Find research datasets worth reusing

Using by-catch camera trapping data for estimating the population size of spotted hyena (Crocuta crocuta)

Spotted hyenas (Crocuta crocuta) are an important carnivore species whose dual role of scavenger and predator is vital to trophic energy flows of systems in which they are found. Where populations of spotted hyenas are small, the environment has few cleaners and carcasses can remain unprocessed. Despite being largely characterized as scavengers, spotted hyenas actively hunt and take down live prey and at high densities can have depressing effects on fragile or choice ungulate populations. In addition, they can alter the structure and composition dynamics of the carnivore guild through direct conflict or indirectly through competition for food and space. Despite their importance to ecosystem function and balance, reliable estimates of spotted hyena densities are rare. This is because unlike lions and leopards, spotted hyenas are generally not regarded as a charismatic species and, as such, survey resources, which are costly, are seldom solely allocated towards surveying them. Nonetheless, being able to confidently estimate spotted hyena numbers is important for the effective management of carnivore and herbivore populations whose dynamics they influence.

opencc-by-4.0Jun 2022View details →

Morphological Data for 95 populations of Silene seeds

Raw data for Area, Perimeter, Length, Width, Aspect Ratio, Circularity, Roundness and Solidity for the lateral and dorsal views of 102 populations belonging to 52 species (49 species of Silene and three related species).

Population structure and demographic analyses of Acanthocybium solandri from the Indo-Pacific and Atlantic oceans

This repository contains scripts, data and results for a populaton genomics study of genetic structure and demography of wahoo, Acanthocybium solandri, published in Journal of Biogeography: Haro-Bilbao et al. (2021) Global connections with some genomic differentiation occur between Indo-Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish. In this work, we generated population allele frequencies for wahoo sampled at 11 locations around the globe using a pooled ezRAD approach. Using thousands of genome-wide SNPs, we demonstrated a significant (but subtle) genetic divide between wahoo from the Indo-Pacific and those from the Atlantic. This genetic differentiation likely occurs against a background of high gene glow throughout the evolutionary history of wahoo, as we inferred from demographic analysis of select population pairs within and between oceanic regions. Analyses contained in this repository are for: (1) Filtering pooled ezRAD allele counts (assembled with dDocent and imputed using poolne_estim); (2) Estimation of genetic differentiation among globally sampled wahoo populations; (3) Estimation of site frequency spectra from joint allele frequencies among select population pairs; (4) Inference of demographic parameters (using δaδi); and (5) Generations of demographic simulation summary statistics. Most of the analyses are performed in R and can be run directly from within the repository directory, this includes: allele filtering, estimation of genetic differentiation, estimaiton of site frequency spectra, and generation of demographic summary statistics. Demographic inference using δaδi requires setup of a Unix environment: input data files and execution scripts are provided, but their implementation needs to be customised.

Extensive population-level sampling reveals clinal variation in (R)-(-)-linalool produced by the flowers of an endemic evening primrose, Oenothera harringtonii

<div></div> <div> <div> The study of floral trait diversity has a long history due to its role in angiosperm diversification. While many studies have focused on visual traits including morphology and color, few have included floral scent despite its importance in pollination. Of the studies that have included floral scent, sampling has been limited and rarely explores variation at the population level. We studied geographic variation in the flowers of Oenothera harringtonii, a rare plant endemic to a vulnerable shortgrass prairie habitat, whose population structure and conservation status are well studied. The self-incompatible flowers of O. harringtonii open at dusk, produce nectar and a strong fragrance, and are pollinated by hawkmoths. We collected floral trait (morphology, scent chemistry and emission rates) data from 650 individuals from 19 wild populations to survey floral variation across the entire range of this species. Similarly, we collected floral data from 49 individuals grown in a greenhouse common garden, to assess whether variation observed in the field is consistent when environment factors (temperature, watering regime, soil) are standardized. We identified 35 floral volatiles representing 5 biosynthetic classes. Population differentiation was stronger for floral scent chemistry than floral morphology. (R)-(−)-linalool was the most important floral trait differentiating populations, exhibiting clinal variation across the distribution of O. harringtonii without any correlated shifts in floral morphology. Populations in the north and west produced (R)-(−)-linalool consistently, those in the east and south largely lacked it, and populations at the center of the distribution were polymorphic. Floral scent emissions in wild populations varied across four years but chemical composition was largely consistent over time. Similarly, volatile emission rates and chemical composition in greenhouse-grown plants were consistent with those of wild populations of origin. Our data set, which represents the most extensive population-level survey of floral scent to date, indicates that such sampling may be needed to capture potentially adaptive geographic variation in wild populations. </div> </div>

Individual growth of the Flathead Knobscaled Lizard, Xenosaurus platyceps, from tropical and temperate populations

Growth rates of ectotherms are frequently affected by environmental conditions, such as temperature, precipitation, and prey availability. However, local adaptation to environmental conditions could influence geographic variation in growth rates. We studied growth rates of the Flathead Knob-scaled Lizard, Xenosaurus platyceps, from a tropical population and a temperate population in Tamaulipas, Mexico. We used a field study and a common garden experiment to examine the extent and potential causes of variation in individual growth rates between these two populations from contrasting environments. Field-determined growth rates in the tropical population were greater than those in the temperate population. In a laboratory common garden experiment that manipulated food availability and temperature for neonates from each population, neonates from the tropical population grew faster than those from the temperate population. Neonates kept at higher temperatures grew faster than those kept at lower temperature. In addition, growth rates of neonates from temperate and tropical populations did not differ at low temperature, but neonates from the tropical population grew faster at the higher temperature than did the neonates from the temperate population. Food treatment did not affect individual growth rates in these lizards, although there was a trend for neonates grown with higher food availability to grow faster. Our results suggest that not only does the warm environment of the tropical population contribute to the observed differences in field growth rates, but there is a genetic difference in the ability of the tropical population to take advantage of the warmer temperatures to increase growth rates.

opencc-zeroDec 2021View details →

Data to accompany from: Effects of neonicotinoid seed treatments on wildbee populations and soybean and corn fields in eastern Ontario

Neonicotinoid-coated corn and soybean seeds are a common crop in Canada and the US. A growing body of research is demonstrating that, through various exposure routes, neonicotinoids can impact a suite of non-target organisms including beneficial insects such as bees. However, to date, only a few studies have examined the effects of neonicotinoids in field settings. We assessed the relationship between agricultural crop soil neonicotinoid levels and wild bee abundance and diversity at 16 agricultural sites representing different soil neonicotinoid levels. We detected clothianidin at 11 sites, thiamethoxam at three sites; imidacloprid was not detected. Hedgerow and crop soils were consistent in terms of where clothianidin was detected; thiamethoxan was not detected in hedgerow soils. Based on model outcomes, fields with higher levels of soil neonicotinoids exhibited significantly lower wild bee abundance and diversity than those with low or no neonicotinoids detected. Crop soil neonicotinoid level, hedgerow floral resource abundance and crop type were consistent predictors of bee abundance across models; only neonicotinoid level and crop type were significant predictors of diversity. Our results are consistent with recent findings in the midwestern US, and underscore the potential risk of soil neonicotinoids to wild bee populations across regions and crop systems.

opencc-by-4.0Apr 2022View details →

Data availability: Random encounter model is a reliable method for estimating population density of multiple species using camera traps

Data of the paper entitled "Random encounter model is a reliable method for estimating population density of multiple species using camera traps" published on Remote Sensing in Ecology and Conservation

Data from: Forest connectivity boosts pollen flow among populations of the oil-producing Nierembergia linariifolia

Context The process of forest fragmentation determines landscapes with isolated forest patches immersed in a distinct matrix. This process may hinder pollinator movement throughout the landscape, which may negatively impact on pollen flow among native plant populations. Objectives We evaluated the effect of the loss of forest connectivity on pollen dispersal by specialized native bees in the oil-producing and self-incompatible Nierembergia linariifolia. Methods We estimated pollen flow between plants of N. linariifolia at an agroecosystem with remnant forest of central Argentina. Six plant populations (source populations) were treated with fluorescent dyes as pollen analogues, and stigmata of recipient plants were collected to seek for dye particles. Dye deposition rate was assessed for plants that were connected through remnant forest to a source population or unconnected by a crop matrix, and at increasing distances to a source population. Results Deposition rate per plant was higher in connected than in unconnected plants, and decreased with increasing distances to a source population in an exponential fashion. Most of the dispersal events between connected plants occurred at the vicinity of a source population. Long dispersal events (up to 1259 m) were recorded between plants located at neighbouring forest patches separated by an agricultural matrix. Conclusions Landscape connectivity through forest remnants is key to enhance pollen flow between self-incompatible plants such as N. linariifolia. Besides, the evidence of pollen dispersal through the agricultural matrix pinpoints the essential role of native pollinators in maintaining pollen flow among unconnected plant populations in fragmented landscapes.

Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients

The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution towards its range periphery and consequently its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers we studied the genetic diversity and structure of 20 populations each of Anthyllis vulneraria along elevational gradients in the Alps from the valleys to the elevational limit (2500 m), and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to a 11.5 °C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in A. vulneraria, this pattern is not likely to be due to less favourable conditions in the North, but due to serial founder effects during the post-glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long-term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low-elevation populations.

SolCAP 8K array genotyping of population 15143

The dataset is a tab-deliminted text file with genotyping information for a diploid potato progeny population derived from a cross of diploid potato clones 12120-03 X 07506-01. The SolCap 8303 Infinium Chip was used for SNP genotyping. It was originally generated for study on genetic mapping of Verticillium wilt resistance. The data was used again for analysis of segregation distortion in the most recent manuscript.

opencc-by-4.0Jul 2022View details →

High-quality video file for Doekes, H.M. and Hermsen, R, "Multiscale selection in spatially structured populations" (2022)

High-quality version of supplementary movie 1 as published with: Doekes, H.M. and Hermsen, R, "Multiscale selection in spatially structured populations" (to be submitted, 2022)

Date advanced functional nuclear magnetic resonance techniques for pediatric population diagnosed with Attention Deficit Hyperactivity Disorder

Attention deficit hyperactivity disorder (ADHD) is highly prevalent childhood-onset neurodevelopment disorder. Several clinical tools are used for ADHD diagnosis such as behavior rating scales, intelligence tests, severity, and dysfunction scales. However, these methods depend to the experience and training of physician increasing human error. DICOM Images using Magnetic Resonance Imaging (MRI) provides quantitative result such as fractional anisotropy or the number of tracts that could be helpful to support ADHD diagnosis.

Triparental ageing in a laboratory population of an insect with maternal care

Parental age at reproduction influences offspring size and survival by affecting pre- and postnatal conditions in a wide variety of species, including humans. However, most investigations into this manifestation of ageing focus upon maternal age effects; the effects of paternal age and interactions between maternal and paternal age are often neglected. Furthermore, even when maternal age effects are studied, pre- and postnatal effects are often confounded. Using a cross-fostered experimental design, we investigated the joint effects of prenatal paternal and maternal and postnatal maternal ages on five traits related to offspring outcomes in a laboratory population of a species of burying beetle, Nicrophorus vespilloides. We found a significant positive effect of the age of the egg producer on larval survival to dispersal. We found more statistical evidence for interaction effects, which acted on larval survival and egg length. Both interaction effects were negative and involved the age of the egg-producer, indicating that age-related prenatal maternal improvements were mitigated by increasing age in fathers and foster mothers. These results agree with an early study that found little evidence for maternal senescence, but it emphasizes that parental age interactions may be an important contributor to ageing patterns. We discuss how the peculiar life history of this species may promote selection to resist the evolution of parental age effects, and how this might have influenced our ability to detect senescence.

opencc-by-4.0Jul 2022View details →

The Large Magellanic Cloud Revealed in Gravitational Waves with LISA: Population Release

The Large Magellanic Cloud (LMC)’s binary populations for study by the Laser Interferometer Space Antenna (LISA) as generated by Keim et al. in a paper submitted to MNRAS (Keim, M. A., Korol, V., Rossi, E. M. The Large Magellanic Cloud Revealed in Gravitational Waves with LISA. Monthly Notices of the Royal Astronomical Society, 2022, submitted). The files include all current double white dwarfs in the LISA band (‘LISABand’), all which will be detectable with a S/N>7 after 4 yrs (‘Detect’), and all which are detached/non-accreting, i.e. sure LISA sources (‘Detached’). This release represents a 2.7*10^9 stellar mass LMC, and includes distribution models based on observation (‘M1’) and simulation (‘M3’). For more information, please refer to Keim et al. (2022). We request that researchers utilising any of these populations cite Keim et al. (2022). The data columns are as follows: Column  1 = Right Ascension (Degrees) Column  2 = Declination (Degrees) Column  3 = Age (Myr, since formation of Main Sequence Pair) Column  4 = Mass of White Dwarf One (Msun) Column  5 = Mass of White Dwarf Two (Msun) Column  6 = Radius of White Dwarf One (Rsun) Column  7 = Radius of White Dwarf Two (Rsun) Column  8 = Orbital Radius (Rsun) Column  9 = Frequency (Hz) Column 10 = Chirp (Hz^2) Column 11 = Latitude (Radians) Column 12 = Longitude (Radians) Column 13 = Amplitude (Defined with a prefactor of 2) Column 14 = Inclination (Radians) Column 15 = Polarization (Radians) Column 16 = Orbital Phase (Radians) Column 17 = Distance (kpc) Column 18 = Mass Transfer (1= Yes, i.e. Roche Lobe Overfill, 0= No)

Data for: Soil microbiota explain differences in herbivore resistance between native and invasive populations of a perennial herb

Soil microbiota can either slow down or facilitate plant invasions through their effects on plant performance. Associations with soil microbiota can also modify other plant traits such as herbivore resistance, which can indirectly affect the outcome of plant introductions. We studied the effects of soil microbiota on the perennial herbaceous legume Lupinus polyphyllus that hosts nitrogen-fixing mutualistic bacteria. We compared the plant performance, herbivore resistance, and volatile organic compounds (VOCs) of plants from native (North American) and invasive (Finnish) populations of the species that were inoculated with intact or autoclaved soil from an invasive population. We found that plants of both origins greatly benefited from the intact soil inoculum with respect to all performance measures considered, suggesting that beneficial nitrogen-fixing rhizobia in the soil play a major role in shaping plant phenotypes. For three traits, effects of the intact soil inoculum were stronger in plants of native origin than in plants of invasive origin (number of leaves, herbivore resistance, and total biomass). With the intact soil inoculum, plants of invasive origin were more resistant to snails than plants of native origin. Strikingly, differences in resistance to snails between plants of different origins disappeared entirely when soil microbes were reduced. Soil inoculum treatment altered the composition of the leaf VOC bouquet similarly regardless of plant origin. Synthesis: These results demonstrate the ability of L. polyphyllus to associate with and benefit from putatively novel soil microbiota including rhizobia, which has likely contributed to its invasion success. Furthermore, it appears that the invasive populations have adapted to be less reliant on their symbionts, which further facilitates species spread. To our knowledge, this is the first study to demonstrate that differences in herbivore resistance between native and invasive plant populations of the same species can depend entirely on soil microbiota.

opencc-by-4.0Jul 2022View details →

Population Census Peru 1876-2017

Population Census Peru 1876-2017

Nuclear genetic diversity and structure of Anastrepha ludens wild populations evidenced by microsatellite markers

The Mexican fruit fly, Anastrepha ludens is an important pest that causes widespread damage to a number of fruit crops in Mexico. The Sterile Insect Technique (SIT) is commonly used for its control. However, the existence of natural barriers can give rise to a population structure in neutral loci and possibly behavioral or adaptive traits that interfere with SIT. For this reason, it is important to understand the genetic diversity and structure of A. ludens populations and to better understand the evolutionary ecology and population processes in view of possible expansions and possible host shifts due to climate change. We genotyped nine nuclear DNA (nDNA) microsatellite loci among fruit fly populations collected from five biogeographic areas within Mexico, Mexican Plateau, the Northeastern Coastal Plain, the Pacific Coast, the Gulf Coast of Mexico, the Soconusco and a laboratory strain. The nuclear genetic diversity was moderate (from He = 0.34 to He = 0.39) within the wild mexfly population. We found that populations were clustered in three genetic groups (K=3). The diversity and genetic structure of A. ludens are produced by environmental and geological conditions as well as local conditions like anthropogenic perturbation which would produce population expansion and the existence of possible predators that would affect the population density. Gene flow showed recent migration among populations. The laboratory strain showed less diversity than the wild samples. Large values of current and ancestral population size suggest high resistance to climatic changes, probably due to biological attributes, such as its polyphagous, multivoltine and high dispersal characteristics. In particular ecosystem fragmentation and perturbation as well as the existence of new plant hosts all of which would probably increase the abundance of flies.

opencc-zeroAug 2022View details →

Older populations of the invader Solidago canadensis exhibit stronger positive plant-soil feedbacks and competitive ability in China

PREMISE The enemy release hypothesis predicts that release from natural enemies, including soil-borne pathogens, liberates invasive plants from a negative regulating force. Nevertheless, invasive plants may acquire novel enemies and mutualists in the introduced range, which may cause variable effects on invader growth. However, how soil microorganisms may influence competitive ability of invasive plants along invasion chronosequences has been little explored. METHODS Using the invasive plant Solidago canadensis, we tested whether longer residence times are associated with stronger negative plant-soil feedbacks and thus weaker competitive abilities at the individual level. We grew S. canadensis individuals from 36 populations with different residence times in competition versus no competition and in three different types of soils: (1) conspecific rhizospheric soils, (2) soil from uninvaded patches, and (3) sterilized soil. For our competitor treatments, we constructed synthetic communities of four native species Bidens parviflora, Solanum nigrum, Kalimeris indica, and Mosla scabra, which naturally co-occur with S. canadensis in the field. RESULTS Solidago canadensis populations with longer residence times experienced stronger positive plant-soil feedbacks and had greater competitive responses (i.e., produced greater above-ground biomass and grew taller) in conspecific rhizospheric soils than in sterilized and uninvaded soils. Moreover, S. canadensis from older populations significantly suppressed above-ground biomass of the native communities in rhizospheric and uninvaded soils but not in sterilized soil. CONCLUSIONS The present results suggest that older populations of S. canadensis experience stronger positive plant-soil feedback, which may enhance their competitive ability against native plant communities.

opencc-zeroAug 2022View details →

Strong isolation by distance among local populations of an endangered butterfly species (Euphydryas aurinia)

The marsh fritillary (Euphydryas aurinia) is a critically endangered butterfly species in Denmark known to be particularly vulnerable to habitat fragmentation due to its poor dispersal capacity. We identified and genotyped 318 novel SNP loci across 273 individuals obtained from 10 small and fragmented populations in Denmark using a genotyping-by-sequencing (GBS) approach to investigate its population genetic structure. Our results showed clear genetic substructuring and highly significant population differentiation based on genetic divergence (FST) among the 10 populations. The populations clustered in three overall clusters and due to further substructuring among these, it was possible to clearly distinguish six clusters in total. We found highly significant deviations from Hardy-Weinberg equilibrium due to heterozygote deficiency within every population investigated which indicates substructuring and/or inbreeding (due to mating among closely related individuals). The stringent filtering procedure that we have applied to our genotype quality could have overestimated the heterozygote deficiency and the degree of substructuring of our clusters but is allowing relative comparisons of the genetic parameters among clusters. Genetic divergence increased significantly with geographic distance, suggesting limited gene flow at spatial scales comparable to the dispersal distance of individual butterflies and strong isolation by distance. Altogether, our results clearly indicate that the marsh fritillary populations are genetically isolated. Further, our results highlight that the relevant spatial scale for conservation of rare, low mobile species may be smaller than previously anticipated.