Biology subjects

Yeager, J.

Publications and source records attributed to Yeager, J..

6 recordsLinked to original sources

bioRxiv2026

Big-team science reveals that patterns of inhibitory control variation in teleost fishes differ from those in mammals and birds

Understanding the evolution of cognition is fundamental to understanding the origins and nature of our own cognitive abilities, with cross-species comparisons providing a cornerstone of this endeavor. Yet, comparative cognition so far has largely focused on endothermic vertebrates, particularly mammals and birds, while ectotherms--representing a substantial proportion of vertebrate diversity--remain relatively understudied. Moreover, variation in experimental methods makes existing data difficult to compare across species. Big-team science offers a way to overcome these limitations by enabling standardized cognitive testing across broad taxonomic scales. Here, we apply this approach to fishes, using inhibitory control as a proof of concept for standardized comparative testing in 444 individuals across 22 teleost species spanning 19 genera. We demonstrate that standardized cognitive testing across such diversity is feasible, while also revealing substantial heterogeneity in the sample. Performance varied markedly among species, but, strikingly, showed only a weak phylogenetic signal, contrasting with patterns previously reported in mammals and birds. In addition, we detected great within-species variation, including differences across research groups, suggesting that performance may reflect not only species-level evolutionary history but also ontogenetic experience and the capacity to adjust decision rules to local conditions. Together, our findings highlight the importance of both evolutionary and environmental sources of cognitive variation and demonstrate that extending standardized comparative approaches beyond traditionally studied endotherms can reveal a more dynamic and complex picture of cognitive evolution across the vertebrate lineage.

animal behavior and cognition↗

bioRxiv2026

Modeling Sex Differences and Neurodegeneration in Repetitive Traumatic Brain Injury Using Drosophila

Traumatic brain injury (TBI) is a public health burden with short-term and long-term consequences for those who survive. Repetitive TBI (rTBI) is highly associated with neurodegenerative diseases such as chronic traumatic encephalopathy. Here, we present a force-adjustable, enhanced CO2-driven Drosophila model of rTBI to investigate locomotor, cognitive, proteomic, and neurodegenerative changes following rTBI. Injured males demonstrate dose-dependent locomotor deficits, while injured females display greater tolerance to rTBI. However, both sexes exhibit significant decision-making deficits. Proteomic analysis revealed changes in proteins linked with locomotory behavior, mitochondria, and energy production post-injury, correlating with observed behavioral phenotypes. Histological analysis revealed increased vacuolization area in rTBI flies. These results suggest that rTBI drives sex-specific behavioral deficits, proteomic disruption, and neurodegeneration. Overall, this enhanced Drosophila rTBI model provides a valuable tool for exploring sexually dimorphic outcomes and understanding the long-term pathophysiology of repetitive brain trauma in the context of neurodegenerative disease. Significance StatementRepetitive traumatic brain injury (rTBI) is linked to long-term cognitive decline and neurodegeneration, yet standardized, scalable models that capture sex-dependent outcomes are limited. We developed an automated, force-adjustable, closed-head Drosophila rTBI apparatus that delivers reproducible injuries without off-target damage, enabling precise control of injury severity across sexes. Using this platform, we show sexually dimorphic survival and locomotor vulnerability, persistent decision-making deficits, and progressive brain pathology marked by vacuolization and apoptosis. Proteomic profiling reveals time-dependent, sex-specific disruption of mitochondrial, oxidative stress, and locomotor-related protein networks, providing mechanistic entry points for discovering modifiers and therapies for repetitive brain trauma.

molecular biology↗

bioRxiv2024

NeoPhAR: Next-generation Phage Therapy for Antimicrobial Resistance

Growing antimicrobial resistance (AMR) infections are among the top contemporary concerns in public healthcare systems which can place considerable burdens on healthcare systems. Phage therapy has long been considered a viable option to help combat AMR infections, including on broad geographic scales. One bottleneck in the application of phage therapy is the accurate matching of host-specific phages to bacterial strains, which is traditionally done using molecular techniques. Here we present an open-access deep learning-based model that shows incredible potential to accurately predict phages for therapeutic use. Our goal is to attenuate the matching process so that specific phages, or a cocktail of phages can be prepared for patients with a high probability of therapeutic success, helping to democratize phage therapy treatments even in low to middle-income countries where genomic resources can be limited, costly, or time prohibitive. We feel this is an important first step towards incorporating and applying bioinformatic practices in promising fields such as phage therapy.

bioinformatics↗

bioRxiv2020

SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability

The emergence of SARS-CoV-2 has resulted in more than 200,000 infections and nearly 9,000 deaths globally so far. This novel virus is thought to have originated from an animal reservoir, and acquired the ability to infect human cells using the SARS-CoV cell receptor hACE2. In the wake of a global pandemic it is essential to improve our understanding of the evolutionary dynamics surrounding the origin and spread of a novel infectious disease. One way theory predicts selection pressures should shape viral evolution is to enhance binding with host cells. We first assessed evolutionary dynamics in select betacoronavirus spike protein genes to predict where these genomic regions are under directional or purifying selection between divergent viral lineages at various scales of relatedness. With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. Next, to gain further insights into factors associated with coronaviruses recognition of the human host receptor, we performed modeling studies of five different coronaviruses and their potential binding to hACE2. Modeling results indicate that interfering with the salt bridges at hot spot 353 could be an effective strategy for inhibiting binding, and hence for the prevention of coronavirus infections. We also propose that a glycine residue at the receptor binding domain of the spike glycoprotein can have a critical role in permitting bat variants of the coronaviruses to infect human cells.

microbiology↗

bioRxiv2019

Orb-weaving spiders show a correlated syndrome of morphology and web structure in the wild

Extended phenotypes are traits that exist outside the physical body of the organism. Despite their potential role in the lives of both the organisms that express them and other organisms that can be influenced by extended phenotypes, the consistency and covariance with morphological and behaviour traits of extended phenotypes is rarely evaluated, especially in wild organisms. We repeatedly measured an extended phenotype that directly influences an organisms prey acquisition, the web structure, of wild orb-weaving spiders (Micrathena vigorsii), which re-build their webs each day. We related web structure traits to behavioural traits and body size (length). Both web diameter and web density were repeatably different among individuals, while reaction to a predation threat was slightly so, but response to a prey stimulus and web symmetry were not. There was a syndrome between morphology and web structure traits, where larger spiders spun webs that were wider, had webs with increased thread spacing, and the spider tended to react more slowly to a predation threat. When a spider built a relatively larger web it was also relatively a less dense and less symmetrical web. The repeatability of web construction and relationship with spider body size we found may be common features of intra-population variation in web structure in spiders. Individual variation along the morphology and web structure syndrome could represent variation in individual foraging strategies, or age-based correlated changes. By estimating the consistency and covariances of extended phenotypes we can begin to evaluate what maintains their variation and how they might evolve.

animal behavior and cognition↗

bioRxiv2019

Collective behaviour is not robust to disturbance, yet parent and offspring colonies resemble each other in social spiders

Groups of animals possess phenotypes such as collective behaviour, which may determine the fitness of group members. However, the stability and robustness to perturbations of collective phenotypes in natural conditions is not established. Furthermore, whether group phenotypes are transmitted from parent to offspring groups is required for understanding how selection on group phenotypes contributes to evolution, but parent-offspring resemblance at the group level is rarely estimated. We evaluated robustness to perturbation and parent-offspring resemblance of collective foraging aggressiveness in colonies of the social spider Anelosimus eximius. Among-colony differences in foraging aggressiveness were consistent over time but changed if the colony was perturbed through the removal of individuals, or via their removal and subsequent return. Offspring and parent colony behaviour were correlated, but only once the offspring colony had settled after being translocated. The parent-offspring resemblance was not driven by a shared elevation but could be due to other environmental factors. Laboratory collective behaviour was not correlated with behaviour in the field. Colony aggression seems sensitive to initial conditions and easily perturbed between behavioural states. Despite this sensitivity, offspring colonies have collective behaviour that resembles that of their parent colony, provided they are given enough time to settle into the environment.

evolutionary biology↗