The importance of genomic variation for biodiversity, ecosystems and people

BR signalling haplotypes contribute to indica-japonica differentiation for grain yield and quality in rice

The functional difference of natural variations in conserved BR signalling genes and the genetic basis of rice indica-japonica differentiation are important yet unknown. Here, we discovered natural variations of the four key components (OsBRI1, OsBAK1, OsGSK3 and OsBZR1) in BR signalling pathway by GWAS using an indicator of indica-japonica differentiation in rice. Two major BR signalling haplotypes (BSHs), caused by co-selected variations of the four genetically unlinked genes, were identified to be highly differentiated between rice subspecies. The genetic contributions of BSHs to grain yield and quality were much higher than that of each component. Introducing alleles of japonica into indica employing substitution lines of OsBAK1, complementation lines of OsGSK3 and genetic populations of OsBRI1/OsBAK1/OsGSK3 confirmed their functional differences between two subspecies. The BSH differentiation led to weaker interaction between OsBRI1 and OsBAK1, stronger autophosphorylation and kinase activity of OsGSK3, less RNA/proteins and stronger phosphorylation of OsBZR1, and weaker BR sensitivity in indica than japonica rice, and regular expression trends of BR-response genes between subspecies, and then synergistically enhanced yield and superior quality of indica. Our results demonstrate that BSHs contribute to rice inter-subspecies diversity, and will provide proof-of-concept breeding strategy and useful targets in crops.

Satellite-observed mountain greening predicts genomic erosion in a grassland medicinal herb over half a century

Mountains are biodiversity hotspots contributing essential benefits to human societies, but global environmental change is rapidly altering their habitats. During the past five decades, increasing temperatures and land-use change in montane and subalpine elevations facilitated the productivity and expansion of competitive vegetation, termed as "greening," with adverse effects on open grassland habitats. Although vegetation greening is well-documented through satellite observations, its impact on the populations and genomic integrity of affected species remains underexplored. Here, we address this challenge by integrating 40 years of remote sensing data with museum genomics and fieldwork to assess the impact of mountain greening on the genomic diversity of grassland plants in the southern Balkan peninsula. We sequenced the genomes of historical and modern populations of Ironwort, a plant of significant medicinal value, and demonstrate widespread genomic erosion across its populations. Our results show that, on average, 6% (0%-20%) of Ironwort's genome is affected by inbreeding accumulation over the past half century, indicating various degrees of population declines. Importantly, we show that genomic erosion is highly predictable by the normalized difference vegetation index (NDVI) rates of change. Our models suggest that faster increases in vegetation density are associated with higher population declines in this grassland species, revealing the negative impacts of increasing productivity in mountain ecosystems. By linking two independent and disparate monitoring indicators, we demonstrate the ability of remote sensing to predict the consequences of environmental change on temporal genomic change in mountain grassland species, with far-reaching implications for protecting natural resources in these fragile ecosystems.

The Anthropocene and the biodiversity crisis: an eco-evolutionary perspective

A major facet of the Anthropocene is global change, such as climate change, caused by human activities, which drastically affect biodiversity with all-scale declines and homogenization of biotas. This crisis does not only affect the ecological dynamics of biodiversity, but also its evolutionary dynamics, including genetic diversity, an aspect that is generally neglected. My tenet is therefore to consider biodiversity dynamics from an eco-evolutionary perspective, i.e. explicitly accounting for the possibility of rapid evolution and its feedback on ecological processes and the environment. I represent the impact of the various avatars of global change in a temporal perspective, from pre-industrial time to the near future, allowing to visualize their dynamics and to set desired values that should not be trespassed for a given time (e.g., +2 °C for 50 years from now). After presenting the impact of various stressors (e.g., climate change) on biodiversity, this representation is used to heuristically show the relevance of an eco-evolutionary perspective: (i) to analyze how biodiversity will respond to the stressors, for example by seeking out more suitable conditions or adapting to new conditions; (ii) to serve in predictive exercises to envision future dynamics (decades to centuries) under stressor impact; (iii) to propose nature-based solutions to the crisis. Significant obstacles stand in the way of the development of such an approach, in particular the general lack of interest in intraspecific diversity, and perhaps more generally a lack of understanding that, we, humans, are only a modest part of biodiversity.

How can biodiversity strategy and action plans incorporate genetic diversity and align with global commitments?

National, subnational, and supranational entities are creating biodiversity strategy and action plans (BSAPs) to develop concrete commitments and actions to curb biodiversity loss, meet international obligations, and achieve a society in harmony with nature. In light of policymakers' increasing recognition of genetic diversity in species and ecosystem adaptation and resilience, this article provides an overview of how BSAPs can incorporate species' genetic diversity. We focus on three areas: setting targets; committing to actions, policies, and programs; and monitoring and reporting. Drawing from 21 recent BSAPs, we provide examples of policies, knowledge, projects, capacity building, and more. We aim to enable and inspire specific and ambitious BSAPs and have put forward 10 key suggestions mapped to the policy cycle. Together, scientists and policymakers can translate high level commitments, such as the Convention on Biological Diversity's Kunming-Montreal Global Biodiversity Framework, into concrete nationally relevant targets, actions and policies, and monitoring and reporting mechanisms.

A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity

Biodiversity is under pressure, mainly due to human activities and climate change. At the international policy level, it is now recognised that genetic diversity is an important part of biodiversity. The availability of high-quality reference genomes gives the best basis for using genetics and genetic diversity towards the global aims of (1) the protection of species, biodiversity, and nature, and (2) the management of biodiversity for achieving sustainable harvesting of nature. Protecting biodiversity is a global responsibility, also resting on small nations, like the Faroe Islands. Being in the middle of the North Atlantic Ocean and having large fisheries activity, the nation has a particular responsibility towards maritime matters. We here provide the reasoning behind the Genome Atlas of Faroese Ecology (Gen@FarE), a project based on our participation in the European Reference Genome Atlas consortium (ERGA). Gen@FarE has three major aims: (1) To acquire high-quality genomes of all eukaryotic species in the Faroe Islands and Faroese waters. (2) To establish population genetics for species of commercial or ecological interest. (3) To establish an information databank for all Faroese species, combined with a citizen science registration database, making it possible for the public to participate in acquiring and maintaining the overview of Faroese species in both terrestrial and marine environments. Altogether, we believe that this will enhance the society's interest in and awareness of biodiversity, thereby protecting the foundations of our lives. Furthermore, the combination of a wide and highly competent ERGA umbrella and more targeted national projects will help fulfil the formal and moral responsibilities that all nations, also those with limited resources, have in protecting biodiversity and achieving sustainability in harvesting from nature.

Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of positive or negative effects of mixed planting on plant resistance, respectively called associational resistance or susceptibility. Here, we identify key genotype pairs responsible for associational resistance to herbivory using the genome-wide polymorphism data of the plant species Arabidopsis thaliana. To quantify neighbor interactions among 199 genotypes grown in a randomized block design, we employ a genome-wide association method named "Neighbor GWAS" and genomic prediction inspired by the Ising model of magnetics. These analyses predict that 823 of the 19,701 candidate pairs can reduce herbivory in mixed planting. We planted three pairs with the predicted effects in mixtures and monocultures, and detected 18-30% reductions in herbivore damage in the mixed planting treatment. Our study shows the power of genomic prediction to assemble genotype mixtures with positive biodiversity effects.

Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)

BACKGROUND

Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.

RESULTS

Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.

CONCLUSIONS

The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.

Improving the Meat and Meat Product Quality of Rare Pork Breeds and Genetic Types

Pork is the most consumed meat globally, particularly in Asia, Europe, and America [...].

Guiding seed movement: environmental heterogeneity drives genetic differentiation in Plathymenia reticulata, providing insights for restoration

Forest and landscape restoration is one of the main strategies for overcoming the environmental crisis. This activity is particularly relevant for biodiversity-rich areas threatened by deforestation, such as tropical forests. Efficient long-term restoration requires understanding the composition and genetic structure of native populations, as well as the factors that influence these genetic components. This is because these populations serve as the seed sources and, therefore, the gene reservoirs for areas under restoration. In the present study, we investigated the influence of environmental, climatic and spatial distance factors on the genetic patterns of Plathymenia reticulata, aiming to support seed translocation strategies for restoration areas. We collected plant samples from nine populations of P. reticulata in the state of Bahia, Brazil, located in areas of Atlantic Forest and Savanna, across four climatic types, and genotyped them using nine nuclear and three chloroplast microsatellite markers. The populations of P. reticulata evaluated generally showed low to moderate genotypic variability and low haplotypic diversity. The populations within the Savanna phytophysiognomy showed values above average for six of the eight evaluated genetic diversity parameters. Using this classification based on phytophysiognomy demonstrated a high predictive power for genetic differentiation in P. reticulata. Furthermore, the interplay of climate, soil and geographic distance influenced the spread of alleles across the landscape. Based on our findings, we propose seed translocation, taking into account the biome, with restricted use of seed sources acquired or collected from the same environment as the areas to be restored (Savanna or Atlantic Forest).

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Evaluating the role of rhizosphere microbial home-field advantage in Betula luminifera adaptation to antimony mining areas

It has been established that the coevolution of plants and the rhizosphere microbiome in response to abiotic stress can result in the recruitment of specific functional microbiomes. However, the potential of inoculated rhizosphere microbiomes to enhance plant fitness and the inheritance of adaptive traits in subsequent generations remains unclear. In this study, cross-inoculation trials were conducted using seeds, rhizosphere microbiome, and in situ soil collected from areas of Betula luminifera grown in both antimony mining and control sites. Compared to the control site, plants originating from mining areas exhibited stronger adaptive traits, specifically manifested as significant increases in hundred-seed weight, specific surface area, and germination rate, as well as markedly enhanced seedling survival rate and biomass. Inoculation with mining microbiomes could enhance the fitness of plants in mining sites through a "home-field advantage" while also improving the fitness of plants originating from control sites. During the initial phase of seedling development, bacteria play a crucial role in promoting growth, primarily due to their mechanisms of metal resistance and nutrient cycling. This study provided evidence that the outcomes of long-term coevolution between plants and the rhizosphere microbiome in mining areas can be passed on to future generations. Moreover, it has been demonstrated that transgenerational inheritance and rhizosphere microbiome inoculation are important factors in improving the adaptability of plants in mining areas. The findings have important implications for vegetation restoration and ecological environment improvement in mining areas.

Complete Chloroplast Genomes of Four Oaks from the Section Cyclobalanopsis Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus Quercus

Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ-trnG-GCC, rbcL-accD, and rpl32-trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.

Hierarchical eco-evo dynamics mediated by the gut microbiome

The concept of eco-evolutionary (eco-evo) dynamics, stating that ecological and evolutionary processes occur at similar time scales and influence each other, has contributed to our understanding of responses of populations, communities, and ecosystems to environmental change. Phenotypes, central to these eco-evo processes, can be strongly impacted by the gut microbiome. The gut microbiome shapes eco-evo dynamics in the host community through its effects on the host phenotype. Complex eco-evo feedback loops between the gut microbiome and the host communities might thus be common. Bottom-up dynamics occur when eco-evo interactions shaping the gut microbiome affect host phenotypes with consequences at population, community, and ecosystem levels. Top-down dynamics occur when eco-evo dynamics shaping the host community structure the gut microbiome.

Quantifying interspecific and intraspecific diversity effects on ecosystem functioning

Rapid environmental changes result in massive biodiversity loss, with detrimental consequences for the functioning of ecosystems. Recent studies suggest that intraspecific diversity can contribute to ecosystem functioning to an extent comparable to contributions of interspecific diversity. Knowledge on the relative importance of these two sources of biodiversity is essential for predicting ecosystem consequences of biodiversity loss and will aid in the prioritization of conservation targets and implementation of management measures. However, our quantitative insights into how interspecific and intraspecific biodiversity loss affects ecosystem functioning and how the effects of these two sources of biodiversity loss on ecosystem functioning can be compared are still very limited. To facilitate such quantitative insights, we extend the interspecific Price partitioning method originally introduced by J. Fox in 2006, previously used to quantify species loss and gain effects on ecosystem functioning, to also account for the effects of intraspecific diversity loss and gain on ecosystem function. Using this extended version can yield the quantitative information required for answering research questions addressing correlations between interspecific and intraspecific diversity effects on ecosystem functioning, identifying interspecific and intraspecific groups with large effects, and assessing whether intraspecific diversity can compensate for losses in interspecific diversity. Applying this method to carefully designed experiments will provide additional insights into how biodiversity loss at different ecological levels contributes to and changes ecosystem functioning.

Performance analysis of conventional and AI-based variant callers using short and long reads

BACKGROUND

The accurate detection of variants is essential for genomics-based studies. Currently, there are various tools designed to detect genomic variants, however, it has always been a challenge to decide which tool to use, especially when various major genome projects have chosen to use different tools. Thus far, most of the existing tools were mainly developed to work on short-read data (i.e., Illumina); however, other sequencing technologies (e.g. PacBio, and Oxford Nanopore) have recently shown that they can also be used for variant calling. In addition, with the emergence of artificial intelligence (AI)-based variant calling tools, there is a pressing need to compare these tools in terms of efficiency, accuracy, computational power, and ease of use.

RESULTS

In this study, we evaluated five of the most widely used conventional and AI-based variant calling tools (BCFTools, GATK4, Platypus, DNAscope, and DeepVariant) in terms of accuracy and computational cost using both short-read and long-read data derived from three different sequencing technologies (Illumina, PacBio HiFi, and ONT) for the same set of samples from the Genome In A Bottle project. The analysis showed that AI-based variant calling tools supersede conventional ones for calling SNVs and INDELs using both long and short reads in most aspects. In addition, we demonstrate the advantages and drawbacks of each tool while ranking them in each aspect of these comparisons.

CONCLUSION

This study provides best practices for variant calling using AI-based and conventional variant callers with different types of sequencing data.

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

BACKGROUND

Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet, comprising two monozygotic twin daughters and their biological parents, using four short and long sequencing platforms (Illumina, BGI, PacBio, and Oxford Nanopore Technology).

RESULTS

The long reads from the monozygotic twin daughters are phased into paternal and maternal haplotypes using the parent-child genetic map and for each haplotype. We also use long reads to generate haplotype-resolved whole-genome assemblies with completeness and continuity exceeding that of GRCh38. Using this Quartet, we comprehensively catalogue the human variant landscape, generating a dataset of 3,962,453 SNVs, 886,648 indels (< 50 bp), 9726 large deletions (≥ 50 bp), 15,600 large insertions (≥ 50 bp), 40 inversions, 31 complex structural variants, and 68 de novo mutations which are shared between the monozygotic twin daughters. Variants underrepresented in previous benchmarks owing to their complexity-including those located at long repeat regions, complex structural variants, and de novo mutations-are systematically examined in this study.

CONCLUSIONS

In summary, this study provides high-quality haplotype-resolved assemblies and a comprehensive set of benchmarking resources for two Chinese monozygotic twin samples which, relative to existing benchmarks, offers expanded genomic coverage and insight into complex variant categories.

Human Impacts on the Vegetation of the Juan Fernández (Robinson Crusoe) Archipelago

The human footprint on marine and terrestrial ecosystems of the planet has been substantial, largely due to the increase in the human population with associated activities and resource utilization. Oceanic islands have been particularly susceptible to such pressures, resulting in high levels of loss of biodiversity and reductions in the numbers and sizes of wild populations. One archipelago that has suffered from human impact has been the Juan Fernández (Robinson Crusoe) Archipelago, a Chilean national park located 667 km west of Valparaíso at 33° S. latitude. The park consists of three principal islands: Robinson Crusoe Island (48 km2); Santa Clara Island (2.2 km2); and Alejandro Selkirk Island (50 km2). The latter island lies 181 kms further west into the Pacific Ocean. No indigenous peoples ever visited or lived on any of these islands; they were first discovered by the Spanish navigator, Juan Fernández, in 1574. From that point onward, a series of European visitors arrived, especially to Robinson Crusoe Island. They began to cut the forests, and such activity increased with the establishment of a permanent colony in 1750 that has persisted to the present day. Pressures on the native and endemic flora increased due to the introduction of animals, such as goats, rats, dogs, cats, pigs, and rabbits. Numerous invasive plants also arrived, some deliberately introduced and others arriving inadvertently. At present, more than three-quarters of the endemic and native vascular species of the flora are either threatened or endangered. The loss of vegetation has also resulted in a loss of genetic variability in some species as populations are reduced in size or go extinct. It is critical that the remaining genetic diversity be conserved, and genomic markers would provide guidelines for the conservation of the diversity of the endemic flora. To preserve the unique flora of these islands, further conservation measures are needed, especially in education and phytosanitary monitoring.

Biodiversity of Indonesian indigenous buffalo: First review of the status, challenges, and development opportunities

In Indonesia, the buffalo is important for small and marginal farmers' livelihood and economic development as a source of food, working animal, and tourist attraction. Therefore, an in-depth study is needed to examine challenges and opportunities for buffalo development in Indonesia. In Indonesia, the buffalo is divided into two types: swamp buffalo and river buffalo. The buffalo population in Indonesia has declined significantly. A decrease of approximately 39.35% was recorded from 2022 to 2017. The decline occurred due to low reproduction rate and suboptimal rearing management systems. There are three buffalo-rearing systems: Intensive, semi-intensive, and extensive. The productivity of buffalo is diverse and closely related to the characteristics of the regional agroecosystem, consistent with existing natural resources and rearing management systems. The diversity of buffalo productivity provides a good opportunity to improve productivity. Improvement of buffalo genetics is urgently needed, by improving mating management, etc., especially to reduce potential inbreeding. In recent years, genetic and molecular research on Indonesian buffalo has made progress, including use of molecular markers, such as microsatellites and single-nucleotide polymorphisms, to evaluate genetic diversity within and among buffalo populations across Indonesia. In addition, studies are being conducted on the relationship of genotype mutations that contribute to appearance and phenotypic performance (heat stress, reproduction, behavior, coat color, and production attributes) in buffaloes. Identification of genetic diversity in local buffaloes can be improved using various genetic and genomic techniques. These findings will form a basis for the targeted conservation of local buffaloes in Indonesia. This study aimed to collect information on the genetic resources of the local buffalo, particularly its status and production system and provide recommendations for developing buffalo production in Indonesia.

Revisiting the Role of Genetic Variation in Adaptation

AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.

Two-level Bayesian interaction analysis for survival data incorporating pathway information

Genetic interactions play an important role in the progression of complex diseases, providing explanation of variations in disease phenotype missed by main genetic effects. Comparatively, there are fewer studies on survival time, given its challenging characteristics such as censoring. In recent biomedical research, two-level analysis of both genes and their involved pathways has received much attention and been demonstrated as more effective than single-level analysis. However, such analysis is usually limited to main effects. Pathways are not isolated, and their interactions have also been suggested to have important contributions to the prognosis of complex diseases. In this paper, we develop a novel two-level Bayesian interaction analysis approach for survival data. This approach is the first to conduct the analysis of lower-level gene-gene interactions and higher-level pathway-pathway interactions simultaneously. Significantly advancing from the existing Bayesian studies based on the Markov Chain Monte Carlo (MCMC) technique, we propose a variational inference framework based on the accelerated failure time model with effective priors to accommodate two-level selection as well as censoring. Its computational efficiency is much desirable for high-dimensional interaction analysis. We examine performance of the proposed approach using extensive simulation. The application to TCGA melanoma and lung adenocarcinoma data leads to biologically sensible findings with satisfactory prediction accuracy and selection stability.

Contemporary changes in phenotypic variation, and the potential consequences for eco-evolutionary dynamics

Most studies assessing rates of phenotypic change focus on population mean trait values, whereas a largely overlooked additional component is changes in population trait variation. Theoretically, eco-evolutionary dynamics mediated by such changes in trait variation could be as important as those mediated by changes in trait means. To date, however, no study has comprehensively summarised how phenotypic variation is changing in contemporary populations. Here, we explore four questions using a large database: How do changes in trait variances compare to changes in trait means? Do different human disturbances have different effects on trait variance? Do different trait types have different effects on changes in trait variance? Do studies that established a genetic basis for trait change show different patterns from those that did not? We find that changes in variation are typically small; yet we also see some very large changes associated with particular disturbances or trait types. We close by interpreting and discussing the implications of our findings in the context of eco-evolutionary studies.

Global determinants of insect mitochondrial genetic diversity

Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.

Understanding and applying biological resilience, from genes to ecosystems

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand 'biological resilience', or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience.

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

Evaluation of the Ecological Environment Affected by Cry1Ah1 in Poplar

Populus is a genus of globally significant plantation trees used widely in industrial and agricultural production. Poplars are easily damaged by Micromelalopha troglodyta and Hyphantria cunea, resulting in decreasing quality. Bt toxin-encoded by the Cry gene has been widely adopted in poplar breeding because of its strong insect resistance. There is still no comprehensive and sufficient information about the effects of Cry1Ah1-modified (CM) poplars on the ecological environment. Here, we sampled the rhizosphere soils of field-grown CM and non-transgenic (NT) poplars and applied 16S rRNA and internal transcribed spacer amplicon Illumina MiSeq sequencing to determine the bacterial community associated with the CM and NT poplars. Based on the high-throughput sequencing of samples, we found that the predominant taxa included Proteobacteria (about 40% of the total bacteria), Acidobacteria (about 20% of the total bacteria), and Actinobacteria (about 20% of the total bacteria) collected from the natural rhizosphere of NT and CM poplars. In addition, studies on the microbial diversity of poplar showed that Cry1Ah1 expression has no significant influence on rhizosphere soil alkaline nitrogen, but significantly affects soil phosphorus, soil microbial biomass nitrogen, and carbon. The results exhibited a similar bacterial community structure between CM varieties affected by the expression of Cry1Ah1 and non-transgenic poplars. In addition, Cry1Ah1 expression revealed no significant influence on the composition of rhizosphere microbiomes. These results broadly reflect the effect of the Bt toxin-encoded by Cry1Ah1 on the ecology and environment and provide a clear path for researchers to continue research in this field in the future.

Species and genetic diversity relationships in benthic macroinvertebrate communities along a salinity gradient

BACKGROUND

Species- and genetic diversity can change in parallel, resulting in a species-genetic diversity correlation (SGDC) and raising the question if the same drivers influence both biological levels of diversity. The SGDC can be either positive or negative, depending on whether the species diversity and the genetic diversity of the measured species respond in the same or opposite way to drivers. Using a traditional species diversity approach together with ultra-conserved elements and high throughput sequencing, we evaluated the SGDCs in benthic macrofauna communities in the Baltic Sea, a geologically young brackish water sea characterised by its steep salinity gradient and low species richness. Assessing SGDCs from six focal marine invertebrate species from different taxonomic groups and with differing life histories and ecological functions on both a spatial and temporal scale gives a more comprehensive insight into the community dynamics of this young ecosystem and the extrinsic factors that might drive the SGDCs.

RESULTS

No significant correlations between species diversity and genetic diversity were found for any of the focal species. However, both negative and positive trends of SGDCs for the individual focal species were observed. When examining the environmental drivers, no common trends between the species were found, even when restricting the analysis to specific taxonomic classes. Additionally, there were no common environmental factors driving the diversity relationships for species sharing the same SGDC trend (positive or negative). Local population dynamics, together with the invasion history of the individual species and their unique adaptation to the distinctive environment of the Baltic Sea, are expected to be of major influence on the outcome of the SGDCs.

CONCLUSIONS

The present results highlight the importance of assessing SGDCs using multiple species, not just a single indicator species. This emphasises a need to pay attention to the ecology and life history of the focal species. This study also provides insight into the large differences in both patterns and drivers of genetic diversity, which is important when including genetic biodiversity in conservation plans. We conclude that the effects of environmental and biological factors and processes that affects diversity patterns at both the community and genetic levels are likely species dependent, even in an environment such as the Baltic Sea with strong environmental gradients.

Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction

Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations.

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen-particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same study system-suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.

A keystone gene underlies the persistence of an experimental food web

Genes encode information that determines an organism's fitness. Yet we know little about whether genes of one species influence the persistence of interacting species in an ecological community. Here, we experimentally tested the effect of three plant defense genes on the persistence of an insect food web and found that a single allele at a single gene promoted coexistence by increasing plant growth rate, which in turn increased the intrinsic growth rates of species across multiple trophic levels. Our discovery of a "keystone gene" illustrates the need to bridge between biological scales, from genes to ecosystems, to understand community persistence.

Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change

BACKGROUND

Understanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations.

RESULTS

Marked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species.

CONCLUSION

Our results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change.

Genetic Diversity on a Rare Terrestrial Orchid, Habenaria linearifolia in South Korea: Implications for Conservation Offered by Genome-Wide Single Nucleotide Polymorphisms

Monitoring intraspecific diversity offers invaluable insights on conservation practices as the variation is the product of species evolution. Accordingly, the role of population genetic diversity has drawn great attention over the last century responding to the biodiversity loss induced by a series of anthropogenic changes. Orchids are one of the most diverse, yet ironically most rapidly disappearing plant groups due to the specialized habitat preferences. Thus, population-level genetic diversity studies may offer a powerful tool for orchid conservation programs. Using the 3 restriction site-associated DNA (3RAD) approach, 2,734 genome-wide single nucleotide polymorphisms (SNPs) were isolated. With the 2,734 SNPs, we investigated genetic diversity and population structure on 72 individuals of Habenaria linearifolia and Habenaria cruciformis in South Korea. Overall, the genetic diversity was well maintained in South Korean Habenaria, but high F _ST values were estimated suggesting large population diversification with limited gene flow. Bayesian assignment analysis revealed a morphologically cryptic diversity pattern in Jeju Island populations, which might serve as an evolutionarily significant unit.

Darwinian genomics and diversity in the tree of life

Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and established laboratory models. Fewer than 18,000 of ∼2,000,000 eukaryotic species (<1%) have a representative genome sequence in GenBank, and only a fraction of these have ancillary information on genome structure, genetic variation, gene expression, epigenetic modifications, and population diversity. This imbalance reflects a perception that human studies are paramount in disease research. Yet understanding how genomes work, and how genetic variation shapes phenotypes, requires a broad view that embraces the vast diversity of life. We have the technology to collect massive and exquisitely detailed datasets about the world, but expertise is siloed into distinct fields. A new approach, integrating comparative genomics with cell and evolutionary biology, ecology, archaeology, anthropology, and conservation biology, is essential for understanding and protecting ourselves and our world. Here, we describe potential for scientific discovery when comparative genomics works in close collaboration with a broad range of fields as well as the technical, scientific, and social constraints that must be addressed.

Why sequence all eukaryotes?

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.

A National Multi-Scale Assessment of Regeneration Deficit as an Indicator of Potential Risk of Forest Genetic Variation Loss

Genetic diversity is essential because it provides a basis for adaptation and resilience to environmental stress and change. The fundamental importance of genetic variation is recognized by its inclusion in the Montréal Process sustainability criteria and indicators for temperate and boreal forests. The indicator that focuses on forest species at risk of losing genetic variation, however, has been difficult to address in a systematic fashion. We combined two broad-scale datasets to inform this indicator for the United States: (1) tree species occurrence data from the national Forest Inventory and Analysis (FIA) plot network and (2) climatically and edaphically defined provisional seed zones, which are proxies for among-population adaptive variation. Specifically, we calculated the estimated proportion of small trees (seedlings and saplings) relative to all trees for each species and within seed zone sub-populations, with the assumption that insufficient regeneration could lead to the loss of genetic variation. The threshold between sustainable and unsustainable proportions of small trees reflected the expectation of age–class balance at the landscape scale. We found that 46 of 280 U.S. forest tree species (16.4%) may be at risk of losing genetic variation. California and the Southeast encompassed the most at-risk species. Additionally, 39 species were potentially at risk within at least half of the seed zones in which they occurred. Seed zones in California and the Southwest had the highest proportions of tree species that may be at risk. The results could help focus conservation and management activities to prevent the loss of adaptive genetic variation within tree species.

The pace of modern life, revisited

Wild populations must continuously respond to environmental changes or they risk extinction. Those responses can be measured as phenotypic rates of change, which can allow us to predict contemporary adaptive responses, some of which are evolutionary. About two decades ago, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine phenotypic responses to specific types of human disturbance. Here, we update the database by adding 5675 new estimates of phenotypic change. Using this newer version of the data base, now containing 7338 estimates of phenotypic change, we revisit the conclusions of four published articles. We then synthesize the expanded database to compare rates of change across different types of human disturbance. Analyses of this expanded database suggest that: (i) a small absolute difference in rates of change exists between human disturbed and natural populations, (ii) harvesting by humans results in higher rates of change than other types of disturbance, (iii) introduced populations have increased rates of change, and (iv) body size does not increase through time. Thus, findings from earlier analyses have largely held-up in analyses of our new database that encompass a much larger breadth of species, traits, and human disturbances. Lastly, we use new analyses to explore how various types of human disturbances affect rates of phenotypic change, and we call for this database to serve as a steppingstone for further analyses to understand patterns of contemporary phenotypic change.

Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

The spatial structure of genomic and phenotypic variation across populations reflects historical and demographic processes as well as evolution via natural selection. Characterizing such variation can provide an important perspective for understanding the evolutionary consequences of changing climate and for guiding ecological restoration. While evidence for local adaptation has been traditionally evaluated using phenotypic data, modern methods for generating and analyzing landscape genomic data can directly quantify local adaptation by associating allelic variation with environmental variation. Here, we analyze both genomic and phenotypic variation of rubber rabbitbrush (Ericameria nauseosa), a foundational shrub species of western North America. To quantify landscape genomic structure and provide perspective on patterns of local adaptation, we generated reduced representation sequencing data for 17 wild populations (222 individuals; 38,615 loci) spanning a range of environmental conditions. Population genetic analyses illustrated pronounced landscape genomic structure jointly shaped by geography and environment. Genetic-environment association (GEA) analyses using both redundancy analysis (RDA) and a machine-learning approach (Gradient Forest) indicated environmental variables (precipitation seasonality, slope, aspect, elevation, and annual precipitation) influenced spatial genomic structure and were correlated with allele frequency shifts indicative of local adaptation at a consistent set of genomic regions. We compared our GEA-based inference of local adaptation with phenotypic data collected by growing seeds from each population in a greenhouse common garden. Population differentiation in seed weight, emergence, and seedling traits was associated with environmental variables (e.g., precipitation seasonality) that were also implicated in GEA analyses, suggesting complementary conclusions about the drivers of local adaptation across different methods and data sources. Our results provide a baseline understanding of spatial genomic structure for E. nauseosa across the western Great Basin and illustrate the utility of GEA analyses for detecting the environmental causes and genetic signatures of local adaptation in a widely distributed plant species of restoration significance.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

The identification of grain size genes by RapMap reveals directional selection during rice domestication

Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.

Sokefun, Yadav S. Disentangling earthworm taxonomic stumbling blocks using molecular markers

Taxonomic classification of earthworms based on anatomical features has created several challenges for systematics and population genetics. This study examines the application of molecular markers, in particular mitochondrial cytochrome oxidase (COI), to facilitate discrimination of closely related earthworm species. Molecular markers have also provided insights into population genetics by aiding assessment of genetic diversity, lineage sorting, and genealogical distributions of populations for several species. Phylogeography—a study that evaluates the geographical distribution of these genealogical lineages and the role of historical processes in shaping their distribution—has also provided insights into ecology and biodiversity. Such studies are also essential to understand the distribution patterns of invasive earthworm species that have been introduced in non-native ecosystems globally. The negative consequences of these invasions on native species include competition for food resources and altered ecosystems. We anticipate that molecular markers such as COI and DNA barcoding offer potential solutions to disentangling taxonomic impediments in earthworms and advancing their systematics and population genetics. 

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change

Background

At any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients can act as a predictor of patterns in changed climates (typically future but possibly paleo-climates), a methodology is provided by AlleleShift of predicting changes in allele frequencies at the population level.

Methods

The prediction procedure involves a first calibration and prediction step through redundancy analysis (RDA), and a second calibration and prediction step through a generalized additive model (GAM) with a binomial family. As such, the procedure is fundamentally different to an alternative approach recently proposed to predict changes in allele frequencies from canonical correspondence analysis (CCA). The RDA step is based on the Euclidean distance that is also the typical distance used in Analysis of Molecular Variance (AMOVA). Because the RDA step or CCA approach sometimes predict negative allele frequencies, the GAM step ensures that allele frequencies are in the range of 0 to 1.

Results

AlleleShift provides data sets with predicted frequencies and several visualization methods to depict the predicted shifts in allele frequencies from baseline to changed climates. These visualizations include 'dot plot' graphics (function shift.dot.ggplot), pie diagrams (shift.pie.ggplot), moon diagrams (shift.moon.ggplot), 'waffle' diagrams (shift.waffle.ggplot) and smoothed surface diagrams of allele frequencies of baseline or future patterns in geographical space (shift.surf.ggplot). As these visualizations were generated through the ggplot2 package, methods of generating animations for a climate change time series are straightforward, as shown in the documentation of AlleleShift and in the supplemental videos.

Availability

AlleleShift is available as an open-source R package from https://cran.r-project.org/package=AlleleShift and https://github.com/RoelandKindt/AlleleShift. Genetic input data is expected to be in the adegenet::genpop format, which can be generated from the adegenet::genind format. Climate data is available from various resources such as WorldClim and Envirem.

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.