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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. ispartof: CONSERVATION GENETICS vol:24 issue:2 pages:181-191 ispartof: location:Netherlands status: published

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Human impacts on the Earth’s biosphere are driving the global biodiversity crisis. Governments are preparing to agree on a set of actions intended to halt the loss of biodiversity and put it on a path to recovery by 2050. We provide evidence that the proposed actions can bend the curve for biodiversity, but only if these actions are implemented urgently and in an integrated manner.

Larger numbers of colonists can be more likely to establish and spread due to the benefits provided by either more individuals (quantity) or a greater diversity of genotypes or phenotypes (genetic diversity). However, the value of higher colonist quantity or genetic diversity varies widely across studies, leaving a great deal of uncertainty in how these respective mechanisms affect colonization success. This variability is potentially driven by differences in which traits are present in respective colonist pools (‘colonist identity’). Studies with high‐performing colonizers (e.g. genotypes pre‐adapted to the colonizing environment) may find increasing quantity or diversity to be beneficial because it increases the chance high‐performers are sampled, while studies with no high‐performers may find no effects of quantity or diversity. Alternatively, quantity and genetic diversity may play little to no role if the smallest populations already contain high‐performing colonists because there is no scope for a sampling effect to operate. We conducted a field mesocosm experiment to determine if variability in the benefits provided by increased quantity or genetic diversity relates to colonist traits. Nine distinct genotypes of Daphnia pulex characterized also by phenotype, were introduced in ‘single’ (one individual) or ‘many’ (nine individuals) introduction quantities and at ‘low’ (monoclonal) and ‘high’ (mixed genotypes) genetic diversities. We found that larger‐bodied D. pulex genotypes benefited less from increased colonist quantity, while increasing genetic diversity tended to have a lower effect on higher growth rate genotypes. Our results show that the trait values of the colonists can determine the benefits gained when colonist quantity or genetic diversity are increased, with potential applications to future research and practical efforts to promote, or prevent, population establishment.

Paz-Vinas et al. (2021) comment on methodological and data-related limits of our paper (Millette et al. 2020), which affect a small proportion of our datasets and analyses. These points do not refute our conclusions. We address their comments and support the call for the development of best practices for future macrogenetics research.

Paz-Vinas, Jensen et al. (2021) comment on data and methodological limits of Millette, Fugère, Debyser et al. (2020)-some affect a small proportion of our data sets and analyses and others need to be tackled more generally. These points do not refute our main conclusion of no strong signal of human impacts on COI variation globally.

Human impacts on genetic diversity are poorly understood yet critical to biodiversity conservation. We used 175 247 COI sequences collected between 1980 and 2016 to assess the global effects of land use and human density on the intraspecific genetic diversity of 17 082 species of birds, fishes, insects and mammals. Human impacts on mtDNA diversity were taxon and scale-dependent, and were generally weak or non-significant. Spatial analyses identified weak latitudinal diversity gradients as well as negative effects of human density on insect diversity, and negative effects of intensive land use on fish diversity. The observed effects were predominantly associated with species turnover. Time series analyses found nearly an equal number of positive and negative temporal trends in diversity, resulting in no net monotonic trend in diversity over this time period. Our analyses reveal critical data and theory gaps and call for increased efforts to monitor global genetic diversity.

Genetic diversity is expected to erode in disturbed habitats through strong selection, local extinctions, and recolonization associated with genetic bottlenecks and restricted gene flow. Despite this general prediction and over three decades of population genetics studies, our understanding of the long-term effect of environmental disturbance on local and regional genetic diversity remains limited. We conducted a population genetic survey of the microcrustacean Daphnia across a landscape subject to anthropogenic stressors from a century of industrial mining. At the local scale we found moderate genetic diversity (i.e., low clonal diversity), characteristic of habitat-specific selective sweeps and local extinctions, but high diversity and strong genetic structure at the regional scale despite the shared watershed of many lakes and exceptional dispersal ability of daphniids. Many habitats experienced changes in species assemblages, with the obligate asexual Daphnia pulex lineages—known only to inhabit ponds—dominating disrupted urban lakes. This habitat transition (pond to lake) was likely facilitated by the disruption of ecological barriers maintaining the genomic separation of these young species. Thus, disrupted habitats can exhibit complex and unexpected genetic patterns of local extinctions and recolonizations, followed by habitat transitions, hybridization and potential speciation events that are difficult to predict and should not be underestimated.

Human impacts on genetic diversity are poorly understood yet critical to understanding the evolutionary capacity of the world’s biodiversity. We combined global estimates of land use and human density with 175,247 mitochondrial sequences to assess human impacts on the intraspecific genetic diversity of 17,082 species of birds, fishes, insects, and mammals. We determined drivers of diversity across geographical space, over time, and at four spatial scales. In both spatial and time series analyses, the magnitude and sign of human impacts depended on taxon, and effects were generally small. Weak latitudinal diversity gradients were also found in birds, fishes, and mammals. Geographic distance was a strong driver of genetic diversity among sequences at large spatial scales. Our analyses provide a first worldwide picture of human impacts on animal genetic diversity and reveals critical gaps in taxonomic, geographic, and temporal data coverage, and calls for increased global efforts to systematically monitor genetic diversity. Statement of authorship All authors contributed to the idea and design of the project. KLM and FJJC contributed to sequence data collection and analysis. VF led statistical analyses. CD led spatial analyses. AGr collected taxonomic information. KLM drafted the manuscript. VF and CD made the figures. AGo supervised the project. All authors contributed to data interpretation and writing of the manuscript. Data accessibility statement All data used in this manuscript are available online in open access, as described in the Methods section. Formatted datasets used in statistical analyses will be archived on an online repository upon manuscript acceptance. Data manipulation and analysis code can be found at https://github.com/VFugere/GenDivProject.

In this study we investigate the extent to which successive range fragmentations, postglacial expansions, and recolonizations influenced intraspecific genetic diversity and patterns of diversification in freshwater zooplankton. Specifically, we explore the global phylogeography of the Holarctic predatory cladoceran Leptodora kindtii Focke, 1844. Phylogenetic analyses based on the mitochondrial cytochrome c oxidase subunit I recover seven deeply divergent lineages (11.8–20.0%) comprising two sister clades within the Nearctic and east Palearctic and three related clades within the west Palearctic. Strong continental endemism was also supported by the nuclear 18S ribosomal gene. Intra-continental divergence levels (, 6%) suggest that many speciation events in Leptodora were initiated by glacial isolation. Demographic and network analyses indicate that in the Nearctic and west Palearctic, regions heavily affected by the Pleistocene glaciations, Leptodora persisted in both classic (e.g., Cascadia, Mississippi, southern Europe) and cryptic refugia (e.g., northeastern Europe, Carpathian basin). Strong signatures of late Pleistocene range expansions and secondary contact were observed in most clades. Deeper intraspecific phylogeographic structure occurs across much finer geographic scales in unglaciated regions of the east Palearctic than across glaciated Nearctic and west Palearctic regions. Leptodora’s ecological and biological characteristics, such as a reliance on temperate, permanent lakes, weak dispersal ability, and specific geological settings likely shaped the complex pattern of diversification in this important planktonic predator. Our data suggest the Pleistocene glaciations were important in the diversification of Holarctic freshwater zooplankton.

Mantel‐based tests have been the primary analytical methods for understanding how landscape features influence observed spatial genetic structure. Simulation studies examining Mantel‐based approaches have highlighted major challenges associated with the use of such tests and fueled debate on when the Mantel test is appropriate for landscape genetics studies. We aim to provide some clarity in this debate using spatially explicit, individual‐based, genetic simulations to examine the effects of the following on the performance of Mantel‐based methods: (1) landscape configuration, (2) spatial genetic nonequilibrium, (3) nonlinear relationships between genetic and cost distances, and (4) correlation among cost distances derived from competing resistance models. Under most conditions, Mantel‐based methods performed poorly. Causal modeling identified the true model only 22% of the time. Using relative support and simple Mantel r values boosted performance to approximately 50%. Across all methods, performance increased when landscapes were more fragmented, spatial genetic equilibrium was reached, and the relationship between cost distance and genetic distance was linearized. Performance depended on cost distance correlations among resistance models rather than cell‐wise resistance correlations. Given these results, we suggest that the use of Mantel tests with linearized relationships is appropriate for discriminating among resistance models that have cost distance correlations

Despite strong interest in understanding how habitat spatial structure shapes the genetics of populations, the relative importance of habitat amount and configuration for patterns of genetic differentiation remains largely unexplored in empirical systems. In this study, we evaluate the relative influence of, and interactions among, the amount of habitat and aspects of its spatial configuration on genetic differentiation in the pitcher plant midge, Metriocnemus knabi. Larvae of this species are found exclusively within the water-filled leaves of pitcher plants (Sarracenia purpurea) in a system that is naturally patchy at multiple spatial scales (i.e., leaf, plant, cluster, peatland). Using generalized linear mixed models and multimodel inference, we estimated effects of the amount of habitat, patch size, interpatch distance, and patch isolation, measured at different spatial scales, on genetic differentiation (F ST) among larval samples from leaves within plants, plants within clusters, and clusters within peatlands. Among leaves and plants, genetic differentiation appears to be driven by female oviposition behaviors and is influenced by habitat isolation at a broad (peatland) scale. Among clusters, gene flow is spatially restricted and aspects of both the amount of habitat and configuration at the focal scale are important, as is their interaction. Our results suggest that both habitat amount and configuration can be important determinants of genetic structure and that their relative influence is scale dependent.