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351 results for “functional genetics”
Functional and genetic diversity changes through time in a cloud forest ant assemblage
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Net N mineralization:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Root biomass:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Soil percent carbon and nitrogen:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Soil pH:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Soil microbial respiration rate:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Genetic overlap and causal inferences between kidney function and cerebrovascular disease
<p><u>Objective:</u> Leveraging large-scale genetic data, we aimed to identify shared pathogenic mechanisms and causal relationships between impaired kidney function and cerebrovascular disease phenotypes.</p> <p><u>Methods:</u> We used summary statistics from genome-wide association studies (GWAS) of kidney function traits (<a name="_Hlk536087805">chronic kidney disease (CKD) diagnosis, estimated glomerular filtration rate (eGFR), and Urinary Albumin-to-Creatinine Ratio (UACR)</a>), and of cerebrovascular disease phenotypes: ischemic stroke and its subtypes, intracerebral hemorrhage (ICH), white matter hyperintensities (WMH) on brain MRI. We (i) tested the genetic overlap between them with polygenic risk scores (PRS), (ii) searched for common pleiotropic loci with pairwise GWAS analyses, and (iii) explored causal associations by employing two-sample Mendelian Randomization (MR).</p> <p><u>Results:</u> A PRS for lower eGFR was associated with higher large-artery stroke (LAS) risk (p=1x10<sup>-4</sup>). Multiple pleiotropic loci were identified between kidney function traits and cerebrovascular disease phenotypes, with 12q24 associated with eGFR and both LAS and small-vessel stroke (SVS), and 2q33 associated with UACR and both SVS and WMH. MR revealed associations of both lower eGFR (OR per 1-log decrement=2.10, 95%CI=1.38-3.21) and higher UACR (OR per 1-log increment=2.35, 95%CI=1.12-4.94) with a higher risk of LAS, as well as between higher UACR and higher risk of ICH.</p> <p><u>Conclusions:</u> Impaired kidney function, as assessed by decreased eGFR and increased UACR, may be causally involved in the pathogenesis of LAS. Increased UACR, previously proposed as a marker of systemic small vessel disease, is involved in ICH risk and shares a genetic risk factor at 2q33 with manifestations of cerebral small vessel disease.</p>
Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries management
<p>The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise, and where many species synchronize their reproduction to seasonal cycles of planktonic productivity. Using genomic data collected from spawning aggregations of Pacific herring (<i>Clupea pallasii</i>) across 1,600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season we observed isolation by distance, indicating that gene flow is limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in reproductive timing when delineating management units for Pacific herring. On several chromosomes we detected linkage disequilibrium extending over millions of base pairs, suggesting the presence of chromosomal rearrangements. The frequencies of putative chromosomal rearrangements differed between populations spawning at different times of year. Spawning phenology was highly correlated with polymorphisms in several genes, in particular <i>SYNE2</i>, which influences the development of retinal photoreceptors in vertebrates. <i>SYNE2 </i>is likely within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (<i>Clupea harengus</i>). The observed genetic diversity likely underlies resource waves provided by spawning herring and demonstrates how population-level genetic diversity can influence ecosystem processes. Given the ecological, economic, and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.</p>
Data from: From ornament to armament or loss of function? Breeding plumage acquisition in a genetically monogamous bird
1. The evolution of conspicuous male traits is thought to be driven by female mate choice or male-male competition. These two mechanisms are often viewed as distinct processes, with most studies focusing on female choice. 2. However, both mechanisms of sexual selection can act simultaneously on the same trait (i.e. dual function) and/or interact in a synergistic or conflicting way. Dual function-traits are commonly assumed to originate through male-male competition before being used in female choice; yet, most studies focusing on such traits could not determine the direction of change, lacking phylogenetic information. 3. We investigated the role of conspicuous male seasonal plumage in male-male competitive interactions in the purple-crowned fairy-wren Malurus coronatus, a cooperatively breeding bird. Male breeding plumage in most Malurus species is selected by female choice through extra-pair mate choice, but unlike its congeners, M. coronatus is genetically monogamous, and females do not seem to choose males based on breeding plumage acquisition. 4. Our study shows that, within groups, subordinate males that were older, and therefore higher-ranked in the queue for breeder position inheritance, produced a more complete breeding plumage. In line with this, subordinate males that were older and/or displayed a more complete breeding plumage were more successful in competitively acquiring a breeder position. 5. A role as a signal of competitive ability was experimentally confirmed by presenting models of males: in breeding colours, these received more aggression from resident breeder males than in non-breeding colours, but elicited limited response from females, consistent with competitors in breeding plumage being perceived as a bigger threat to the breeder male. 6. The role of the conspicuous breeding plumage in mediating male-male interactions might account for its presence in this genetically monogamous species. Since phylogenetic reconstructions suggest a past female choice function in M. coronatus, this could represent a sexual trait that shifted functions, or a dual function-trait that lost one function. These evolutionary scenarios imply that intra- and inter-sexual functions of ornaments may be gained or lost independently, and offer new perspectives in understanding the complex dynamics of sexual selection.
Data from: Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana
Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes and anal plates exhibit striking differences between Drosophila mauritiana and Drosophila simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.
Data from: Genetic drivers of pancreatic islet function
Nearly all gene loci that have been associated with type 2 diabetes play a role in pancreatic islet function. To evaluate the role of islet gene expression in the etiology of diabetes, we sensitized a genetically diverse mouse population with a Western diet and carried out genome-wide association mapping of diabetes-related phenotypes. We quantified mRNA abundance in the islets, and identified 18,775 expression quantitative trait loci. We applied mediation analysis to identify candidate causal driver genes at loci where numerous transcripts co-map. These include two genes previously associated with monogenic diabetes (PDX1 and HNF4A), as well as three genes with nominal association with diabetes-related traits in humans (FAM83E, IL6ST, and SAT2). We grouped transcripts into gene modules and show that these modules enrich for physiological pathways that also map to distinct loci. We identified and mapped regulatory loci for modules enriched with transcripts specific for α-cells, and another specific for δ-cells. However, no single module enriched for β-cell-specific transcripts, reflecting heterogeneity within the β-cell population. A module enriched in transcripts associated with branched chain amino acid metabolism was the most strongly correlated with clinical traits that reflect insulin resistance. Although the mice in this study were not overtly diabetic, the analysis of pancreatic islet gene expression under dietary-induced stress, enabled us to identify genes and pathways linked to diabetes-associated clinical traits. Our analysis reveals a high degree of concordance between diabetes-associated loci in the mouse with those found in human populations, and demonstrates how the mouse can provide evidence to support nominal associations found in human genome-wide association mapping.
Data from: The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler
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Data from: Relationships between adaptive and neutral genetic diversity and ecological structure and function: a meta-analysis
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Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries management
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Data from: Genetic dissection of adaptive form and function in rapidly-speciating cichlid fishes
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Data from: Genetic variation, simplicity and evolutionary constraints for function-valued traits
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Data from: Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana
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Genetic overlap and causal inferences between kidney function and cerebrovascular disease
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Data from: Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse
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Data from: Genetic drivers of pancreatic islet function
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.