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.
Aquatic species represent a vast diversity of metazoans, provide humans with the most abundant animal protein source, and are of increasing conservation concern, yet landscape genomics is dominated ...by research in terrestrial systems. We provide researchers with a roadmap to plan aquatic landscape genomics projects by aggregating spatial and software resources and offering recommendations from sampling to data production and analyses, while cautioning against analytical pitfalls. Given the unique properties of water, we discuss the importance of considering freshwater system structure and marine abiotic properties when assessing genetic diversity, population connectivity, and signals of natural selection. When possible, genomic datasets should be parsed into neutral, adaptive, and sex-linked datasets to generate the most accurate inferences of eco-evolutionary processes.
Proliferation of genome-scale studies on aquatic species have resulted from the decreasing costs of high-throughput sequencing combined with novel computational approaches.
Our increasing understanding of the genomes of aquatic species has enabled the annotation of loci that are adaptive, sex linked, and associated with phenotype, allowing the inference of evolutionary and demo-genetic processes from spatio-temporal genetic patterns.
Recent improvements in climate and habitat data for aquatic systems provide a more precise characterization of aquatic niches, facilitating landscape genomics.
Many landscape genetic analytical methods have recently been developed specifically for aquatic systems.
We provide a list of spatial and genomic resources as part of a ‘roadmap’ to guide future aquatic landscape genomic studies.
Alluvial aquifers are key components of river floodplains and biodiversity worldwide, but they contain extreme environmental conditions and have limited sources of carbon for sustaining food webs. ...Despite this, they support abundant populations of aquifer stoneflies that have large proportions of their biomass carbon derived from methane. Methane is typically produced in freshwater ecosystems in anoxic conditions, while stoneflies (Order: Plecoptera) are thought to require highly oxygenated water. The potential importance of methane-derived food resources raises the possibility that stonefly consumers have evolved anoxia-resistant behaviors and physiologies. Here we tested the anoxic and hypoxic responses of 2,445 stonefly individuals in three aquifer species and nine benthic species. We conducted experimental trials in which we reduced oxygen levels, documented locomotor activity, and measured survival rates. Compared to surface-dwelling benthic relatives, stoneflies from the alluvial aquifer on the Flathead River (Montana) performed better in hypoxic and anoxic conditions. Aquifer species sustained the ability to walk after 4–76 h of anoxia vs. 1 h for benthic species and survived on average three times longer than their benthic counterparts. Aquifer stoneflies also sustained aerobic respiration down to much lower levels of ambient oxygen. We show that aquifer taxa have gene sequences for hemocyanin, an oxygen transport respiratory protein, representing a possible mechanism for surviving low oxygen. This remarkable ability to perform well in low-oxygen conditions is unique within the entire order of stoneflies (Plecoptera) and uncommon in other freshwater invertebrates. These results show that aquifer stoneflies can exploit rich carbon resources available in anoxic zones, which may explain their extraordinarily high abundance in gravel-bed floodplain aquifers. These stoneflies are part of a novel food web contributing biodiversity to river floodplains.
•Community genomic evolution is influenced by community and environmental effects.•Landscape genetics and community genetics remain largely independent disciplines.•Landscape community genomics (LCG) ...melds landscape genetics with community genetics.•LCG helps to avoid misinterpreting the relative effects of the community versus the environment.•Recent advances in genomic sequencing are the key to adopting LCG approaches.
Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between environmental and community effects. Failure to consider both effects on evolutionary dynamics simultaneously can lead to incomplete, spurious, or erroneous conclusions about the mechanisms driving genomic variation. We highlight the need for a landscape community genomics (LCG) framework to help to motivate and challenge scientists in diverse fields to consider a more holistic, interdisciplinary perspective on the genomic evolution of multi-species communities in complex environments.
New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. ...The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.
ABSTRACT
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors ...and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
Estimating the effective population size and effective number of breeders per year (Nb) can facilitate early detection of population declines. We used computer simulations to quantify bias and ...precision of the one‐sample LDNe estimator of Nb in age‐structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5%–10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence Nb estimation. Precision was higher for 100 SNPs (H ≈ 0.30) than for 15 microsatellites (H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when Nb was small (Nb < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that Nb = 50 when the true Nb = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject Nb = 500 when the true Nb = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in Nb when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate Nb for age structured populations (https://github.com/popgengui/agestrucnb/), which should help biologists develop sensitive monitoring programmes for early detection of changes in Nb and population declines.
Gravel-bed river floodplains occur in river corridors around the globe. One key habitat of these floodplains are alluvial aquifers that provide habitat for a wide range of obligate groundwater ...species. Multiple species of the amphipod genus
Stygobromus
commonly occur in alluvial aquifers, as well as in karstic phreatic systems, but few studies have investigated the population structure and its relevance to the biogeography of the genus. Using reduced representation genome sequencing, RAD-seq, we investigated the population structure and genetic connectivity of an undescribed
Stygobromus
species in several alluvial aquifers on floodplains of the Flathead River, Montana (USA). Amphipods were genetically similar (pairwise
F
ST
ranging from 0.0061 to 0.0092) at multiple sites within floodplains but three genetic clusters were segregated among floodplains (pairwise
F
ST
ranging from 0.0303 to 0.0547), suggesting some geographic isolation of populations. These floodplain aquifers are separated by bedrock canyons that could be migration barriers resulting in the observed spatial segregation of populations.
Agencies currently utilize several proxy tests, related to level of compaction (density) and moisture content, to assess the quality of a recycled pavement during construction. These proxy tests are ...not completely able to indicate sufficient quality or stability of recycled pavements under trafficking or surfacing, especially at early ages. The lack of sound and rapid tests for use in process control and acceptance during construction limits the use of the recycling techniques by agencies, therefore they do not fully benefit from the advantages that pavement recycling offers. This study evaluates the viability of currently available simple and practical stiffness tests (i.e., soil stiffness gauge and light weight deflectometer tests), deformation resistance tests (i.e., Marshall hammer test), and penetration resistance tests (i.e., dynamic cone penetration test) to characterize the properties of asphalt-treated cold recycled mixtures. The scope of the work included laboratory testing of 18 different cold recycled mixtures, prepared through different processes combining different binding agents and filler types, at different curing times via the selected tests. The collected data were analyzed to evaluate these tests in relation to their repeatability characteristics and versatility to capture the performance of recycled materials with respect to changes in curing time, type of stabilizing/recycling agent, and presence of active filler. The data obtained showed the ability of these tests to capture the effect of curing. Moreover, these tests were found to be sensitive to changes in the recycling agent type, recycling agent content, and presence of active filler.
PDF
