Genetic variation is fundamental to population fitness and adaptation to environmental change. Human activities are driving declines in many wild populations and could have similar effects on genetic ...variation. Despite the importance of estimating such declines, no global estimate of the magnitude of ongoing genetic variation loss has been conducted across species. By combining studies that quantified recent changes in genetic variation across a mean of 27 generations for 91 species, we conservatively estimate a 5.4%–6.5% decline in within‐population genetic diversity of wild organisms since the industrial revolution. This loss has been most severe for island species, which show a 27.6% average decline. We identified taxonomic and geographical gaps in temporal studies that must be urgently addressed. Our results are consistent with single time‐point meta‐analyses, which indicated that genetic variation is likely declining. However, our results represent the first confirmation of a global decline and provide an estimate of the magnitude of the genetic variation lost from wild populations.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
The MinION sequencer is increasingly being used for the detection and outbreak surveillance of pathogens due to its rapid throughput. For RNA viruses, MinION's new direct RNA sequencing is the next ...significant development. Direct RNA sequencing studies are currently limited and comparisons of its diagnostic performance relative to different DNA sequencing approaches are lacking as a result. We sought to address this gap and sequenced six subtypes from the mycovirus CHV-1 using MinION's direct RNA sequencing and DNA sequencing based on a targeted viral amplicon. Reads from both techniques could correctly identify viral presence and species using BLAST, though direct RNA reads were more frequently misassigned to closely related CHV species. De novo consensus sequences were error prone but suitable for viral species identification. However, subtype identification was less accurate from both reads and consensus sequences. This is due to the high sequencing error rate and the limited sequence divergence between some CHV-1 subtypes. Importantly, neither RNA nor amplicon sequencing reads could be used to obtain reliable intra-host variants. Overall, both sequencing techniques were suitable for virus detection, though limitations are present due to the error rate of MinION reads.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Monitoring the evolutionary responses of species to ongoing global climate change is critical for informing conservation. Population genomic studies that use samples from multiple time points ...(“temporal genomics”) are uniquely able to make direct observations of change over time. Consequently, only temporal studies can show genetic erosion or spatiotemporal changes in population structure. Temporal genomic studies directly examining climate change effects are currently rare but will likely increase in the coming years due to their high conservation value. Here, we highlight four key genetic indicators that can be monitored using temporal genomics to understand how species are responding to climate change. All indicators crucially rely on having a suitable baseline that accurately represents the past condition of the population, and we discuss aspects of study design that must be considered to achieve this.
Population genomic studies that use samples from multiple time points (“temporal genomics”) are uniquely able to make direct observations of change over time, and are critical to documenting how species are responding to climate change. Here, we highlight some key genetic indicators that can be monitored using temporal genomics to understand how species are responding to climate change: genetic erosion, spatiotemporal population structure, hybridization, and adaptation.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Polymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss in genetic diversity at such loci constitutes an extinction risk ...and should be monitored in species of conservation concern. However, effective implementations of genome‐wide immune polymorphism sets into high‐throughput genotyping assays are scarce. Here, we report the design and validation of a microfluidics‐based amplicon sequencing assay to comprehensively capture genetic variation in Alpine ibex (Capra ibex). This species represents one of the most successful large mammal restorations recovering from a severely depressed census size and a massive loss in diversity at the major histocompatibility complex (MHC). We analysed 65 whole‐genome sequencing sets of the Alpine ibex and related species to select the most representative markers and to prevent primer binding failures. In total, we designed ~1,000 amplicons densely covering the MHC, further immunity‐related genes as well as randomly selected genome‐wide markers for the assessment of neutral population structure. Our analysis of 158 individuals shows that the genome‐wide markers perform equally well at resolving population structure as RAD‐sequencing or low‐coverage genome sequencing data sets. Immunity‐related loci show unexpectedly high degrees of genetic differentiation within the species. Such information can now be used to define highly targeted individual translocations. Our design strategy can be realistically implemented into genetic surveys of a large range of species. In conclusion, leveraging whole‐genome sequencing data sets to design targeted amplicon assays allows the simultaneous monitoring of multiple genetic risk factors and can be translated into species conservation recommendations.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Identifying local adaptation in bottlenecked species is essential for conservation management. Selection detection methods have an important role in species management plans, assessments of adaptive ...capacity, and looking for responses to climate change. Yet, the allele frequency changes exploited in selection detection methods are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods have across bottlenecked populations. In this study, simulations were used to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). The meticulously recorded demographic history of the Alpine ibex was used to generate comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in outliers identified in empirical Alpine ibex RADseq derived SNP data. Within the simulated data set, the false positive rates were high for all selection detection methods (FST outlier scans and Genetic‐Environment Association analyses) but fell substantially when two or more methods were combined. True positive rates were consistently low and became negligible with increased stringency. Despite finding many outlier loci in the empirical Alpine ibex SNPs, none could be distinguished from genetic drift‐driven false positives. Unfortunately, the low true positive rate also prevents the exclusion of recent local adaptation within the Alpine ibex. The baselines and stringent approach outlined here should be applied to other bottlenecked species to ensure the risk of false positive, or negative, signals of selection are accounted for in conservation management plans.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Duckweeds, including the common duckweed Lemna minor, are increasingly used to test eco‐evolutionary theories. Yet, despite its popularity and near‐global distribution, the understanding of its ...population structure (and genetic variation therein) is still limited. It is essential that this is resolved, because of the impact genetic diversity has on experimental responses and scientific understanding. Through whole‐genome sequencing, we assessed the genetic diversity and population genomic structure of 23 natural Lemna spp. populations from their natural range in Switzerland. We used two distinct analytical approaches, a reference‐free kmer approach and the classical reference‐based one. Two genetic clusters were identified across the described species distribution of L. minor, surprisingly corresponding to species‐level divisions. The first cluster contained the targeted L. minor individuals and the second contained individuals from a cryptic species: Lemna japonica. Within the L. minor cluster, we identified a well‐defined population structure with little intra‐population genetic diversity (i.e., within ponds) but high inter‐population diversity (i.e., between ponds). In L. japonica, the population structure was significantly weaker and genetic variation between a subset of populations was as low as within populations. This study revealed that L. japonica is more widespread than previously thought. Our findings signify that thorough genotype‐to‐phenotype analyses are needed in duckweed experimental ecology and evolution.
We investigated the genetic diversity and population structure of the common duckweed Lemna minor. Through whole‐genome sequencing of 23 natural populations in Switzerland, we identified two genetic clusters, including a cryptic species, L. japonica. While L. minor showed a well‐defined population structure, L. japonica showed weaker population structure. The findings highlight the widespread distribution of L. japonica and underscore the importance of genetic studies in improving our understanding of duckweed ecology and evolution, particularly when it comes to leveraging L. minor for eco‐evolutionary research.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Millette et al. (Ecology Letters, 2020, 23:55–67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data ...from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Across its range, the Atlantic Puffin Fratercula arctica is divided into four separate genetic clusters that correspond with geography and/or size differences. However, in the Western Atlantic High ...Arctic, there is a Puffin colony (Thule) that comprises two discrete size phenotypes. Using whole genome sequencing data of six Thule individuals from these two phenotypes, we found that Thule consists of three distinct genetic clusters, with no signs of recent interbreeding. Our results suggest the beginnings of a potential northward shift of boreal Atlantic Puffins in the West Atlantic, consistent with responses to a warming High Arctic climate.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Intramuscular accumulation of triacylglycerol, in the form of lipid droplets (LD), has gained widespread attention as a hallmark of metabolic disease and insulin resistance. Paradoxically, LDs also ...amass in muscles of highly trained endurance athletes who are exquisitely insulin sensitive. Understanding the molecular mechanisms that mediate the expansion and appropriate metabolic control of LDs in the context of habitual physical activity could lead to new therapeutic opportunities. Herein, we show that acute exercise elicits robust upregulation of a broad program of genes involved in regulating LD assembly, morphology, localization, and mobilization. Prominent among these was perilipin-5, a scaffolding protein that affects the spatial and metabolic interactions between LD and their surrounding mitochondrial reticulum. Studies in transgenic mice and primary human skeletal myocytes established a key role for the exercise-responsive transcriptional coactivator PGC-1α in coordinating intramuscular LD programming with mitochondrial remodeling. Moreover, translational studies comparing physically active versus inactive humans identified a remarkably strong association between expression of intramuscular LD genes and enhanced insulin action in exercise-trained subjects. These results reveal an intimate molecular connection between intramuscular LD biology and mitochondrial metabolism that could prove relevant to the etiology and treatment of insulin resistance and other disorders of lipid imbalance.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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