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.
13
datasets available to search
ShareScore release 0.9.0
Dataset results
13 results for “neutralization theory”
Data from: Invasions of an obligate asexual daphnid species support the nearly neutral theory
<p><span>To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (<em>dN/dS</em>) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual <em>Daphnia pulex</em> invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded <em>D. pulex</em> lineages (JPN1 and JPN2) and compared the <em>dN/dS</em> ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in <em>dN/dS</em> occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the <em>dN/dS</em> ratio for the obligate asexual <em>D. pulex</em> was well explained by the NNT.</span></p>
Data from: Invasions of an obligate asexual daphnid species support the nearly neutral theory
Open the record for dataset details and reuse information.
A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations
<p>Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that form two large-small pairs. We sequenced thousands of ultraconserved elements (UCEs) of the Fiji bush-warbler<i> Horornis ruficapilla</i>, a passerine distributed on these four Fijian islands, and performed a demographic analysis to test hypotheses of the effects of island size and distance on rates of gene flow. Our demographic analysis inferred low levels of gene flow from each large island to its small counterpart and little or none in the opposite direction. The difference in the distance between these two island pairs manifested itself in lower levels of gene flow between more distant islands. Both findings are generally concordant with classic island biogeography. The amount of reduction in gene flow based on distance was consistent with predictions from island biogeographic equations, while the reduction from small to large islands was possibly greater than expected. These findings offer a hypothesis and framework to guide future study of inter-island gene flow in archipelagos as the study of island biogeography progresses into the genomic era.</p>
Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species-pair
<p><b>Aim:</b> Estimating genetic diversity is key for understanging biogeographic and evolutionary processes. However, gathering genetic information is not feasible for all taxa or populations, particularly in the tropical regions. Identifying proxies for inferring such values has thus become essential. Here, we built on the niche centrality hypothesis (NCH; or central-abundance hypothesis) and the nearly neutral theory of evolution (NNT) to identify some of such proxies using a montane tropical conifer species-pair as model. The NCH predicts more genetic diversity under optimal ecological conditions, which should also allow for more efficient purifying selection, according to the NNT.</p> <p><b>Location:</b> The Transmexican Volcanic Belt, central Mexico.</p> <p><b>Taxa:</b> A fir species-pair endemic to central Mexico,<b> </b><i>Abies flinckii </i>and<i> A. religiosa.</i></p> <p><b>Methods:</b> We estimated patterns of genetic diversity from nuclear SSRs (<i>A</i>, <i>H</i><sub>E</sub>), and gene-coding sequences (<i>π</i><sub>S</sub>, <i>π</i><sub>N</sub>), together with the efficacy of purifying selection, measured as <i>π</i><sub>N</sub>/<i>π</i><sub>S</sub>. After testing for niche overlap, we used several geographic and ecological proxies (i.e. longitude, latitude, elevation, estimated area, and distance to the niche centroid in the present and in the LGM) to predict genetic diversity and <i>π</i><sub>N</sub>/<i>π</i><sub>S</sub> using general linear models.</p> <p><b>Results:</b> Populations at the west of the Trans Mexican Volcanic Belt (TVB) had lower genetic diversity than populations in the east of this mountain chain. Both species had significant niche overlap. The principal predictors for neutral genetic diversity (<i>H</i><sub>E</sub>, <i>A</i> and <i>π</i><sub>S</sub>) were longitude and latitude, followed by the current distance to the niche centroid; the efficiency of purifying selection was mostly accounted for by the current distance to the niche centroid (which was also correlated to elevation). No correlation was observed between genetic diversity or <i>π</i><sub>N</sub>/<i>π</i><sub>S</sub> and current population area.</p> <p><b>Main conclusions:</b> Historical and ecological factors have to be taken into account for explaining the amounts of genetic diversity in mountain tropical species. Following the NTT, populations closer to the niche centroid are more efficient at eliminating slightly deleterious mutations than marginal stands, independently of their size or geographical location (longitude). Expanding the central-abundance theory within the scope of the NTT might help reconciling conflicting views concerning the extent of its empirical support.</p>
Data from: Diversity and tectonics: predictions from neutral theory
Open the record for dataset details and reuse information.
A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations
Open the record for dataset details and reuse information.
Data from: Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods
Open the record for dataset details and reuse information.
Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species-pair
Open the record for dataset details and reuse information.
Data from: Wolf in sheep's clothing: model misspecification undermines tests of the neutral theory for life histories
Understanding the processes behind change in reproductive state along life-history trajectories is a salient research program in evolutionary ecology. Two processes, state dependence and heterogeneity, can drive the dynamics of change among states. Both processes can operate simultaneously, begging the difficult question of how to tease them apart in practice. The Neutral Theory for Life Histories (NTLH) holds that the bulk of variations in life-history trajectories is due to state dependence and is hence neutral: Once previous (breeding) state is taken into account, variations are mostly random. Lifetime reproductive success (LRS), the number of descendants produced over an individual's reproductive life span, has been used to infer support for NTLH in natura. Support stemmed from accurate prediction of the population-level distribution of LRS with parameters estimated from a state dependence model. We show with Monte Carlo simulations that the current reliance of NTLH on LRS prediction in a null hypothesis framework easily leads to selecting a misspecified model, biased estimates and flawed inferences. Support for the NTLH can be spurious because of a systematic positive bias in estimated state dependence when heterogeneity is present in the data but ignored in the analysis. This bias can lead to spurious positive covariance between fitness components when there is in fact an underlying trade-off. Furthermore, neutrality implied by NTLH needs a clarification because of a probable disjunction between its common understanding by evolutionary ecologists and its translation into statistical models of life-history trajectories. Irrespective of what neutrality entails, testing hypotheses about the dynamics of change among states in life histories requires a multimodel framework because state dependence and heterogeneity can easily be mistaken for each other.
Data from: Wolf in sheep's clothing: model misspecification undermines tests of the neutral theory for life histories
Open the record for dataset details and reuse information.
Data from: Adding ecological and evolutionary processes to restoration biodiversity offset models using neutral theory
Open the record for dataset details and reuse information.
Data from: Phanerozoic diversity and neutral theory
Although Phanerozoic increases in the global richness, local richness, and evenness of marine invertebrates are well documented, a common explanation for these patterns has been difficult to identify. Evidence is presented here from marine invertebrate communities that there is a Phanerozoic increase in the fundamental biodiversity number (θ), which describes diversity and relative abundance distributions in neutral ecological theory. If marine ecosystems behave according to the rules of Hubbell's Neutral Theory of Biodiversity and Biogeography, the Phanerozoic increase in θ suggests three possible mechanisms for the parallel increases in global richness, local richness, and evenness: (1) an increase in the per-individual probability of speciation, (2) an increase in the area occupied by marine metacommunities, and (3) an increase in the density (per-area abundance) of marine organisms. Because speciation rates have declined over time and because there is no clear evidence for an increase in metacommunity area through the Phanerozoic, the most likely of these is an increase in the spatial density of marine invertebrates over the Phanerozoic, an interpretation supported by previous studies of fossil abundance. This, coupled with a Phanerozoic rise in body size, suggests that an increase in primary productivity through time is the primary cause of Phanerozoic increases in θ, global richness, local richness, local evenness, abundance, and body size.
Data from: Phanerozoic diversity and neutral theory
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.