Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
38
datasets available to search
ShareScore release 0.7.1
Dataset results
38 results for “phylogenetic relatedness”
Data from: SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness
Open the record for dataset details and reuse information.
Data from: Joint effect of phylogenetic relatedness and trait selection on the elevational distribution of Rhododendron species
Open the record for dataset details and reuse information.
Data from: Exploring trophic role similarity and phylogenetic relatedness between species in food webs
Open the record for dataset details and reuse information.
Relatedness and the composition of communities over time: evaluating phylogenetic community structure in the late Cenozoic record of bivalves
Understanding the mechanisms that prevent or promote the coexistence of taxa at local scales is critical to understanding how biodiversity is maintained. Competitive exclusion and environmental filtering are two processes thought to limit which taxa become established in a community. However, determining the relative importance of the two processes is a complex task, especially when the critical initial stages of colonization cannot be directly observed. Here, we explore the use of phylogenetic community structure for identifying filtering mechanisms in a fossil community. We integrated a time-calibrated molecular phylogeny of bivalve genera with a spatial dataset of late Cenozoic bivalves from the Pacific coast of North America to characterize how the community that was present in the semi-restricted San Joaquin Basin (SJB) embayment of present-day California was phylogenetically structured. We employed phylogenetic distance-based metrics across six time bins spanning 27-2.5 Ma and found no evidence of significant clustering or evenness in the SJB community when compared to communities randomly assembled from the regional source pool. Additionally, we found that new colonizers into the SJB were not significantly more or less closely related to native taxa than expected by chance. These findings suggest that neither competitive exclusion nor environmental filtering were overwhelmingly influential factors shaping the composition of the SJB community over time. We further discuss interpretations of these patterns in light of current understandings in community phylogenetics and reiterate the critical role historical perspectives play in how community assembly rules are assessed.
Dataset: Plant-plant facilitation increases with reduced phylogenetic relatedness along an elevation gradient
<p>Environmental conditions can modify the intensity and sign of ecological interactions. The stress gradient hypothesis (SGH) predicts that facilitation becomes more important than competition under stressful conditions. To properly test this hypothesis, it is necessary to account for all (not a subset of) interactions occurring in the communities and consider that species do not interact at random but following a specific pattern. We aim to assess elevational changes in facilitation, in terms of species richness, frequency and intensity of the interaction as a function of the evolutionary relatedness between nurses and their associated species. We sampled nurse and their facilitated plant species in two 1000-2000 m. elevation gradients in Mediterranean Chile where low temperature imposes a mortality filter on seedlings. We first estimated the relative importance of facilitation as a mechanism adding new species to communities distributed along these gradients. We then tested whether the frequency and intensity of facilitation increases with elevation, taking into account the evolutionary relatedness of the nurse species and the facilitated species.</p> <p>We found that nurses increase the species richness of the community by up to 35%. Facilitative interactions are more frequent than competitive interactions (56% vs. 44%) and facilitation intensity increased with elevation for interactions involving distantly related lineages. Our results highlight the importance of including an evolutionary dimension in the study of facilitation to have a clearer picture of the mechanisms enabling species to coexist and survive under stressful conditions. This knowledge is especially relevant to conserve vulnerable and threatened communities facing new climate scenarios, such as those located in Mediterranean-type ecosystems.</p>
Data from: Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria
Background: Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. Results: Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. Conclusions: The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.
Phylogenetic relatedness among Cladosporium leaf endophytes predicts their ability to reduce the severity of a poplar leaf rust disease
<p>More closely related organisms are expected to function more similarly than distantly related organisms due to shared ancestry and functional trait heritability. However, there have been few tests of this hypothesis for fungal leaf endophytes, which can modify host plant disease severity by a variety of mechanisms. We tested whether phylogenetic relatedness within <i>Cladosporium</i>, a genus including many common fungal leaf endophyte species, predicts endophyte effects on cottonwood leaf rust disease severity caused by <i>Melampsora ×</i> <i>columbiana</i>. First, we used multilocus sequence typing to infer phylogenetic relationships among 96 <i>Cladosporium </i>isolates collected from wild cottonwood trees growing in Pacific Northwest of North America. Next, we conducted a double-inoculation leaf-disk assay (endophyte inoculated first, then rust pathogen) for a subset of 50 <i>Cladosporium </i>isolates to characterize disease modification for the endophyte isolates; data on endophytes parasitizing rust was collected simultaneously for each isolate. We used generalized linear models to link disease modification and mycoparisitic ability to endophyte phylogeny, while accounting for endophyte geographic origin. We recognized 17 distinct species of <i>Cladosporium</i>; all fifty isolates of <i>Cladosporium</i> reduced rust disease severity in our leaf disk assay (by as much as 79% and as little as 45%). <i>Cladosporium </i>phylogeny was a significant predictor of rust disease severity and was also correlated with mycoparasitism. The geographic origin of the isolates explained only a small amount of the overall variation in disease reduction. Our results demonstrate that fungal endophyte phylogenetic relatedness can help predict differences in endophyte function.</p>
Data from: Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility
A central goal of invasion biology is to elucidate mechanisms regulating community invasibility. Darwin's naturalization hypothesis, one of the oldest hypotheses in invasion biology, emphasizes the importance of phylogenetic relatedness (PR) between resident and invader species for predicting invasibility. Alternatively, a recent extension of the diversity-invasibility hypothesis predicts that phylogenetic diversity (PD) of resident communities influences invasibility. Neither of these hypotheses has undergone rigorous experimental testing, and the relative contributions of PR and PD, whose effects tend to be confounded with each other, to community invasibility are unknown. Here we consider both perspectives together by independently manipulating PR and PD in laboratory bacterial assemblages. We found that while invader abundance declined significantly as PR increased, it was unaffected by PD. Likewise, we found that resident-invader functional similarity, not functional diversity of resident communities, was a significant predictor of invader abundance. Nevertheless, invader abundance was better predicted by PR than functional similarity. These results highlight the importance of considering species evolutionary relationships, especially the phylogenetic relatedness between resident and invader species, for the prediction, prevention and management of biological invasions.
Data from: Invasion status and phylogenetic relatedness predict cost of heterospecific pollen receipt: implications for native biodiversity decline
Understanding the mechanisms by which invasive species affect native plants is a central challenge. Invasive plants have been shown to reduce pollinator visitation to natives and increase pollen quantity limitation. However, visitation and conspecific pollen delivery are only two components of the pollination process; post-pollination interactions on the stigma (heterospecific pollen [HP] receipt) could intensify pre-pollination responses to invasion. Here we used meta-analysis to test the hypotheses that invasive plants are more detrimental as HP donors than natives ones, and that HP donors that are closely related to the recipients have stronger effects on fruit and seed production compared to distantly related ones. Invasive HP donors reduced fruit and seed production of recipients to a greater degree than native ones, and this was more intense for HP donors closely related to natives. Related donors were more detrimental overall. Synthesis: These results suggest that the total effect of invasive plants on native plant reproductive success could be greater than what is inferred from visitation and conspecific pollen transfer alone. Furthermore, these results indicate that invasive species can reduce reproductive success of native species even if pollinator visitation rates remain unaltered. Thus, we highlight the need to evaluate pre- and post-pollination processes in order to fully understand the potential effects of invasive species on the reproductive success and maintenance of native plant populations.
Data from: Phylogenetic relatedness, phenotypic similarity, and plant-soil feedbacks
Open the record for dataset details and reuse information.
Phylogenetic relatedness among Cladosporium leaf endophytes predicts their ability to reduce the severity of a poplar leaf rust disease
Open the record for dataset details and reuse information.
Data from: Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility
Open the record for dataset details and reuse information.
Data from: Invasion status and phylogenetic relatedness predict cost of heterospecific pollen receipt: implications for native biodiversity decline
Open the record for dataset details and reuse information.
Dataset: Plant-plant facilitation increases with reduced phylogenetic relatedness along an elevation gradient
Open the record for dataset details and reuse information.
Data from: Differences in endophyte communities of introduced trees depend on the phylogenetic relatedness of the receiving forest
Open the record for dataset details and reuse information.
Data from: Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria
Open the record for dataset details and reuse information.
Relatedness and the composition of communities over time: evaluating phylogenetic community structure in the late Cenozoic record of bivalves
Open the record for dataset details and reuse information.
Data from: Plant competitive interactions and invasiveness: searching for the effects of phylogenetic relatedness and origin on competition intensity
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.