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MESA inlists for 'Revisiting the Red Giant Branch Hosts KOI-3886 and $\iota$ Draconis. Detailed Asteroseismic Modeling and Consolidated Stellar Parameters' by Campante et al.

MESA inlists used in preparation of the paper 'Revisiting the Red Giant Branch Hosts KOI-3886 and $\iota$ Draconis. Detailed Asteroseismic Modeling and Consolidated Stellar Parameters' by Campante et al. Two folders are provided in the .zip file: <ul> <li>TL_Pipeline — inlists (MESA release version 12115) used to build the grid of stellar models used in Sect. 4.1 of the paper.</li> <li>JO_Pipeline — inlists (MESA release version 12778) used to build both grids of stellar models used in Sect. 4.2 of the paper.</li> </ul>

opencc-zeroMar 2023View details →

Host population effects on ectomycorrhizal fungi

Geographic distinctions in the affinity of tree populations for select ectomycorrhizal fungi (EMF) may occur where strong edaphic pressures act on fungal communities and their hosts. We examine this premise for Pseudotsuga menziesii var. menziesii of southwest British Columbia, using ten native seedlots collected from a range of mean annual precipitation (MAP), as a proxy for podzolization extent and phosphorus (P) deficiencies, and evaluated in contrasting low P and high P soils. After two growing seasons, seedling biomass in the high P soil dwarfed that of the low P soil, and better growth rates under high P were detected for populations from very dry and very wet origins. EMF communities on the high P soil displayed more symmetry among host populations than the low P soil (average community dissimilarity of 0.20% vs 0.39%, respectively). Seedling foliar P% differed slightly but significantly in relation to MAP of origin. EMF species richness varied significantly among host populations but independently of climatic parameters. There were significant shifts in EMF species abundance related to seedlot MAP, particularly on the low P soil where nonlinear relationships were found for Wilcoxina mikolae, Hyaloscypha finlandica, and Rhizopogon villosulus. Despite efforts to enhance colonization by native fungi, the predominance of ruderal EMF species hindered a realistic evaluation of local adaptation among host-fungi populations. Nevertheless, the shifting affinity in taxa abundance and wider community disparity on low P soil reflected the potential for a consequential host genetic effect related to geographical patterns in P availability across temperate rainforests

Dataset for manuscript "Host-related and environmental factors influence long-term ectoparasite infestation dynamics of mouse lemurs in northwestern Madagascar" to be published in the American Journal of Primatology

This Excel-file contains three datasets, corresponding to the initial raw dataset resulting from all ectoparasite inspections (n = 2,241), the merged dataset used for host-related and temporal modeling (n = 1940), and the even more condensed dataset with one datapoint per individual used for climatic modeling (n = 583), respectively.

Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara

Abstract Bacteria colonize specific niches in the animal gut. However, the genetic basis of these associations is often unclear. The proteobacterium Frischella perrara is a widely distributed gut symbiont of honey bees. It colonizes a specific niche in the hindgut and causes a characteristic melanization response. Genetic determinants required for the establishment of this association, or its relevance for the host, are unknown. Here, we independently isolated three point mutations in genes encoding the DNA-binding protein integration host factor (IHF) in F. perrara. These mutants abolished the production of an aryl polyene metabolite causing the yellow colony morphotype of F. perrara. Inoculation of microbiota-free bees with one of the mutants drastically decreased gut colonization of F. perrara. Using RNAseq we found that IHF affects the expression of potential colonization factors, including genes for adhesion (Type 4 pili), interbacterial competition (Type 6 secretion systems), and secondary metabolite production (colibactin and aryl polyene biosynthesis). Gene deletions of these components revealed different colonization defects depending on the presence of other bee gut bacteria. Interestingly, one of the T6SS mutants did not induce the scab phenotype anymore, despite colonizing at high levels, suggesting an unexpected role in bacteria-host interaction. IHF is conserved across many bacteria and may also regulate host colonization in other animal symbionts.

Clownfish Hosting Anemone Location Data from GBIF

This is a location dataset derived from GBIF location data for the 10 Clownfish hosting anemones. The data was downloaded, filtered, and used to create range maps in R. The species included are: <ol> <li>Cryptodendrum adhaesivum</li> <li>Entacmaea quadricolor</li> <li>Heteractis aurora</li> <li>Heteractis crispa</li> <li>Heteractis magnifica</li> <li>Heteractis malu</li> <li>Macrodactyla doreensis</li> <li>Stichodactyla gigantea</li> <li>Stichodactyla haddoni</li> <li>Stichodactyla mertensii</li> </ol>

Host influence on life history traits of Ceratitis capitata Wiedemann in an arid region of Argentina

<pre>Data set of life history traits of Ceratitis capitata recovered from peaches, plums, and figs grown under climatic conditions of an irrigated oasis in San Juan, Argentina.</pre>

Data for: The impact of wildlife and environmental factors on hantavirus infection in host and its translation into human risk

Identifying factors that drive infection dynamics in reservoir host populations is essential in understanding human risk from wildlife-originated zoonoses. We studied zoonotic Puumala orthohantavirus (PUUV) in the host, the bank vole (Myodes glareolus), populations in relation to the host population, rodent and predator community and environment-related factors and whether these processes are translated into human infection incidence. We used 5-year rodent trapping and bank vole PUUV serology data collected from 30 sites located in 24 municipalities in Finland. We found that PUUV seroprevalence was negatively associated with the abundance of red foxes, but this process did not translate into human disease incidence, which showed no association with PUUV seroprevalence. The abundance of weasels, the proportion of juvenile bank voles in the host populations and rodent species diversity were negatively associated with the abundance index of PUUV-positive bank voles, which, in turn, showed a positive association with human disease incidence. Our results suggest certain predators, high proportion of young bank vole individuals and a diverse rodent community, may reduce PUUV risk for humans through their negative impacts on the abundance of infected bank voles.

Parasitoid development and superparasitism in invasive versus native widow spider host egg sacs

The brown widow spider, Latrodectus geometricus, is a hazardous and highly invasive species globally. One of the suggested mechanisms enhancing this spider's invasiveness is lower susceptibility to natural enemies compared to other widow species. The parasitoid wasp, Philolema latrodecti, is known to attack egg sacs of L. geometricus, as well as those of other species of Latrodectus. Despite its potential importance as a natural enemy of L. geometricus, little is known about the development of this wasp and factors mediating its parasitism success. We investigated the development of this parasitoid in two widow spider host species, one native to Israel, the white widow, L. pallidus, and the invasive brown widow, L. geometricus. We compared wasp developmental success in egg sacs exposed to increasing wasp densities. We found increased wasp emergence and brood size, and smaller emerging wasp body size, with increasing wasp density. Across all wasp densities, more and larger parasitoids developed in the egg sacs of the native host species, L. pallidus, compared to the invasive host species, L. geometricus. Parasitoid sex ratio was highly female-biased and the proportion of males increased with wasp density, suggesting local mate competition. Overall, our results suggest that L. pallidus is a better host for the egg sac parasitoid P. latrodecti, which could give a competitive advantage to the less-affected invasive brown widow spider.

Tracing the future of epidemics: Coincident niche distribution of host animals and disease incidence revealed climate-correlated risk shifts of main zoonotic diseases in China

This dataset contains host occurrence data from NACRC database and disease incidence data for the paper "Tracing the future of epidemics: Coincident niche distribution of host animals and disease incidence revealed climate-correlated risk shifts of main zoonotic diseases in China".

Patterns of host plant use do not explain mushroom body expansion in Heliconiini butterflies

The selective pressures leading to the elaboration of downstream, integrative processing centres, such as the mammalian neocortex or insect mushroom bodies, are often unclear. In Heliconius butterflies, the mushroom bodies are three to four times larger than their Heliconiini, and the largest known in Lepidoptera. Heliconiini lay almost exclusively on Passiflora, which exhibit a remarkable diversity of leaf shape, and it has been suggested that the mushroom body expansion of Heliconius may have been driven by the cognitive demands of recognising and learning the leaf shapes of local host plants. We test this hypothesis using two complementary methods: i) phylogenetic comparative analyses to test whether variation in mushroom body size is associated with the morphological diversity of host plants exploited across the Heliconiini; and ii) shape learning experiments using six Heliconiini species. We found that variation in the range of leaf morphologies used by Heliconiini was not associated with mushroom body volume. Similarly, we find interspecific differences in shape learning ability, but Heliconius are not overall better shape learners than other Heliconiini. Together these results suggest that the visual recognition and learning of host plants was not a main factor driving the diversity of mushroom body size in this tribe.

opencc-by-4.0Apr 2023View details →

Developmental period of Brachymeria nosatoi Habu (Hymenoptera: Chalcididae) on different host pupae

Screening of intercrop herbivores as alternative hosts for Brachymeria nosatoi Habu (Hymenoptera: Chalcididae), the pupal parasitoid of coconut leaf eating caterpillar, Opisina arenosella Walker (Lepidoptera: Oecophoridae). The developmetal period of B. nosatoi (days) was recorded on pupae of five herbivores, including the natural host, on which the parasitoid had completed its life cycle. Between host species differences in developmental period were tested for using ANOVA in GenStat. The residuals were homogenous and normally distributed (Bartlett’s test: v2 = 4.13, df = 4, P = 0.389; Shapiro–Wilk test: W = 0.975, P = 0.377).

opencc-by-4.0Apr 2023View details →

Developmental parameters of Opisina arenosella Walker (Lepidoptera: Oecophoridae) on alternative host plants

Survival and development of Opisina arenosella Walker (Lepidoptera: Oecophoridae), the leaf eating caterpillar of coconut, were studied on three host plants on which comparatively high feeding rates were observed: Artocarpus heterophyllus Lam. (Jack fruit), Elaeis guineensis Jacq. (Oil palm) and Anacardium occidentale L. (Cashew), plus coconut palm (Cocos nucifera L.). A freshly hatched first instar O. arenosella larva was transferred onto the leaf in a glass beaker and reared on them. Fresh leaves were provided every 48 h until pupation of O. arenosella larvae. The larval period, pupal period and the longevity of the successfully developing adult female moths were recorded. For each plant species, there were ten replicates yielding adult moths. Data on the length of O. arenosella developmental stages and adult longevity had homogenous variance (Bartlett’s test on residuals from ANOVA of developmental time across plant species: Larval period, v2 = 5.13, df = 3, P = 0.163; Pupal period, v2 = 0.15, df = 3, P = 0.986; Longevity, v2 = 1.58, df = 3, P = 0.664) and were normally distributed (Shapiro–Wilk test: Larval period, W = 0.978, P = 0.632; Pupal period, W = 0.981, P = 0.714; Longevity, W = 0.974, P = 0.472). Thus, the effects of plant species on each of these measures were tested using one-way ANOVA in GenStat. Aggregation of factor levels was used to evaluate differences between treatments when overall results were significant (Crawley 1993). The larval period differed significantly across all four plant species presented and was shortest when on coconut. Pupal periods were also shortest on coconut but did not differ among larvae fed on the three intercrops. The longevity of adult females was unaffected by the species of plant on which larvae had fed.

Data for: Dispersal-limited symbionts exhibit unexpectedly wide variation in host specificity

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macroevolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode versus multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. Comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts.

opencc-by-4.0Jun 2022View details →

Host symbiont gene reconciliation supplementary material

Cinara aphids dataset was obtained from the data of article by Manzano-Marin et al. ISME, 2019, and we chose a representative subset of the species present in the gene trees. We used an exterior source for the phylogeny for the enterobacteria present in the gene trees using Annotree (Mendler et al., Nucleic Acids Research, 2019) (for the one that are not associated to Cinara aphids, and are thus "free living" in this setting).  Helicobacter pylori dataset was constructed by Alexia Nguyen Trung, gathering available whole genome sequences on NCBI with assigned geo populations on NCBI or pubMLST.  A phylogenetic tree was built based on the concatenation of universal-unicopy genes (322 genes), and a sample of 113 strains representing the diversity of H. pylori in the old world (excluding strains from the Americas) was obtained using Treemmer (Menardo et al, BMC Bioinformatics, 2018). Then, 6 non pylori strains were added (H. hepaticus, H. acinonychis, H. canadensis, H felis, H. bizzozeronii, H. cetorum), as an external group.  In this study we considered the 1034 gene families, including 322 universal unicopy family, which displayed strains from the external group and from at least 3 continents. The taleoutput repository contains the recphyloxml outputs of the methods used in the paper, am stands for the approach with amalgamation of the universal unicopy genes to construct a strain tree, while nc refers to the results with the tree constructed from the concatenate, and then the repositories refer to the putative population trees 1, 2, 3 and 4. 0u_0 is the strains genes reconciliation in recphyloxml format. 0upper is the host strains reconciliation in recphyloxml format. Finally, the last repository contains the simulated dataset. It was generated using Sagephy https://compbio.engr.uconn.edu/software/sagephy/ https://doi.org/10.1093/bioinformatics/btz081 For each instance, a host tree, a symbiont tree, and 5 gene trees were generated. We used the parameters proposed in https://doi.org/10.1145/3307339.3342168 \cite{kordi_inferring_2019}, as representative of small (D 0.133, T 0.266, L 0.266), medium (D 0.3, T 0.6, L 0.6) and high (D 0.6, T 1.2, L 1.2) transfer rates, without replacing transfers. The software enables to specify an inter transfer rate, corresponding to the probability for a gene transfer between different hosts. When a horizontal transfer is chosen during generation of the gene tree (inside a symbiont tree and knowing a host/symbiont reconciliation), the transfer is chosen to be an inter host one with the inter transfer rate. So an inter transfer rate of 0 corresponds to only intra transfer, and of 1 corresponds to a case where transfers are only between symbionts in separate hosts. We constructed two simulated datasets, one with a combination of the different rates for the DTL parameters (varrates), and one with only medium rates but with different rates of "inter" and "intra" transfers (coevol). For the first dataset, we used all 9 combinations of small, medium and high rates for the symbiont generation and the gene generation, with only intra host gene transfer (i.e. an inter transfer rate of zero). For the second dataset, we used only medium rates for both symbiont and genes generation, but we used 6 inter transfer rates going from 0 to 1.  For both datasets, and for each set of rates, we generated 50 instances consisting of 1 host tree with 100 leaves, 1 symbiont tree and 5 gene trees, each generated in the pruned version of the other trees (branch that do not reach present are pruned before the generation of the next tree). We then kept each host leaves with a probability of 0.08 to simulate unexhaustive sampling, resulting in host trees with an average size of 8 leaves. This ended up to 399 instances for the first dataset and 226 instances for the second one, and at least 29 instances of 5 genes for each set of parameters. Each repositiory is a simulation instance, varrates_k_l_i correspond to simulation number i with lower rate k and upper rate l. genes, symbiont, species are repositories containing the trees in newick of the genes, symbiont and host in newick. Gene trees are unrooted. Lower matching is a matching between gene and symbiont leaves, upper matching between symbiont and host leaves, gene_host_matching is a matching between gene and host leaves. Transfer list contains one file for each gene and with all transfers simulated, donor and receiver symbiont internal nodes. Each instance also contains the output of tale used in the paper, with the three heuristic, the 2-level symbiont gene (_2l), the 3-level sequential heuristic (_dec) and the 3-level monte carlo approach (_mc) with 50 iterations. All the launch were with 5 rounds of parameters estimation (the default usage). The 0u_0 contain a sampled symbiont gene reconciliation in recphyloxml, and for the 3-level heuristics, 0upper a corresponding host symbiont reconciliation in recphyloxml (multiple ones for the montecarlo i_upper and iu_0 for i from 0 to 49). A known error in the recphyloxml transcription script, now corrected, has induced some errors in some of the recphyloxml files : for some transfers the indicated receiver species is the donor and not the receiver, however redundancy in the format makes it possible to retrieve the information by looking at the matching species in the next event of the gene, that will be the receiver species, we chose to leave it this way instead of relaunching all the computations, as it has no impact on the figures and results presented in our article (mostly constructed using the freq files). The files freq contains information on the frequencies of the different events summed up over gene symbionts reconciliation, lower_log_likelihood contains the log likelihood of the host and symbiont trees knowing the genes (the probability of the genes knowing the host and symbiont).

opencc-by-4.0Nov 2023View details →

Fig. 2 in Icosiella Neglecta (Nematoda, Onchocercidae) In Ukraine: Occurrence, Hosts, Morphological And Molecular Characterisation

Fig. 2. Icosiella neglecta in host leg (A) and throat (B) muscles.

opencc-by-4.0Nov 2023View details →

Fig. 1 in Icosiella Neglecta (Nematoda, Onchocercidae) In Ukraine: Occurrence, Hosts, Morphological And Molecular Characterisation

Fig. 1. Studied localities in Ukraine. Numbers correspond to those in table 1.

Graft‐host coupling changes can lead to engraftment arrhythmia: A computational study

This dataset contains examples and raw data related to the cited publication (doi: 10.1113/jp284244). Computational models derived from histological images are provided. Raw values in the data spreadsheet are given as fraction of simulations for a particular configureation that resulted in graft-initiated host excitation.

A meta-analysis of how parasites affect host consumption rates

Parasites are known to mediate trophic interactions and can, for example, modify how consumers acquire resources. These modifications of host feeding behaviour can be imposed through three interconnected mechanisms affecting: (1) host food acquisition, (2) host food digestion or (3) host energy budgets. As a result, infected hosts may consume more, less or the same amount of food compared to their uninfected conspecifics. It is commonly assumed that infected hosts have lower consumption rates than uninfected hosts, but a comprehensive quantitative synthesis investigating the effects of parasites on host consumption rate has been lacking thus far. To fill this knowledge gap, we systematically searched for experimental studies that evaluated changes in consumption rate of infected vs uninfected hosts. In total, we extracted 158 effect sizes from 68 studies. We then performed meta-analyses of mean differences in host consumption rates and their variation. The analyses were carried out for all taxonomic groups as well as separately for vertebrate and invertebrate hosts. The main-effects meta-analyses confirmed a generally negative effect of parasites on host consumption rates; infected hosts consumed on average 25% less food than their uninfected conspecifics. In addition, there was a significant increase in the variability in host consumption rate, on average by 25%, indicating that parasites can have variable effects on the foraging behaviour of their hosts. The meta-regression models revealed that several moderator variables related to host and parasite characteristics influence host consumption rate. Experimental infection had a stronger influence on variance effects than natural infection. Parasitic infections reduced consumption rate of vertebrate hosts by 28% and thus more strongly than those of invertebrates, which were reduced by 22%. We conclude with recommendations to facilitate future ecological research syntheses on host-parasite interactions and beyond.

opencc-zeroMay 2023View details →

Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

Despite the vast diversity of phytophagous insects that feed on vascular plants (tracheophytes), insects that feed on bryophytes remain understudied. Agromyzidae, one of the most species-rich phytophagous clades in Diptera, consists mainly of leaf-mining species that feed on tracheophytes. However, a recent discovery of thallus-mining species on liverworts and hornworts within the Liriomyza group of Phytomyzinae provides an opportunity to study host shifts between tracheophytes and bryophytes. This study aimed to explore the origin and diversification of thallus-miners and estimate the pattern and timing of host shifts. Phylogenetic analysis of Phytomyzinae has revealed that the thallus-mining agromyzids formed a separate clade, which was sister to a fern pinnule-miner. The diversification of bryophyte-associated agromyzids since the Oligocene involved multiple host shifts across various bryophyte taxa. The diversification of the thallus-mining Phytoliriomyza may have occurred at the same time as the leaf-mining agromyzid flies on herbaceous plants, indicating a dynamic history of interactions between bryophytes and herbivores in angiosperms-dominated ecosystems.