Find research datasets worth reusing

Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL

The domesticated crop maize and its wild progenitor, teosinte, have been used in numerous experiments to investigate the nature of divergent morphologies. This study examines a poorly understood region on the fifth chromosome of maize associated with a number of traits under selection during domestication using a QTL mapping population specific to the fifth chromosome. In contrast with other major domestication loci in maize where large effect, highly pleiotropic, single genes are responsible for phenotypic effects, our study found the region on chromosome five fractionates into multiple QTL regions, none with singularly large effects. The smallest 1.5 LOD support interval for a QTL contained 54 genes, one of which was a MADS MIKCC transcription factor, a family of proteins implicated in many developmental programs. We also used simulated trait datasets to investigate the power of our mapping population to identify QTL for which there is a single underlying causal gene. This analysis showed that while QTL for traits controlled by single genes can be accurately mapped, our population design can detect no more than ~4.5 QTL per trait even when there are 100 causal genes. Thus when a trait is controlled by 5 or more genes in the simulated data, the number of detected QTL can represent a simplification of the underlying causative factors. Our results show how a QTL region with effects on several domestication traits may be due to multiple linked QTL of small effect as opposed to a single gene with large and pleiotropic effects.

opencc-zeroMay 2019View details →

Data from: A link between heritable parasite resistance and mate choice in dung beetles

Parasites play a central role in the adaptiveness of sexual reproduction. Sexual selection theory suggests a role for parasite resistance in the context of mate choice, but the evidence is mixed. The parasite-mediated sexual selection (PMSS) hypothesis derives a number of predictions, among which that resistance to parasites is heritable, and that female choice favours parasite resistance genes in males. Here we tested the PMSS hypothesis using the dung beetle Onthophagus taurus, a species that can be heavily parasitised by Macrocheles merdarius mites, which are known to affect adult survival. We investigated the heritability of resistance to M. merdarius, as well as whether female O. taurus impose a mating bias against males susceptible to mite infestation. Female choice for parasite resistance is difficult to disentangle from the possibility that females are simply choosing less parasitised males due to naturally selected benefits of avoiding contracting those parasites. This is especially likely for ectoparasites, such as mites. We tackled this problem by performing a mate choice trial first, and then measuring a male's resistance to mite infestation. Resistance to mite infestation exhibited significant levels of additive genetic variance. Although we found no relationship between mating success and parasite resistance, males with greater resistance to infestation mated for longer. If females control copula duration, given that short copulations often result in mating failure, female choice could act on parasite resistance.

opencc-zeroDec 2012View details →

Data from: A genomic island linked to ecotype divergence in Atlantic cod

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in "genomic mosaics" during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or "genomic island", as potentially associated with ecological divergence and suggest a selective sweep involved in ecological divergence. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although underlying mechanisms are still unknown, the results suggest that "genomic mosaics" of differentiation may even be found under high levels of gene flow, and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

Data from: Linking phenological shifts to species interactions through size-mediated priority effects

1. Inter-annual variation in seasonal weather patterns causes shifts in the relative timing of phenological events of species within communities, but we currently lack a mechanistic understanding of how these phenological shifts affect species interactions. Identifying these mechanisms is critical to predicting how inter-annual variation affects populations and communities. 2. Species' phenologies, particularly the timing of offspring arrival, play an important role in the annual cycles of community assembly. We hypothesize that shifts in relative arrival of offspring can alter interspecific interactions through a mechanism called size-mediated priority effects (SMPE), in which individuals that arrive earlier can grow to achieve a body size advantage over those that arrive later. 3. In this study, we used an experimental approach to isolate and quantify the importance of SMPE for species interactions. Specifically, we simulated shifts in relative arrival of the nymphs of two dragonfly species to determine the consequences for their interactions as intraguild predators. 4. We found that shifts in relative arrival altered not only predation strength but also the nature of predator-prey interactions. When arrival differences were great, SMPE allowed the early arriver to prey intensely upon the late arriver, causing exclusion of the late arriver from nearly all habitats. As arrival differences decreased, the early arriver's size advantage also decreased. When arrival differences were smallest, there was mutual predation, and the two species coexisted in similar abundances across habitats. Importantly, we also found a nonlinear scaling relationship between shifts in relative arrival and predation strength. Specifically, small shifts in relative arrival caused large changes in predation strength while subsequent changes had relatively minor effects. 5. These results demonstrate that SMPE can alter not only the outcome of interactions but also the demographic rates of species and the structure of communities. Elucidating the mechanisms that link phenological shifts to species interactions is crucial for understanding the dynamics of seasonal communities as well as for predicting the effects of climate change on these communities.

opencc-zeroDec 2018View details →

Data from: Blood-brain barrier impairment and hypoperfusion are linked in cerebral small vessel disease

Objective: To investigate the link between BBB permeability and CBF and the relation with white matter hyperintensities (WMHs) in cerebral small vessel disease (cSVD). Methods: Twenty-seven patients with cSVD received dynamic susceptibility contrast and dynamic contrast-enhanced MRI to determine CBF and BBB permeability (expressed as leakage rate and volume), respectively. Structural MR images were segmented into normal appearing white matter (NAWM) and WMHs, for which a perilesional zone was defined. In these regions, we investigated the BBB permeability, CBF, and their relation using Pearson correlation r. Results: We found a decrease in CBF of 2.2 mL/min/100g(p<0.01) and an increase in leakage volume of 0.7%(p<0.01) per mm closer to the WMHs in the perilesional zones. Lower CBF values correlated with higher leakage measures in the NAWM and WMHs (-0.53

Data from: Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa

Fitness costs play a key role in the evolutionary dynamics of antibiotic resistance in bacteria by generating selection against resistance in the absence of antibiotics. Although the genetic basis of antibiotic resistance is well understood, the precise molecular mechanisms linking the genetic basis of resistance to its fitness cost remain poorly characterized. Here, we examine how the system-wide impacts of mutations in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin resistance in Pseudomonas aeruginosa. Rifampin resistance mutations reduce transcriptional efficiency, and this explains 76% of the variation in fitness among rpoB mutants. The pleiotropic consequence of rpoB mutations is that mutants show altered relative transcript levels of essential genes. We find no evidence that global transcriptional responses have an impact on the fitness cost of rifampin resistance as revealed by transcriptome sequencing (RNA-Seq). Global changes in the transcriptional profiles of rpoB mutants compared to the transcriptional profile of the rifampin-sensitive ancestral strain are subtle, demonstrating that the transcriptional regulatory network of P. aeruginosa is robust to the decreased transcriptional efficiency associated with rpoB mutations. On a smaller scale, we find that rifampin resistance mutations increase the expression of RNAP due to decreased termination at an attenuator upstream from rpoB, and we argue that this helps to minimize the cost of rifampin resistance by buffering against reduced RNAP activity. In summary, our study shows that it is possible to dissect the molecular mechanisms underpinning variation in the cost of rifampin resistance and highlights the importance of genome-wide buffering of relative transcript levels in providing robustness against resistance mutations. IMPORTANCE Antibiotic resistance mutations carry fitness costs. Relative to the characteristics of their antibiotic-sensitive ancestors, resistant mutants show reduced growth rates and competitive abilities. Fitness cost plays an important role in the evolution of antibiotic resistance in the absence of antibiotics; however, the molecular mechanisms underlying these fitness costs is not well understood. We applied a systems-level approach to dissect the molecular underpinnings of the fitness costs associated with rifampin resistance in P. aeruginosa and showed that most of the variation in fitness cost can be explained by the direct effect of resistance mutations on the enzymatic activity of the mutated gene. Pleiotropic changes in transcriptional profiles are subtle at a genome-wide scale, suggesting that the gene regulatory network of P. aeruginosa is robust in the face of the direct effects of resistance mutations.

opencc-zeroDec 2016View details →

Data from: Defector clustering is linked to cooperation in a pathogenic bacterium

Spatial clustering is thought to favour the evolution of cooperation because it puts cooperators in a position to help each other. However, clustering also increases competition. The fate of cooperation may depend on how much cooperators cluster relative to defectors, but these clustering differences have not been the focus of previous models and experiments. By competing siderophore-producing cooperator and defector strains of the opportunistic pathogen Pseudomonas aeruginosa in experimental microhabitats, we found that at the spatial scale of individual interactions, cooperator clustering lowers cooperation, but defector clustering favours cooperation. A theoretical model and individual-based simulations show these counterintuitive effects can arise when competition and cooperation occur at a single resource-determined scale, with population dynamics crucially allowing cooperators and defectors to cluster differently. The results suggest that cooperation relies on the regulation of sufficient defector clustering relative to cooperator clustering, which may be important in bacteria, social amoeba, and cancer inhibition.

opencc-zeroDec 2017View details →

Data from: Aspiration-based coevolution of link weights promotes cooperation in the spatial prisoner's dilemma game

In this article, we propose an aspiration-based coevolution of link weights, and we explore how this affects the evolution of cooperation in the spatial prisoner's dilemma game. In particular, an individual will increase the weight of its link to its neighbors only if the payoff received via this interaction will exceed a pre-defined aspiration. Conversely, if the received payoff is below this aspiration, the link weight with the corresponding neighbor will be decreased. Our simulation results show that an appropriate aspiration level leads to a high-cooperation plateau, whereas a too high or a too low aspiration will impede the evolution of cooperation. We explain these findings with a comprehensive analysis of transition points and with a systematic analysis of typical configuration patterns. The presented results provide further theoretical insights with regards to the impact of different aspiration levels on cooperation in human societies.

opencc-zeroDec 2015View details →

Data from: Re-evaluating the distribution of cooperative breeding in birds: is it tightly linked with altriciality?

The evolution of cooperative breeding (CB) in birds has aroused intensive interest for decades, largely due to the paradox that some adults forgo independent breeding to help others. While much effort has been directed at understanding the adaptive significance of CB behavior, much less effort has been spent on understanding its origin. Ligon and Burt argued that the evolution of altriciality played a key role in the origin of CB since CB occurs more frequently in altricial lineages than expected if developmental mode and CB evolved independently and that both traits arose early in the avian tree of life. We mapped presence or absence of CB, and precocial or altricial development on a recent phylogeny of all birds to re-evaluate their conclusions. Our results suggest altriciality may be more recently derived than previously thought, and that CB species clustered in a derived land bird clade (especially within Passeriformes) where we reconstructed many gains and losses. We did find a link between cooperative breeding and altriciality. However, since CB also occurs in precocial species, has not evolved in many altricial clades, and may have evolved prior to altriciality (based on some classifications of which species have CB), it is not clear whether altriciality is linked to other factors, such as benefits to group living, that are necessary for the acquisition of CB behavior, or whether altriciality may have been a driving force in the evolution of CB itself. The relative importance of these other factors versus altriciality for the origin of CB needs to be considered.

opencc-zeroDec 2015View details →

Data from: On the link between functional traits and growth rate: meta-analysis shows effects change with plant size, as predicted

A plant's growth rate is seen as a central element of its ecological strategy, and as determined by its traits.Yet the literature is inconsistent about the empirical correlation between functional traits and growth, casting doubt on the capacity of some prominent traits to influence growth rate. We propose that traits should influence growth in a way that depends on the size of individual plants. We outline mechanisms and hypotheses based on new theoretical work, and test these predictions in tree species using a meta-analysis of 103 studies (> 500 correlations) for five traits (specific leaf area, wood density, maximum height, seed mass and maximum assimilation rate).We also recorded data for 14 other traits commonly used in the trait literature.To capture the effects of plant size, we tested for a shift in the direction of correlation between growth rates and each trait across three ontogenetic stages: seedling,sapling and adult. Results were consistent with predictions, although there were some limitations arising from unequal numbers of observation across ontogenetic stages.Specific leaf area was correlated with relative growth rate in seedlings but not in adult plants.Correlations of growth with wood density were not affected by ontogenetic stage. Seed mass, assimilation rate and maximum height were correlated with relative growth rate only in one ontogenetic stage category: seedlings,seedlings and adults,respectively. Although we were able to confirm several of our theoretical predictions,major knowledge gaps still exist in the trait literature.For example,for one third of the traits considered,the majority (> 75%) of reported correlations with growth came from the same ontogenetic stage. Synthesis: We show for some traits, how trait-growth correlations change in a predictable way with plant size.Our understanding of plant strategies should shift away from describing species as having a fixed growth strategy throughout their life (on a continuous axis from slow to fast growth), in favour of a size-dependent growth trajectories.

opencc-zeroSep 2019View details →

Data from: Differential female sociality is linked with the fine-scale structure of sexual interactions in replicate groups of red junglefowl, Gallus gallus

Recent work indicates that social structure has extensive implications for patterns of sexual selection and sexual conflict. However, little is known about the individual variation in social behaviours linking social structure to sexual interactions. Here, we use network analysis of replicate polygynandrous groups of red junglefowl (Gallus gallus) to show that the association between social structure and sexual interactions is underpinned by differential female sociality. Sexual dynamics are largely explained by a core group of highly social, younger females, which are more fecund and more polyandrous, and thus associated with more intense postcopulatory competition for males. In contrast, less fecund females from older cohorts, which tend to be socially dominant, avoid male sexual attention by clustering together and perching on branches, and preferentially reproduce with dominant males by more exclusively associating and mating with them. Collectively, these results indicate that individual females occupy subtly different social niches, and demonstrate that female sociality can be an important factor underpinning the landscape of intra-sexual competition and the emergent structure of animal societies.

opencc-zeroDec 2012View details →

Data from: An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles

Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used to define phylogenetic relationships in the approach. We used Escherichia coli K12 genome as the reference genome and its 4195 proteins were used in the current analysis. We compared our approach with two existing methods and our initial results show that the predictions have outperformed two of the existing approaches. In addition, we have validated our method using a targeted protein-protein interaction network derived from protein-protein interaction database STRING. Our preliminary results indicates that improvement in function prediction can be attained by using coevolution-based similarity measures and the runs on to the same scale instead of computing them in different scales. Our method can be applied at the whole-genome level for annotating hypothetical proteins from prokaryotic genomes.

opencc-zeroDec 2016View details →

Data from: Linking intra-specific trait variation to community abundance dynamics improves ecological predictability by revealing a growth-defence trade-off

1.Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in inter-specific interactions and population dynamics. In turn, variation in species' interactions and densities can alter the strength and direction of trait change. The resulting feedback between species′ traits and abundance permits a wide range of community dynamics that would not be expected from ecological theories purely based on species abundances. Despite the theoretical importance of these interrelated processes, unambiguous experimental evidence of how intraspecific trait variation modifies species interactions and population dynamics and how this feeds back to influence trait variation is currently required. 2.We investigate the role of trait-mediated demography in determining community dynamics and examine how ecological interactions influence trait change. We concurrently monitored the dynamics of community abundances and individual traits in an experimental microbial predator-prey-resource system. Using this data, we parameterized a trait dependent community model to identify key ecologically relevant traits and to link trait dynamics with those of species abundances. 3.Our results provide clear evidence of a feedback between trait change, demographic rates and species dynamics. The inclusion of trait-abundance feedbacks into our population model improved the predictability of ecological dynamics from r-squared of 34% to 57% and confirmed theoretical expectations of density dependent population growth and species interactions in the system. 4.Additionally, our model revealed that the feedbacks were underpinned by a trade-off between population growth and anti-predatory defence. High predator abundance was linked to a reduction in prey body size. This prey size decrease was associated with a reduction in its rate of consumption by predators and a decrease in its resource consumption. 5.Modelling trait-abundance feedbacks allowed us to pinpoint the underlying life history trade-off which links trait and abundance dynamics. These results show that accounting for trait-abundance feedbacks has the potential to improve understanding and predictability of ecological dynamics.

Data from: Macrophage migration inhibitory factor is involved in ectopic endometrial tissue growth and peritoneal-endometrial tissue interaction in vivo: a plausible link to endometriosis development

Pelvic inflammation is a hallmark of endometriosis pathogenesis and a major cause of the disease's symptoms. Abnormal immune and inflammatory changes may not only contribute to endometriosis-major symptoms, but also contribute to ectopic endometrial tissue growth and endometriosis development. A major pro-inflammatory factors found elevated in peritoneal fluid of women with endometriosis and to be overexpressed in peritoneal fluid macrophages and active, highly vascularized and early stage endometriotic lesions, macrophage migration inhibitory factor (MIF) appeared to induce angiogenic and inflammatory and estrogen producing phenotypes in endometriotic cells in vitro and to be a possible therapeutic target in vivo. Using a mouse model where MIF-knock out (KO) mice received intra-peritoneal injection of endometrial tissue from MIF-KO or syngeneic wild type (WT) mice and vice versa, our current study revealed that MIF genetic depletion resulted in a marked reduction ectopic endometrial tissue growth, a disrupted tissue structure and a significant down regulation of the expression of major inflammatory (cyclooxygenease-2), cell adhesion (αv and β3 integrins), survival (B-cell lymphoma-2) and angiogenic (vascular endothelial cell growth) factorsrelevant to endometriosis pathogenesis, whereas MIF add-back to MIF-KO mice significantly restored endometriosis-like lesions number and size. Interestingly, cross-experiments revealed that MIF presence in both endometrial and peritoneal host tissues is required for ectopic endometrial tissue growth and pointed to its involvement in endometrial-peritoneal interactions. This study provides compelling evidence for the role of MIF in endometriosis development and its possible interest for a targeted treatment of endometriosis.

opencc-by-nc-sa-4.0Nov 2015View details →

Data from "Linked Coupled Cluster Monte Carlo"

<p>We consider a new formulation of the stochastic coupled cluster method in terms of the similarity transformed Hamiltonian. We show that improvement in the granularity with which the wavefunction is represented results in a reduction in the critical population required to correctly sample the wavefunction for a range of systems and excitation levels and hence leads to a substantial reduction in the computational cost. This development has the potential to substantially extend the range of the method, enabling it to be used to treat larger systems with excitation levels not easily accessible with conventional deterministic methods.</p>

opennotspecifiedDec 2013View details →

FIGURE 41. A in Taxonomic history and invasion biology of two Phyllonorycter leaf miners (Lepidoptera: Gracillariidae) with links to taxonomic and molecular datasets

FIGURE 41. A preliminary DNA barcode (COI) library for global gracillariid species.

opencc-by-3.0-usDec 2023View details →

Mechano-sensitive super-enhancers govern atherosclerosis-linked genes in vascular endothelial cells

<p>Supplemental Table S1-2 of the manuscript in submission</p>

opencc-by-4.0Jun 2019View details →

FIGURE 17 Periclimenes incertus Borradaile, 1915 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology

FIGURE 17 Periclimenes incertus Borradaile, 1915, ovigerous female, RMNH.CRUS.D.53946. A, left third pereiopod; B, idem dactylus. Scale bar: A = 1 mm; B = 0.2 mm.

opencc-by-4.0Jun 2019View details →

FIGURE 13 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology

FIGURE 13 Periclimenes subcorallum sp. nov., ovigerous female paratype (pocl. 1.45 mm), RMNH.CRUS.D.57575. A, left third pereiopod; B, idem, dactylus; C, left fourth pereiopod; D, idem, dactylus; E, left fifth pereiopod; F, idem, dactylus. Scale bar: A, C, E = 1 mm; B, D, F = 0.07 mm.