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opencc-by-4.0Dec 2019View details →

Co-authoring graphs of research teams in a laboratory in computer science

Our aim is to study inter-organisational collaborations initiated by researchers in their research activity. We considered the co-authoring graph involving at least researchers from LORIA (<a href="https://www.loria.fr/fr/">https://www.loria.fr/fr/</a>), a French laboratory in computer science. The dataset is collected from the open French archive HAL (<a href="https://data.archives-ouvertes.fr/">https://data.archives-ouvertes.fr/</a>). Each file encodes (in <a href="http://www.graphviz.org/about/">DOT</a>) the co-authoring graph of a team of LORIA. A node represents a researcher, two nodes are linked only if the corresponding researchers published together over the three considered years 2017, 2018 and 2019. An affiliation attribute is attached to each considered node. The name of researchers and the teams as well as the HAL:id are anonymised. Only affiliations remain the same.

opencc-zeroDec 2020View details →

Ecological factors mediate immunity and parasitic co-infection in sea fan octocorals

The interplay among environment, demography, and host-parasite interactions is a challenging frontier. In the ocean, fundamental changes are occurring due to anthropogenic pressures, including increased disease outbreaks on coral reefs. These outbreaks often include multiple parasites, calling into question how coral immunity functions in this complex milieu. Corals provide an interesting model to study ecological immunity during co-infection, being highly sensitive to environmental change, susceptible to many diseases, and defended by the innate immune system. Our work investigates the interplay of factors influencing coral co-infection using metrics of the innate immune response: levels of cellular immunity and the expression of candidate immune genes. We used existing copepod infections and live pathogen inoculation with Aspergillus fungus to test the effect of sequential co-infections in a laboratory experiment. We profile significant increases in the expression of the immune recognition gene Tachylectin 5A in response to both of these naturally occurring parasites of the Caribbean sea fan octocoral, Gorgonia ventalina. Cellular immunity increased significantly by 8.16% in copepod infections compared to controls and single Aspergillus infections. We evaluated immunity in reef populations and again detected activation of cellular immunity, with a 13.6% increase in copepod infections and no detectable increase in fungal infections. Thus, cellular immunity measured in the field and lab were similar, increasing with copepod infections and not Aspergillus. We found random co-occurrence of copepods and fungus across 15 reefs in Puerto Rico, suggesting other factors prevail in structuring parasite infection. Sea fan colony size strongly predicted infection by the copepod parasite. Moreover, the effect of parasitic infection on immunity was small relative to the explanatory power of site differences and coral cover, and roughly equivalent to the effect of reproductive status. We suggest that host size, reproductive status, live coral cover, and site-specific factors have large effects on parasitic infections and host immunity that overwhelm effects of the parasites on each other. Thus, host size and site-specific features emerge as critical drivers in this multi-parasite system. Parsing the effects of immunity and ecological factors in coral co-infection shows how disease depends on more than one host and one parasite.

opencc-by-4.0Dec 2020View details →

Metaproteomics analysis of SARS-CoV-2-infected patient samples reveals presence of potential co-infecting microorganisms

Supplemental data for SARS-CoV-2 patient sample metaproteomics analysis

opencc-zeroDec 2020View details →

Co-infection best predicts respiratory viral infection in a wild host

1) The dynamics of directly transmitted pathogens in natural populations are likely to result from the combined effects of host traits, pathogen biology and interactions among pathogens within a host. Discovering how these factors work in concert to shape variation in pathogen dynamics in natural host – multi‐pathogen systems is fundamental to understanding population health. 2) Here, we describe temporal variation in incidence and then elucidate the effect of hosts trait, season, and pathogen co‐occurrence on host infection risk using one of the most comprehensive studies of co‐infection in a wild population: a suite of seven directly‐transmitted, viral and bacterial, respiratory infections from a four‐year study of 200 free‐ranging African buffalo (Syncerus caffer). 3) Incidence of upper respiratory infections was common throughout the study – five out of the seven pathogens appeared to be consistently circulating throughout our study population. One pathogen exhibited clear outbreak dynamics in our final study year and another was rarely detected. 4) Co‐infection was also common in this system. The strongest indicator of pathogen occurrence for respiratory viruses was, in fact, the presence of other viral respiratory infections. Host traits had minimal effects on odds of pathogen occurrence but did modify pathogen‐pathogen associations. In contrast, only season predicted bacterial pathogen occurrence. 5) Though a combination of environmental, behavioral, and physiological factors work together to shape disease dynamics, we found pathogen associations best determined infection risk. Our study demonstrates that, in absence of very fine‐scale data, the intricate changes among these factors are best represented by co‐infection.

opennotspecifiedJan 2018View details →

Fig. 1 in Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses

Fig. 1. Host association and geographical distribution of the CoV sequences analyzed here. Countries within large-scale geographical regions are colored according to the number of CoV analyzed. Pie charts indicate the host-association of the CoV sequences included within each geographical area, with the colors indicating the different families of bat hosts. The map was built using mapchart (https://mapchart.net).

opennotspecifiedJan 2018View details →

Fig. 2 in Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses

Fig. 2. Phylogenetic overview of CoV sequences analyzed here. The tree reflects a Bayesian analysis of 935 bp of the RdRp gene (data set RdRp_CoV_1), rooted using two sequences from gamma coronaviruses (GenBank accession numbers EF584911-2). Genus specific clusters identified in our study are colored based on the host genus, as indicated. Posterior probabilities> 0.90 supporting each cluster are shown. Branch lengths are scaled according to the number of substitutions per site. The three bars around the tree show the frequency within each cluster of (i) host genera, (ii) host species and (iii) sampling locations, from the innermost to the most exterior. Sequences showing characters with frequency <10%, between 10 and 50%, and> 50% are colored black, grey and light grey, respectively. For the "host species" bar, only sequences belonging to the host genus characterizing the cluster (frequency> 50%) have been colored; sequences associated with hosts only characterized at the genus level are indicated in yellow. The ICTV classification of virus clusters is indicated when available. The figure was generated using iTOL.

opencc-zeroDec 2020View details →

Data from: Group-level variation in co-feeding tolerance between two sanctuary-housed communities of chimpanzees (Pan troglodytes)

Social tolerance in group-living animals can be viewed as a counterweight against competitive interests necessary to obtain coexistence equilibrium and maintain group cohesion. As such, it forms an interesting phenomenon to study at the group-level, but how can this be done most informatively? Here, we use three group-level co-feeding assays and social network analysis to study social tolerance in two groups of chimpanzees living under similar circumstances within a sanctuary to i) reassess whether social tolerance may be a group-specific parameter in chimpanzees and derive inferences about its long-term stability, and ii) compare the characteristics and resultant patterns between two established and one new assay. We show that the three assays expose the same (predicted) group-level differences in social tolerance as in the previous study eight years ago, thereby providing preliminary evidence for stability in group-specific levels of social tolerance in chimpanzees, despite changing group compositions. Furthermore, from an experimental point of view, we identify the new assay as more valid than the two established ones based on the consideration that resources may deplete at different rates across groups, which would consequently alter the need for tolerance differentially. We discuss implications for the study of social tolerance and highlight the importance of taking into account intraspecific variation in social animals.

opencc-zeroDec 2010View details →

Data from: Small-scale variation in fuel loads differentially affects two co-dominant bunchgrasses in a species-rich pine savanna

Ecological disturbances frequently control the occurrence and patterning of dominant plants in high-diversity communities like C4 grasslands and savannas. In such ecosystems disturbance-related processes can have important implications for species, and for whole communities when those species are dominant, yet mechanistic understanding of such processes remains fragmentary. Multiple bunchgrass species commonly co-dominate disturbance-dependent and species-rich pine savannas, where small-scale fuel heterogeneity may influence bunchgrass survival and growth following fires. We quantified how fire in locally varying fuel loads influenced dynamics of dominant C4 bunchgrasses in a species-rich pine savanna in southeastern Louisiana, USA. We focused on two congeneric, co-dominant species (Schizachyrium scoparium and S. tenerum) with similar growth forms, functional traits and reproductive strategies to highlight effects of fuel heterogeneity during fires. In experimental plots with either reduced or increased fuels versus controls with unmanipulated fuels, we compared: 1) bunchgrass damage and 2) mortality from fires; 3) subsequent growth and 4) flowering. Compared to controls, fire with increased fuels caused greater damage, mortality and subsequent flowering, but did not affect post-fire growth. Fire with reduced fuels had no effect on any of the four measures. The two species responded differently to fire with increased fuels – S. scoparium incurred measurably more damage and mortality than S. tenerum. Logistic regression indicated that the larger average size of S. tenerum tussocks made them resistant to more severe burning where fuels were increased. We speculate that locally increased fuel loading may be important in pine savannas for creating colonization sites because where fuels are light or moderate, dominant bunchgrasses persist through fires. Small-scale heterogeneity in fires, and differences in how species tolerate fire may together promote shared local dominance by different bunchgrasses.

opencc-zeroDec 2010View details →

Data from: Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum (LGM). Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of Northeast Australia. Our results demonstrate at least two episodes of vicariance due to climate-driven forest contractions: one in the early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.

Data from: Pollinator-mediated interactions between cultivated papaya and co-flowering plant species

Many modern crop varieties rely on animal pollination to set fruit and seeds. Intensive crop plantations usually do not provide suitable habitats for pollinators so crop yield may depend on the surrounding vegetation to maintain pollination services. However, little is known about the effect of pollinator-mediated interactions among co-flowering plants on crop yield or the underlying mechanisms. Plant reproductive success is complex, involving several pre- and post-pollination events; however, the current literature has mainly focused on pre-pollination events in natural plant communities. We assessed pollinator sharing and the contribution to pollinator diet in a community of wild and cultivated plants that co-flower with a focal papaya plantation. In addition, we assessed heterospecific pollen transfer to the stigmatic loads of papaya and its effect on fruit and seed production. We found that papaya shared at least one pollinator species with the majority of the co-flowering plants. Despite this, heterospecific pollen transfer in cultivated papaya was low in open-pollinated flowers. Hand pollination experiments suggest that heterospecific pollen transfer has no negative effect on fruit production or weight, but does reduce seed production. These results suggest that co-flowering plants offer valuable floral resources to pollinators that are shared with cultivated papaya with little or no cost in terms of heterospecific pollen transfer. Although HP reduced seed production, a reduced number of seeds per se is not negative, given that from an agronomic perspective the number of seeds does not affect the monetary value of the papaya fruit.

opencc-zeroDec 2018View details →

Data from: Revisiting the relative growth rate hypothesis for gymnosperm and angiosperm species co‐occurrence

Premise of the study: It is unclear to what extent the co-occurrence of angiosperm and gymnosperm species in some marginal ecosystems is explained by reduced growth in angiosperms due to carbon (C) limitation, and by high stress tolerance in gymnosperms associated with lack of vessels and resource conservation. Methods: We examined growth patterns and traits associated with C balance in four evergreen angiosperm species (including one vesselless species, Drimys winteri) and three gymnosperm tree species of a cold-temperate rainforest in southern Chile. We measured the mean basal area increment for the first 50 (BAI50) and the last 10 years (BAI10), wood density, leaf lifespan, and non-structural carbohydrate (NSC) concentrations in different organs. Key results: BAI50 was 6-fold higher in angiosperms than in gymnosperms, and c. 4-fold higher in Drimys than in the fastest growing gymnosperm. BAI10 and aboveground NSC concentrations were significantly higher and leaf lifespan lower in angiosperms than in gymnosperms; these differences though were largely driven by the slow growth and low NSC concentrations of the Cupressaceae species (Pilgerodendron uviferum), while the two Podocarpaceae showed similar BAI10 and NSC concentrations to angiosperms. In angiosperms, NSC and starch concentrations were generally higher in species with lower BAI10, indicating no severe C limitation. Conclusions: The co-occurrence of angiosperms and gymnosperms in cold-temperate rainforests of southern Chile is not explained by growth disadvantages and C limitation in angiosperms. High leaf longevity, but not lack of vessels, appeared to favor resource conservation and C balance in some gymnosperms (Podocarpaceae). In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.

Data from: Competing for blood: the ecology of parasite resource competition in human malaria-helminth co-infections

Ecological theory suggests that co-infecting parasite species can interact within hosts directly, via host immunity and/or via resource competition. In mice, competition for red blood cells (RBCs) between malaria and bloodsucking helminths can regulate malaria population dynamics, but the importance of RBC competition in human hosts was unknown. We analyzed infection density (i.e. the concentration of parasites in infected hosts), from a 2-year deworming study of over 4,000 human subjects. After accounting for resource-use differences among parasites, we find evidence of resource competition, priority effects, and a competitive hierarchy within co-infected individuals. For example, reducing competition via deworming increased Plasmodium vivax densities 2.8-fold, and this effect is limited to bloodsucking hookworms. Our ecological, resource-based perspective sheds new light into decades of conflicting outcomes of malaria-helminth co-infection studies with significant health and transmission consequences. Beyond blood, investigating within-human resource competition may bring new insights for improving human health.

Data from: Comparing genetic diversity and demographic history in co-distributed wild South American camelids

Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1,000 individuals. For vicuña this bottleneck is inferred to have taken place ~3,300 years ago, but to have occurred more recently for guanaco at ~2,000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.

opencc-zeroDec 2016View details →

Data from: Co-occurrence of related asexual, but not sexual, lineages suggests that reproductive interference limits coexistence

We used randomizations to analyse patterns of co-occurrence of sexual and apomictic (asexual) members of the North American Crepis agamic complex (Asteraceae). We expect strong asymmetry in reproductive interactions in Crepis: apomicts produce clonal seeds with no need for pollination and are not subject to reproductive interference from co-occurring relatives. However, because they still produce some viable pollen, apomicts can reduce reproductive success of nearby sexual relatives, potentially leading to eventual local exclusion of sexuals. Consistent with this, randomizations reveal that sexuals are over-represented in isolated sites, while apomicts freely co-occur. Incorporation of taxonomic and phylogenetic evidence indicates that this pattern is not driven by local origins of asexuals. Our evidence that patterns of local co-occurrence are structured by reproductive interference suggests an underappreciated role for these interactions in community assembly, and highlights the need for explicit tests of the relative contributions of ecological and reproductive interactions in generating patterns of limiting similarity.

Data from: Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species' and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co‐occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model (JSDM) that integrates these distinct observational approaches by incorporating species co‐occurrence data into a SDM. JSDMs estimate distributions of multiple species simultaneously and allow decomposition of species co‐occurrence patterns into components describing shared environmental responses and residual patterns of co‐occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia. Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM. Eucalypt species that interbreed had similar environmental responses but had negative residual co‐occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities. Environmental and residual correlations estimated from JSDMs can help indicate whether co‐occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDMs take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.

opencc-zeroDec 2012View details →

Data from: Outcomes of co-infection by two potyviruses: implications for the evolution of manipulative strategies

Recent studies have documented effects of plant-viruses on host plants that appear to enhance transmission by insect vectors. But, almost no empirical work has explored the implications of such apparent manipulation for interactions among co-infecting pathogens. We examined single and mixed infections of two potyviruses, Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV), that frequently co-occur in cucurbitaceae populations and share the same aphid vectors. We found that ZYMV isolates replicated at similar rates in single and mixed infections, while WMV strains accumulated to signficantly lower levels in the presence of ZYMV. Furthermore, ZYMV induced changes in leaf colour and volatile emissions that enhanced aphid (Aphis gossypii) recruitment to infected plants. In contrast, WMV did not elicit strong effects on plant-aphid interactions. Nevertheless, WMV was still readily transmitted from mixed infections, despite fairing poorly in in-plant competition. These findings suggest that pathogen effects on host-vector interactions may well influence competition among co-infecting pathogens. For example, if non-manipulative pathogens benefit from the increased vector traffic elicited by manipulative competitors, their costs of competition may be mitigated to some extent. Conversely, the benefits of manipulation may be limited by free-rider effects in systems where there is strong competition among pathogens for host resources and/or access to vectors.

opencc-zeroJun 2019View details →

Data from: Geography best explains global patterns of genetic diversity and post-glacial co-expansion in marine turtles

For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to post-glacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial dataset encompassing 23 previously identified lineages from all 7 marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian Model Averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.

opencc-zeroDec 2016View details →

Data from: Multi-DICE: R package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes

Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest, and composite likelihood optimization. Here, we introduce the R package Multi-DICE, a wrapper program that exploits existing simulation software for straight-forward and flexible execution of hierarchical model-based inference using the aSFS, which is derived from genomic-scale data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding event pulses, and specifying flexible hyperprior distributions. In sum, Multi-DICE provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a valuable tool for comparative phylogeography and population genomics.

opencc-zeroMar 2020View details →

"Chancing on a spectacle:" co-occurring animal migrations and interspecific interactions

Migrations of diverse wildlife species often converge in space and time, with their journeys shaped by similar forces (i.e., geographic barriers and seasonal resources and conditions); we term this "co-migration." Supporting this, recent studies have elucidated co-migrations and seasonal patterns that govern the location and timing of multiple species' journeys. Beyond their significance as natural wonders, species with overlapping migrations may interact ecologically, with potential effects on population and community dynamics. Direct and indirect ecological interactions including predation and competition between migrant species remain poorly understood, in part because migration is the least-studied phase of animals' annual cycles. To address this gap, we conducted a literature review to examine whether animal migration studies incorporate multiple species and to what extent they investigate interspecific interactions between co-migrants. Following a key word search, we read all migration research papers in 23 relevant peer-reviewed journals during 2008-2017. Thirty percent of animal migration papers reported two or more species with coinciding migrations, suggesting that co-migrations are common, although few studies investigated or discussed these mixed-species migrations further. Synthesizing those that did explore this phenomenon, we present examples and describe five types of ecological interactions between migrating species, including predator-prey, host-parasite, and commensal relationships. Deepening ecological knowledge of interspecific interactions among migratory animal communities will enhance understanding of the drivers of migration and could improve predictions about wildlife responses to global change. Further research focused on multi-species migrations could also inform conservation efforts for migratory animal populations, many of which are declining or shifting, with unexplored consequences for other co-migratory species.