Biology subjects

York, R. A.

Publications and source records attributed to York, R. A..

5 recordsLinked to original sources

bioRxiv2026

Differential impacts of fall versus spring prescribed burns on microbial biomass, richness, and composition in young mixed conifer forests

Prescribed burns aim to restore ecological processes and mitigate high-severity wildfire risks. Historically, California wildfires occur in summer or fall, but due to limited burning opportunities, prescribed burns occur in fall and spring. Yet, whether the burn season affects ecological outcomes is largely unknown. Here, we test prescribed burn season impacts on soil burn severity, bacterial and fungal abundance, richness, and composition as assessed with 16S and 18S qPCR and 16S and ITS2 Illumina MiSeq. We implemented a Before-After-Control-Impact design with 9 California montane mixed conifer forest stands (4 fall, 4 spring, 1 unburned control). We assessed resilience by collecting 6 sub-samples per stand at 6 time points ranging from pre-fire to 3 days, 1 and 6 months, and 1 and 2 years after fall and spring burns. Fall burns significantly reduced bacterial and fungal abundance and richness, whereas spring burns did not. Indeed, at 24 days after fall burns compared to pre-fire, bacterial and fungal richness were reduced by 24-30%, with richness of ectomycorrhizal fungi reduced by 45% and saprobic fungi by 28%. After the fall burn, fungal richness recovered within a year and fungal abundance within 6 months, whereas bacterial abundance and richness recovered in 2 years. Bacterial and fungal communities experienced compositional turnovers after both burns, with the emergence of several genera of "fire-loving" pyrophilous bacteria (Massilia, Paenibacillus) and fungi (Geminibasidium, Pyronema, Neurospora). Our findings suggest that, although seasonal differences were evident, both fall and spring prescribed burns mitigate wildfire impacts while promoting the succession of pyrophilous microbes.

microbiology↗

bioRxiv2021

Mechanosensory input shapes Drosophila motor behavior through Patterned Spontaneous Network Activity

Neural activity sculpts circuit wiring in many animals. In vertebrates, patterned spontaneous network activity (PaSNA) generates sensory maps and establishes local circuits 1-3. However, it remains unclear how PaSNA might shape neuronal circuits and behavior in invertebrates. Previous work in the developing Drosophila embryo discovered spontaneous muscle activity that did not require synaptic transmission, and hence was myogenic, preceding PaSNA 4-6. These studies, however, monitored muscle movement, not neural activity, and were therefore unable to observe how myogenic activity might relate to subsequent neural network engagement. Here we use calcium imaging to directly record neural activity and characterize the emergence of PaSNA. We demonstrate that the spatiotemporal properties of PaSNA are highly stereotyped across embryos, arguing for genetic programming. Consistent with previous observations, we observe neural activity well before it becomes patterned, initially emerging during the myogenic stage. Remarkably, inhibition of mechanosensory input as well as inhibition of muscle contractions results in premature and excessive PaSNA, demonstrating that muscle movement serves as a brake on this process. Finally, using an optogenetic strategy to selectively disrupt mechanosensory inputs during PaSNA, followed by quantitative modeling of larval behavior, we demonstrate that mechanosensory modulation during development is required for proper larval foraging. This work thus provides a foundation for using the Drosophila embryo to study the role of PaSNA in circuit formation, provides mechanistic insight into how PaSNA is entrained by motor activity, and demonstrates that spontaneous network activity is essential for locomotor behavior. These studies argue that sensory feedback during the earliest stages of circuit formation can sculpt locomotor behaviors through innate motor learning. HighlightsO_LIPaSNA in the Drosophila embryonic CNS is spatiotemporally stereotyped C_LIO_LIMechanosensory neurons negatively modulate PaSNA C_LIO_LIEmbryonic PaSNA is required for larval locomotor behavior C_LI

neuroscience↗

bioRxiv2020

TREBLE: a generalizable framework for high-throughput behavioral analysis

Uncovering relationships between neural activity and behavior represents a critical challenge, one that would benefit from facile tools that can capture complex structures within large datasets. Here we demonstrate a generalizable strategy for capturing such structures across diverse behaviors: Time-REsolved BehavioraL Embedding (TREBLE). Using data from synthetic trajectories, adult and larval Drosophila, and mice we show how TREBLE captures both continuous and discrete behavioral dynamics, can uncover variation across individuals, detect the effects of optogenetic perturbation in unbiased fashion, and reveal structure in pose estimation data. By applying TREBLE to moving mice, and medial entorhinal cortex (MEC) recordings, we show that nearly all MEC neurons encode information relevant to specific movement patterns, expanding our understanding of how navigation is related to the execution of locomotion. Thus, TREBLE provides a flexible framework for describing the structure of complex behaviors and their relationships to neural activity.

animal behavior and cognition↗

bioRxiv2020

Modular genetic control of social status in a cichlid fish

Social hierarchies are ubiquitous in social species and profoundly influence physiology and behavior. Androgens like testosterone have been strongly linked to social status, yet the molecular mechanisms regulating social status are not known. The African cichlid fish Astatotilapia burtoni is a powerful model species for elucidating the role of androgens in social status given their rich social hierarchy and genetic tractability. Dominant A. burtoni males possess large testes, bright coloration, and perform aggressive and reproductive behaviors while non-dominant males do not. Social status in A. burtoni is in flux, however, as males alter their status depending on the social environment. Due to a teleost-specific whole-genome duplication, A. burtoni possess two androgen receptor (AR) paralogs, ARα and ARβ, providing a unique opportunity to disentangle the role of gene duplication in the evolution of social systems. Here, we used CRISPR/Cas9 gene editing to generate AR mutant A. burtoni and performed a suite of experiments to interrogate the mechanistic basis of social dominance. We find that ARβ, but not ARα, is required for testes growth and bright coloration, while ARα, but not ARβ, is required for the performance of reproductive behavior and aggressive displays. Both receptors are required to reduce flees from females and either AR is sufficient for attacking males. Thus, social status in A. burtoni is inordinately dissociable and under the modular control of two AR paralogs. This type of non-redundancy may be important in facilitating social plasticity in A. burtoni and other species whose social status relies on social experience.Significance Statement Social rank along a hierarchy determines physiological state and behavioral performance. A ubiquitous feature of social hierarchies is the communication of rank through non-physical signaling systems (e.g., coloration) and aggression, traits that correlate with the reproductive status of an individual. Despite the links identified between social status, physiology, and behavior, the molecular basis of social status is not known. Here, we genetically dissect social status in the African cichlid fish Astatotilapia burtoni using CRISPR/Cas9 gene editing. We show that two distinct androgen receptor (AR) genes control social status in a highly modular manner. This type of coordination of social status may be fundamental across species that rely on social information to optimally guide physiology and behavior.Competing Interest StatementThe authors have declared no competing interest.View Full Text

animal behavior and cognition↗

bioRxiv2018

Hormonal regulation of social ascent and temporal patterns of behavior in an African cichlid

For many species, social rank determines which individuals perform certain social behaviors and when. Higher ranking or dominant (DOM) individuals maintain status through aggressive interactions and perform courtship behaviors while non-dominant (ND) individuals do not. In some species ND individuals ascend (ASC) in social rank when the opportunity arises. Many important questions related to the mechanistic basis of social ascent remain to be answered. We probed whether androgen signaling regulates social ascent in male Astatotilapia burtoni, an African cichlid whose social hierarchy can be readily controlled in the laboratory. As expected, androgen receptor (AR) antagonism abolished reproductive behavior during social ascent. However, we discovered multiple AR-dependent--and AR-independent--temporal behavioral patterns that typify social ascent and dominance. AR antagonism in ASC males reduced the speed of behavioral performance compared to DOM males. Socially ascending males, independent of AR activation, were more likely than DOM males to follow aggressive displays with another aggressive display. Further analyses revealed differences in the sequencing of aggressive and courtship behaviors, wherein DOM males were more likely than ASC males to follow male-directed aggression with courtship displays. Strikingly, this difference was driven mostly by ASC males taking longer to transition from aggression to courtship, suggesting ASC males can perform certain DOM-typical temporal behavioral patterns. Our results indicate androgen signaling drives social ascent, but hormonal signaling and social experience shape the full suite of DOM-typical behavioral patterns.

animal behavior and cognition↗