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69 results for “trait shift”
Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>This archive contains the code and datasets generated in the associated manuscript: "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits". We provide instructions, environments and scripts to reproduce the presented analyses.</p>
Data from: Trait-dependent distributional shifts in fruiting of common British fungi
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Seasonal elevational dynamics of Central Himalayan mammals and birds: occurrences, richness metrics, abundance centres, boundary shifts, traits, and phylogeny
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Idiosyncratic shifts in life-history traits at species’ geographic range edges
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Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands
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Data from: Modeling the effects of climate-change induced shifts in reproductive phenology on temperature-dependent traits
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Data from: Nitrogen addition and warming modulate the pathogen impact on plant biomass by shifting intraspecific functional traits and reducing species richness
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Data from: Losing the trait without losing the signal: evolutionary shifts in communicative colour signalling
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Asymmetric interspecific competition drives shifts in signalling traits in fan-throated lizards
<p>Interspecific competition can occur when species are unable to distinguish between conspecific and heterospecific mates or competitors when they occur in sympatry. Selection in response to interspecific competition can lead to shifts in signalling traits - a process termed as agonistic character displacement. In two fan-throated lizard species- <i>Sitana laticeps</i>and <i>Sarada darwini,</i> females are morphologically indistinguishable and male agonistic signalling behaviour is similar. Consequently, in areas where these species overlap, males engage in interspecific aggressive interactions. To test whether interspecific male aggression between <i>S. laticeps</i> and <i>S. darwini</i> results in agonistic character displacement, we quantified species recognition and signalling behaviour using staged encounter assays with both conspecifics and heterospecifics across sympatric and allopatric populations of both species. We found an asymmetric pattern, wherein males of <i>S. laticeps</i>but not <i>S. darwini</i> showed differences in competitor recognition and agonistic signalling traits (morphology and behaviour) in sympatry compared to allopatry. This asymmetric shift in traits is likely due to differences in competitive abilities between species and can minimize competitive interactions in zones of sympatry. Overall, our results support agonistic character displacement, and highlight the role of asymmetric interspecific competition in driving shifts in social signals. </p>
Dataset: Species presence, trait and philogeny database. Data from: Shift from trait convergence to divergence along old field succession. Journal of Vegetation Science.
<p>This dataset was use in the manuscript "Shift from trait convergence to divergence along old field succession" publish at Journal of Vegetation Science. It contains the data of species presence at three different plots and species trait values (SLA, LDMC, height, seed weight and Phylogeny). We show that at the initial stage of succession, there is a scale-invariant pattern of trait convergence. On the contrary, in the late and intermediate stages of succession we observed that trait divergence became frequent at smaller grains and extents. The trend along the chronosequence is consistent with the theoretical hypothesis that predicts a shift from convergence to divergence along succession.</p>
Data from: Floral trait evolution associated with shifts between insect and wind pollination in the dioecious genus Leucadendron (Proteaceae)
Transitions between animal and wind pollination have occurred in many lineages and have been linked to various floral modifications, but these have seldom been assessed in a phylogenetic framework. In the dioecious genus Leucadendron (Proteaceae), transitions from insect to wind pollination have occurred at least four times. Using analyses that controlled for relatedness among Leucadendron species, we investigated how these transitions shaped the evolution of floral structural and signaling traits, including the degree of sexual dimorphism in these traits. Pollen grains of wind-pollinated species were found to be smaller, more numerous, and dispersed more efficiently in wind than were those of insect-pollinated species. Wind-pollinated species also exhibited a reduction in spectral contrast between showy subtending leaves and background foliage, reduced volatile emissions, and a greater degree of sexual dimorphism in color and scent. Uniovulate flowers and inflorescence condensation are conserved ancestral features in Leucadendron and likely served as exaptations in shifts to wind pollination. These results offer insights into the key modifications of male and female floral traits involved in transitions between insect and wind pollination.
Data from: Inference of adaptive shifts for multivariate correlated traits
To study the evolution of several quantitative traits, the classical phylogenetic comparative framework consists of a multivariate random process running along the branches of a phylogenetic tree. The Ornstein-Uhlenbeck (OU) process is sometimes preferred to the simple Brownian Motion (BM) as it models stabilizing selection toward an optimum. The optimum for each trait is likely to be changing over the long periods of time spanned by large modern phylogenies. Our goal is to automatically detect the position of these shifts on a phylogenetic tree, while accounting for correlations between traits, which might exist because of structural or evolutionary constraints. We show that, in the presence shifts, phylogenetic Principal Component Analysis (pPCA) fails to decorrelate traits efficiently, so that any method aiming at finding shift needs to deal with correlation simultaneously. We introduce here a simplification of the full multivariate OU model, named scalar OU (scOU), which allows for noncausal correlations and is still computationally tractable. We extend the equivalence between the OU and a BM on a re-scaled tree to our multivariate framework. We describe an Expectation Maximization algorithm that allows for a maximum likelihood estimation of the shift positions, associated with a new model selection criterion, accounting for the identifiability issues for the shift localization on the tree. The method, freely available as an R-package (PhylogeneticEM) is fast, and can deal with missing values. We demonstrate its efficiency and accuracy compared to another state-of-the-art method (l1ou) on a wide range of simulated scenarios, and use this new framework to re-analyze recently gathered datasets on New World Monkeys and Anolis lizards.
Data from: Evidence of trait shifts in response to forest disturbance in Taiwanese Carabus masuzoi (Coleoptera: Carabidae)
Shifts of functional traits are important because phenotypic responses of species to environmental changes caused by natural and anthropogenic disturbances are fundamental in determining the risk of population extinction. This study tested the effect of forest thinning on the body shape and male genital size of an endemic ground beetle species Carabus masuzoi (Imura and Satô 1989) (Coleoptera, Carabidae) in cypress plantations started approximately 30 years ago in central Taiwan. The beetles were sampled and compared from (1) natural broadleaf forest, (2) non-thinned cypress plantation, and (3) 45% thinned cypress plantation. Female prothorax length from the non-thinned plantation was significantly greater than that of the natural forest, and the 45% thinned plantation had a higher frequency of the small (S-type) and a lower frequency of the large (L-type) male genitalia than in the natural forest. The results indicated that, within a short ecological time frame, the prothorax shapes and male genital sizes of C. masuzoi populations might respond to changes induced by different forest types and forest thinning, respectively. We hypothesized that the difference in thoracic shape was related to locomotory ability in forest understories, whereas the changes in male genital sizes might have been a result of different levels of intraspecific sexual selection, random effects of population fluctuations/dispersal or pleiotropy.
Data from: A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait
While the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral genome is gradually reduced – and ultimately reversed into a deleterious effect – over the course of an experimental adaptive trajectory in which a primitive form of novel cooperation evolved. This reduction and reversal of a positive social allelic effect is driven solely by changes in the genetic context in which the gene is expressed as new mutations are sequentially fixed during adaptive evolution, and explicitly demonstrates a significant evolutionary change in the genetic architecture of an ecologically important social trait.
Data from: Hormonal, behavioral, and life-history traits exhibit correlated shifts in relation to population establishment in a novel environment
Climate change, habitat alteration, range expansions, and biological invasions are all predicted to require rapid shifts in multiple traits including behavior and life history, both for initial population establishment and subsequent adaptation. Hormonal mechanisms likely play a key role in facilitating or constraining plastic and genetic responses for suites of traits, but few studies have evaluated their role in shaping contemporary adaptation or diversification. We examined multiple phenotypic adjustments and associated hormonal changes following a recent (early 1980s) colonization event, in which a temperate-breeding songbird, the dark-eyed junco (Junco hyemalis), became established in the Mediterranean climate of San Diego, California. The milder climate has led to an extended breeding season and year-round residency, and we document shifts in multiple sexually selected behaviors and plumage traits. Testosterone titers in San Diego were elevated for longer but with a lower peak value compared to a nearby native-range population, and correlations between testosterone and related traits were similar within and among populations. A common garden study indicated that changes in testosterone likely represent plastic responses to the less seasonal environment of the city, providing the context against which subsequent genetic changes in morphology likely occurred. We argue that correlated shifts in multiple traits, organized by underlying physiology, may be a generally important element of many successful adjustments to changing environments.
Data from: Nitrogen enrichment and warming shift community functional composition via distinct mechanisms: the role of intraspecific trait variability and species turnover
<p>1. Global change factors may shift community functional composition by driving species turnover (species occurrence and species relative abundance) and intraspecific trait variability. However, their relative contribution in determining the functional response of community to global change, especially nitrogen enrichment and warming, remains unclear.</p> <p>2. We conducted a fully factorial field experiment in a Tibetan alpine meadow to examine responses of plant community functional composition to nitrogen enrichment and warming by quantifying seven plant functional traits in each plot. Using the sum of squares decomposition, we further disentangled the relative contribution of intraspecific trait variability and species turnover to changes in community functional composition.</p> <p>3. We found that nitrogen enrichment caused a shift of plant community toward a more resource-acquisitive strategy, while warming resulted in a shift toward a more resource-conservative strategy. Plant intraspecific trait variability controls shifts in community functional composition in response to nitrogen enrichment, whereas species turnover (especially change in species relative abundance) mainly explains warming-induced shifts. Nitrogen enrichment and warming did not show significant interactive effects on plant functional composition.</p> <p>4. These findings suggest that nitrogen enrichment and warming can alter community functional composition of alpine meadow through distinct mechanisms. Plant intraspecific trait variability confers functional resilience of Tibetan alpine meadows under nitrogen enrichment, but warming could induce significant turnover of species that pronouncedly impacts community functioning in this highland ecosystem.</p>
Farmer-mediated shifts in drought tolerance traits across an aridity gradient in an indigenous food security crop
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Data from: Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.
Data from: A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait
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Data from: Detecting hidden diversification shifts in models of trait-dependent speciation and extinction
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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.