Biology subjects

Hughes, A. C.

Publications and source records attributed to Hughes, A. C..

15 recordsLinked to original sources

bioRxiv2026

Global Patterns and Drivers of Bee Diversity and Endemism on Islands

Islands harbor a disproportionate share of global biodiversity1, yet insects, even invaluable pollinators such as bees2, remain underrepresented in island biogeography research3. Here, we present the first global checklist of island bees, recording 4,140 species across 306 islands. Although islands comprise only [~]5% of Earths land area, they support [~]20% of global bee diversity, and 43% of insular species are endemic, making up [~]8% of all known bee species. Island bee species richness, mirroring continental trends4, peaks at mid-latitudes. Native richness increases with island area and declines with isolation, consistent with patterns in other taxa5. The strength of species-area relationships varies among biomes and is steepest in mediterranean-type systems, which also support disproportionately high bee richness relative to flowering plant diversity. Endemism is highest on large tropical islands, reflecting extensive in situ diversification. Major centers of bee endemism include Madagascar, Malesia (e.g. the Greater Sundas and New Guinea), and Hawaii, where a single large radiation of Hylaeus (Nesoprosopis) dominates6. Among islands capable of supporting endemic species, endemism scales strongly with total richness. These findings highlight the need to integrate island bee diversity into global conservation planning and position bees as a model for understanding insect evolution and conservation on islands.

ecology↗

bioRxiv2026

Enhancer-based AAV approach for selective AADC delivery reduces motor symptoms and dyskinesia in Parkinson's mouse models

Degeneration of midbrain dopamine (DA) neurons and the resulting loss of striatal dopamine signaling are hallmarks of Parkinsons disease (PD). Although the dopamine precursor levodopa (L-DOPA) provides symptomatic relief, prolonged treatment often leads to abnormal involuntary movements (dyskinesia). Previous adeno-associated virus (AAV) approaches delivering aromatic L-amino acid decarboxylase (AADC) to the striatum under a ubiquitous promoter enhanced local dopamine synthesis and improved PD motor deficits, but this broad targeting strategy limited insight into the cellular populations underlying the behavioral improvements. Here, we engineered enhancer-driven AAVs to direct AADC expression to defined striatal and midbrain cell populations and paired these regulatory elements with a blood-brain barrier-penetrant capsid to enable both systemic and direct delivery. Targeted expression restored motor performance at reduced L-DOPA doses and decreased dyskinesia-like behaviors, producing improvements comparable to or greater than those achieved with ubiquitous expression. Distinct neuronal and non-neuronal populations each supported motor rescue but improved different behavioral domains to different extents, indicating complementary cell type-specific roles within PD-relevant circuits. Together, these findings establish enhancer-driven, cell type-specific AADC delivery as a better-tolerated strategy that enables rescue of motor deficits at lower L-DOPA doses in PD models.

neuroscience↗

bioRxiv2025

Sociality and nesting strategy shape the bimodal diversity gradient in bees

Bees are dominant pollinators across native and agricultural plant communities, yet the drivers of their patterns of geographic distribution and functional diversity remain poorly understood. Notably, bees exhibit a bimodal latitudinal diversity gradient, peaking in species diversity in temperate and arid regions rather than the tropics despite their close ecological and evolutionary ties to flowering plants, which show the opposite pattern. Here, we investigated whether two key life history traits thought to shape where bees can live--sociality and nesting strategy--may influence this pattern. We compiled data on sociality and nesting strategy for 4,293 bee species and combined it with a comprehensive phylogeny, curated global occurrence records, and newly-developed models of trait evolution to test 1) whether sociality and nesting biology are evolutionarily correlated, 2) how these life history traits shape bees climatic niches and niche breadths, and 3) whether the evolutionary dynamics of these traits may explain the bimodal latitudinal gradient in bee diversity. We find that the evolution of above-ground nesting is closely tied to the evolution of social behavior, but this trait combination has evolved rarely across the evolutionary history of bees. Where this combination does arise, species that are both social and above-ground nesters tend to have narrower climatic niches and are associated with environments that are warmer, wetter, and experience little seasonal temperature variation, making them more prevalent in tropical bee communities. Together, our results indicate that the bimodal diversity gradient in bees is driven by phylogenetic niche conservatism, where most bee lineages retain ancestral traits suited to arid environments and the derived syndrome necessary for thriving in the tropics evolves rarely.

evolutionary biology↗

bioRxiv2024

Differential prevalence and risk factors for infection with coronaviruses in bats collected during 2020 in Yunnan Province, China

Coronaviruses (CoVs) pose a threat to human health globally, as highlighted by severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and the COVID-19 pandemic. Bats from the Greater Mekong Subregion (GMS) are an important natural reservoir for CoVs. Here we report the differential prevalence of CoVs in bats across biological and ecological factors within Yunnan Province. We also show the coexistence of CoVs in individual bats and identify an additional putative host for SARS-related CoV, with higher dispersal capacity than other known hosts. Notably, 11 SARS-related coronaviruses (SARSr-CoVs) were discovered in horseshoe bats and a Chinese water myotis bat by pan-CoV detection and Illumina sequencing. Our findings facilitate an understanding of the fundamental features of the distribution and circulation of CoVs in nature as well as zoonotic spillover risk in the One health framework.

microbiology↗

bioRxiv2024

Buzz-world: Global patterns and drivers of buzzing bees and poricidal plants

Foraging behavior frequently plays a major role in driving the geographic distribution of animals. Buzzing to extract protein-rich pollen from flowers is a key foraging behavior used by bee species across at least 83 genera (these genera comprise [~]58% of all bee species). Although buzzing is widely recognized to affect the ecology and evolution of bees and flowering plants (e.g., buzz-pollinated flowers), global patterns and drivers of buzzing bee biogeography remain unexplored. Here, we investigate the global species distribution patterns within each bee family and how patterns and drivers differ with respect to buzzing bee species. We found that both distributional patterns and drivers of richness typically differed for buzzing species compared to hotspots for all bee species and when grouped by family. A major predictor of the distribution, but not species richness overall for buzzing members of four of the five major bee families included in analyses (Andrenidae, Halictidae, Colletidae and to a lesser extent, Apidae) was the richness of poricidal flowering plant species, which depend on buzzing bees for pollination. As poricidal plant richness was highest in areas with low wind and high aridity, we discuss how global hotspots of buzzing bee biodiversity are likely driven by both biogeographic factors and plant host availability. Whilst we explored global patterns with State-level data, higher resolution work is needed to explore local level drivers of patterns, but from a global perspective, buzz-pollinated plants clearly play a greater role in the ecology and evolution of buzzing bees than previously predicted.

ecology↗

bioRxiv2023

Locus Coeruleus Norepinephrine Neurons Facilitate Orbitofrontal Cortex Remapping and Behavioral Flexibility

To guide behavior, brain regions such as the orbitofrontal cortex (OFC) retain complex information about current tasks and expected outcomes in cellular representations referred to as cognitive maps. When actions produce undesirable results, OFC cognitive maps must update to promote behavioral change. Here, we show that this remapping is driven by the locus coeruleus (LC), a small brainstem nucleus that contains most of the brains norepinephrine (NE)-releasing neurons. In a task that tests behavioral flexibility in rodents, LC-NE activity correlated with task acuity and altered depending on trial outcome. Silencing LC neurons caused perseverative behavior and impeded cognitive remapping in OFC, while enhancing LC activity disrupted the ability of new maps to stabilize. These findings reveal a novel role for bidirectional LC-NE signaling in regulation of OFC cognitive map stability and promotion of flexible behavior that differs from the traditional function of this circuit as a global arousal signal.

neuroscience↗

bioRxiv2023

SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis

SwrA activates flagellar gene expression in Bacillus subtilis to increase the frequency of motile cells in liquid and elevate flagellar density to enable swarming over solid surfaces. Here we use ChIP-seq to show that SwrA interacts with many sites on the chromosome in a manner that depends on the response regulator DegU. We identify a DegU-specific inverted repeat DNA sequence and show that SwrA synergizes with phosphorylation to increase DegU DNA binding affinity. We further show that SwrA increases the size of the DegU footprint expanding the region bound by DegU towards the promoter. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription more that could be explained by deactivation. We conclude that SwrA/DegU forms a heteromeric complex that enables both remote binding and interaction between the activator and RNA polymerase in the context of an interceding UP element. We speculate that multimeric activators that resolve cis-element spatial conflicts are common in bacteria and likely act on flagellar biosynthesis loci and other long operons of other multi-subunit complexes. IMPORTANCEIn Bacteria, the sigma subunit of RNA polymerase recognizes specific DNA sequences called promoters that determine where gene transcription begins. Some promoters also have sequences immediately upstream called an UP element that is bound by the alpha subunit of RNA polymerase and is often necessary for transcription. Finally, promoters may be activated by transcription factors that bind DNA specific sequences and help recruit RNA polymerase to weak promoter elements. Here we show that the promoter for the 32 gene long flagellar operon in Bacillus subtilis requires an UP element and is activated by a heteromeric transcription factor of DegU and SwrA. Our evidence suggests that SwrA oligomerizes DegU over the DNA to allow RNA polymerase to interact with DegU and the UP element simultaneously. Heteromeric activator complexes are known but poorly-understood in bacteria and we speculate they may be needed to resolve spatial conflicts in the DNA sequence.

microbiology↗

bioRxiv2023

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 has led to increased sampling of related sarbecoviruses circulating primarily in horseshoe bats. These viruses undergo frequent recombination and exhibit spatial structuring across Asia. Employing recombination-aware phylogenetic inference on bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed just [~]1-3 years prior to their emergence in humans. Phylogeographic analyses examining the movement of related sarbecoviruses demonstrate that they traveled at similar rates to their horseshoe bat hosts and have been circulating for thousands of years in Asia. The closest-inferred bat virus ancestor of SARS-CoV likely circulated in western China, and that of SARS-CoV-2 likely circulated in a region comprising southwest China and northern Laos, both a substantial distance from where they emerged. This distance and recency indicate that the direct ancestors of SARS-CoV and SARS-CoV-2 could not have reached their respective sites of emergence via the bat reservoir alone. Our recombination-aware dating and phylogeographic analyses reveal a more accurate inference of evolutionary history than performing only whole-genome or single gene analyses. These results can guide future sampling efforts and demonstrate that viral genomic fragments extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.

evolutionary biology↗

bioRxiv2023

BeeDC: An R package and globally synthesised and flagged bee occurrence dataset

Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We present BeeBDC, a new R package, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation.

ecology↗

bioRxiv2023

A Novel Single Vector Intersectional AAV Strategy for Interrogating Cellular Diversity and Brain Function

As the discovery of cellular diversity in the brain accelerates, so does the need for functional tools that target cells based on multiple features, such as gene expression and projection target. By selectively driving recombinase expression in a feature-specific manner, one can utilize intersectional strategies to conditionally promote payload expression only where multiple features overlap. We developed Conditional Viral Expression by Ribozyme Guided Degradation (ConVERGD), a single-construct intersectional targeting strategy that combines a self-cleaving ribozyme with traditional FLEx switches. ConVERGD offers benefits over existing platforms, such as expanded intersectionality, the ability to accommodate larger and more complex payloads, and a vector design that is easily modified to better facilitate rapid toolkit expansion. To demonstrate its utility for interrogating neural circuitry, we employed ConVERGD to target an unexplored subpopulation of norepinephrine (NE)-producing neurons within the rodent locus coeruleus (LC) identified via single-cell transcriptomic profiling to co-express the stress-related endogenous opioid gene prodynorphin (Pdyn). These studies showcase ConVERGD as a versatile tool for targeting diverse cell types and reveal Pdyn-expressing NE+ LC neurons as a small neuronal subpopulation capable of driving anxiogenic behavioral responses in rodents.

neuroscience↗

bioRxiv2021

Gaps in global wildlife trade monitoring leave amphibians vulnerable

As the biodiversity crisis continues, we must redouble efforts to understand and curb pressures pushing species closer to extinction. One major driver is the unsustainable trade of wildlife. Trade in internationally regulated species gains the most research attention, but this only accounts for a minority of traded species and we risk failing to appreciate the scale and impacts of unregulated legal trade. Despite being legal, trade puts pressure on wild species via: direct collection, introduced pathogens, and invasive species. Smaller species-rich vertebrates, such reptiles, fish, and amphibians, may be particularly vulnerable to trading because of gaps in regulations, small distributions, and demand of novel species. Here we combine data from five sources: online web searches in six languages, CITES trade database, LEMIS trade database, IUCN assessments, and a recent literature review, to characterise the global trade in amphibians, and also map use by purpose including meat, pets, medicinal and for research. We show that 1,215 species are being traded (17% of amphibian species), almost three times previous recorded numbers, 345 are threatened, and 100 data deficient or unassessed. Traded species origin hotspots include South American, China, and Central Africa; sources indicate 42% of amphibians are taken from the wild. Newly described species can be rapidly traded (mean time lag of 6.5 years), including threatened and unassessed species. The scale and limited regulation of the amphibian trade, paired with the triptych of connected pressures (collection, pathogens, invasive species), warrants a re-examination of the wildlife trade status-quo, application of the precautionary principle in regards to wildlife trade, and a renewed push to achieve global biodiversity goals.

ecology↗

bioRxiv2021

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.

microbiology↗

bioRxiv2020

A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19

The unprecedented epidemic of pneumonia caused by a novel coronavirus, HCoV-19, in China and beyond has caused public health concern at a global scale. Although bats are regarded as the most likely natural hosts for HCoV-191,2, the origins of the virus remain unclear. Here, we report a novel bat-derived coronavirus, denoted RmYN02, identified from a metagenomics analysis of samples from 227 bats collected from Yunnan Province in China between May and October, 2019. RmYN02 shared 93.3% nucleotide identity with HCoV-19 at the scale of the complete virus genome and 97.2% identity in the 1ab gene in which it was the closest relative of HCoV-19. In contrast, RmYN02 showed low sequence identity (61.3%) to HCoV-19 in the receptor binding domain (RBD) and might not bind to angiotensin-converting enzyme 2 (ACE2). Critically, however, and in a similar manner to HCoV-19, RmYN02 was characterized by the insertion of multiple amino acids at the junction site of the S1 and S2 subunits of the Spike (S) protein. This provides strong evidence that such insertion events can occur in nature. Together, these data suggest that HCoV-19 originated from multiple naturally occurring recombination events among those viruses present in bats and other wildlife species.

microbiology↗

bioRxiv2019

Redlisting the redlist: a global analysis of species distributions and biodiversity

Global conservation and research has come to rely on the IUCN species range-maps to direct research, allocate funding and define and design protected areas. However, IUCN species range-maps may be created on the basis of little actual data. Though the IUCN methods may be suitable for well known species, they may be liable unreliable for lesser known species or areas. In such cases, human biases may limit the usefulness of the output maps and potentially misdirect conservation funding and protection. Possible errors in these IUCN maps has global implications for the preservation of biodiversity, as flawed data leads to flawed decisions, which are of critical importance to the protection of the biodiversity of this planet. Ultimately we show that the current IUCN \"expert-assessment based\" range-maps may hinder rather than assist global conservation, as errors ranged from tens to thousands of kilometres (between recorded distributions and IUCN-maps), and for some taxa under 50% of records fell within their mapped-ranges. IUCN maps are being used globally to evaluate global conservation and protection, yet up to 85.4% of IUCN species-range boundaries follow political-boundaries, making using IUCN maps to evaluate the protected-area system and its efficacy impossible. The current availability of data, methods and computer-power has relegated these maps in the wake of more empirically based methods, and better use of available data provides the ability to make better conservation decisions, especially for highly threatened species and regions.

ecology↗

bioRxiv2019

Attacked from above and below, new observations of cooperative and solitary predators on roosting cave bats

Predation of bats in their roosts has previously only been attributed to a limited number of species such as various raptors, owls, and snakes. However, in situations where due to over-crowding and limited roost space, some individuals may be forced to roost in suboptimal conditions, such as around the entrances of caves and may thus be vulnerable to predation by species which would normally be unlikely to predate bats whilst roosting inside caves. Here, we describe the first documented cooperative hunting of the Large-billed Crow, Corvus macrorhynchos Wagler, 1827 (Passeriformes: Corvidae) and opportunistic predation by the Yellow-headed water monitor, Varanus cumingi Martin, 1839 (Squamata: Varanidae) in the worlds largest colony of Geoffroys Rousette, Rousettus amplexicaudatus (E. Geoffroy Saint-Hilaire, 1810) (Chiroptera: Pteropidae) in the Island of Samal, Mindanao, Philippines.

animal behavior and cognition↗