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268 results for “michigan”
Annual tree growth for Red and Sugar Maples in six forest plots distributed around Ann Arbor, MI and around the University of Michigan Biological Station (UMBS), 1999 to 2022
The dataset contains the annual growth, in mm, of over 200 red and sugar maple trees. All trees are located in established study sites in the vicinity of Ann Arbor or UMBS.
Ozone Concentrations and Ozone Flux at the Univerity of Michigan Biological Station PROPHET Tower from 2002-2005
Measurements of ozone, sensible heat, and latent heat fluxes and plant physiological parameters were made at a northern mixed hardwood forest located at the University of Michigan Biological Station in northern Michigan from June 27 to September 28, 2002. These measurements were used to calculate total ozone flux and partitioning between stomatal and non-stomatal sinks. Total ozone flux varied diurnally with maximum values reaching 100 8mol m-2 h-1 at midday and minimums at or near zero at night. Mean daytime canopy conductance was 0.5 mol m-2 s-1. During daytime, non-stomatal ozone conductance accounted for as much as 66% of canopy conductance, with the non-stomatal sink representing 63% of the ozone flux. Stomatal conductance showed expected patterns of behaviour with respect to photosynthetic photon flux density (PPFD) and vapour pressure defecit (VPD). Non-stomatal conductance for ozone increased monotonically with increasing PPFD, increased with temperature (T) before falling off again at high T, and behaved similarly for VPD. Day-time non-stomatal ozone sinks are large and vary with time and environmental drivers, particularly PPFD and T. This information is crucial to deriving mechanistic models that can simulate ozone uptake by different vegetation types.
Michigan Rodents Distribution at the University of Michigan Biological Station, Pellston, MI, from 1883 to 2007
Distribution of rodents in northern Michigan documented by Dr. Phil Myers, et al. We use museum and other collection records to document large and extraordinarily rapid changes in the ranges and relative abundance of 9 species of mammals in the northern Great Lakes region (white-footed mice, woodland deer mice, southern red-backed voles, woodland jumping mice, eastern chipmunks, least chipmunks, southern flying squirrels, northern flying squirrels, common opossums). These species reach either the southern or the northern limit of their distributions in this region. Changes consistently reflect increases in species of primarily southern distribution (white-footed mice, eastern chipmunks, southern flying squirrels, common opossums) and declines by northern species (woodland deer mice, southern red-backed voles, woodland jumping mice, least chipmunks, northern flying squirrels). White-footed mice and southern flying squirrels have extended their ranges over 225 km since 1980, and at particularly well-studied sites in Michigan's Upper Peninsula, small mammal assemblages have shifted from numerical domination by northern species to domination by southern species. Repeated re-sampling at some sites suggests that southern species are replacing northern ones rather than simply being added to the fauna. Observed changes are consistent with predictions from climatic warming but not with predictions based on recovery from logging or changes in human populations. Because of the abundance of these focal species (the 8 rodent species make up 96.5% of capture records of all forest-dwelling rodents in the region and 70% of capture records of all forest-dwelling small mammals) and the dominating ecological roles they play, these changes substantially affect the composition and structure of forest communities. They also provide an unusually clear example of change that is likely to be the result of climatic warming in communities that are experienced by large numbers of people.
Michigan GLBRC Extensive Sites at the Kellogg Biological Station, Hickory Corners, MI (2008 to 2011)
Dataset Abstract The Great Lakes Bioenergy Research Center’s (GLBRC) Extensive Sites are farm-scale fields located on working farms. Fields of corn, switchgrass, and restored prairie are represented at each of 10 locations in 13 counties in Michigan. original data source http://lter.kbs.msu.edu/datasets/106
Settlement Trees, Southern Michigan Level 0
We provide a Level 0 record of trees from 41 counties in the southern two-thirds of Michigan's Lower Peninsula transcribed from Public Land Surveys conducted by surveyors from the General Land Office of the United States in the 1800s. Posts were set every half mile in townships that were typically 6 miles by 6 miles square. Surveyors recorded details about the one to four trees closest (but typically recorded information for the two closest trees) to the posts and included information about the tree name (taxonomic specificity ranged by surveyor), tree diameter (inches), and distance and bearing from the post. Our records include the tree information and the location of the posts from which the tree information came from. These Level 0 tree data were aggregated to the 8km grid resolution Level 1 product (see msb-paleon.26 package). That product was then statistically smoothed using a statistical model that accounts for zero-inflated continuous data with smoothing based on generalized additive modeling techniques and approximate Bayesian uncertainty estimates for the Level 2 products estimating aboveground biomass (msb-paleon.23), density (msb-paleon.24), and basal area (msb-paleon.25). The data processing steps and associated code are available in the GitHub repository: https://github.com/PalEON-Project/PLS_products. These products are used in the manucript, Paciorek et al., 2020, Statistically-estimated tree biomass, stem, and basal area for the upper Midwestern United States at the time of Euro-American settlement (https://www.biorxiv.org/content/10.1101/856526v1). This material is based upon work supported by the National Science Foundation under grants #DEB-1241874, 1241868, 1241870, 1241851, 1241891, 1241846, 1241856, 1241930.
Settlement Trees, Northern Michigan Level 0
We provide a Level 0 record of trees from 43 counties Michigan's Upper Peninsual and the northern one-third of Michigan's Lower Peninsula from Public Land Surveys conducted by surveyors from the General Land Office of the United States in the 1800s. Posts were set every half mile in townships that were typically 6 miles by 6 miles square. Surveyors recorded details about the one to four trees closest (but typically recorded information for the two closest trees) to the posts and included information about the tree name (taxonomic specificity ranged by surveyor), tree diameter (inches), and distance and bearing from the post. Our records include the tree information and the location of the posts from which the tree information came from. These Level 0 tree data were aggregated to the 8km grid resolution Level 1 product (see msb-paleon.26 package). That product was then statistically smoothed using a statistical model that accounts for zero-inflated continuous data with smoothing based on generalized additive modeling techniques and approximate Bayesian uncertainty estimates for the Level 2 products estimating aboveground biomass (msb-paleon.23), density (msb-paleon.24), and basal area (msb-paleon.25). The data processing steps and associated code are available in the GitHub repository: https://github.com/PalEON-Project/PLS_products. These products are used in the manucript, Paciorek et al., 2020, Statistically-estimated tree biomass, stem, and basal area for the upper Midwestern United States at the time of Euro-American settlement (https://www.biorxiv.org/content/10.1101/856526v1). This material is based upon work supported by the National Science Foundation under grants #DEB-1241874, 1241868, 1241870, 1241851, 1241891, 1241846, 1241856, 1241930.
Transcriptome analysis of invasive Gypsophila paniculata (baby's breath) populations from Michigan and Washington, USA.
<p>Invasive species provide an opportune system to investigate how populations respond to new or changing environments. While the impacts of invasive species increase annually, many gaps in our understanding of how these species invade, adapt, and thrive in the areas they are introduced to remain. Using the perennial forb <i>Gypsophila paniculata</i> as a study system, we aimed to investigate how invasive species respond to different environments. Baby's breath (<i>Gypsophila paniculata</i>) was introduced to North America in the late 1800's and has since spread throughout the northwestern United States and western Canada. We used an RNA-seq approach to explore how molecular processes may be contributing to the success of invasive <i>G. paniculata</i> populations that are thought to share similar genetic backgrounds across distinct habitats. Transcription profiles were constructed for root, stem, and leaf tissue from seedlings collected from a sand dune ecosystem in Petoskey, MI (PSMI) and a sagebrush ecosystem in Chelan, WA (CHWA). Using these data we assessed differential gene expression between the two populations and identified SNPs within differentially expressed genes. We identified 1,146 transcripts that were differentially expressed across all tissues between the two populations. GO processes enriched by genes displaying higher expression in PSMI were associated with increased nutrient starvation, while enriched processes in CHWA were associated with abiotic stress. Only 7.4% of the differentially expressed genes across all three tissues contained SNPs differing in allele frequencies of at least 0.5 between the populations. In addition, common garden studies found the two populations differed in germination rate and seedling emergence success, but not in above- and below-ground tissue allocation. Our results suggest that the success of invasive <i>G. paniculata</i> across these two environments is likely the result of plasticity in molecular processes responding to different environmental conditions, although some genetic divergence may also be contributing to these differences.</p>
On the anomalous shapes of native copper crystals from the Michigan Copper Country
<p>Raw NanoSIMS image data files and metadata files with analytical conditions for each analysis. Data associated with manuscript "On the anomalous shapes of native copper crystals from the Michigan Copper Country" by Boulliard, Aléon and Gaillou, accepted in European Journal of Mineralogy, 2021.</p>
17th Michigan Vol. Inf. Reg. Monument
At 2 p.m., May 12th, two Ninth Corps brigades were ordered to attack the Confederate works one-quarter mile southeast of this spot. The 17th Michigan was on the extreme left of the Federal line. As the regiment approached its objective, Brig. Gen. James Lane's North Carolina Brigade emerged from the thick woods and struck it on the left flank in the bloody hand-to-hand fighting that followed, the 17th Michigan lots its national colors and 189 of the 225 men it carried into battle. Three soldiers later received the Medal of Honor for their brave but unsuccessful efforts to save the colors. 3D model from photos generated with photogrammetry software 3DF Zephyr v4.530 processing 44 images. Marker is near Spotsylvania, Virginia, in Spotsylvania County. Marker is on Burnside Drive, on the right when traveling east. Located near tour stop seven (Heth's Salient) on the driving tour of Spotsylvania Battlefield unit of the Fredericksburg and Spotsylvania National Military Park. Source: Objaverse 1.0 / Sketchfab
The gut microbiome of wild American marten in the Upper Peninsula of Michigan
<p>Directory Information for The gut microbiome of wild American marten in the Upper Peninsula of Michigan<br> #######</p> <p>"R Code" contains:</p> <p>--- "marten_phyobj.rds" is the phyloseq object that can be directly imported for statistical analysis if the user prefers not to go entire QIIME2 pipeline. The phyloseq object was created from QIIME2 artifacts from the "QIIMEpipe.html" pipeline: the cleaned rooted tree, the cleaned taxonomy table and the cleaned ASV table. <strong>This requires the command "readRDS()" to import. <em>The "load()" command will not work.</em></strong></p> <p><br> --- "Stat.Rmd" Markdown file for "Stat.html"</p> <p>--- "Stat.html" knitted statistical analysis file to view the studies outputs quickly</p> <p>--- "Stat.R" R code if user prefers over Rmarkdown</p> <p>#######</p> <p>"QIIME" contains:<br> --- "martendemux.qza" demultiplexed QIIME2 artifact</p> <p>--- "martendemux.qzv" visualization output of demultiplexed sequence that can be viewed at qiimeview.org</p> <p>--- "MartenMeta.tsv" metadata file for QIIME2 pipeline and statistical analysis</p> <p>--- "QIIMepipe.html" code for bioinformatic pipeline for downstream analysis</p> <p>- "Sequences" folder:<br> --- "R1_demultiplxed_pairedend_marten.fastq.gz" forward reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2.</p> <p>--- "R2_demultiplxed_pairedend_marten.fastq.gz" reverse reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2.<br> </p>
Temporal data from camera trap captures of raccoons (Procyon lotor) and coyote (Canis latrans) across urban-rural gradient Michigan 2015-2020
<p>Temporal data and trap success for raccoons (<em>Procyon lotor</em>) and coyotes (<em>Canis latrans</em>) across an urban-rural gradient in Michigan, from 2015 to 2020. These data are associated with the article "Temporal refuges of a subordinate carnivore vary across rural-urban gradient" in the journal Ecology and Evolution. </p>
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
<p>Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (<em>Coregonus clupeaformis</em>) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management. </p>
Carbon sequestration in intact rare ecosystems and their encroaching forests (Michigan, USA)
<p>Rising atmospheric carbon dioxide levels are impacting global temperatures, ecological systems, and human societies. Natural carbon sequestration through the conservation of soil and native ecosystems may slow or reduce the amount of CO<sub>2</sub> in the atmosphere, and thus slow or mitigate the rate of global warming. Most of the research investigating carbon sequestration in natural systems occurs in forested ecosystems, however rare ecosystems such as coastal plain marshes and wet-mesic sand prairie collectively may serve as significant carbon sinks. Our objectives were to measure and assess the importance of carbon sequestration in three rare ecosystems (oak-pine barrens, coastal plain marsh, and wet-mesic sand prairie) in western Lower Michigan. We measured carbon in standing vegetation, dead organic matter, and soils within each ecosystem and adjacent encroaching forested areas. Driven by tree carbon, total carbon stocks in encroaching areas were greater than in intact rare ecosystems. Soil organic carbon was greater in all intact ecosystems, though only significantly so in coastal plain marsh. Principal components analysis explained 72% of the variation and revealed differences between intact ecosystems and their encroaching areas. Linear models using the ratio of red to green light reflectance successfully predicted SOC in intact coastal plain marsh and wet-mesic sand prairie. Our results infer the importance of these rare ecosystems in sequestering carbon in soils and support the need to establish federal or state management practices for the conservation of these systems.</p>
Underwater video of lake whitefish Coregonus clupeaformis spawning in lake Michigan
<p>The lake whitefish <em>Coregonus clupeaformis,</em> <em>dikameg</em> in Anishinaabemowin, holds cultural importance, and is a mainstay of commercial, recreational, and subsistence fisheries throughout North America. In the Laurentian Great Lakes, declines in recruitment, since the early 2000s, have raised concerns among stewards and fishery managers. A more detailed understanding of the lake whitefish mating system could help resolve potential recruitment bottlenecks and thus inform appropriate stewardship actions. Herein, we describe, for the first time, a single lake whitefish spawning event captured using high-resolution underwater videography. From 94 h spent on the water, we captured and analyze a 4.5 min video clip that shows pre-mating, mating, and post-mating behaviour of a male and female lake whitefish from Lake Michigan. The clip shows a number of what we interpret as courtship, site-selection, and spawning behaviours culminating in release of about 20 eggs in a single spawning event. Behaviours that included travelling, physical contact, chasing, circling, orienting, and gamete release are described and time-referenced to a video supplement. This single observation is part of a larger project to assess lake whitefish spawning behaviour in the wild but is noteworthy in that it provides new insights into the spawning behaivour of lake whitefish and appears consistent with reproductive behaviours observed in European coregonines.</p>
Vegetation Density and Greenness Change Index (GCI), Southeast Michigan, 1990-2000-2010
<p>The vegetation density composites in 1990, 2000, and 2010 and greenness change index (GCI) between 2000 and 2010 for the Detroit-area counties of Oakland, Macomb, and Wayne.</p>
Data from: Two for the price of one: eDNA metabarcoding reveals temporal and spatial variability of mussel and fish co-distributions in Michigan riverine systems
<p>Freshwater mussels (family Unionidae) are among the world's most endangered taxa, with almost 75% of North American taxa classified as a species of concern, threatened, or endangered. Despite the critical importance of comprehensive distributional data for the conservation of unionids and fishes, these data are often lacking because of the labor and resources associated with traditional survey methods. During their larval stage, unionid mussels use various fish species as obligate hosts, making native fish species vital to unionid persistence and an understanding of host distribution similarly important. Here, we utilized an eDNA metabarcoding approach to evaluate patterns of co-distribution of unionid mussels and fishes along ~362 km of the densely sampled Grand River network as well as the outlets of 19 tributaries along the eastern shore of Lake Michigan, USA. We detected a total of 21 mussel and 40 fish taxa, with distinctive composition of both mussel and fish assemblages across tributaries and differences in fish taxa between sampling periods. Notably, we detected more mussel taxa within the Grand River watershed than at the outlets of all 20 rivers combined. Within the Grand River network, two fish taxa (<em>Pylodictus</em> <em>olivaris</em> and <em>Cyprinella</em>) were found more frequently in areas of high mussel diversity, and three fish taxa more frequently in areas of low mussel diversity (<em>Umbra</em>, Leuciscidae, and <em>Etheostoma</em>). There was little difference between eDNA detections of mussels from samples collected in June versus August, but we detected significantly more fish taxa in August compared to June. Taken together, our findings demonstrate the value of eDNA metabarcoding for evaluating co-distribution of ecologically connected taxa. The use of eDNA as a tool for determining distributions of mussels and their obligate hosts may facilitate conservation efforts for these imperiled taxa.</p>
Low Kirtland's Warbler fledgling survival in Wisconsin plantations relative to Michigan plantations
<p>The Kirtland's Warbler (<em>Setophaga kirtlandii</em>) is a formerly endangered habitat specialist that breeds mainly in young jack pine (<em>Pinus banksiana</em>) forests in northern Lower Michigan, USA. The species is conservation-reliant and depends on habitat management. Management actions have primarily focused on creating jack pine plantations, but the species also breeds in red pine (<em>Pinus resinosa</em>) plantations in central Wisconsin, USA. However, the plantations were not intended as breeding habitat and have suboptimal pine densities. While nesting success is similar between low-density red pine plantations and optimal jack pine habitat, it is not clear if low-density red pine plantations support high fledging survival. If high-quality nesting and post-fledging habitat are not synonymous, fledgling survival and breeding population recruitment may be low. We characterized survival, habitat use, and movement patterns of dependent Kirtland's Warbler fledglings in Wisconsin red pine plantations and compared fledgling survival between Wisconsin and Michigan. Mayfield cumulative survival estimates at 30 days post-fledging were 0.20 for Wisconsin fledglings and 0.43 to 0.78 for Michigan fledglings. Logistic exposure cumulative survival estimates for Wisconsin fledglings were 0.23 to 0.34 at 30 days post-fledging. Fledglings in Wisconsin used areas where vegetation cover and density of red and jack pine were high relative to available areas but not at greater proportions than what was available. Our findings demonstrate that red pine plantations with low pine densities were not equally suitable as nesting and post-fledging habitat, as fledgling survival rates were low. We hypothesize that habitat structure, and not particular pine species, likely contributed to reduced fledgling survival in Wisconsin. Thus, we recommend including red pine as a component in managed Kirtland's Warbler habitat only if tree densities approach optimal levels.</p>
Genotype data for wild lupin populations from central Michigan
<p>Habitat degradation can have significant effects on native species inhabiting natural ecosystems. Within oak barrens and oak-pine barrens ecosystems, there is a complex interspecies interaction between the federally endangered Karner blue butterfly (<em>Lycaeides melissa samuelis</em>) and its obligate host plant, wild lupine (<em>Lupinus perennis</em> L.). Recruitment of wild lupine is critical for maintaining butterfly populations; however, this recruitment can be impeded by habitat fragmentation. Reduced recruitment can result in low genetic diversity in isolated populations, limiting its adaptive potential to respond to environmental change. This study was aimed at understanding the genetic diversity and population structure of wild lupine populations throughout central and west Michigan. We identified significant population structure across most of the populations sampled, with only two sites not significantly different from each other. No sites within our study area displayed statistically significant levels of inbreeding. There are also at least two genetic clusters of wild lupine present within our study region, although there is significant overlap among these groups, indicating that genetic differentiation among clusters may be limited.</p>
Figure 2 in First data on water mite (Acari, Hydrachnidia) assemblages of Point Rosa Marsh, Harrison Township, Michigan, USA, and their use as environmental bioindicators of aquatic health
Figure 2 Point Rosa Marsh along Lake St. Clair, Harrison Township, Michigan, USA. (A) Taken at
Figure 1 in First data on water mite (Acari, Hydrachnidia) assemblages of Point Rosa Marsh, Harrison Township, Michigan, USA, and their use as environmental bioindicators of aquatic health
Figure 1 Map of Lake St. Clair Metropark with inset showing placement in the Lake St. Clair
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
OpenNeuro
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.