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opencc-zeroDec 2022View details →

Combined measures of mimetic fidelity explain imperfect mimicry in a brood parasite–host system

The persistence of imperfect mimicry in nature presents a challenge to mimicry theory. Some hypotheses for the existence of imperfect mimicry make differing predictions depending on how mimetic fidelity is measured. Here, we measure mimetic fidelity in a brood parasite–host system using both trait-based and response-based measures of mimetic fidelity. Cuckoo finches Anomalospiza imberbis lay imperfectly mimetic eggs that lack the fine scribbling characteristic of eggs of the tawny-flanked prinia Prinia subflava, a common host species. A trait-based discriminant analysis based on Minkowski functionals—that use geometric and topological morphometric methods related to egg pattern shape and coverage—reflects this consistent difference between host and parasite eggs. These methods could be applied to quantify other phenotypes including stripes and waved patterns. Furthermore, by painting scribbles onto cuckoo finch eggs and testing their rate of rejection compared to control eggs (i.e. a response-based approach to quantify mimetic fidelity), we show that prinias do not discriminate between eggs based on the absence of scribbles. Overall, our results support relaxed selection on cuckoo finches to mimic scribbles, since prinias do not respond differently to eggs with and without scribbles, despite the existence of this consistent trait difference.

Data and Code for: Resistance is futile: Weaker selection for resistance by abundant parasites increases prevalence and depresses host density

We model host evolution of costly resistance to infection and its dependence on environmental factors, such as nutrients. We find that higher nutrients can increase infection prevalence AND select for lower resistance. In turn, the model predicts that lower resistance drives infection prevalence even higher while depressing host density. The attached code performs the model analysis, produces the published figures, and conducts statistical analysis on the data (described below). We conducted a mesocosm experiment with mixtures of zooplankton host (Daphnia dentifera) genotypes, algal resources (Ankistrodesmus falcatus), and fungal parasites (Metschnikowia bicuspidata). Mesocosm populations were supplied with low or high nutrients (5 or 50 ug/L phosphorus and 100 or 1000 ug/L nitrogen). We measured densities of hosts along with age class (juvenile or adult), sex, infections status, and egg number and chlorophyll densities; these data are a subset of data published previously Walsman et al. Functional Ecology (<a href="https://doi.org/10.1111/1365-2435.14030">https://doi.org/10.1111/1365-2435.14030</a>; data at <a href="https://doi.org/10.5061/dryad.mw6m905zg">https://doi.org/10.5061/dryad.mw6m905zg</a>). For the first time, we also report genotype frequencies for the mixed genotype treatments. Importantly, we found that high nutrients increased infection prevalence as well as selecting for the host genotype less resistant to infection; the resulting host evolution increased infection prevalence further and depressed host density. These data and code may be reused with citation of the corresponding publication ("'Resistance is futile': Weaker selection for resistance by abundant parasites increases prevalence and depresses host density" in The American Naturalist).

Cloacal microbiomes of sympatric and allopatric Sceloporus lizards vary with environment and host relatedness

Animals and their microbiomes exert reciprocal influence; the host's environment, physiology, and phylogeny can impact the composition of the microbiome, while the microbes present can affect host behavior, health, and fitness. While some microbiomes are highly malleable, specialized microbiomes that provide important functions can be more robust to environmental perturbations. Recent evidence suggests Sceloporus virgatus has one such specialized microbiome, which functions to protect eggs from fungal pathogens during incubation. Here, we examine the cloacal microbiome of three different Sceloporus species (spiny lizards; Family Phrynosomatidae) – Sceloporus virgatus, Sceloporus jarrovii, and Sceloporus occidentalis. We compare two species with different reproductive modes (oviparous vs. viviparous) living in sympatry: S. virgatus and S. jarrovii. We compare sister species living in similar habitats (riparian oak-pine woodlands) but different latitudes: S. virgatus and S. occidentalis. And, we compare three populations of one species (S. occidentalis) living in different habitat types: beach, low-elevation forest, and the riparian woodland. We found differences in beta diversity metrics between all three comparisons, although those differences were more extreme between animals in different environments, even though those populations were more closely related. Similarly, alpha diversity varied among the S. occidentalis populations and between S. occidentalis and S. virgatus, but not between sympatric S. virgatus and S. jarrovii. Despite these differences, all three species and all three populations of S. occcidentalis had the same dominant taxon, Enterobacteriaceae. The majority of the variation between groups was in low abundance taxa and at the ASV level, and responded to habitat differences, geographic distance, and host relatedness. Understanding wild microbiomes and factors that influence their composition is important to understanding the ecology and evolution of the host animals.

Out of the 'host' box: Extreme off-host conditions alter the infectivity and virulence of a parasitic bacterium

Disease agents play an important role in the ecology and life history of wild and cultivated populations and communities. While most studies focus on the adaptation of parasites to their hosts, the adaptation of free-living parasite stages to their external (off-host) environment may tell us a lot about the factors that shape the distribution of parasites. Pasteuria ramosa is an endoparasitic bacterium of the water flea Daphnia with a wide geographic distribution. Its transmission stages rest outside of the host and thus experience varying environmental regimes. We examined the life history of P. ramosa populations from four environmental conditions (i.e., groups of habitats): the factorial combinations of summer-dry water bodies or not, and winter-freeze water bodies or not. Our goal was to examine how the combination of winter temperature and summer dryness affects the parasite's ability to attach to its host and to infect it. We subjected samples of the four groups of habitats to temperatures of 20, 33, 46 and 60˚C in dry and wet conditions, and exposed a susceptible clone of Daphnia magna to the treated spores. We found that spores that had undergone desiccation endured higher temperatures better than spores kept wet, both regarding attachment and subsequent infection. Furthermore, spores treated with heightened temperatures were much less infective and virulent. Even under high temperatures (60˚C), exposed spores from all populations were able to attach to the host cuticle, albeit they were unable to establish infection. Our work highlights the sensitivity of a host-free resting stage of a bacterial parasite to the external environment. Long heatwaves and harsh summers, which are becoming more frequent due to recent climate changes, may therefore pose a problem for parasite survival.

opencc-by-4.0Nov 2022View details →

Data: Fate of intravenously administered umbilical cord mesenchymal stromal cells and interactions with the host's immune system

This data set includes all the raw data collected for the following article: "Fate of intravenously administered umbilical cord mesenchymal stromal cells and interactions with the host's immune system".

Data for: Aggressive hosts are undeterred by a cuckoo's hawk mimicry, but probably make good foster parents

Parasites face a trade-off if the highest quality hosts are also most resistant to exploitation. For brood parasites, well-defended host nests may be both harder to parasitize and harder to predate, leading to better survival of parasitic chicks. This trade-off could be accentuated if brood-parasitic adaptations to reduce front-line defences of hosts, such as mimicry of hawks by Cuculus cuckoos, do not deter hosts which aggressively mob raptors. Here we investigate the costs and benefits to the African cuckoo (Cuculus gularis) of specializing on a highly aggressive host species, the fork-tailed drongo (Dicrurus adsimilis). Field experiments showed that drongos strongly attacked and mobbed both cuckoo and hawk models, implying that hawk mimicry does not deter front-line defences against African cuckoos. Attacks on cuckoo and hawk models generally declined after the egg stage but attacks on snake models sharply increased, suggesting drongos may treat hawks more like cuckoos than predators. We suggest that the cost to cuckoos of parasitizing an aggressive host may be alleviated by subsequent benefits to their offspring, since drongo nests survived better than nests of other species with similar nesting ecology. These results are indicative of a trade-off between host quality and susceptibility for a brood parasite.

opencc-by-4.0Jan 2023View details →

Catalog of Cool Host Stars with Established Rotation Periods

Catalog of 249 late K- and M-type exoplanet host stars with rotation periods obtained from the literature or new analysis of space- or ground-based time-series photometry as of August 2022.  Model-based, metallicity-dependent corrections are provided but not included in gyrochronological age estimates.   Please cite the reference paper if any information from this table is used.   Table 1 in Gaidos et al. 2023, in press, in CDS format.

opencc-by-4.0Dec 2022View details →

Part 1: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file Data.One.Focb-2.tar contains 22 files of paired-end reads from F. oxysporum f.sp. cubense tropical race 1 isolate N2 (SRA accession: SRR550150, SRR550151), and F. oxysporum f.sp. cubense TR4 isolates Hainan.B2 (SRR550152), My-1 (SRR7226877), La-2 (SRR7226878), Vn-2 (SRR7226879), Leb1.2C (SRR7226880), JV11 (SRR7226881), Phi2.6C (SRR7226882), Pak1.1A (SRR7226883), UK0001 (SRR9733598).

opencc-by-4.0Dec 2022View details →

Part 2: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file Data.One.Focb.tar contains 16 files of paired-end reads from F. oxysporum f.sp. cubense TR4 isolates II-5 (SRA accession: SRR10054446), S1B8 (SRR10054447), JV14 (SRR10054448), FOC.TR4-5 (SRR10054449), FOC.TR4-1 (SRR10054450), Col2 (SRR10103605), Col4 (SRR10125423), Col17 (SRR10747097).

opencc-by-4.0Jan 2023View details →

Part 4: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogen

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file reads.tar contains 44 files of paired-end reads from F. oxysporum f.sp. lycopersici isolate Fol069 (SRA accession: SRR307106, SRR307107, SRR307113, SRR307115, SRR307123, SRR307257, SRR307266), isolate Fol072 (SRR307122, SRR307092, SRR307091, SRR307090, SRR307086, SRR307281, SRR307250), isolate Fol4287 (SRR7690004, SRR3139043), and F. oxysporum f.sp. radicis-cucumerinum isolate Forc016 (SRR3139027, SRR3139028), isolate Forc024 (SRR3139029, SRR3139030), isolate Forc031 (SRR3139031, SRR3139032).

opencc-by-4.0Jan 2023View details →

Utilizing traditional and remote sensing techniques to assess Colorado potato beetle host preference in the Columbia Basin -- 2021 Data

This is a remote sensing dataset collected in 2021 that contains orthomosaic images, shape files, analysis scripts, and derived numerical data from each plot. Data was collected using the protocol described here: <a href="https://www.protocols.io/view/usda-ars-potato-genetics-lab-drone-data-collection-bp2l6148dvqe/v1">https://www.protocols.io/view/usda-ars-potato-genetics-lab-drone-data-collection-bp2l6148dvqe/v1</a> Provided are "field map" files that denote the location and contents of each plot, a folder from each date that contains the 10 band orthomosiac, surface model image, a cropped and rotated image, shape files indicating the location of each plot, and derived data. The analysis can be replicated by following along with workflow listed in file named: rondon_cpb_2021.R. Derived data from this experiment can be found it the file named: "Rondon_CPB_data_2021_UAS_all.csv" If you have any questions or comments regarding this dataset please contact Dr. Max Feldman via email: max.feldman@usda.gov

opencc-zeroFeb 2023View details →

Data from: Hidden variable models reveal the effects of infection from changes in host survival

The impacts of disease on host vital rates can be demonstrated using longitudinal studies, but these studies can be expensive and logistically challenging. We examined the utility of hidden variable models to infer the individual effects of infectious disease from population-level measurements of survival when longitudinal studies are not possible. Our approach seeks to explain temporal deviations in population-level survival after introducing a disease causative agent when disease prevalence cannot be directly measured by coupling survival and epidemiological models. We tested this approach using an experimental host system (Drosophila melanogaster) with multiple distinct pathogens to validate the ability of the hidden variable model to infer per-capita disease rates. We then applied the approach to a disease outbreak in harbor seals (Phoca vituline) that had data on observed strandings but no epidemiological data. We found that our hidden variable modeling approach could successfully detect the per-capita effects of disease from monitored survival rates in both the experimental and wild populations. Our approach may prove useful for detecting epidemics from public health data in regions where standard surveillance techniques are not available and in the study of epidemics in wildlife populations, where longitudinal studies can be especially difficult to implement.

opencc-zeroFeb 2023View details →

Individual variation in the avian gut microbiota: The influence of host state and environmental heterogeneity

<div class="abstract-group metis-abstract"> <div class="article-section__content en main"> The gut microbiota have important consequences for host biological processes and there is some evidence that they also affect fitness. However, the complex, interactive nature of ecological factors that influence the gut microbiota has scarcely been investigated in natural populations. We sampled the gut microbiota of wild great tits (Parus major) at different life stages allowing us to evaluate how microbiota varied with respect to a diverse range of key ecological factors of two broad types: (1) host state, namely age and sex, and the life history variables, timing of breeding, fecundity and reproductive success; and (2) the environment, including habitat type, the distance of the nest to the woodland edge, and the general nest and woodland site environments. The gut microbiota varied with life history and the environment in many ways that were largely dependent on age. Nestlings were far more sensitive to environmental variation than adults, pointing to a high degree of flexibility at an important time in development. As nestlings developed their microbiota from one to two weeks of life, they retained consistent (i.e., repeatable) among-individual differences. However these apparent individual differences were driven entirely by the effect of sharing the same nest. Our findings point to important early windows during development in which the gut microbiota are most sensitive to a variety of environmental drivers at multiple scales, and suggest reproductive timing, and hence potentially parental quality or food availability, are linked with the microbiota. Identifying and explicating the various ecological sources that shape an individual's gut bacteria is of vital importance for understanding the gut microbiota's role in animal fitness. </div> </div> <div class="pb-dropzone"> </div>

opencc-by-4.0Mar 2023View details →

Exploring Host-Binding Machineries of Mycobacteriophages with AlphaFold2

Coordinates of AlphaFold2 predicted structures presented in the publication "Exploring Host-Binding Machineries of Mycobacteriophages with AlphaFold2".

opencc-zeroMar 2023View details →

Data for: Strong effects of food quality on host life history do not scale to impact parasitoid efficacy or life history

Parasitoids are small insects, (e.g., small wasps or flies) that reproduce by laying eggs on or within host arthropods. Parasitoids make up a large proportion of the world's biodiversity and are popular agents of biological control. Idiobiont parasitoids paralyze their hosts upon attack and thus are expected to only target hosts large enough to support offspring development. Host resources generally impact host attributes and life histories including size, development, and life span. Some argue slow host development in response to resource quality increases parasitoid efficacy (i.e., a parasitoid's ability to successfully reproduce on or within a host) due to longer host exposure to parasitoids. However, this hypothesis is not always supported and does not consider variation in other host traits in response to resources that may be important for parasitoids (e.g., variation in host size is known to impact parasitoid efficacy). In this study, we test whether trait variation within host developmental stages in response to host resources is more important for parasitoid efficacy and life histories than trait variation across host developmental stages. We exposed seed beetle hosts raised on a food quality gradient to mated female parasitoids and measured the number of hosts parasitized and parasitoid life history traits at the scale of host stage- and age-structure. Our results suggest host food quality does not cascade to impact idiobiont parasitoid life histories despite large food quality effects on host life history. Instead, variation in host life histories across host developmental stages better predicts parasitoid efficacy and life histories, suggesting finding a host in a specific instar is more important for idiobiont parasitoids than finding hosts on or within higher quality resources.

opencc-by-4.0Mar 2023View details →

MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids

This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann et al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.01.530589v1">bioRxiv</a>, 2023. Article Summary Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (Gorilla gorilla gorilla, Gorilla beringei beringei), three chimpanzee subspecies (Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii), and bonobos (Pan paniscus), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family Dialisteraceae, though we find that overall, co-phylogeny patterns are frequently disrupted in humans.

opencc-zeroMar 2023View details →

Data from: Fungal symbionts generate water-saver and water-spender plant drought strategies via diverse effects on host gene expression

Panicum hallii var hallii HAL2 plants were inoculated individually with six foliar fungal endophytes or fungus-free controls and subjected to 5% or 20% soil moisture treatments. The fungi were selected for their previously observed effects on plant drought physiology, inducing either a "water saver" or a "water spender" strategy in the host. Plants were grown in enclosed microcosms to prevent cross-contamination and each treatment and control included 6 replicates. All fungi were Ascomycetes isolated from plants in central Texas. Plants were monitored for height, wilt, water loss, and survival. At the harvest, we also measured biomass and leaf colonization by the fungi and flash-froze leaf tissue for transcriptomic analyses. Both plant response and gene expression data are provided.

opencc-by-4.0Apr 2021View details →

Dataset for: Effect of developmental temperatures on Aphidius colemani host-foraging behavior at high temperature

This is the dataset for the following study; Effect of developmental temperatures on Aphidius colemani host-foraging behavior at high temperature. We explored how three rearing temperatures (10, 20, and 28°C) affected host-foraging behaviors and associated traits under warm conditions in the insect parasitoid Aphidius colemani.

opencc-by-4.0Nov 2010View details →

Figure 1 in Parasites as secret files of the trophic interactions of hosts: the case of the rufousbellied thrush Los parásitos como archivos secretos en las interacciones tróficas con sus hospederos: el caso del Zorzal Colorado

Figure 1. Relationship between body weight in grams (independent variable) of adult rufous-bellied thrushes (Turdus rufiventris) and species richness of parasites (dependent variable).