Biology subjects

Sauer, E.

Publications and source records attributed to Sauer, E..

6 recordsLinked to original sources

bioRxiv2026

PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data

Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI's integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ~15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI's utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.

genomics↗

bioRxiv2024

A high lipid diet leads to greater pathology and lower tolerance during infection

Despite the clear effect of food resources on wildlife disease dynamics, few studies have investigated how shifts in diet, specifically macronutrient content, shape vertebrate host responses to infection. While each individual macronutrient plays a vital role in physiological processes necessary for pathogen defense, it is often difficult to disentangle the role of an individual macronutrient on disease pathology. We explored the effects of dietary macronutrient composition on disease pathology and feeding behavior of canaries (Serinus canaria domestica) infected with Mycoplasma gallisepticum (MG). First, we provided canaries with isocaloric diets comprised of identical ingredients that varied in macronutrient content (high-protein or high-lipid) then MG- or sham-inoculated birds. We then offered both diets to canaries before and after MG- and sham-inoculation. In experiment one, high protein diet birds consumed more food than high lipid diet birds and experienced a more pronounced decrease in food intake after infection. High protein diet birds were more tolerant to MG infection, exhibiting reduced pathology when compared to high lipid diet birds, despite the two treatments having similar levels of MG-specific antibodies and MG loads. When birds had access to both diets, they consumed more of the high protein diet and experienced pathology for less time than lipid or protein restricted birds. These results highlight that macronutrient makeup of the diet can shape host tolerance and pathology and thus affect host-pathogen transmission dynamics. Summary StatementMacronutrient composition of the diet shapes tolerance in an avian host pathogen system. Birds that had greater access to protein exhibited reduced pathology despite similar pathogen loads when compared with birds with greater access to lipids.

ecology↗

bioRxiv2023

Critical reproductive behaviors in Scaled Quail and Northern Bobwhite are affected by thermal variability and mean temperature

Animals can respond differently to shifting thermal variability versus thermal averages, both of which are changing due to climate warming. How these thermal variables affect parental care behaviors can reveal the ability of parents to modify their behaviors to meet the competing demands of their offsprings thermal needs and self-maintenance, which becomes critical in suboptimal thermal conditions. Further, the time frame used to examine the interplay between temperature and behavioral shifts (e.g., seasonal patterns in care vs. drivers of individual care decisions) can provide different information about the plasticity of parental care behavior. We investigated the relationship between thermal means, thermal variability, and incubation behaviors across multiple timescales in Scaled Quail and Northern Bobwhite. Both species decreased off-bout length during periods of high thermal variability, a novel finding among studies of avian parental behavior. Further relationships between thermal endpoints (mean vs. variation) and behavior differed depending on the temporal scale. For instance, total daily time spent off the nest was not influenced by daily average temperature, yet individual off-bout duration increased with increasing average temperature in the two hours prior to the off-bout. These results provide evidence that thermal-behavioral relationships differ across scales and likely represent a birds ability to modify their incubation strategy to rapidly respond to the immediate thermal environment (altering individual off-bout length based on temperature) to meet self-maintenance needs while resulting in a similar outcome for their nest (total daily off-bout time). However, longer off-bout durations during high temperature events can come with reproductive costs, sometimes resulting in acute offspring mortality when eggs or chicks experience lethal temperatures.

animal behavior and cognition↗

bioRxiv2022

A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics.

AO_SCPLOWBSTRACTC_SCPLOWDirekli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a [~]14,000 year old 2.59X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten "Taurasian tur" likely survived Late Pleistocene climatic change in a Taurus Mountain refugia and its genomic fate is unknown.

genomics↗

bioRxiv2021

Do host-consumed resources increase endoparasitic but decrease ectoparasitic infections?

Habitat loss and disease outbreak play a major role in the decline of biodiversity. Habitat degradation is often associated with reduced food resources, which can lead to less investment in host immunity and increased infections. However, pathogens use host resources for replication and pathogen traits, such as infecting hosts internally or short generation times, might allow pathogens to rapidly capitalize on host-consumed nutrients. Thus, it is unclear whether increased food consumption by hosts should reduce or amplify pathogen levels. We conducted experiments on Cuban treefrogs (Osteopilus septentrionalis) to test how food availability affects infection levels of Ranavirus and the fungal pathogen Batrachochytrium dendrobatidis (Bd), which are both associated with mass die-offs of amphibians. Given that Ranavirus is an endoparasite with a much shorter generation time than the ectoparasitic Bd, we postulated that Ranavirus might be able to capitalize on host-consumed resources more quickly than Bd. We hypothesized that increased food availability to hosts might reduce Bd infections more than Ranavirus infections. As predicted, augmenting food access decreased Bd infection intensity, but increased Ranavirus infection intensity. Future work should assess whether pathogen traits, such as generation time and endo- versus ectoparasitism, generally affect whether food resources more positively benefit hosts or pathogens.

ecology↗

bioRxiv2018

Impacts of thermal mismatches on chytrid fungus Batrachochytrium dendrobatidis prevalence are moderated by life stage, body size, elevation and latitude

Global climate change is increasing the frequency of unpredictable weather conditions; however, it remains unclear how species-level and geographic factors, including body size and latitude, moderate impacts of unusually warm or cool temperatures on disease. Because larger hosts and lower-latitude hosts generally have slower acclimation times, we hypothesized that their disease susceptibility increases under \"thermal mismatches\", or differences between baseline climate and the temperature during surveying. Here, we examined how thermal mismatches interact with body size, life stage, habitat, latitude, elevation, phylogeny, and IUCN conservation status to predict infection prevalence of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in a global analysis of 38,967 amphibian hosts. As hypothesized, we found that the susceptibility of larger hosts and hosts from lower latitudes was strongly influenced by thermal mismatches. Furthermore, hosts of conservation concern are more susceptible than others following thermal mismatches, suggesting that thermal mismatches might have contributed to recent amphibian declines.\n\nData Accessibility StatementShould the manuscript be accepted, the data supporting the results will be archived in an appropriate public repository such as Dryad or Figshare and the data DOI will be included at the end of the article.

ecology↗