Find research datasets worth reusing

opencc-zeroDec 2015View details →

Data from: Phylogenetic diversity reveals hidden patterns related to population source and species pools during restoration

A phylogenetic perspective of community assembly can reveal new insights into how variation within dominant species interacts with the local species pool to influence the structure of restored plant communities. Many studies have examined the effect of dominant species in structuring plant communities, but few have investigated their effect on phylogenetic diversity (PD). We established grassland in a post-agricultural field using two population sources (cultivars and local ecotypes) of three dominant grasses (Sorghastrum nutans, Andropogon gerardii and Schizachyrium scoparium) with three unique pools of subordinate species that varied in PD but not taxonomic or life-form diversity. We tested the effect of the population source treatment on two metrics of community PD (net relatedness index [NRI] and nearest taxon index [NTI]) during the first 4 years of restoration. The NRI measures the overall pairwise phylogenetic distance between all pairs of taxa in a community. By contrast, NTI measures the pairwise distance between closely related taxa in a community. Population sources had a transitory effect on community phylogenetic structure over time. Local ecotypes decreased the abundance of closely related eudicots, monocots (low +NRI and +NTI values) and volunteer species (−NTI) more than cultivars. However, population sources did not affect ecologically conservative species (i.e. species with intermediate-to-poor ecological tolerance and a high degree of fidelity to prairie habitats). Thus, cultivars might have a positive effect on community phylogenetic diversity more than local ecotypes by decreasing the abundance of a phylogenetically diverse community of less closely related volunteer species. Differences in PD of seed mixes were maintained in the community of high-fidelity species, but did not affect PD of the unsown (volunteer) species in the assembling community. Synthesis and applications. This is the first experiment to show consequences of using different seed sources on phylogenetic diversity (PD) in grassland restoration. Phylogenetics can reveal the effects of population sources on the abundance of volunteer species not evident through traditional analyses of species diversity. The PD of seed mixes or establishing communities, or other assessments of phylogenetic relationships, by restoration practitioners is recommended as a metric to allow consequences of the evolutionary patterns among species to be included in conservation planning. Increased accessibility of phylogenetic tools will allow the application of PD in restoration monitoring.

opencc-zeroDec 2016View details →

Data from: Species pool functional diversity plays a hidden role in generating β-diversity

Functional trait diversity is used as a way to infer mechanistic processes that drive community assembly. While functional diversity within communities is often viewed as a response variable, here we present and test a framework for how functional diversity among taxa in the regional species pool drive the assembly of communities among habitats. We predicted that species pool functional diversity should work with environmental heterogeneity to drive β-diversity. We tested these predictions by modeling empirical patterns in invertebrate communities from 570 streams in 52 watersheds. Our analysis of the field data provided strong support for the inclusion of both functional diversity and environmental heterogeneity in the models, and our predictions were supported when the community was analyzed all together. However, analyses within individual functional feeding guilds revealed strong context dependency in the relative importance of functional diversity, γ-richness, and environmental heterogeneity on β-diversity. We interpret the results to mean that functional diversity can play an important role in driving β-diversity; however, within guilds the nature of interspecific interactions and species pool size complicate the relationship. Future research should test this conceptual model across different ecosystems and in experimental settings using metacommunity mecocosms to enhance our understanding the role that functional variation plays in generating spatial biodiversity patterns.

opencc-zeroDec 2017View details →

Data from: Global patterns in helminth host specificity: phylogenetic and functional diversity of regional host species pools matter

Host specificity has a major influence on a parasite's ability to shift between human and animal host species. Yet there is a dearth of quantitative approaches to explore variation in host specificity across biogeographical scales, particularly in response to the varying community compositions of potential hosts. We built a global dataset of intermediate host associations for nine of the world's most widespread helminth parasites (all of which infect humans). Using hierarchical models, we asked if realised parasite host specificity varied in response to regional variation in the phylogenetic and functional diversities of potential host species. Parasites were recorded in 4-10 zoogeographical regions, with some showing considerable geographical variation in observed versus expected host specificity. Parasites generally exhibited the lowest phylogenetic host specificity in regions with the greatest variation in prospective host phylogenetic diversity, namely the Neotropical, Saharo-Arabian and Australian regions. Globally, we uncovered notable variation in parasite host shifting potential. Observed host assemblages for Hydatigera taeniaeformis and Hymenolepis diminuta were less phylogenetically diverse than expected, suggesting limited potential to spillover into unrelated hosts. Host assemblages for Echinococcus granulosus, Mesocestoides lineatus and Trichinella spiralis were less functionally diverse than expected, suggesting limited potential to shift across host ecological niches. By contrast, Hydatigera taeniaeformis infected a higher functional diversity of hosts than expected, indicating strong potential to shift across hosts with different ecological niches. We show that the realised phylogenetic and functional diversities of infected hosts are determined by biogeographical gradients in prospective host species pools. These findings emphasise the need to account for underlying species diversity when assessing parasite host specificity. Our framework to identify variation in realised host specificity is broadly applicable to other host-parasite systems and will provide key insights into parasite invasion potential at regional and global scales.

opencc-zeroDec 2015View details →

Data from: Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq

Understanding the genomic basis of adaptive divergence in the presence of gene flow remains a major challenge in evolutionary biology. In prickly sculpin (Cottus asper), an abundant euryhaline fish in northwestern North America, high genetic connectivity among brackish-water (estuarine) and freshwater (tributary) habitats of coastal rivers does not preclude the build-up of neutral genetic differentiation and emergence of different life history strategies. Because these two habitats present different osmotic niches, we predicted high genetic differentiation at known teleost candidate genes underlying salinity tolerance and osmoregulation. We applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to explore adaptive divergence between two estuarine and two tributary habitats. Paired-end sequence reads were mapped against genomic contigs of European Cottus, and the gene content of candidate regions was explored based on comparisons with the threespine stickleback genome. Genes showing signals of repeated differentiation among brackish-water and freshwater habitats included functions such as ion transport and structural permeability in freshwater gills, which suggests that local adaptation to different osmotic niches might contribute to genomic divergence among habitats. Overall, the presence of both repeated and unique signatures of differentiation across many loci scattered throughout the genome is consistent with polygenic adaptation from standing genetic variation and locally variable selection pressures in the early stages of life history divergence.

opencc-zeroDec 2020View details →

Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species

Despite their suitability for studying evolution, many conifer species have large and repetitive giga-genomes (16-31Gbp) that create hurdles to producing high coverage SNP datasets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within Pinaceae, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost-saving benefits of pool-seq and exome-capture to discover SNPs in two conifer species, Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco, Pinaceae) and jack pine (Pinus banksiana Lamb., Pinaceae). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong positive correlation with those estimated by sequencing the same population as individuals (r > 0.948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are likely due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r > 0.973). Our work addresses bioinformatic challenges in non-model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralog sites, and suggests the combination of pool-seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.

opencc-zeroJul 2021View details →

Data from: Consequences of aboveground invasion by non-native plants into restored vernal pools do not prompt changes in belowground processes

Given the frequent overlap between biological plant invasion and ecological restoration efforts it is important to investigate their interactions to sustain desirable plant communities and modify long-term legacies both above and belowground. To address this relationship, we used natural reference, invaded, and constructed vernal pools in the Central Valley of California to examine potential changes in direct and indirect plant effects on soils associated with biological invasion and active restoration ecosystem disturbances. Our results showed that through a shift in vegetation composition and changes in the plant community tissue chemistry, invasion by non-native plant species has the potential to transform plant inputs to soils in vernal pool systems. In particular, we found that while non-native litter decomposition was driven by seasonal and interannual variability, associated with changes in precipitation, the overall decomposition for non-native litter was drastically lower than native species. This shift has important implications for long-term alterations in plant-based inputs to soils in a negative feedback to nutrient cycling. Moreover, these results were independent of historic active restoration efforts. Despite the consistent shift in plant litter decomposition rates and community composition, we did not detect associated shifts in belowground function associated with invasion by non-native plants. Instead, soil C:N ratios and microbial biomass did not differ between invaded and reference naturally occurring pools but were reduced in the manipulated restored pools independent of invasion levels. Our results suggest that while there is an observed invasive positive feedback aboveground, this trajectory is not necessarily represented belowground and restoration legacies were still dominant ten years after practices were applied. Restoration practices that limit invasive plant feedbacks and account for soil legacy recovery, therefore offer the best solution for disturbed ephemeral ecosystems.

opencc-zeroMay 2022View details →

Genomic variation within the maize Stiff Stalk heterotic germplasm pool

The Stiff Stalk heterotic group is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and to a lesser extent B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four ex-Plant Variety Protection lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40 which is a Pioneer Hi-Bred early Stiff Stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13 to 2.18 Gbp with N50 scaffold lengths greater than 200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas and transposable element annotation was conducted using de novo and homology-directed methodologies. In comparison to the reference inbred B73, synteny analyses revealed extensive collinearity across the five Stiff Stalk genomes, although unique components of the maize pan-genome were detected. Comparison of this set of Stiff Stalk genome sequences with the original Stiff Stalk population revealed that these inbreds represent only a proportion of variation in the original Stiff Stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original Stiff Stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent Stiff Stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pan-genome.

opencc-zeroSep 2021View details →

Data and scripts from: Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

<ul> <li>The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only ~6Mya have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved.</li> <li>Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. </li> <li>We find that two recently described species from northeast Brazil's Atlantic forest were the earliest to diverge, strongly suggesting a South American common ancestor of Manihot. Ancestral state reconstruction indicates early Manihot diversification in dry forests, with numerous independent episodes of new habitat colonization including into savannas and rainforests within South America. We identify the closest wild relatives to M. esculenta including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species including M. glaziovii, a species used widely in breeding programs. Finally, we show that this wild-to-crop introgression substantially shapes the mutation load in cassava.</li> <li>Our findings provide a detailed case study for neotropical evolutionary history in a diverse and widespread group, and a robust phylogenomic framework for future Manihot and cassava research.</li> </ul>

opencc-by-4.0Jan 2023View details →

Geophysical data collected at Obsidian Pool Thermal Area, Yellowstone National Park, in 2015-2016

Geophysical data (EMI, GTEM, Seismic, Resistivity) collected over Obsidian Pool Thermal Area, Yellowstone National Park, in 2015 and 2016.

opencc-zeroMar 2023View details →

Data set from: Phylogenetic structure of alien plant species pools from European donor habitats

Aim. Many plant species native to Europe have naturalized worldwide. We tested whether the phylogenetic structure of the species pools of European habitats is related to the proportion of species from each habitat that have naturalized outside Europe (habitat's donor role) and whether the donated species are more phylogenetically related to each other than expected by chance. Location. Europe (native range), the rest of the World (invaded range). Time period. Last c. 100 years. Major taxa studied. Angiospermae. Methods. We selected 33 habitats in Europe and analyzed their species pools, including 9,636 plant species, of which 2,293 have naturalized outside Europe. We assessed the phylogenetic structure of each habitat as the difference between the observed and expected mean pairwise phylogenetic distance (MPD) for (a) the whole species pool and (b) subgroups of species that have naturalized outside Europe and those that have not. We used generalized linear models to test for the effects of the phylogenetic structure and the level of human influence on the habitats' donor role. Results. Habitats strongly to moderately influenced by humans often showed phylogenetically clustered species pools. Within the clustered species pools, those species that have naturalized outside Europe showed a random phylogenetic structure. Species pools of less human-influenced natural habitats varied from phylogenetically clustered to overdispersed, with donated naturalized species also often showing random patterns within the species pools. Donor roles in both habitat groups increased with increasing MPD within habitats. Main conclusions. European human-influenced habitats donate closely related species that often naturalize in disturbed habitats outside their native range. Natural habitats donate species from different lineages with various ecological strategies that allow them to succeed in different habitats in the invaded range. However, in most cases, the naturalized species donated are phylogenetically random subsets of the donor habitats' species pools. Aim. Many plant species native to Europe have naturalized worldwide. We tested whether the phylogenetic structure of the species pools of European habitats is related to the proportion of species from each habitat that have naturalized outside Europe (habitat's donor role) and whether the donated species are more phylogenetically related to each other than expected by chance. Location. Europe (native range), the rest of the World (invaded range). Time period. Last c. 100 years. Major taxa studied. Angiospermae. Methods. We selected 33 habitats in Europe and analyzed their species pools, including 9,636 plant species, of which 2,293 have naturalized outside Europe. We assessed the phylogenetic structure of each habitat as the difference between the observed and expected mean pairwise phylogenetic distance (MPD) for (a) the whole species pool and (b) subgroups of species that have naturalized outside Europe and those that have not. We used generalized linear models to test for the effects of the phylogenetic structure and the level of human influence on the habitats' donor role. Results. Habitats strongly to moderately influenced by humans often showed phylogenetically clustered species pools. Within the clustered species pools, those species that have naturalized outside Europe showed a random phylogenetic structure. Species pools of less human-influenced natural habitats varied from phylogenetically clustered to overdispersed, with donated naturalized species also often showing random patterns within the species pools. Donor roles in both habitat groups increased with increasing MPD within habitats. Main conclusions. European human-influenced habitats donate closely related species that often naturalize in disturbed habitats outside their native range. Natural habitats donate species from different lineages with various ecological strategies that allow them to succeed in different habitats in the invaded range. However, in most cases, the naturalized species donated are phylogenetically random subsets of the donor habitats' species pools.

opencc-by-4.0Jan 2023View details →

Dataset: Bed Stability of Step-Pool Channels with Macrorough Sidewalls

The data set includes the cumulative sediment outflow data and the digital elevation model (DEM) data of flume experiments conducted at the Laboratory of Hydraulics, Hydrology, and Glaciology (VAW) at ETH Zurich.

opencc-zeroMay 2023View details →

Rock pools as a source of environmental DNA for the detection of the threatened Pilbara olive python (Liasis olivaceus barroni)

Environmental DNA (eDNA) research is transforming biomonitoring at a global scale, but applicability to reptiles has been restricted because of their presumed low shedding rate. Consequently, eDNA may have considerable limitations as a biomonitoring tool in Australia where 40% of the terrestrial vertebrates are reptiles. However, there is a need to evaluate if method improvements such as targeting certain substrates, improves the ability to detect reptile eDNA. The Pilbara olive python (Liasis olivaceus barroni) is an uncommon and elusive Australian top predator with a high conservation priority. Like many other snake species, Pilbara olive pythons are challenging to monitor with traditional survey methods, therefore exploring an eDNA-based approach is highly relevant. The pythons are known to occasionally reside in rock pools. Thus, development of a reliable eDNA-based approach to detect the pythons in water would provide a needed alternative method. Here we use a previously developed metabarcoding assay targeting reptiles, to sequence a total of 228 water samples collected from 40 rock pools from six broad locations across the Pilbara region of Western Australia, and we confirm the presence of Pilbara olive python eDNA in 37 samples from 12 of those pools at three of the six broad sampling locations. Other vertebrate taxa, including other reptiles, amphibians, mammals and birds were also detected. Our documented ability to detect Pilbara olive python eDNA from rock pool water samples represents an important step towards eDNA-based precision monitoring of this species.

opencc-by-4.0Aug 2023View details →

Repeatome turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

The present repository provides zipped archives containing the results of the RepeatExplorer2 runs of individual as well as comparative repeat analyses in beet genomes.   Sugar beet (Beta vulgaris subsp. vulgaris) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation. We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera Beta and Patellifolia. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section Corollinae/Nanae. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia species to the formation of patchwork chromosomes in Corollinae/Nanae species.  We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.

opencc-by-4.0Sep 2023View details →

Evolution of impact melt pools on Titan - data files

Data files to produce figures in the manuscript entitled 'Evolution of impact melt pools on Titan' written by Klara Kalousova, Shigeru Wakita, Christophe Sotin, Catherine D. Neish, Jason M. Soderblom, Ondrej Soucek, and Brandon C. Johnson and submitted to Journal of Geophysical Research: Planets.

opencc-by-4.0Oct 2023View details →

ICON-LES for FESSTVaL: Jogi cold pool 2021-06-29

Dataset used in How Variable are Cold Pools?  Leah D. Grant, Bastian Kirsch, Jennie Bukowski, Nicholas M. Falk, Christine A. Neumaier, Mirjana Sakradzija Susan C. van den Heever, and Felix Ament submitted to Geophysical Research Letters

closedIPD-NOFeb 2026View details →

Korean Nationwide Multicenter Pooled Registry of Drug-Eluting Stents

ClinicalTrials.gov study NCT03507205. IPD Sharing: NO. Countries: 1. Publications: 5.

restrictedIPD-UNDECIDEDFeb 2026View details →

Expanding Pancreas Donor Pool by Evaluation of Unallocated Organs After Brain Death - The EXPLORE Study

ClinicalTrials.gov study NCT04127266. IPD Sharing: Not stated. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

QTc Intervals in Former Preterm/Extreme Low Birth Weight Infants: a Pooled Study Proposal

ClinicalTrials.gov study NCT05243537. IPD Sharing: UNDECIDED. Countries: 2. Publications: 4.

closedIPD-NOFeb 2026View details →

Pooled Mutant KRAS-Targeted Long Peptide Vaccine Combined With Nivolumab and Ipilimumab for Patients With Resected Mismatch Repair Protein (MMR-p) Colorectal and Pancreatic Cancer

ClinicalTrials.gov study NCT04117087. IPD Sharing: NO. Countries: 1. Publications: 0.