Biology subjects

Parker, B. J.

Publications and source records attributed to Parker, B. J..

18 recordsLinked to original sources

bioRxiv2026

Evolution of endogenized densoviral elements across aphid species

AO_SCPLOWBSTRACTC_SCPLOWEndogenous viral elements (EVEs) are widespread across animal genomes, yet the processes governing EVE evolution and diversification remain poorly understood. Here, we characterize the evolution of densoviral EVEs and exogenous densoviruses across the aphid tribe Macrosiphini, an agriculturally important group in which exogenous densoviruses and their endogenous derivatives have been linked to the plastic production of wings. Using new genome assemblies, transcriptomics, and phylogenetic analysis, we find that EVE content varies extensively across species. Moreover, we discovered a novel densovirus that is vertically transmitted, but phylogenetic incongruence between other densoviruses and their hosts suggests that horizontal transmission may also occur. Finally, we show that EVE-mediated regulation of wing plasticity extends across species that use different environmental signals to induce winged offspring. Our study shows that in this system, the evolution of EVEs is highly variable and lineage-specific, generating genomic patterns that cannot be predicted from host evolutionary relationships.

evolutionary biology↗

bioRxiv2025

Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont

AO_SCPLOWBSTRACTC_SCPLOWHeritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont strains. Despite their importance, we lack a clear understanding of how novel traits arise in symbiosis and how this diversity influences host ecology in natural populations. The aphid facultative symbiont Regiella insecticola is ideally suited to this question because of its strong lineage-specific variation in host benefits. By generating 20 high-quality genomes, we found that Regiellas evolution is driven largely by gene gains mediated by mobile genetic elements. We identified a plasmid (pRILSR1) that encodes a type IV secretion system and a highly expressed predicted effector that has been convergently acquired by Regiella strains from pea aphids. Notably, only pRILSR1-bearing strains confer protection against the specialist fungal pathogen Pandora neoaphidis, indicating that gains and losses of the plasmid underlie the evolution of this key defensive phenotype. Using a multi-year field study, we further show that the pRILSR1 plasmid is strongly associated with Regiella found in pea aphid populations adapted to specific host plants, driving variation in symbiont-mediated defense across populations. Together, our results show that mobile genetic elements generate key adaptive traits in microbial symbionts and, in doing so, drive phenotypic divergence among host populations.

evolutionary biology↗

bioRxiv2025

Overlooked neuroanatomical markers of face processing and developmental prosopagnosia in posteromedial cortex

Recent functional imaging studies implicate human posteromedial cortex (PMC)--composed of the posterior cingulate cortex, the precuneus, and retrosplenial cortex--in face processing. Separately, anatomical studies have identified previously overlooked cortical folds (sulci) in PMC associated with higher-level cognitive abilities. Here, we tested whether these newly identified sulci support face processing in neurotypical individuals and individuals with developmental prosopagnosia (DP). After manually labeling 1,642 sulci in 164 hemispheres, we first identified a gradient of face selectivity along the anterior-posterior axis of PMC that was consistent across three samples, including DP individuals. Second, we discovered a new anatomical locus in PMC that differed structurally and functionally between neurotypical and DP individuals. Finally, data-driven analysis revealed that right-hemisphere PMC sulcal morphology was associated with face recognition ability. These findings reveal a sulcal network in PMC that supports face processing, and they identify the first structural neuroanatomical marker of face processing deficits in PMC.

neuroscience↗

bioRxiv2025

CS-Fold: Advancing RNA Structure Predictions through Phylogenetic Modelling of Compensatory Mutations in Deep Neural Networks

Accurate prediction of RNA secondary structures is essential for understanding the conformation, function, and interactions of RNA. Leveraging co-evolutionary information across species through multiple sequence alignments (MSAs) has been proven to be effective in improving molecular structure predictions. However, existing deep learning approaches do not explicitly incorporate compensatory substitutions along the phylogenetic trees, which are crucial for capturing structural conservation through evolution. To address this, we developed CS-Fold, a novel deep learning framework that integrates compensatory substitutions likelihoods as constraints using likelihood estimation and Monte Carlo algorithms. These likelihoods, representing evolutionary changes along phylogenetic trees, are encoded in a sparse matrix that guides the attention mechanism of a Pairformer-based architecture. A custom loss function and an unrolled post-processing algorithm enforce adherence to the solution space constrained by these evolutionary constraints. CS-Fold achieves a substantial 5% improvement in the F1 score compared to the current mainstream approaches, demonstrated through evaluations on cross-family datasets, including 604 human RNA families from the Rfam database. Our model offers novel insights and incorporates additional evolutionary information beyond traditional MSAs and folding strategies, providing a robust and innovative solution for RNA secondary structure prediction.

bioinformatics↗

bioRxiv2024

Draft genome sequence of the glasshouse-potato aphid Aulacorthum solani

AO_SCPLOWBSTRACTC_SCPLOWAulacorthum solani is a worldwide agricultural pest aphid capable of feeding on a wide range of host plants. This insect causes mechanical damage to crops and is a vector of plant viruses. We found that the publicly available genome for A. solani is contaminated with another aphid species, and we produced a new genome using a barcoded isogenic laboratory line. We produced Oxford Nanopore and Illumina reads to generate a draft assembly, and we sequenced RNA to aid in the annotation of our assembly. Our A. solani draft genome is 671 Mbp containing 7,020 contigs with an N50 length of 196 kb with a BUSCO completeness of 98.6%. Out of the 24,981 genes predicted by E-GAPx, 22,804 were annotated with putative functions based on homology to other aphid species. This genome will provide a useful resource for the community of researchers studying aphids from agricultural and genomic perspectives.

genomics↗

bioRxiv2023

Pathogen-microbiome interactions and the virulence of an entomopathogenic fungus

AO_SCPLOWBSTRACTC_SCPLOWBacteria shape interactions between hosts and fungal pathogens. In some cases, bacteria associated with fungi are essential for pathogen virulence. In other systems, host associated microbiomes confer resistance against fungal pathogens. We studied an aphid-specific entomopathogenic fungus called Pandora neoaphidis in the context of both host and pathogen microbiomes. Aphids host several species of heritable bacteria, some of which confer resistance against Pandora. We first found that spores that emerged from aphids that harbored protective bacteria were less virulent against subsequent hosts and did not grow on plate media. We then used 16S amplicon sequencing to study the bacterial microbiome of fungal mycelia and spores during plate culturing and host infection. We found that the bacterial community is remarkably stable in culture despite dramatic changes in pathogen virulence. Last, we used an experimentally transformed symbiont of aphids to show that Pandora can acquire hostassociated bacteria during infection. Our results uncover new roles for bacteria in the dynamics of aphidpathogen interactions and illustrate the importance of the broader microbiological context in studies of fungal pathogenesis.

microbiology↗

bioRxiv2023

Untangling an insect virome from its endogenous viral elements

AO_SCPLOWBSTRACTC_SCPLOWInsects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have therefore employed high-throughput sequencing of RNA, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. In this study, we use a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-reduced RNAseq to characterize the bacteria and viruses found in individual insects. We then characterized the frequency of a heritable Flavivirus and an Ambidensovirus in our population. We next generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing. This analysis showed that the Ambidensovirus, previously described from an RNAseq viral screen, is not a exogenous virus and instead is a transcribed endogenous viral element in the M. euphorbiae genome. Our study generates key insight into an important agricultural pest and highlights a widespread challenge for the study of viral diversity using RNAseq.

genomics↗

bioRxiv2023

Plasma cells are formed in waning germinal centers via an affinity-independent process

Long-lived plasma cells (PCs) secrete antibodies that can provide sustained immunity against infection. It has been proposed that high affinity cells are preferentially selected into this compartment, potentiating the immune response. Here we used single cell RNA-seq to track the development of Ighg2A10 cells, specific for the Plasmodium falciparum circumsporozoite protein (PfCSP) within the germinal center (GC). We identified cells differentiating into memory B cells (MBC) or PCs and estimated their affinity by V(D)J sequencing. While pre-memory cells were of lower affinity than GC B cells generally, the affinity of pre-PC cells was indistinguishable. Rather, a larger proportion of cells differentiated into PCs in waning GCs. These later emigrants replaced early arrivals in the bone marrow allowing the development of a high affinity PC compartment.

immunology↗

bioRxiv2023

Sulcal morphology of posteromedial cortex substantially differs between humans and chimpanzees

Recent studies identify a surprising coupling between evolutionarily new sulci and the functional organization of human posteromedial cortex (PMC). Yet, no study has compared this modern PMC sulcal patterning between humans and non-human hominoids. To fill this gap in knowledge, we first manually defined 918 sulci in 120 chimpanzee (Pan Troglodytes) hemispheres and 1619 sulci in 144 human hemispheres. We uncovered four new PMC sulci, and quantitatively identified species differences in incidence, depth, and surface area. Interestingly, some PMC sulci are more common in humans and others, in chimpanzees. Further, we found that the prominent marginal ramus of the cingulate sulcus differs significantly between species. Contrary to classic observations, the present results reveal that the surface anatomy of PMC substantially differs between humans and chimpanzees -- findings which lay a foundation for better understanding the evolution of neuroanatomical-functional and neuroanatomical-behavioral relationships in this highly expanded region of the human cerebral cortex.

neuroscience↗

bioRxiv2022

CRMnet: a deep learning model for predicting gene expression from large regulatory sequence datasets

Recent large datasets measuring the gene expression of millions of possible gene promoter sequences provide a resource to design and train optimised deep neural network architectures to predict expression from sequences. High predictive performance due to the modelling of dependencies within and between regulatory sequences is an enabler for biological discoveries in gene regulation through model interpretation techniques. To understand the regulatory code that delineates gene expression, we have designed a novel deep-learning model (CRMnet) to predict gene expression in Saccharomyces cerevisiae. Our model outperforms the current benchmark models and achieves a Pearson correlation coefficient of 0.971. Interpretation of informative genomic regions determined from model saliency maps, and overlapping the saliency maps with known yeast motifs, support that our model can successfully locate the binding sites of transcription factors that actively modulate gene expression. We compare our models training times on a large compute cluster with GPUs and Google TPUs to indicate practical training times on similar datasets.

bioinformatics↗

bioRxiv2022

Variation in density, immune gene suppression, and co-infection outcomes among strains of the aphid endosymbiont Regiella insecticola

AO_SCPLOWBSTRACTC_SCPLOWMany insects harbor heritable beneficial microbes that influence host phenotypes. Across systems, divergent symbiont strains have been shown to establish at different densities within hosts. This genetic variation is important evolutionarily because within-host density has been linked to the costs and benefits of the symbiosis for both partners. Studying the factors shaping within-host density is therefore important to our broader understanding of host-microbe coevolution. Here we focused on different strains of Regiella insecticola, a facultative symbiont of aphids. We first demonstrated that different strains of Regiella consistently establish in pea aphids at drastically different densities. We then found that variation in density is correlated with the expression levels of two key insect immune system genes (phenoloxidase and hemocytin), with immune gene suppression correlating with higher Regiella density. We then performed an experiment where we established co-infections of a higher- and lower-density Regiella strain, and we showed that the higher-density strain is better able to persist in co-infections than the lower-density strain. Together, our results point to a potential mechanism for strain-level variation in symbiont density in this system, and further suggest that symbiont fitness may be increased by establishing at higher density within hosts. Our work highlights the importance of within-host dynamics shaping symbiont evolution.

evolutionary biology↗

bioRxiv2022

Functionally and structurally distinct fusiform face area(s) in over 1000 participants

The Fusiform Face Area (FFA) is a widely studied region causally involved in face perception. Even though cognitive neuroscientists have been studying the FFA for over two decades, answers to foundational questions regarding the structure, function, and connectivity of the FFA from a large (N>1000) group of participants are still lacking. To fill this gap, we quantified structural, functional, and connectivity features of fusiform face-selective regions in 1080 participants in the Human Connectome Project (HCP). After manually defining over 4,000 fusiform face-selective regions, we report five main findings. First, 68.94% of hemispheres have two cortically separate regions (pFus-faces/FFA-1 and mFus-faces/FFA-2). Second, in 26.48% of hemispheres, pFus-faces/FFA-1 and mFus-faces/FFA-2 are spatially contiguous, yet functionally and structurally distinct. Third, pFus-faces/FFA-1 is more face-selective than mFus-faces/FFA-2, and the two regions have distinct functional connectivity fingerprints. Fourth, pFus-faces/FFA-1 is cortically thinner and more heavily myelinated than mFus-faces/FFA-2. Fifth, face-selective patterns and functional connectivity fingerprints of each region were more similar in monozygotic than dizygotic twins and more so than structural gradients. As we share our areal definitions with the field, future studies can explore how structural and functional features of these regions will inform theories regarding how visual categories are represented in the brain.

neuroscience↗

bioRxiv2022

Hominoid-specific sulcal variability is related to face perception ability

Human perception requires complex cortical networks that function at neuroanatomical scales of microns and temporal scales of milliseconds. Despite this complexity, what if just one morphological feature of the brain could predict perceptual ability? Here, we tested this hypothesis with pre-registered analyses of neuroanatomy and face perception in neurotypical controls (NTs) and individuals with developmental prosopagnosia (DPs). Results show that the length of the mid-fusiform sulcus (MFS), a hominoid-specific tertiary sulcus in ventral temporal cortex (VTC), was shorter in DPs than NTs. Furthermore, individual differences in MFS length in the right, but not left, hemisphere predicted individual differences in face perception. These results support theories linking brain structure and function to perception, as well as indicate that one feature - variability in MFS length - can predict face perception. Finally, these findings add to growing evidence supporting a role of morphological variability of late developing, tertiary sulci and individual differences in cognition.

neuroscience↗

bioRxiv2021

In vitro neurons learn and exhibit sentience when embodied in a simulated game-world

Integrating neurons into digital systems to leverage their innate intelligence may enable performance infeasible with silicon alone, along with providing insight into the cellular origin of intelligence. We developed DishBrain, a system which exhibits natural intelligence by harnessing the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins, are integrated with in silico computing via high-density multielectrode array. Through electrophysiological stimulation and recording, cultures were embedded in a simulated game-world, mimicking the arcade game Pong. Applying a previously untestable theory of active inference via the Free Energy Principle, we found that learning was apparent within five minutes of real-time gameplay, not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organise in a goal-directed manner in response to sparse sensory information about the consequences of their actions.

synthetic biology↗

bioRxiv2021

A new tripartite landmark in posterior cingulate cortex

Understanding brain structure-function relationships, and their development and evolution, is central to neuroscience research. Here, we show that morphological differences in posterior cingulate cortex (PCC), a hub of functional brain networks, predict individual differences in macroanatomical, microstructural, and functional features of PCC. Manually labeling 4,319 sulci in 552 hemispheres, we discovered a consistently localized shallow cortical indentation (termed the inframarginal sulcus; ifrms) within PCC that is absent from neuroanatomical atlases, yet co-localized with a region within the cognitive control, but not default mode, network. Morphological analyses in humans and chimpanzees showed that unique properties of the ifrms differ across the lifespan and between hominoid species. Intriguingly, the consistency of the ifrms also debunks the uniqueness of the morphology of Einsteins PCC. These findings support a classic theory that shallow, tertiary sulci serve as landmarks in association cortices. They also beg the question: how many other cortical indentations have we missed?

neuroscience↗

bioRxiv2020

Intraspecific variation in immune gene expression and heritable symbiont density

AO_SCPLOWBSTRACTC_SCPLOWHost genetic variation plays an important role in the structure and function of heritable microbial communities. Recent studies have demonstrated that insects use immune mechanisms to regulate heritable symbionts. Here we test the hypothesis that variation in symbiont density within hosts is linked to intraspecific differences in the immune response to harboring symbionts. We show that pea aphids (Acyrthosiphon pisum) harboring the bacterial endosymbiont Regiella insecticola (but not all other species of symbionts) suppress expression of key immune genes. We then functionally link immune suppression with symbiont density using RNAi. The pea aphid species complex is comprised of multiple reproductively-isolated host plant-adapted populations. These biotypes have distinct patterns of heritable symbiont infections: for example, aphids from the Trifolium biotype are strongly associated with Regiella. Using RNAseq, we compare patterns of gene expression in response to Regiella in aphid genotypes from multiple biotypes, and we show that Trifolium aphids experience no immune gene suppression from Regiella and host symbionts at lower densities. We then generated F1 hybrids between two biotypes and found that symbiont density and immune suppression are both intermediate in hybrids. We suggest that in this system, Regiella symbionts are suppressing aphid immune mechanisms to increase their density, but that some hosts have adapted to prevent immune suppression in order to control symbiont numbers. The specific immune mechanisms suppressed by Regiella have been previously demonstrated to combat pathogens in aphids, and thus this work highlights the immune systems complex dual role in interacting with both beneficial and harmful microbes. AO_SCPLOWUTHORC_SCPLOW SO_SCPLOWUMMARYC_SCPLOWHeritable microbes are found in most insects including agriculturally and medically relevant pests. Explaining the variation in the distribution and abundance of symbionts in natural populations is critical to understanding these interactions. This work contributes to our mechanistic understanding of an important model of host-microbe symbiosis and suggests more broadly that variation in insect immune responses plays a role in intraspecific variation in host-symbiont interactions. Our work also suggests that antagonistic coevolution can play a role in host-microbe interactions even when microbes are transmitted vertically and provide a clear benefit to their hosts.

evolutionary biology↗

bioRxiv2020

Intraspecific variation in symbiont density in an insect-microbe symbiosis

AO_SCPLOWBSTRACTC_SCPLOWMany insects host vertically-transmitted microbes, which can confer benefits to their hosts but are costly to maintain and regulate. A key feature of these symbioses is variation: for example, symbiont density can vary among host and symbiont genotypes. However, the evolutionary forces maintaining this variation remain unclear. We studied variation in symbiont density using the pea aphid (Acyrthosiphon pisum) and the bacterium Regiella insecticola, a symbiont that can protect its host against fungal pathogens. We found that relative symbiont density varies both between two Regiella phylogenetic clades and among aphid biotypes. Higher-density symbiont infections are correlated with stronger survival costs, but variation in density has little effect on the protection Regiella provides against fungus. Instead, we found that in some aphid genotypes, a dramatic decline in symbiont density precedes the loss of a symbiont infection. Together, our data suggest that the optimal density of a symbiont infection is likely different from the perspective of aphid and microbial fitness. Regiella might prevent loss by maintaining high within-host densities, but hosts do not appear to benefit from higher symbiont numbers and may be advantaged by losing costly symbionts in certain environments. The standing variation in symbiont density observed in natural populations could therefore be maintained by antagonistic coevolutionary interactions between hosts and their symbiotic microbes.

evolutionary biology↗

bioRxiv2017

Unravelling the genomic basis and evolution of the pea aphid male wing dimorphism

Wing dimorphisms have long served as models for examining the ecological and evolutionary tradeoffs associated with alternative morphologies [1], yet the mechanistic basis of morph determination remains largely unknown. Here we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing dimorphism, wherein males exhibit one of two alternative morphologies that differ dramatically in a set of correlated traits that inclused the presence or absence of wings [2-4]. Unlike the environmentally-induced asexual female aphid wing polyphenism [5], the male wing polymorphism is genetically determined by a single uncharacterized locus on the X chromosome called aphicarus (\"aphid\" plus \"Icarus\", api) [6, 7]. Using recombination and association mapping, we localized api to a 130kb region of the pea aphid genome. No nonsynonymous variation in coding sequences strongly associated with the winged and wingless phenotypes, indicating that api is likely a regulatory change. Gene expression level profiling revealed an aphid-specific gene from the region expressed at higher levels in winged male embryos, coinciding with the expected stage of api action. Comparison of the api region across biotypes (pea aphid populations specialized to different host plants that began diverging ~16,000 years ago [8, 9]) revealed that the two alleles were likely present prior to biotype diversification. Moreover, we find evidence for a recent selective sweep of a wingless allele since the biotypes diversified. In sum, this study provides insight into how adaptive, complex traits evolve within and across natural populations.

evolutionary biology↗