Biology subjects

Penn, A.

Publications and source records attributed to Penn, A..

6 recordsLinked to original sources

bioRxiv2026

Genomic history and ecology of local adaptation in sky-island Arabidopsis thaliana

Adaptation to local environments in isolated habitats may produce independent solutions to similar ecological challenges, yielding insight into the predictability of evolution. Alpine plants on tropical sky-islands, in particular, must cope with extreme diurnal fluctuations in temperature and radiation. These populations may undergo parallel local adaptation to high elevation, or alternatively, distinct local adaptations due to intermountain heterogeneity. For instance, abiotic stress on mountain peaks could select for stress tolerance or stress escape/bet-hedging strategies. We tested these hypotheses in experiments with 163 newly sequenced Arabidopsis thaliana genotypes from East Africa. Genomic history followed geography: Ugandan genotypes were the most divergent, and Ethiopian genotypes more closely related. Effective population size decreased towards the present on all mountains, in concert with declining climatic suitability since the end of the African Humid Period. Genotypes from the colder and seasonally drier mountains showed strong seed dormancy, rapid flowering, short/curved inflorescences. In contrast, genotypes from the milder and less seasonal mountains showed less seed dormancy, delayed flowering, and long/erect inflorescences. Elevational clines found in multiple mountains included seed dormancy-release with short (vs. long) stratification, and shorter inflorescences, at higher elevations. In a genome-wide association study (GWAS) with inflorescence length, we detected the TCP5 transcription factor, but these variants only segregated in some mountains and showed an elevational allele frequency cline at only one mountain. Allele reuse based on GWAS was greater between Ethiopian populations (QTL allele-frequency r > 0.9 for most traits), and generally lower between Uganda and the rest. Results indicate limited evidence of parallel local adaptation along elevation, suggesting that dwarf inflorescences are selected for in multiple mountain tops, while bet-hedging prevails in cold and seasonally dry sky-islands, and divergent selection along elevation in other traits can evolve in mountains with milder climates. Overall these results suggest a long history of isolation and ecological complexity limit the predictability of local adaptation.

evolutionary biology↗

bioRxiv2025

Ultrastructure of Inputs to the Granule Cell Domain of the Dorsal Cochlear Nucleus

The granule cell domain of the cochlear nucleus (GCD) receives input from multimodal brain regions including the second cervical spinal ganglion, the spinal trigeminal nucleus, the cuneate nucleus, and the lateral reticular nucleus. Most of the input are in the form of large mossy fibers and small boutons containing round synaptic vesicles and forming asymmetric synapses. A smaller number of inputs arise from the lateral reticular nucleus and the spinal trigeminal nucleus that contain pleomorphic synaptic vesicles implying inhibitory action. This circumstance positions the GCD for integrating polysensory excitatory and inhibitory inputs at the earliest stages of auditory processing, which suggests a role for segregating sound streams. The structural substrate for such a function is naturally elaborate. Mossy fibers from these different origins are large, multilobed endings that form synaptic glomeruli with postsynaptic targets that include granule cells, unipolar brush cells, cartwheel cells, and chestnut cells, which in turn project to principal cells in the dorsal cochlear nucleus (DCN). Numerous synapses contribute to the integration of the different modalities, but the organization of these synapses is still not well understood. We investigated this issue by labelling the presynaptic endings of different somatosensory inputs using biotinylated dextran amine or Phaseolus vulgaris leucoagglutinin, and studying their post-synaptic relationships in the GCD. The anterogradely-labeled endings and associated targets were visualized by light and electron microscopy. Following computer-aided, three-dimensional reconstructions, we found that unipolar brush cells are the main target of the C2 DRG and cuneate nucleus. Mossy fibers from the spinal trigeminal nucleus project to Golgi cells, an inhibitory neuron. In contrast, inhibitory boutons originated from the lateral reticular nucleus. These results reveal that somatosensory integration in the granule cell domain is achieved by distinctive synaptic wiring and specialized chemical signaling.

neuroscience↗

bioRxiv2025

Age-related changes in the gut microbiota of a long-lived seabird suggest divergence from mammalian models

Gut microbiota plays key roles in shaping host development, immunity, and physiology. The assembly of vertebrate gut microbiota during early life follows relatively predictable trajectories across several mammalian species, largely driven by maternal transmission routes. However, birds lack these transmission mechanisms due to their oviparity, potentially leading to different age-related microbiota patterns. Here, we investigate gut microbiota variation in Atlantic puffin (Fratercula arctica) chicks and adults across six British populations using 16S rRNA amplicon sequencing. We find that chick microbiotas show strong population-level structuring that disappears in adults, with spatial patterns particularly pronounced in anaerobic bacteria. Puffin microbiotas become increasingly individualised and aerotolerant with age, while taxonomic richness remains stable - patterns that contrast with the convergent, richness-increasing trajectories observed in several mammalian species. Our results suggest that environmental exposure drives early-life microbiota assembly in birds, highlighting the value of avian systems for understanding vertebrate microbiota development beyond mammals.

ecology↗

bioRxiv2025

It's all in the timing: vegetative phase change alters selection under drought and contributes to local adaptation

The timing of developmental transitions is critical for adaptation, aligning stress-tolerant and sensitive stages with harsh and benign periods. At the same time, tradeoffs can promote diversity in development within populations. While geographic clines in developmental timing are often documented, there are few documented genetic tradeoffs in stress tolerance across developmental stages. Here, we study the juvenile-to-adult vegetative phase change (VPC), a conserved transition marked by changes in leaf morphology and physiology. In Arabidopsis, we found strong rank-changing genotype-by-environment interactions for fitness depending on the stage of drought exposure, indicating tradeoffs and stage-specific mechanisms of drought adaptation. Adult plants significantly increased water-use efficiency under drought, while juveniles did not, indicating lower juvenile plasticity. VPC timing varied with climate in Iberia, where genotypes from warm, dry climates transitioned earlier than those from cool, moist climates. However, SNPs associated with VPC timing and drought fitness showed little global geographic variation, suggesting tradeoffs maintain diversity across the species range. Genome-wide association mapping revealed candidate loci for VPC timing and stage-specific drought responses, several validated in T-DNA lines. Our results show that VPC timing contributes to drought adaptation and that genetic tradeoffs across developmental stages help maintain natural diversity.

plant biology↗

bioRxiv2024

Neighbor sensing through rhizodeposits in sorghum affects plant physiology and productivity

Plant-plant interactions play a crucial role in shaping the growth environment for crops, impacting their productivity and stress response. The interaction between plants aboveground has been studied and incorporated into breeding programs that select for plants that reduce aboveground competition between plants. However, few studies have focused on belowground interactions, and these looked at combined interactions and root partitioning in the soil. This study focuses on the developmental and physiological responses of sorghum (Sorghum bicolor L.) genotypes to neighboring sorghum plants. In this study, we used two growing methods: i) a focal plant surrounded by neighboring plants in the same pot but without shading, and ii) a focal plant grown either alone or surrounded by neighbors, irrigated with nutrient solution passed through pots (leachates) with or without plants. Our results showed that the presence of neighbors in the same pot led to reduced size-dry weight height, and leaf area of the focal plant. In addition, the presence of neighbors reduced stomatal conductance and PSII quantum yield. While the response direction was similar across tested genotypes, the magnitude varied. The results were repeated when neighboring plants were not grown in the same pot, but the nutrient solution passed through the root system of plants of the neighboring genotype. Furthermore, we saw a reduction in assimilation rate and stomatal conductance when plants were exposed to either the physical presence of neighbors or leachate. We did not find differences in root architecture in either treatment. These results show plants change their growth in response to neighbors and that the signal is carried through the liquid phase of the soil. Our findings provide insights into sorghum plants responses to below-ground signaling from neighboring plants and lay the foundation for future studies enabling increased crop performance under high-density planting conditions.

plant biology↗

bioRxiv2021

Kismet/CHD7/CHD8 affects gut biomechanics, the gut microbiome, and gut-brain axis in Drosophila melanogaster

The gut-brain axis may contribute to the pathophysiology of neurodevelopmental disorders, yet it is often unclear how risk genes associated with these disorders affect gut physiology in a manner that could impact microbial colonization. We addressed this question using Drosophila melanogaster with a null mutation in kismet, the ortholog of chromodomain helicase DNA-binding protein (CHD) family members CHD7 and CHD8. In humans, CHD7 and CHD8 are risk genes for neurodevelopmental disorders with co-occurring gastrointestinal symptoms. We found kismet mutant flies have a significant increase in gastrointestinal transit time, indicating functional homology of kismet with CHD7/CHD8 in vertebrates. To measure gut tissue mechanics, we used a high-precision force transducer and length controller, capable of measuring forces to micro-Newton precision, which revealed significant changes in the mechanics of kismet mutant guts, in terms of elasticity, strain stiffening, and tensile strength. Using 16S rRNA metagenomic sequencing, we also found kismet mutants have reduced diversity of gut microbiota at every taxonomic level and an increase in pathogenic taxa. To investigate the connection between the gut microbiome and behavior, we depleted gut microbiota in kismet mutant and control flies and measured courtship behavior. Depletion of gut microbiota rescued courtship defects of kismet mutant flies, indicating a connection between gut microbiota and behavior. In striking contrast, depletion of gut microbiome in the control strain reduced courtship activity. This result demonstrated that antibiotic treatment can have differential impacts on behavior that may depend on the status of microbial dysbiosis in the gut prior to depletion. We propose that Kismet influences multiple gastrointestinal phenotypes that contribute to the gut-brain axis to influence behavior. Based on our results, we also suggest that gut tissue mechanics should be considered as an element in the gut-brain communication loop, both influenced by and potentially influencing the gut microbiome and neuronal development.

developmental biology↗