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

Wastewater and warming effects on aquatic invertebrates: Experimental insights into multi-level biodiversity consequences

Wastewater effluents and global warming affect freshwater ecosystems and impact their crucial biodiversity. Our study aimed at characterizing individual and combined impacts of wastewater effluent and increased water temperature (as one aspect of climate change) on model freshwater communities. We tested the effect of experimental treatments on genetic diversity, survival, body weight, total lipid content, lipidome and metabolome of individual species as well as community composition and phylogenetic diversity. In a 21-day mesocosm experiment we assessed the responses of a simplified freshwater food web comprising of moss and seven species of benthic macroinvertebrate shredders and grazers (mayflies, stoneflies, caddisflies and amphipods) to four treatments in a full factorial design: control, increased water temperature, wastewater and a multiple stressor treatment combining increased temperature and wastewater. Physiological responses varied among taxa, with species-specific sensitivities observed in survival and lipid content. The lowest total lipid content was observed in caddisflies and a mayfly subjected to multiple stressor treatment. The effects of stressors were reflected in the altered metabolic pathways and lipid metabolism of the individual taxa, with differential treatment effects also observed between taxa. A notable decrease in phylogenetic diversity was observed across all experimental communities. Gammarus fossarum demonstrated a high susceptibility to environmental stressors at the genetic level. Hence, while commonly used indicators of ecosystem health (e.g. community composition) remained stable, molecular indicators (e.g. phylogenetic diversity, metabolome and lipidome) responded readily to experimental treatments. These findings underscore the vulnerability of macroinvertebrates to environmental stressors, even over relatively short exposure periods. They highlight the importance of molecular indicators in detecting immediate ecological impacts, offering valuable information for conservation strategies and understanding the ecological consequences in freshwater ecosystems.

Highly clustered mating networks in naturally fragmented riparian tree populations

Understanding how spatial patterns of mating and gene flow respond to habitat loss and geographical isolation is a crucial aspect of forest fragmentation genetics. Naturally fragmented riparian tree populations exhibit unique characteristics that significantly influence these patterns. In this study, we investigate mating patterns, pollen-mediated gene flow, and genetic diversity in relict populations of Frangula alnus in southern Spain by testing specific hypotheses related to the riparian habitat. We employ a novel approach that combines paternity analysis, particularly suited for small and isolated populations, with complex network theory and Bayesian models to predict mating likelihood among tree pairs. Our findings reveal a prevalence of short-distance pollination, resulting in spatially driven local mating clusters with a distinct subset of trees being highly connected in the mating network. Additionally, we observe numerous pollination events over distances of hundreds of metres and considerable pollen immigration. Local neighbourhood density is the primary factor influencing within-population mating patterns and pollen dispersal; moreover, mating network properties reflect the population's size and spatial configuration. Conversely, among-population pollen dispersal is mainly determined by tree size, which influences floral display. Our results do not support a major role of directional pollen dispersal in longitudinal trends of genetic diversity. We provide evidence that long-term fragmented tree populations persist in unique environments that shape mating patterns and impose constraints to pollen-mediated gene flow. Nevertheless, even seemingly strongly isolated populations can maintain functional connectivity over extended periods, especially when animal-mediated mating networks promote genetic diversity, as in this riparian tree species.

Riverscape community genomics: A comparative analytical approach to identify common drivers of spatial structure

Genetic differentiation among local groups of individuals, that is, genetic β-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic β-diversity within and among many species and demonstrate how this riverscape community genomics approach can be applied to identify common drivers of genetic structure. Our study evaluated genetic β-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N = 24) were partitioned into discrete subpopulations (K = 2-7). We used partial redundancy analysis to compare species-specific genetic β-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x̄ = 62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the stream hierarchy model. We discuss our conclusions regarding conservation and management and identify the 8-digit hydrologic unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.

Comparative landscape genomics has arrived with a splash

Comparative methods are central for understanding the distribution of biodiversity. Assessing spatial variation of multiple species can identify biodiversity drivers across landscapes, including on the genetic level. Molecular ecology approaches have expanded in spatial precision, from phylogeography to landscape genetics, as have molecular tools that now allow genome-scale inferences for virtually any organism. These welcome increases in genomic data richness, however, have not been matched by growth in the multispecies dimension, and empirical studies continue to focus predominantly on single species. In this issue of Molecular Ecology, Zbinden et al. (Molecular Ecology, 2022, 32) present a landmark achievement for comparative landscape genomics, surveying an impressive 31 species of fishes, sampled from 75 locations in the White River Basin and genotyping each species for thousands of SNPs. Zbinden et al. (Molecular Ecology, 2022, 32) draw upon the statistical tools of landscape genetics to comprehensively interrogate four hypotheses-that populations of multiple freshwater fish species are isolated by river distance, barriers to dispersal, stream hierarchy or environment. Stream hierarchy overwhelmingly predicts population structure within co-distributed fish species pointing to commonalities among species at the large landscape scale (100s of km). The tight alignment between intraspecific genetic spatial structure and stream hierarchies, moreover, provides clear validation for conservation and fisheries management to use watershed divisions as distinct management units.

Fish germ cell cryobanking and transplanting for conservation

The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond.

Importance of timely metadata curation to the global surveillance of genetic diversity

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.

Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value

Spatial patterns of genetic variation compared across species provide information about the predictability of genetic diversity in natural populations, and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni- a major river system from the Guiana Shield -, to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, the mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as gold mining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow, and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.

Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish

To conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence. We found that neutral genetic population structure was largely explainable by restricted gene flow among drainages. However, environmental associations revealed that ecological variables had a similar power to explain overall genetic variation, and greater power to explain body shape variation, than the included neutral covariables. Hydrological and thermal variables were the strongest environmental predictors and were correlated with traits previously linked to heritable habitat-associated dimorphism in rainbowfishes. In addition, climate-associated genetic variation was significantly associated with morphology, supporting heritability of shape variation. These results support the inference of evolved functional differences among localities, and the importance of hydroclimate in early stages of diversification. We expect that substantial evolutionary responses will be required in tropical rainforest endemics to mitigate local fitness losses due to changing climates.

Phenotypic variation among silverside populations (Atherinopsidae: Atherinella brasiliensis) from distinct environments in Northeastern Brazil

The successful adaptation of populations to a wide range of environments is a central topic in ecology. Based on the assumption that body shape may affect survival, we evaluated to what extent biotic and abiotic factors are capable of inducing morphological changes in Brazilian silverside populations (Atherinella brasiliensis). To reach this goal, we compared 18 morphological traits of specimens from five ecosystems representing three types of environment (estuary, coastal lagoon, reservoir). Populations from estuaries displayed greater anal fin area and greater caudal fin aspect ratio and area. Populations from coastal lagoons had more compressed bodies, larger heads, and slightly broader caudal peduncles. The fish from estuaries and coastal lagoons had longer caudal peduncles, larger pelvic fins and larger eye area. Population from reservoir had more depressed bodies and greater oral protrusion. Food availability explained 31% of the observed ecomorphological patterns. Overall, the morphology of the respective populations was consistent with each type of environment, making it possible to associate phenotypic variation with habitat and feeding patterns, although abiotic factors were more significant than biotic factors. In conclusion, landlocked populations of A. brasiliensis are sustainable and add to current knowledge of phenotypical variability in a species widely distributed along the Western Atlantic coast.

Spatial Variations and Influencing Factors of River Networks in River Basins of China

Analysis of the spatial variations in river networks and the related influencing factors is crucial for the management and protection of basins. To gain insight into the spatial variations and influencing factors of river networks between large basins, in this study, three river basins from north to south in China (Songhua River Basin, Yellow River Basin and Pearl River Basin) were selected for investigation. First, based on a digital elevation model, different river networks with six drainage accumulation thresholds of three basins were extracted using ArcGIS. The optimal networks were determined through fitting the relationship between the accumulation threshold and related drainage density. Then, we used two indicators, drainage density and water surface ratio, to characterize the spatial variations of three basins. Finally, Pearson’s correlation coefficients were calculated between those two indicators and natural/human influencing factors. The results showed that drainage density and water surface ratio decreased from north to south in China and were negatively correlated with natural/human influencing factors. Drainage density was more influenced by natural factors than by human factors, while the opposite was true for water surface ratio. These findings may provide some basis for the management and protection of the river network.

A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded insightful results for conservation.

Dispersal behaviour and riverine network connectivity shape the genetic diversity of freshwater amphipod metapopulations

Theory predicts that the distribution of genetic diversity in a landscape is strongly dependent on the connectivity of the metapopulation and the dispersal of individuals between patches. However, the influence of explicit spatial configurations such as dendritic landscapes on the genetic diversity of metapopulations is still understudied, and theoretical corroborations of empirical patterns are largely lacking. Here, we used microsatellite data and stochastic simulations of two metapopulations of freshwater amphipods in a 28,000 km² riverine network to study the influence of spatial connectivity and dispersal strategies on the spatial distribution of their genetic diversity. We found a significant imprint of the effects of riverine network connectivity on the local and global genetic diversity of both amphipod species. Data from 95 sites showed that allelic richness significantly increased towards more central nodes of the network. This was also seen for observed heterozygosity, yet not for expected heterozygosity. Genetic differentiation increased with instream distance. In simulation models, depending on the mutational model assumed, upstream movement probability and dispersal rate, respectively, emerged as key factors explaining the empirically observed distribution of local genetic diversity and genetic differentiation. Surprisingly, the role of site‐specific carrying capacities, for example by assuming a direct dependency of population size on local river size, was less clear cut: while our best fitting model scenario included this feature, over all simulations, scaling of carrying capacities did not increase data‐model fit. This highlights the importance of dispersal behaviour along spatial networks in shaping population genetic diversity.

Opportunities and challenges of macrogenetic studies

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.

Charting a course for genetic diversity in the UN Decade of Ocean Science

The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.

The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead (Oncorhynchus mykiss) Populations across the Elwha River Watershed

Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers.

By Animal, Water, or Wind: Can Dispersal Mode Predict Genetic Connectivity in Riverine Plant Species?

Seed dispersal is crucial to gene flow among plant populations. Although the effects of geographic distance and barriers to gene flow are well studied in many systems, it is unclear how seed dispersal mediates gene flow in conjunction with interacting effects of geographic distance and barriers. To test whether distinct seed dispersal modes (i.e., hydrochory, anemochory, and zoochory) have a consistent effect on the level of genetic connectivity (i.e., gene flow) among populations of riverine plant species, we used unlinked single-nucleotide polymorphisms (SNPs) for eight co-distributed plant species sampled across the Rio Branco, a putative biogeographic barrier in the Amazon basin. We found that animal-dispersed plant species exhibited higher levels of genetic diversity and lack of inbreeding as a result of the stronger genetic connectivity than plant species whose seeds are dispersed by water or wind. Interestingly, our results also indicated that the Rio Branco facilitates gene dispersal for all plant species analyzed, irrespective of their mode of dispersal. Even at a small spatial scale, our findings suggest that ecology rather than geography play a key role in shaping the evolutionary history of plants in the Amazon basin. These results may help improve conservation and management policies in Amazonian riparian forests, where degradation and deforestation rates are high.