Biology subjects

Murray, E. A.

Publications and source records attributed to Murray, E. A..

8 recordsLinked to original sources

bioRxiv2026

Low-Coverage Genome Sequencing Outperforms Target Enrichment Phylogenomics

Genome-scale data have transformed phylogenetic inference, yet most studies continue to rely on reduced-representation approaches that target a subset of loci to reduce cost and increase taxon sampling. Although effective, these methods require specialized laboratory workflows, constrain long-term data reuse, and may perform poorly with degraded DNA. Low-coverage whole genome sequencing (lcWGS) offers a streamlined alternative: shallow to moderate sequencing of complete genomes followed by bioinformatic extraction of loci of interest. Despite its promise, lcWGS has not been rigorously benchmarked against targeted enrichment using historical museum specimens. Here, we directly compared lcWGS and ultraconserved element (UCE) target enrichment across taxonomically diverse bee specimens collected between 1934 and 2021. Both data types were generated from the same Illumina libraries, enabling a controlled, head-to-head evaluation. Using standard UCE analytical pipelines, we quantified locus recovery, gene-tree support, and phylogenetic performance across sequencing methods and specimen age classes. We further assessed recovery of additional marker classes, including mitogenomes, BUSCO loci, and UCEs from a newly-designed, expanded probe set. Across all age categories, lcWGS consistently outperformed target enrichment, recovering more UCE loci and substantially longer alignments, with the largest gains observed in highly degraded specimens. Gene trees derived from lcWGS exhibited higher mean bootstrap support and greater topological concordance, translating into improved species-tree inference. In addition, lcWGS enabled recovery of markedly more non-target loci, expanding analytical flexibility beyond the original marker set. These results demonstrate that lcWGS not only matches but frequently exceeds the performance of targeted enrichment in museum-based phylogenomics, while providing broader genomic utility. As sequencing costs continue to decline, lcWGS represents a robust and forward-looking strategy for phylogenetic research, particularly in taxa with modest genome sizes and challenging DNA quality.

evolutionary biology↗

bioRxiv2022

The Chalcidoidea bush of life - a massive radiation blurred by mutational saturation

Capturing phylogenetic signal from a massive radiation can be daunting. The superfamily Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. Chalcidoidea are mostly parasitoid wasps that until now included 27 families, 87 subfamilies and as many as 500,000 estimated species. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 Ultra-Conserved Elements (UCEs) for 433 taxa including all extant families, over 95% of all subfamilies and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between molecular results and our collective morphological and biological knowledge, we detected insidious bias driven by the saturation of nucleotide data and highlighted morphological convergences. Our final results are based on a concatenated analysis of the least saturated exons and UCE data sets (2054 loci, 284,106 sites). Our analyses support a sister relationship with Mymarommatoidea. Seven of the previously recognized families were not monophyletic, so foundations for a new classification are discussed. Biology appears potentially more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a shift from smaller soft-bodied wasps to larger and more heavily sclerotized wasps. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a Middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea underwent a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about host taxa of chalcid wasps, their fossil record, and Earths paleogeographic history.

evolutionary biology↗

bioRxiv2021

Selective prefrontal-amygdala circuit interactions underlie social and nonsocial valuation in rhesus macaques

Lesion studies in macaques suggest dissociable functions of the orbitofrontal cortex (OFC) and medial frontal cortex (MFC), with OFC being essential for goal-directed decision making and MFC supporting social cognition. Bilateral amygdala damage results in impairments in both of these domains. There are extensive reciprocal connections between these prefrontal areas and the amygdala; however, it is not known whether the dissociable roles of OFC and MFC depend on functional interactions with the amygdala. To test this possibility, we compared the performance of male rhesus macaques (Macaca mulatta) with crossed surgical disconnection of the amygdala and either MFC (MFC x AMY, n=4) or OFC (OFC x AMY, n=4) to a group of unoperated controls (CON, n=5). All monkeys were assessed for their performance on two tasks to measure: (1) food-retrieval latencies while viewing videos of social and nonsocial stimuli in a test of social interest, and (2) object choices based on current food value using reinforcer devaluation in a test of goal-directed decision making. Compared to the CON group, the MFC x AMY group, but not the OFC x AMY group, showed significantly reduced food-retrieval latencies while viewing videos of conspecifics, indicating reduced social valuation and/or interest. By contrast, on the devaluation task, group OFC x AMY, but not group MFC x AMY, displayed deficits on object choices following changes in food value. These data indicate that the MFC and OFC must functionally interact with the amygdala to support normative social and nonsocial valuation, respectively. Significance StatementAscribing value to conspecifics (social) vs. objects (nonsocial) may be supported by distinct but overlapping brain networks. Here we test whether two nonoverlapping regions of the prefrontal cortex, the medial frontal cortex and the orbitofrontal cortex, must causally interact with the amygdala to sustain social valuation and goal-directed decision making, respectively. We found that these prefrontal-amygdala circuits are functionally dissociable, lending support for the idea that medial frontal and orbital frontal cortex make independent contributions to cognitive appraisals of the environment. These data provide a neural framework for distinct value assignment processes and may enhance our understanding of the cognitive deficits observed following brain injury or in the development of mental health disorders.

animal behavior and cognition↗

bioRxiv2021

Interaction between decision-making and interoceptive representations of bodily arousal in frontal cortex

Decision-making and representations of arousal are intimately linked. Behavioral investigations have classically shown that either too little or too much bodily arousal is detrimental to decision-making, indicating that there is an inverted U relationship between bodily arousal and performance. How these processes interact at the level of single neurons as well as the neural circuits involved are unclear. Here we recorded neural activity from orbitofrontal cortex (OFC) and dorsal anterior cingulate cortex (dACC) of macaque monkeys while they made reward-guided decisions. Heart rate (HR) was also recorded and used as a proxy for bodily arousal. Recordings were made both before and after subjects received excitotoxic lesions of the bilateral amygdala. In intact monkeys, higher HR facilitated reaction times (RTs). Concurrently, a set of neurons in OFC and dACC selectively encoded trial-by-trial variations in HR independent of reward value. After amygdala lesions, HR increased and the relationship between HR and RTs was reversed. Concurrent with this change, there was an increase in the proportion of dACC neurons encoding HR. Applying a novel population-coding analysis, we show that after bilateral amygdala lesions the balance of encoding in dACC is skewed away from signaling either reward value or choice direction towards HR coding around the time that choices are made. Taken together, the present results provide insight into how bodily arousal and decision-making are signaled in frontal cortex. Significance statementHow bodily arousal states influence decision-making has been a central question in psychology, but the neural mechanisms are unclear. We recorded heart rate, a measure of bodily arousal, while simultaneously monitoring neural activity in orbitofrontal cortex (OFC) and dorsal anterior cingulate cortex (dACC) of macaques making reward-guided decisions. In intact macaques higher HR was associated with shorter reaction times. Concurrently, the activity of a set of neurons in OFC and dACC selectively encoded HR. Following amygdala lesions, HR generally increased and now the relationship between HR and reaction times was reversed. At the neural level, the balance of encoding in dACC shifted towards signaling HR, suggesting a specific mechanism through which bodily arousal influences decision-making.

neuroscience↗

bioRxiv2020

Autonomic arousal tracks outcome salience not valence in monkeys making social decisions

The evolutionary and neural underpinnings of human prosociality are still largely unknown. A growing body of evidence suggests that some species find the sight of another individual receiving a reward reinforcing, often called vicarious reinforcement. One hypothesis is that vicarious reward is reinforcing because it is arousing like a primary reward. We evaluated this hypothesis by measuring the autonomic pupil response of eight monkeys across two laboratories in two different versions of a vicarious reinforcement paradigm. Monkeys were cued as to whether an upcoming reward would be delivered to them, another monkey, or nobody and could accept or decline the offer. As expected, all monkeys in both laboratories showed a marked preference for juice to the self, together with a reliable prosocial preference for juice to a social partner compared to juice to nobody. However, contrary to the autonomic arousal hypothesis, we found that pupils were widest in anticipation of juice to the self, moderately-sized in anticipation of juice to nobody, and narrowest in anticipation of juice to a social partner. This effect was seen across both laboratories and regardless of specific task parameters. The seemingly paradoxical pupil effect can be explained by a model in which pupil size tracks outcome salience, prosocial tendencies track outcome valence, and the relation between salience and valence is U-shaped.

animal behavior and cognition↗

bioRxiv2018

Orthogonal Representations of Reward Magnitude, Certainty, and Volatility in the Macaque Orbitofrontal Cortex

Categorical knowledge about the probabilistic and volatile nature of resource availability can improve foraging strategies, yet we have little understanding of how the brain represents such knowledge. Neurons in the orbitofrontal cortex (OFC) of macaques encode several decision variables (e.g., reward magnitude, probability) that could influence choice behavior. Here we investigated whether OFC neurons also represent two aspects of reward predictability: certainty and volatility. Rhesus monkeys performed a visual stimulus-reward association task in which a set of simple shapes preceded the delivery of reward, and they learned the nature of each shapes reward association along two dimensions. One involved the certainty of a reward outcome; rewards can be either deterministic (and therefore certain) or probabilistic (uncertain). A second dimension reflected the volatility of an outcome; reward schedules can be either stable over time or volatile. During stimulus presentation, the activity of OFC neurons reflected both categorical certainty and categorical volatility, in addition to reward magnitude. These three characteristics were represented orthogonally by three distinct neural populations of similar size. These findings point to a more general role for OFC in processing reward information than one restricted to encoding parametric valuations such as reward magnitude and probability.

neuroscience↗

bioRxiv2017

Anterolateral entorhinal-hippocampal imbalance in older adults disrupts object pattern separation

The entorhinal cortex (EC) is among the earliest brain areas to deteriorate in Alzheimers disease (AD). However, the extent to which functional properties of the EC are altered in the aging brain, even in the absence of clinical symptoms, is not understood. Recent human fMRI studies have identified a functional dissociation within the EC, similar to what is found in rodents. Here, we used high-resolution fMRI to identify a specific hypoactivity in the anterolateral EC (alEC) commensurate with major behavioral deficits on an object pattern separation task in asymptomatic older adults. Only subtle deficits were found in a comparable spatial condition, with no associated differences in posteromedial EC between young and older adults. We additionally link this condition to previously reported dentate/CA3 hyperactivity, both of which were associated with object mnemonic discrimination impairment. These results provide novel evidence of alEC-dentate/CA3 circuit dysfunction in cognitively normal aged humans.

neuroscience↗

bioRxiv2017

Amygdala Input Differentially Influences Prefrontal Local Field Potential And Single Neuron Encoding Of Reward-Based Decisions

Reward-guided behaviors require functional interaction between amygdala, orbital (OFC), and medial (MFC) divisions of prefrontal cortex, but the neural mechanisms underlying these interactions are unclear. Here, we used a decoding approach to analyze local field potentials (LFPs) recorded from OFC and MFC of monkeys engaged in a stimulus-choice task, before and after excitotoxic amygdala lesions. Whereas OFC LFP responses were strongly modulated by the amount of reward associated with each stimulus, MFC responses best represented which stimulus subjects decided to choose. This was counter to what we observed in the level of single neurons where their activity was closely associated with the value of the stimuli presented on each trial. After lesions of the amygdala, stimulus-reward value and choice encoding were reduced in OFC and MFC, respectively. However, while the lesion-induced decrease in OFC LFP encoding of stimulus-reward value mirrored changes in single neuron activity, reduced choice encoding in MFC LFPs was distinct from changes in single neuron activity. Thus, LFPs and single neurons represent different information required for decision-making in OFC and MFC. At the circuit-level, amygdala input to these two areas play a distinct role in stimulus-reward encoding in OFC and choice encoding in MFC.

neuroscience↗