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.
47
datasets available to search
ShareScore release 0.9.0
Dataset results
47 results for “evolutionary determinism”
Data for: Cephalopod Sex Determination and its Ancient Evolutionary Origin
<p>This repository contains the chromosome-level genome assembly, annotation, and genome hub files of the California two-spot octopus (<em>Octopus bimaculoides</em>). These data resulted in the discovery of the cephalopod sex chromosomes. Read the paper in <em>Current Biology </em>here: https://doi.org/10.1016/j.cub.2025.01.005. </p>
Fig. 1 in (macro-) Evolutionary ecology of parasite diversity: From determinants of parasite species richness to host diversification
Fig. 1. Expression of the basic transmission rate (R0) for the case of microparasites (i.e. viruses) and macroparasites (i.e. helminths with direct transmission) (for derivations of these expressions see Morand and Deter, 2008), emphasizing the importance of two host traits, longevity and density, as likely determinants of parasite invasion and then parasite species richness. In the right panel, relationships showing that both density and longevity are in allometry with host body mass (after Brown, 1995).
Fig. 2 in (macro-) Evolutionary ecology of parasite diversity: From determinants of parasite species richness to host diversification
Fig. 2. (A) Variability of ectoparasite species richness among 113 families of mammals (20 orders) (data from Kim, 1985;see Poulin and Morand, 2004). (B) Ectoparasite species richness is related to mammal diversification. The statistical analysis follows Nunn et al. (2004), where the change in the number of descendent clades is related to the change in the number of ectoparasite species, estimated using a modified version of the independent contrast method (Agapow and Isaac, 2002), for each node of the mammal phylogeny (from Binida-Emonds et al., 2007).
Figure 2 in Phylogeny of sex-determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap?
Figure 2. Phylogenetic reconstruction of sex-determining mechanisms in squamate reptiles based on the molecular tree according to Townsend et al. (2004). For details see legend to Figure 1.
Figure 3 in Phylogeny of sex-determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap?
Figure 3. Phylogenetic reconstruction of sex-determining mechanisms in squamate reptiles based on the molecular tree according to Vidal & Hedges (2005). For details see legend to Figure 1.
Figure 1 in Phylogeny of sex-determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap?
Figure 1. Parsimony analysis of sex-determining mechanisms in squamate reptiles based on the 'morphological' tree. Circles indicate maximum-likelihood reconstructions of ancestral states, only nodes with significant reconstruction are shown (tested by likelihood-ratio test). Numbers in parentheses indicate the counts of species within a genus that share
Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments
<p><span>Machine learning can be as good as maximum likelihood when reconstructing phylogenetic topologies and determining the best evolutionary model on four taxon alignments.</span></p> <p><span>Phylogenetic tree reconstruction with molecular data is important in many fields of life science research. The gold standard in this discipline is the Maximum Likelihood tree reconstruction method. Here we show that for quartet trees, Machine Learning using neural networks can be as good as the Maximum Likelihood method to infer the best tree topology and the best model of sequence evolution for nucleotide as well as amino acid sequences. For this purpose we simulated data sets for a wide range of branch lengths, evolutionary models and model parameters and compared the topologies and inferred models obtained with Machine learning with those obtained with the Maximum Likelihood and the Neighbour Joining method. Our results show that neural networks are a promising avenue for determining relatedness between taxa, which is likely to accelerate the construction of phylogenetic trees in the future, while maintaining a high accuracy.</span></p>
Comparative genomics of sex-determination-related genes reveals shared evolutionary patterns between bivalves and mammals, but not fruit flies
Open the record for dataset details and reuse information.
Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments
Open the record for dataset details and reuse information.
Evolutionary history of grazing and resources determine herbivore exclusion effects on plant diversity
Ecological models predict that the effects of mammalian herbivore exclusion on plant diversity depend on resource availability and plant exposure to ungulate grazing over evolutionary time. Using an experiment replicated in 57 grasslands on six continents, with contrasting evolutionary history of grazing, we tested how resources (mean annual precipitation and soil nutrients) determine herbivore exclusion effects on plant diversity, richness, and evenness. Here we show that at sites with a long history of ungulate grazing, herbivore exclusion reduced plant diversity by reducing both richness and evenness, and the responses of richness and diversity to herbivore exclusion decreased with mean annual precipitation. At short with a short history of grazing, the effects of herbivore exclusion were not related to precipitation but differed for native and exotic plant richness. Thus, plant species’ evolutionary history of grazing continues to shape the response of the world’s grasslands to changing mammalian herbivory.
The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds
<p><span><span><span><span><span><span><span><span><span><span><span><b>Aim</b>: Variation in species diversity among different geographic areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions,anda long time available for the accumulation of species (know as the "time-for-speciation effect"). Here, we examine the relative importance of the three aforementionedprocesses in shaping the geographic diversity patterns of a large radiation of passerine birds.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Location</b>: Global</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Time period</b>: Early Miocene to present</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Major taxa studied</b>: Babblers (Aves: Passeriformes)</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods</b>: Using a comprehensive phylogeny of extant species (~90% sampled) and distributions of the world's babblers, we reconstructed their biogeographic history and analysed the diversification dynamics. We examined how species richness correlates with the timing of regional colonization, the number of immigration events and the rate of speciation within all 13 geographic distribution regions.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results</b>: We found thatbabblers likely originated in the Sino-Himalayan Mountains (SHM) in the early Miocene, suggesting a long time for diversification and species accumulation within the SHM. Regression analyses showed the regional diversity of babblers can be well explained by the timing of the first colonization within of these areas, while differences in rates of speciation or immigration have far weaker effects. Nonetheless, the rapid speciation of <i>Zosterops</i>during the Pleistocene has accounted for the increased diversification and accumulation of species in the oceanic islands.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Main conclusions</b>: Our results suggest that the global diversity patterns of babblers have predominantly been shaped by the time-for-speciation effect. Our findings also support an origin centred in tropical and subtropical parts of the SHM, with a cradle of recent diversification in the oceanic islands of the Indo-Pacific region, which provides new insights into the generation of global biodiversity hotspots.</span></span></span></span></span></span></span></span></span></span></span></p>
Strong selective environments determine evolutionary outcome in time-dependent fitness seascapes
<p>The impact of fitness landscape features on evolutionary outcomes has attracted considerable interest in recent decades. However, evolution often occurs under time-dependent selection in so-called fitness seascapes where the landscape is under flux. Fitness seascapes are an inherent feature of natural environments, where the landscape changes owing both to the intrinsic fitness consequences of previous adaptations and extrinsic changes in selected traits caused by new environments. The complexity of such seascapes may curb the predictability of evolution. However, empirical efforts to test this question utilising a comprehensive set of regimes are lacking. Here we employed an in vitro microbial model system to investigate differences in evolutionary outcomes between time-invariant and -dependent environments, including all possible temporal permutations, with three subinhibitory antimicrobials and a viral parasite (phage) as selective agents. Expectedly, time-invariant environments caused stronger directional selection for resistances compared to time-dependent environments. Intriguingly, however, multidrug resistance outcomes in both cases were largely driven by two strong selective agents (rifampicin and phage) out of four agents in total. These agents either caused cross-resistance or obscured the phenotypic effect of other resistance mutations, modulating the evolutionary outcome overall in time-invariant environments and as a function of exposure epoch in time-dependent environments. This suggests that identifying strong selective agents and their pleiotropic effects is critical for predicting evolution in fitness seascapes, with ramifications for evolutionarily informed strategies to mitigate drug resistance evolution. </p>
Evolutionary determinants of non-seasonal breeding in wild chacma baboons
<p><span>Animal reproductive phenology varies from strongly seasonal to non-seasonal, sometimes among closely related or sympatric species. While the extent of reproductive seasonality is often attributed to environmental seasonality, this fails to explain many cases of non-seasonal breeding in seasonal environments. We investigated the evolutionary determinants of non-seasonal breeding in a wild primate, the chacma baboon (<em>Papio ursinus</em>), living in a seasonal environment with high climatic unpredictability. We tested three hypotheses proposing that non-seasonal breeding has evolved in response to (1) climatic unpredictability, (2) reproductive competition between females favoring birth asynchrony, and (3) individual, rank-dependent variations in optimal reproductive timing. We found strong support for an effect of reproductive asynchrony modulated by rank: (i) birth synchrony is costly to subordinate females, lengthening their interbirth intervals, (ii) females alter their reproductive timings (fertility periods and conceptions) in relation to previous conceptions in the group, and (iii) the reported effect of birth synchrony on interbirth intervals weakens the intensity of reproductive seasonality at the population level. This study emphasizes the importance of sociality in mediating the evolution of reproductive phenology in group-living organisms, a result of broad significance for understanding key demographic parameters driving population responses to increase climatic fluctuations.</span></p>
Evolutionary and ecological processes determining properties of the $\bm G$-matrix
<p>The $\bm G$-matrix is the matrix of additive genetic variances and covariances for a vector of phenotypes. Here we apply the classical theory for the balance between selection drift and mutations to find the contributions to $\bm G$ from each locus. The fitness is approximated by a linear function of phenotypes. Fluctuations in the environment generate variation in the coefficients of the fitness function. We show that the $\bm G$-matrix can be decomposed into 4 additive components generated by selection, drift, mutations and environmental fluctuations. Selection is on average counteracted by the other three processes included in Fisher's concept of the deterioration of the environment, in accordance with Frank's approximate conservation law proposing that the response to selection at stasis on average is canceled by effects of drift and mutations. The theory illustrates that Fisher's fundamental theorem cannot be used to accumulate selection through time to describe adaption unless the other effects are corrected for. Another implication of the analyses is that the factor loadings to the eigenvector of the $\bm G$-matrix with the least eigenvalue are likely to indicate which characters contributing the most to the fitness function. This is information notoriously difficult to obtain in natural populations. </p>
Evolutionary history and climate co-determine the geographical variation in pollination modes of angiosperms in China
<p><span><strong>Aim:</strong> </span><span>Pollination is an essential stage of angiosperm reproduction and the mode of pollination plays a major role in driving evolutionary and ecological responses of plants to environmental changes. However, the effects of climate, evolutionary history and floral traits (i.e. plant sexual systems) on pollination mode variation remain unclear. Here, we explored the biogeographic patterns in pollination mode frequency, and tested the hypothesis that insect pollination prevails in warm humid regions with old floras due to high pollinator dependence, whereas wind pollination is more frequent in arid regions with younger floras and is more strongly associated with dioecy.</span></p> <p><span><strong>Location</strong>: </span><span>China</span></p> <p><span><strong>Time</strong> <strong>period</strong>: </span><span>Since the Last Glacial Maximum</span></p> <p><span><strong>Major taxa studied</strong>:</span><span> Angiosperms</span></p> <p><span><strong>Methods</strong>:</span><span> Using data on pollination modes and geographic ranges of 29,719 angiosperm species in China, we mapped the biogeographic </span><span>pattern of pollination mode frequency</span><span>. Phylogenetic logistic regressions and </span><span>generalized linear mixed models </span><span>were employed to evaluate the relative importance of climate, evolutionary history (represented by phylogenetic conservatism and grid-level mean genus age) and sexual systems on variations in pollination modes across species and space.</span></p> <p><span><strong>Results</strong>: </span><span>E</span><span>volutionary history was the strongest correlate of pollination mode variation across species and space. The proportion of insect-pollinated species was higher in warm humid regions with old floras, but lower in arid regions with young floras. </span><span>Evolutionary history and temperature dominated variations in pollination mode frequency in warm humid areas, while precipitation dominated in arid areas.</span><span> Climate mainly influenced geographic patterns in pollination mode frequency</span><span> indirectly via its effects on species richness and plant sexual systems.</span></p> <p><span><strong>Main</strong> <strong>conclusions</strong>: </span><span>Our results showed that </span><span>geographic pattern in angiosperm pollination mode frequency is </span><span>dominated by evolutionary history followed by climate</span><span>, which extended previous findings of climate-driven mechanisms. Our findings demonstrate the importance to incorporate evolutionary history in understanding the mechanisms underlying the functional biogeography of plant traits.</span></p>
A key evolutionary step determining osmoregulatory ability for freshwater colonisation in early life stages of fish
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Colonisation of freshwater habitats by marine animals is a remarkable evolutionary event that has enriched biodiversity in freshwater ecosystems. The acquisition of tolerance to hypotonic stress during early life stages is presumed to be essential for their successful freshwater colonisation, but very little empirical evidence has been obtained to support this idea. This study aimed to comprehend the evolutionary changes in osmoregulatory mechanisms that enhance larval freshwater tolerance in amphidromous fishes, which typically spend their larval period in marine (ancestral) habitats and the rest of their life history stages in freshwater (derived) habitats. We compared the life history patterns and changes in larval survivorship and gene expression depending on salinity among three congeneric marine-originated amphidromous goby species (<em>Gymnogobius</em>), which had been suggested to differ in their larval dependence on freshwater habitats. An otolith microchemical analysis and laboratory-rearing experiment confirmed the presence of freshwater residents only in <em>G. urotaenia</em> and higher larval survivorship of this species in the freshwater condition than in the obligate amphidromous <em>G. petschiliensis</em> and <em>G. opperiens</em>. Larval whole-body transcriptome analysis revealed that <em>G. urotaenia</em> from both amphidromous and freshwater-resident populations exhibited the greatest differences in expression levels of several osmoregulatory genes, including <em>aqp3</em>, which is critical for water discharge from their body during early fish development. The present results consistently support the importance of enhanced freshwater tolerance and osmoregulatory plasticity in larval fish to establish freshwater forms, and further identify key candidate genes for larval freshwater adaptation and colonisation in the goby group.</p> </div> </div> </div>
Evolutionary and ecological processes determining properties of the $\bm G$-matrix
Open the record for dataset details and reuse information.
The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds
Open the record for dataset details and reuse information.
Evolutionary determinants of non-seasonal breeding in wild chacma baboons
Open the record for dataset details and reuse information.
Evolutionary history and climate co-determine the geographical variation in pollination modes of angiosperms in China
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.