indicator recently adopted in the Convention on Biological Diversity's Kunming–Montreal Global Biodiversity Framework. As developers and advocates of the N e 500 indicator, we agree with this assessment, and acknowledge that N e does not comprehensively predict changes in allelic variation. In this article we briefly summarize several major points in Allendorf et al. and provide practical suggestions to better account for allelic variation during indicator assessments. These suggestions include reporting major declines in N c as part of genetic assessments, clearly articulating the intention and caveats of the N e 500 indicator, integrating simulations into genetic assessments, and assessing the number of genetically distinct populations. We conclude that the N e 500 indicator remains a valuable metric uniquely capable of capturing critical aspects of a species' genetic status while remaining accessible and interpretable to policymakers and other non‐geneticists. By acknowledging the limitations of focusing solely on N e and providing options for more thorough and nuanced understandings of genetic diversity, we hope to guide future usage of the N e 500 indicator and help bridge the gap between conservation genetics theory and practice.