Environmental and geographic variables are effective surrogates for genetic variation in conservation planning

Spatial Analysis of the Ecogeographic Diversity of Wild Creeping Cucumber (Melothria pendula L.) for In Situ and Ex Situ Conservation in Mexico

Melothria pendula L., a wild relative of cucurbit crops, is also used for food and as a medicinal plant in Mexico. The objective of this study was to ecogeographically characterize the known populations of M. pendula in Mexico, determining its adaptive range and possible sites for in situ and ex situ conservation. To achieve this goal, we compiled a dataset of 1270 occurrences of M. pendula from herbarium and botanical databases and individual observations. Adaptive scenarios were generated through the development of an ecogeographic land characterization (ELC) map, preceded by the identification of abiotic variables influencing the species' distribution. Eleven bioclimatic, edaphic, and geophysical variables were found to be important for the species' distribution. The ELC map obtained contained 21 ecogeographic categories, with 14 exhibiting the presence of M. pendula. By analyzing ecogeographic representativeness, 111 sites of high interest were selected for the efficient collection of M. pendula in Mexico. Eight high-priority hotspots for future in situ conservation of M. pendula were also identified based on their high ecogeographic diversity, with only three of these hotspots located within protected natural areas. In this study, ecogeographic approaches show their potential utility in conservation prioritization when genetic data are scarce, a very common condition in crop wild relatives.

Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China

BACKGROUND

Michelia lacei W.W.Smith (Magnoliaceae), was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both action plans of 2012 and 2021. This evergreen tree is known for its high ornamental and scientific value, but it faces significant threats due to its extremely small population size and narrow geographical distribution. The study aims to understand the genetic structure, diversity, and demographic history of this species to inform its conservation strategies.

RESULTS

The analysis of transcriptome data from 64 individuals across seven populations of M. lacei identified three distinct genetic clusters and generated 104,616 single-nucleotide polymorphisms (SNPs). The KM ex-situ population, originating from Longling County, exhibited unique genetic features, suggesting limited gene flow. The genetic diversity was substantial, with significant differences between populations, particularly between the KM lineage and the OTHER lineage. Demographic history inferred from the data indicated population experienced three significant population declines during glaciations, followed by periods of recovery. We estimated the effective population size (Ne) of the KM and OTHER lineages 1,000 years ago were 85,851 and 416,622, respectively. Gene flow analysis suggested past gene flow between populations, but the KM ex-situ population showed no recent gene flow. A total of 805 outlier SNPs, associated with four environmental factors, suggest potential local adaptation and showcase the species' adaptive potential. Particularly, the BZ displayed 515 adaptive loci, highlighting its strong potential for adaptation within this group.

CONCLUSIONS

The comprehensive genomic analysis of M. lacei provides valuable insights into its genetic background and highlights the urgent need for conservation efforts. The study underscores the importance of ex-situ conservation methods, such as seed collection and vegetative propagation, to safeguard genetic diversity and promote population restoration. The preservation of populations like MC and BZ is crucial for maintaining the species' genetic diversity. In-situ conservation measures, including the establishment of in-situ conservation sites and community engagement, are essential to enhance protection awareness and ensure the long-term survival of this threatened plant species.

Conservation macrogenetics: harnessing genetic data to meet conservation commitments

Genetic biodiversity is rapidly gaining attention in global conservation policy. However, for almost all species, conservation relevant, population-level genetic data are lacking, limiting the extent to which genetic diversity can be used for conservation policy and decision-making. Macrogenetics is an emerging discipline that explores the patterns and processes underlying population genetic composition at broad taxonomic and spatial scales by aggregating and reanalyzing thousands of published genetic datasets. Here we argue that focusing macrogenetic tools on conservation needs, or conservation macrogenetics, will enhance decision-making for conservation practice and fill key data gaps for global policy. Conservation macrogenetics provides an empirical basis for better understanding the complexity and resilience of biological systems and, thus, how anthropogenic drivers and policy decisions affect biodiversity.

Complementary Analysis and Implementation Plan for Conservation of Crop Wild Relatives in Finland

Crop wild relatives (CWR) are valuable wild plant species that can be used as genetic resources providing adaptive traits to crop plants and therefore they play an important role in future food security. This paper describes in situ and ex situ conservation planning of CWR species in Finland and includes the following parts: (a) drafting of the national CWR priority list, (b) undertaking the in situ conservation gap analysis and (c) identifying ex situ conservation gaps and multi-species collecting sites for the CWR in Finland. As a result of the study, essential information was acquired, which will enhance future planning of active science-based practical conservation of CWR in Finland. Based on the new data and earlier work, a number of conservation recommendations are presented. This national work has been carried out in connection with the larger Nordic regional CWR co-operation.

On the Prospects of In Situ Conservation of Medicinal- and Aromatic-Plant Genetic Resources at Ancient-Hillfort Sites: A Case Study from Lithuania

Twenty-three ancient-hillfort sites were investigated to evaluate the potential for the in situ conservation of medicinal- and aromatic-plant populations. An evaluation of the site's suitability was carried out by employing three major groups of criteria: species-specific, site-specific, and threat assessment. The species-specific criteria included the total species number, target species number, the cover-abundance of the target species estimated by mean Braun-Blanquet score, and, as an additional criterion, the number and cover-abundance of crop wild relatives. The site-specific criteria included site evaluation with respect to climatic region, the area size of a site, the habitat type, and the site's protection status. The threat assessment was focused on anthropogenic activities, such as recreational, agricultural, and others. The total number of vascular plant species inventoried was 264, including 82 species of medicinal and aromatic plants (MAP). There was a strong and highly significant correlation between the total and the MAP species numbers (r_s = 0.77, p < 0.001), and the two most species-rich sites, Žuklijai and Pamiškė, contained the highest total and MAP species numbers. The investigated hillfort sites covered the populations of 49 species, or about 33% of the priority species list, with 5 or more populations. The most frequent species, Hypericum perforatum, occurred at 21 sites. The twenty-three hillfort sites represent three of the four climatic regions and six of the ten climatic subregions of Lithuania. Although these hillfort sites are quite small (1.24 ± 0.75 ha on average, without buffer zone), they are scattered across the country and are state-protected as archaeological objects, which makes them suitable for the in situ conservation of MAP genetic resources. In addition, seven hillfort sites (30.4% of the investigated ones) belong to the European network of special areas of conservation of habitats (Natura 2000), thus increasing their international importance. The threat assessment showed that anthropogenic activities (recreational, agricultural, etc.) are among the major factors affecting target-species populations.

Molecular ecology meets systematic conservation planning

Integrative and proactive conservation approaches are critical to the long-term persistence of biodiversity. Molecular data can provide important information on evolutionary processes necessary for conserving multiple levels of biodiversity (genes, populations, species, and ecosystems). However, molecular data are rarely used to guide spatial conservation decision-making. Here, we bridge the fields of molecular ecology (ME) and systematic conservation planning (SCP) (the 'why') to build a foundation for the inclusion of molecular data into spatial conservation planning tools (the 'how'), and provide a practical guide for implementing this integrative approach for both conservation planners and molecular ecologists. The proposed framework enhances interdisciplinary capacity, which is crucial to achieving the ambitious global conservation goals envisioned for the next decade.

Primates facing climate crisis in a tropical forest hotspot will lose climatic suitable geographical range

Global climate changes affect biodiversity and cause species distribution shifts, contractions, and expansions. Climate change and disease are emerging threats to primates, and approximately one-quarter of primates' ranges have temperatures over historical ones. How will climate changes influence Atlantic Forest primate ranges? We used habitat suitability models and measured potential changes in area and distributions shifts. Climate change expected in 2100 may change the distribution area of Atlantic Forest primates. Fourteen species (74%) are predicted to lose more than 50% of their distribution, and nine species (47%) are predicted to lose more than 75% of their distribution. The balance was negative, indicating a potential future loss, and the strength of the reduction in the distribution is related to the severity of climate change (SSP scenarios). Directional shifts were detected to the south. The projected mean centroid latitudinal shift is ~ 51 km to the south for 2100 SSP5-8.5 scenario. The possibility of dispersal will depend on suitable routes and landscape configuration. Greenhouse gas emissions should be urgently reduced. Our results also emphasize that no more forest loss is acceptable in Atlantic Forest, and restoration, canopy bridges, friendly agroecosystems, and monitoring of infrastructure projects are urgent to enable dealing with climate change.

Environmental and topographic drivers of amphibian phylogenetic diversity and endemism in the Iberian Peninsula

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study. Our main hypothesis assumes that topography along with contemporary and historical climate are drivers of phylogenetic diversity and endemism, but that the strength of these predictors may be weaker at the regional scale than it tends to be at the global scale. We mapped spatial patterns of Iberian amphibians' phylogenetic diversity and endemism, using previously published phylogenetic and distribution data. Furthermore, we compiled spatial data on topographic and climatic variables related to the water-energy availability, topography, and historical climatic instability hypotheses. To test our hypotheses, we used Spatial Autoregressive Models and selected the best model to explain diversity patterns based on Akaike Information Criterion. Our results show that, out of the variables tested in our study, water-energy availability and historical climate instability are the most important drivers of amphibian diversity in Iberia. However, as predicted, the strength of these predictors in our case study is weaker than it tends to be at global scales. Thus, additional drivers should also be investigated and we suggest caution when interpreting these predictors as surrogates for different components of diversity.

Assessing ex situ genetic and ecogeographic conservation in a threatened but widespread oak after range-wide collecting effort

Although the genetic diversity and structure of in situ populations has been investigated in thousands of studies, the genetic composition of ex situ plant populations has rarely been studied. A better understanding of how much genetic diversity is conserved ex situ, how it is distributed among locations (e.g., botanic gardens), and what minimum sample sizes are needed is necessary to improve conservation outcomes. Here we address these issues in a threatened desert oak species, Quercus havardii Rydb. We assess the genetic, geographic, and ecological representation of 290 plants from eight ex situ locations, relative to 667 wild individuals from 35 in situ locations. We also leverage a recent dataset of >3000 samples from 11 other threatened plants to directly compare the degree of genetic conservation for species that differ in geographic range size. We found that a majority of Q. havardii genetic diversity is conserved; one of its geographic regions is significantly better conserved than the other; genetic diversity conservation of this widespread species is lower than documented for the 11 rarer taxa; genetic diversity within each garden is strongly correlated to the number of plants and number of source populations; and measures of geographic and ecological conservation (i.e., percent area and percent of ecoregions represented) were typically lower than the direct assessment of genetic diversity (i.e., percent alleles). This information will inform future seed sampling expeditions to ensure that the intraspecific diversity of threatened plants can be effectively conserved.

Evolving spatial conservation prioritization with intraspecific genetic data

Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change.

State of ex situ conservation of landrace groups of 25 major crops

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation.

Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (N_e). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.

Estimation of wetland biodiversity based on the hydrological patterns and connectivity and its potential application in change detection and monitoring: A case study of the Sanjiang Plain, China

A high biodiversity conservation value of a specific area generally indicates biodiversity priorities, making biodiversity conservation planning more reasonable. However, the spatial prioritization of biodiversity cannot easily indicate temporal changes because the data of many species are difficult to obtain in even a single period, let alone repeated surveys. Here, we show that the easily available wetland hydrological pattern and connectivity (HCP) variables are effective surrogates for the monitoring of biodiversity conservation value. We used the Systematic Conservation Planning (SCP) method to evaluate the historical biodiversity conservation value (BCV), represented by Irreplaceability Index, by integrating the predicted spatial distribution of biodiversity features in 1995. We then calculated the wetland HPC indexes in randomly setup samples within a certain radius and analysed the correlation between the BCV and HPC indexes with a regression method. Finally, we further simulated the numerical and spatial changes of the BCV in different periods to illustrate its variation regularity. We found that the BCV considerably decreased in the study area. In conclusion, we confirmed that the wetland HPC indexes are significantly correlated with and can simulate the BCV indicator. We further identified the spatial locations of these degraded areas and proposed conservation and restoration scenarios for the study area. This study verified the impacts of HPC changes on wetland biodiversity caused by human-induced land use change; it also provides a reference for long-term assessment of wetland biodiversity change. SIGNIFICANCE STATEMENT: Among other abilities, effective biodiversity conservation should have the abilities to both prioritize the conservation value and detect its spatial changes. However, the assessment of biodiversity conservation value needs sufficient and high-quality species occurrence data and multi-period comparison. Here, we find that the relatively well accessible wetland hydrological pattern and connectivity indexes are effective surrogates for the change detection of wetland biodiversity conservation value. This means that wetland biodiversity conservation planners can monitor the biodiversity conservation situations without resource-consuming investigations to obtain species' occurrence data and repeated prioritization of the conservation value.

Incorporating putatively neutral and adaptive genomic data into marine conservation planning

The availability of genomic data for an increasing number of species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic data can inform spatial conservation prioritization (SCP), but they focus on metrics of diversity and distinctness derived primarily from neutral genetic data sets. Identifying adaptive genetic markers can provide important information regarding the capacity for populations to adapt to environmental change. Yet, the effect of including metrics based on adaptive genomic data into SCP in comparison to more widely used neutral genetic metrics has not been explored. We used existing genomic data on a commercially exploited species, the giant California sea cucumber (Parastichopus californicus), to perform SCP for the coastal region of British Columbia (BC), Canada. Using a RAD-seq data set for 717 P. californicus individuals across 24 sampling locations, we identified putatively adaptive (i.e., candidate) single nucleotide polymorphisms (SNPs) based on genotype-environment associations with seafloor temperature. We calculated various metrics for both neutral and candidate SNPs and compared SCP outcomes with independent metrics and combinations of metrics. Priority areas varied depending on whether neutral or candidate SNPs were used and on the specific metric used. For example, targeting sites with a high frequency of warm-temperature-associated alleles to support persistence under future warming prioritized areas in the southern coastal region. In contrast, targeting sites with high expected heterozygosity at candidate loci to support persistence under future environmental uncertainty prioritized areas in the north. When combining metrics, all scenarios generated intermediate solutions, protecting sites that span latitudinal and thermal gradients. Our results demonstrate that distinguishing between neutral and adaptive markers can affect conservation solutions and emphasize the importance of defining objectives when choosing among various genomic metrics for SCP.

Using environmental and geographic data to optimize ex situ collections and preserve evolutionary potential

Maintenance of biodiversity through seed banks and botanical gardens, where the wealth of species' genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections if trade-offs exist among cost, effort, and conserving species evolutionary potential, particularly when genetic data are not available. We evaluated the genetic consequences of population preservation informed by geographic (isolation by distance [IBD]) and environmental (isolation by environment [IBE]) distance for ex situ collections for which population provenance is available. We used 19 genetic and genomic data sets from 15 plant species to assess the proportion of population genetic differentiation explained by geographic and environmental factors and to simulate ex situ collections prioritizing source populations based on pairwise geographic distance, environmental distance, or both. Specifically, we tested the impact prioritizing sampling based on these distances may have on the capture of neutral, functional, or putatively adaptive genetic diversity and differentiation. Individually, IBD and IBE explained limited population genetic differences across all 3 genetic marker classes (IBD, 10-16%; IBE, 1-5.5%). Together, they explained a substantial proportion of population genetic differences for functional (45%) and adaptive (71%) variation. Simulated ex situ collections revealed that inclusion of IBD, IBE, or both increased allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections based on environmental and geographic distance data can optimize genetic variation captured ex situ. For the vast majority of plant species for which there is no genetic information, these data are invaluable to conservation because they can guide preservation of genetic variation needed to maintain evolutionary potential within collections.

Evaluating surrogates of genetic diversity for conservation planning

Protected-area systems should conserve intraspecific genetic diversity. Because genetic data require resources to obtain, several approaches have been proposed for generating plans for protected-area systems (prioritizations) when genetic data are not available. Yet such surrogate-based approaches remain poorly tested. We evaluated the effectiveness of potential surrogate-based approaches based on microsatellite genetic data collected across the Iberian Peninsula for 7 amphibian and 3 reptilian species. Long-term environmental suitability did not effectively represent sites containing high genetic diversity (allelic richness). Prioritizations based on long-term environmental suitability had similar performance to random prioritizations. Geographic distances and resistance distances based on contemporary environmental suitability were not always effective surrogates for identification of combinations of sites that contain individuals with different genetic compositions. Our results demonstrate that population genetic data based on commonly used neutral markers can inform prioritizations, and we could not find an adequate substitute. Conservation planners need to weigh the potential benefits of genetic data against their acquisition costs.

Crop wild relatives of the United States require urgent conservation action

The contributions of crop wild relatives (CWR) to food security depend on their conservation and accessibility for use. The United States contains a diverse native flora of CWR, including those of important cereal, fruit, nut, oil, pulse, root and tuber, and vegetable crops, which may be threatened in their natural habitats and underrepresented in plant conservation repositories. To determine conservation priorities for these plants, we developed a national inventory, compiled occurrence information, modeled potential distributions, and conducted threat assessments and conservation gap analyses for 600 native taxa. We found that 7.1% of the taxa may be critically endangered in their natural habitats, 50% may be endangered, and 28% may be vulnerable. We categorized 58.8% of the taxa as of urgent priority for further action, 37% as high priority, and 4.2% as medium priority. Major ex situ conservation gaps were identified for 93.3% of the wild relatives (categorized as urgent or high priority), with 83 taxa absent from conservation repositories, while 93.1% of the plants were equivalently prioritized for further habitat protection. Various taxonomic richness hotspots across the US represent focal regions for further conservation action. Related needs include facilitating greater access to and characterization of these cultural-genetic-natural resources and raising public awareness of their existence, value, and plight.

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

BACKGROUND

As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis).

RESULTS

Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus.

CONCLUSION

The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks

Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta-analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied river systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.

Global conservation of species' niches

Environmental change is rapidly accelerating, and many species will need to adapt to survive¹. Ensuring that protected areas cover populations across a broad range of environmental conditions could safeguard the processes that lead to such adaptations^1-3. However, international conservation policies have largely neglected these considerations when setting targets for the expansion of protected areas⁴. Here we show that-of 19,937 vertebrate species globally^5-8-the representation of environmental conditions across their habitats in protected areas (hereafter, niche representation) is inadequate for 4,836 (93.1%) amphibian, 8,653 (89.5%) bird and 4,608 (90.9%) terrestrial mammal species. Expanding existing protected areas to cover these gaps would encompass 33.8% of the total land surface-exceeding the current target of 17% that has been adopted by governments. Priority locations for expanding the system of protected areas to improve niche representation occur in global biodiversity hotspots⁹, including Colombia, Papua New Guinea, South Africa and southwest China, as well as across most of the major land masses of the Earth. Conversely, we also show that planning for the expansion of protected areas without explicitly considering environmental conditions would marginally reduce the land area required to 30.7%, but that this would lead to inadequate niche representation for 7,798 (39.1%) species. As the governments of the world prepare to renegotiate global conservation targets, policymakers have the opportunity to help to maintain the adaptive potential of species by considering niche representation within protected areas^1,2.

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

Systematic conservation planning for intraspecific genetic diversity

Intraspecific diversity informs the demographic and evolutionary histories of populations, and should be a main conservation target. Although approaches exist for identifying relevant biological conservation units, attempts to identify priority conservation areas for intraspecific diversity are scarce, especially within a multi-specific framework. We used neutral molecular data on six European freshwater fish species (Squalius cephalus, Phoxinus phoxinus, Barbatula barbatula, Gobio occitaniae, Leuciscus burdigalensis and Parachondrostoma toxostoma) sampled at the riverscape scale (i.e. the Garonne-Dordogne river basin, France) to determine hot- and coldspots of genetic diversity, and to identify priority conservation areas using a systematic conservation planning approach. We demonstrate that systematic conservation planning is efficient for identifying priority areas representing a predefined part of the total genetic diversity of a whole landscape. With the exception of private allelic richness (PA), classical genetic diversity indices (allelic richness, genetic uniqueness) were poor predictors for identifying priority areas. Moreover, we identified weak surrogacies among conservation solutions found for each species, implying that conservation solutions are highly species-specific. Nonetheless, we showed that priority areas identified using intraspecific genetic data from multiple species provide more effective conservation solutions than areas identified for single species or on the basis of traditional taxonomic criteria.

Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus)

Background

Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents impacting the physiology of organisms. With one of the highest salinity level, the Mediterranean Sea provides an excellent model to investigate adaptive genomic divergence underlying salinity adaptation. In the present study, we combined six genome scan methods to detect potential genomic signal of selection in the striped red mullet (Mullus surmuletus) populations distributed across a wide salinity gradient. We then blasted these outlier sequences on published fish genomic resources in order to identify relevant potential candidate genes for salinity adaptation in this species.

Results

Altogether, the six genome scan methods found 173 outliers out of 1153 SNPs. Using a blast approach, we discovered four candidate SNPs belonging to three genes potentially implicated in adaptation of M. surmuletus to salinity. The allele frequency at one of these SNPs significantly increases with salinity independently from the effect of longitude. The gene associated to this SNP, SOCS2, encodes for an inhibitor of cytokine and has previously been shown to be expressed under osmotic pressure in other marine organisms. Additionally, our results showed that genome scan methods not correcting for spatial structure can still be an efficient strategy to detect potential footprints of selection, when the spatial and environmental variation are confounded, and then, correcting for spatial structure in a second step represents a conservative method.

Conclusion

The present outcomes bring evidences of potential genomic footprint of selection, which suggest an adaptive response of M. surmuletus to salinity conditions in the Mediterranean Sea. Additional genomic data such as sequencing of a full-genome and transcriptome analyses of gene expression would provide new insights regarding the possibility that some striped red mullet populations are locally adapted to their saline environment.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4579-z) contains supplementary material, which is available to authorized users.