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opencc-zeroJun 2023View details →

Dataset for: How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes

For nearly 15 years now, environmental DNA has demonstrated its effectiveness in monitoring biodiversity. Methodological and technical improvements have significantly enhanced the field. However, the effect of factors such as sequence coverage, bioinformatic filtration and primer choice have been less explored or need to be optimized according to specific survey objectives and study site characteristics. We evaluated these factors to help optimize monitoring fish biodiversity in North American temperate lakes. We sampled water for fish community eDNA analysis in 12 lakes from southwestern Québec, Canada. The lakes were selected to encompass a wide range of surface areas and species richness. We sampled water from a total of 520 sites (25 to 50 per lake) and analyzed three mitochondrial DNA regions (12S rRNA; 16S rRNA; and cytb) using NovaSeq sequencing. Our results, based on rarefied count matrices (from a sequencing depth of 100,000 to a minimum depth of 1,000 reads per sample), showed that keeping only species in each sample if they represented at least one thousandth (species minimum read proportion threshold = 0.001) of the sample's reads was adequate to remove false positives and had a limited negative impact on true positives with low read counts. The sequencing depth was found to have a negligible impact on the accuracy of fish community assessment in a given lake. With the same sequencing depth and a complete local reference database for each primer set, a single primer set produced similar species richness medians than the combination of two or three primer sets. Overall, 12S and 16S detected more species and provided more consistent community profiles than cytb. Based on our observations, we suggest using the 12S MiFish-U primer set and applying a minimum proportion of 0.001 reads per species and site to monitor north-temperate lentic freshwater fish communities.

publicJun 2023View details →

Dataset for: How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes

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publicJun 2022View details →

Assessing the conservation priority of freshwater lake sites based on taxonomic, functional and environmental uniqueness

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publicNov 2024View details →

Comparing eDNA and transect methods for aquatic biodiversity assessment in lakes and ponds

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edi36/100

Lakes of Missouri Volunteer Program (LMVP) and University of Missouri: Missouri Statewide Lake Assessment Data (MO-SLAP), 1978-2013

The Lakes of Missouri Volunteer Program (LMVP) is funded by the U.S. Environmental Protection Agency through the Missouri Department of Natural Resources and coordinated by the School of Natural Resources at the University of Missouri. It was created in 1992 and began with four lakes in the Kansas City area. Since then about 200 volunteers have participated and water samples have been collected on over 50 different lakes around the state. The goals of the LMVP are: 1) to determine the current water quality based on productivity or trophic state of Missouri's lakes, 2) to monitor for changes in water quality over time, and 3) to educate the public about lake ecology and water quality issues. Volunteers take water samples to measure algae, nitrogen, phosphorus, inorganic suspended solids, and measure Secchi transparency in the field. Many lakes have several sample sites. The water samples are analyzed at the University of Missouri-Columbia, Department of Fisheries and Wildlife limnology laboratory. An annual data report is compiled containing the results of the data from all of the public lakes. This report is sent to all interested parties including the volunteers, government agencies and lake associations. The process starts in the spring when an LMVP staff and volunteer meet at the lake. The volunteer is given all of the equipment and trained by the staff on the proper collection and processing procedures.

openCC0Apr 2017View details →

edi36/100

Talus microbes and plant assessment for the upper Green Lake Valley from 2007 to 2008.

It is increasingly recognized that species distributions are driven by both abiotic factors and biotic interactions. Despite much recent work incorporating competition, predation, and mutualism into species distribution models (SDMs), the focus has been confined to aboveground macroscopic interactions. Biotic interactions between plants and soil microbial communities are understudied as potentially important drivers of plant distributions. Some soil bacteria promote plant growth by cycling nutrients, while others are pathogenic; thus they have a high potential for influencing plant occurrence. We investigated the influence of soil bacterial clades on the distributions of bryophytes and 12 vascular plant species in a high elevation talus-field ecosystem in the Rocky Mountain Front Range, Colorado, USA. We used an information- theoretic criterion (AICc) modeling approach to compare SDMs with the following different sets of predictors: abiotic variables, abiotic variables and other plant abundances, abiotic variables and soil bacteria clade relative abundances, and a full model with abiotic factors, plant abundances, and bacteria relative abundances. We predicted that bacteria would influence plant distributions both positively and negatively, and that these interactions would improve prediction of plant species distributions. We found that inclusion of either plant or bacteria biotic predictors generally improved the fit, deviance explained, and predictive power of the SDMs, and for the majority of the species, adding information on both other plants and bacteria yielded the best model. Interactions between the modeled species and biotic predictors were both positive and negative, suggesting the presence of competition, parasitism, and facilitation. While our results indicate that plant–plant co-occurrences are a stronger driver of plant distributions than plant–bacteria co-occurrences, they also show that bacteria can explain parts of plant distributions that remain

openCC (other)Dec 2018View details →

opencc-zeroSep 2020View details →

Data from: Paleolimnological assessment of wildfire-derived atmospheric deposition of trace metal(loid)s and major ions to subarctic lakes (Northwest Territories, Canada)

Wildfires release terrestrial elements to the atmosphere as aerosols, and these events are becoming more frequent and intense in the Arctic boreal forest as the climate is warming. We quantified the impact of atmospheric deposition of aerosols from local wildfires on metal(loid) fluxes using macroscopic charcoal accumulation rates, historical fire mapping, and element concentrations in 210Pb‐dated lake sediment from five subarctic lakes with small catchments. Lake sediments showed small but significant increases in fluxes (median = 5–10%) for 22 trace metals, metalloids, or major ions following fire events. The impact of wildfire aerosols on element fluxes was mostly due to short‐term (≤2 years) increasing sedimentation rate (6 ± 41% increase), whereas sediment element concentrations were not strongly impacted. Wildfire‐associated deposition to lake sediments was mainly composed of Ca, Al, Fe, Mg, K, Mn, and Na, which are major constituents of ash from burned biomass, but changes in sediment flux were greatest for Sb, As, Ni, Ba, Mn, Mo, and Sr compared to pre‐disturbance conditions. Compared to anthropogenic sources of pollution, wildfire‐associated atmospheric fluxes of metal contaminants to the lakes (e.g., Hg, Pb, As, Sb, and Cd) were low. This study provides quantitative estimates of wildfire impacts on atmospheric geochemical fluxes to subarctic lakes, which can be used for modeling larger‐scale impacts under changing fire regimes.

opencc-zeroDec 2012View details →

Data from: The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing

During speciation-with-gene-flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome-wide patterns of genetic differentiation, especially if the variance due to the previously mentioned factors is partitioned. In North American lake whitefish (Coregonus clupeaformis), glacial lineages that diverged in allopatry about 60,000 years ago and came into contact 12,000 years ago have independently evolved in several lakes into two sympatric species pairs (a normal benthic and a dwarf limnetic). Variable degrees of reproductive isolation between species pairs across lakes offer a continuum of genetic and phenotypic divergence associated with adaptation to distinct ecological niches. To disentangle the complex array of genetically based barriers that locally reduce the effective migration rate between whitefish species pairs, we compared genome-wide patterns of divergence across five lakes distributed along this divergence continuum. Using restriction site associated DNA (RAD) sequencing, we combined genetic mapping and population genetics approaches to identify genomic regions resistant to introgression and derive empirical measures of the barrier strength as a function of recombination distance. We found that the size of the genomic islands of differentiation was influenced by the joint effects of linkage disequilibrium maintained by selection on many loci, the strength of ecological niche divergence, as well as demographic characteristics unique to each lake. Partial parallelism in divergent genomic regions likely reflected the combined effects of polygenic adaptation from standing variation and independent changes in the genetic architecture of postzygotic isolation. This study illustrates how integrating genetic mapping and population genomics of multiple sympatric species pairs provide a window on the speciation-with-gene-flow mechanism.

opencc-by-4.0Nov 2024View details →

Code_Lake_drought_Assessment

Lake drought: definition, global assessment, and hotspots. 1. 'Lake_area_1km2.xlsx' includes monthly lake area series from 1985 to 2018 for lakes with mean area > 1km2 (162413 lakes across the globe). The first column is lake ID from HydroLakes (https://www.hydrosheds.org/products/hydrolakes) and lake area data is from the GLEV dataset (https://zenodo.org/records/4646621). 2. 'Lake_point.shp' includes 162413 lakes with other attributions from HydroLakes. 3. 'Lake_drought_frequency_trend.xlsx' includes the MK trend results for all studied lakes. 4. 'Lake_drought.m' indicates the MATLAB code for identifying lake droughts and calculating the trends. 5. 'hotspot_regions.shp' indicates the hotspot region (Southern United States and Southeast Australia) 6. 'hotspot_climate.xlsx' indicates the annual anomalies of climatic factors (temperature, precipitation, and VPD).

opencc-zeroFeb 2022View details →

Assessing the population genetic structure of introduced rainbow trout (Oncorhynchus mykiss) in the Lake Tahoe basin: A case for understanding hybridization potential during the reintroduction of the native Endangered Species Act listed Lahontan cutthroat trout (O. clarkii henshawi)

Hybridization with introduced or invasive species is a major threat and driver of population declines in native salmonids. The rainbow trout (Oncorhynchus mykiss, RBT) has been widely introduced globally and represents an important invasive species, often establishing entrenched naturalized populations. The cutthroat trout (Oncorhynchus clarkii, CT), a close congener, is particularly susceptible to competition and hybridization from RBT introductions which has led to range-wide population declines and loss of CT genetic variation. The Lahontan CT (O. c. henshawi, LCT) whose historic distribution included the Lake Tahoe basin, was extirpated by the 1940s due to overfishing and introduction of nonnative salmonids, including now naturalized RBT. Here, we characterize genetic variation of RBT in a subset of Lake Tahoe tributaries to assess potential homing of RBT to streams for spawning, thereby informing LCT reintroduction. Diploid reproductively viable RBT were stocked annually into Lake Tahoe from the late 1800s until the mid-2000s by California and Nevada fish and wildlife agencies, planting the same commonly raised hatchery strains over time. Since 2007, triploid RBT comprise the bulk of RBT planted. Despite extensive dispersal from stocking locations, our analyses revealed variation in population differentiation among tributaries, with individuals from spatially proximate streams clustering across multiple population genetic analyses. Although subtle, we detected evidence for genetic differentiation among tributaries from the southern, western, and northern regions, including surprising structure involving a single tributary. These results illustrate the extent of differentiation within and among streams and could inform possibilities for and implications of RBT removal and LCT reintroduction.

Fig. 3 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 3 Correlation between the samples positions obtained on the first axes of the PCA based on microscopy and HTS diatom composition of the samples. There is a highly significant correlation (p <0.001, R 2 = 31%) between both axes

Fig. 4 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 4 Comparison of the diatom assemblages heterogeneity inside each lake, obtained with HTS and microscopy. Inside lake assemblage heterogeneity is the sum of the Bray-Curtis distances between the three samples of a lake. Correlation is significant (Pearson correlation p <0.001) and follows a linear model (p <0.001, R 2 = 50.8%) (see black line)

Fig. 6 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 6 Correlations of diversity indices obtained with microscopy and HTS. All correlations are significant and follow linear models (see Table 1)

Fig. 2 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 2 Correlation between both distance matrices (Bray-Curtis distances) calculated between diatom compositions of samples obtained with microscopy and HTS

Fig. 5 in Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

Fig. 5 Comparison of diversity indices obtained with microscopy and HTS. Classes boundaries for α diversity: c1 <0.675 ≤ c2 <1.100 ≤ c3 <1.525 ≤ c4 <1.950 ≤ c5 <2.375 ≤ c6 <2.800 ≤ c7 <3.225 ≤ c8 <3.650 ≤ c9 <4.075 ≤ c10. For β diversity: c1 <0.7 ≤ c2 <0.8 ≤ c3 <0.9 ≤ c4 <1.0 ≤ c5 <1.1 ≤ c6 <1.2 ≤ c7 <1.3 ≤ c8 <1.4 ≤ c9 <1.5 ≤ c10. For ϒ diversity: c1 <1.04 ≤ c2 <1.48 ≤ c3 <1.92 ≤ c4 <2.36 ≤ c5 <2.80 ≤ c6 <3.24 ≤ c7 <3.68 ≤ c8 <4.12 ≤ c9 <4.56 ≤ c10

opencc-zeroDec 2017View details →

Data from: A review of the defining chemical properties of soda lakes and pans: an assessment on a large geographic scale of Eurasian inland saline surface waters

The aim of this study is to evaluate the definition of water chemical type, with particular attention to soda brine characteristics by assessing ionic composition and pH values on a large geographic scale and broad salinity (TDS) range of Eurasian inland saline surface waters, in order to rectify the considerable confusion about the exact chemical classification of soda lakes and pans. Data on pH and on the concentration of eight major ions were compiled into a database drawn from Austria, China, Hungary, Kazakhstan, Mongolia, Russia, Serbia, and Turkey. The classification was primarily based on dominant ions exceeding an equivalent percentage of 25 (> 25e%) of the total cations or anions, and the e% rank of dominant ions was also identified. We identified four major types: waters dominated by (1) Na-HCO3 (10.0%), (2) Na-HCO3 + CO3 (31.4%), (3) Na-Cl (45.9%), and (4) Na-SO4 (12.7%), considering only the first ion by e% rank. These major types can be divided into 30 subtypes in the dataset, taking into account the e% rank of all dominant ions. The major and subtypes of soda brine can be divided into "Soda" and "Soda-Saline" types. "Soda type" when Na+ and HCO3– + CO32– are the first in the rank of dominant ions (> 25e%), and "Soda-Saline type" when Na+ is the first in the rank of dominant cations and the sum of HCO3– + CO32– concentration exceeds 25e%, but it is not the first in the rank of dominant anions. Soda-saline type can be considered as a separate evolutionary stage between Soda and Saline types respect to the geochemical interpretation by saturation indexes of brines. The obtained overlapping ranges in distribution demonstrate that a pH measurement alone is not a reliable indicator to classify the permanent alkaline "soda type" and various other types of temporary alkaline waters.

ClinicalTrials.gov32/100

A Study to Assess Infection Rate of Severe Acute Respiratory Syndrome - CoronaVirus 2 (SARS-CoV-2) and It's Affect on Quality of Life in Adult Volunteers in Lake County, Illinois

ClinicalTrials.gov study NCT04611230. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.

restrictedIPD-UNDECIDEDFeb 2026View details →

publicApr 2022View details →

Assessing the population genetic structure of introduced rainbow trout (Oncorhynchus mykiss) in the Lake Tahoe basin: A case for understanding hybridization potential during the reintroduction of the native Endangered Species Act listed Lahontan cutthroat trout (O. clarkii henshawi)

Open the record for dataset details and reuse information.