Biology subjects

Fisher, B. L.

Publications and source records attributed to Fisher, B. L..

11 recordsLinked to original sources

bioRxiv2026

Global homeostatic forces shape the composition of a hyperdiverse tropical insect fauna

Despite comprising the bulk of terrestrial biodiversity, we know surprisingly little about insect faunas, particularly in the tropics. Here, we characterize the insect fauna of Madagascar, a global biodiversity hotspot, based on extensive DNA metabarcoding of Malaise trap and leaf litter samples. We estimate that the fauna comprises at least 250,000 species, only 5% of which are currently recorded. The ecological and taxonomic composition is surprisingly similar to that of temperate forests. We show that this is likely caused by global homeostatic forces shaping net diversification rates after colonization of Madagascar rather than by the composition of colonizing lineages. Features differing from temperate forests include the dearth of parasitoids and richness of beetles. Understanding the forces shaping these patterns is key in sustainable management of tropical insect faunas.

evolutionary biology↗

bioRxiv2026

Genome assemblies and annotations of the poneroid ants Platythyrea mocquerysi (Ponerinae) and Stigmatomma oregonense (Amblyoponinae)

We present draft genome assemblies for two poneroid ant species with distinctive life history traits: Platythyrea mocquerysi Emery, 1899 (Ponerinae) and Stigmatomma oregonense Wheeler, 1915 (Amblyoponinae). Platythyrea mocquerysi is a Malagasy ant in which larvae produce secretions from a ventral tubercle that are consumed by adults, representing an unusual form of larva-to-adult trophallaxis. Stigmatomma oregonense, a North American "dracula ant," feeds non-lethally on larval haemolymph. Using PacBio HiFi long-read sequencing, we assembled the P. mocquerysi genome (187 Mb, 307 scaffolds, N50 = 5.26 Mb, BUSCO 99.2% complete) and the S. oregonense genome (262 Mb, 1,189 scaffolds, N50 = 0.84 Mb, BUSCO 98.3% complete). These genomes encode 10,860 and 12,354 protein-coding genes, respectively. Repeat content is higher in S. oregonense than in P. mocquerysi, 54.3% against a lower bound of 15.7%. Most of the difference is in unclassified repeats, which we show to be diverged transposable elements. Comparative analysis with two additional poneroid genomes from closely related species reveals that genome size variation across poneroid ants is largely explained by transposable element dynamics, with notable expansions in several gene families including carboxylesterases, serine proteases, and lipid metabolism genes in Amblyoponinae. These genomes provide essential resources for investigating the molecular basis of unconventional brood management strategies in ants.

genomics↗

bioRxiv2026

Beyond Gloger's rule: multiple biogeographic drivers of dark and red colouration in ants

Colour is a key trait involved in camouflage, physiological protection and thermoregulation. Yet environmental drivers of colour variation remain poorly understood at large spatial scales. Glogers rule predicts animals should be darker in warmer and wetter climates, and in a complex version, redder in warmer and drier climates. Here, we present the first test of the complex Glogers rule in insects using 34,331 images of 10,400 ant species across 586 assemblages worldwide. We decompose species mean colouration into two orthogonal axes, linked to darkness and redness. Assemblages were darker under high UV-B radiation and low dry-season precipitation, consistent with UV protection and desiccation resistance via melanisation. Canopy height increased both axes, suggesting camouflage. In contrast, higher mean temperature of the warmest quarter increased redness, as predicted by the complex Glogers rule. Ant colouration cannot be explained by one macroecological rule but reflects environmental drivers acting independently on darkness and redness.

ecology↗

bioRxiv2026

Inhibition of Slc17a7 expressing neurons in the basolateral amygdala which project to the nucleus accumbens shapes the fidelity of motivated behavior

Adaptive behavior depends on the ability to form predictive associations between environmental cues and biologically relevant outcomes. Classical models posit that projections from the basolateral amygdala (BLA) to the nucleus accumbens (NAc) promote reward seeking, whereas projections to the central amygdala facilitate defensive responding. However, accumulating evidence indicates that molecular identity and inhibitory dynamics introduce additional layers of functional heterogeneity within these pathways. Genetically defined subsets of BLA[->]NAc neurons can drive either reward-related or aversive behaviors, and single-cell imaging studies show that cue-responsive BLA ensembles undergo an inhibitory shift as conditioning progresses. How these molecular and inhibitory mechanisms interact within defined projections to shape motivated behavior remains unclear. To address this, we examined Vglut1-expressing BLA[->]NAc neurons (Vglut1BLA[->]NAc), the predominant excitatory population within this pathway. Whole-cell electrophysiology revealed that reward conditioning increases inhibitory synaptic input onto Vglut1BLA[->]NAc neurons and reduces intrinsic excitability. Using a dual-recombinase chemogenetic strategy, we found that selective inhibition of this projection enhances acquisition of a cued reward task, increases instrumental reward seeking, and elevates reward valuation in a two-choice preference assay. Similar enhancement was observed in a fear-discrimination task, where inhibition of Vglut1BLA[->]NAc neurons improved differentiation between threat- and safety-associated cues. These findings identify inhibitory regulation of Vglut1BLA[->]NAc neurons as a key mechanism that strengthens stimulus-outcome associations. By demonstrating that conditioning-associated inhibitory plasticity modulates this major BLA output pathway, the work refines prevailing models of BLA[->]NAc function and highlights inhibition as an important contributor to the fidelity of motivated behavior.

neuroscience↗

bioRxiv2025

High-throughput phenomics of global ant biodiversity

The big data era in biology is underway, but the study of organismal form has been slow to capitalize on advances in imaging and computation. Modern imaging can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Within the open science initiative Antscan, we applied high-throughput synchrotron X-ray microtomography to capture phenotypes across a diverse and ecologically dominant insect group -- ants. We provide 2193 whole-body 3D ant datasets from 792 species to broadly cover the ant phylogeny with a global scope, also pairing phenomic data with genome sequencing projects. Scans acquired with standardized parameters facilitate automated analysis and free access to data can broaden the audience and incentivize methods development. Antscan presents a scalable approach to create libraries of diverse anatomies, heralding a new era of studies on the evolution, structure, and function of organismal phenotypes.

zoology↗

bioRxiv2024

Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar

We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, weekly Malaise trap samples were collected at 203 locations within 100 sites in Sweden and at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of COI (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.

ecology↗

bioRxiv2024

Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens

Natural history collections serve as invaluable repositories of biodiversity data. Large-scale genomic analysis would greatly expand the utility and accessibility of museum collections but the high cost and time-intensive nature of genomic methods limit such projects, particularly for invertebrate specimens. This paper presents an innovative, cost-effective and high-throughput approach to extracting genomic DNA from diverse insect specimens using single-phase reverse immobilization (SPRI) beads. We optimized PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 6-11 cents per sample. Our method was validated against three widely used extraction protocols, and showed comparable DNA yield and amplification success to the widely used Qiagen DNeasy kit. We successfully applied the protocol in a high-throughput manner, extracting DNA from 3,786 insect specimens across a broad range of ages, taxonomies, and tissue types. A detailed protocol is provided to facilitate the adoption of the method by other researchers. By improving one of the most crucial steps in any molecular project, this SPRI bead-based DNA extraction approach has significant potential for enabling large-scale museomics projects, thereby increasing the utility of historical collections for biodiversity research and conservation efforts.

genomics↗

bioRxiv2024

Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods

Modern DNA-based biodiversity surveys result in massive-scale data, including up to millions of species - of which most are rare. Making the most of such data for inference and prediction requires modelling approaches that can relate species occurrences to environmental and spatial predictors, while incorporating information about their taxonomic or phylogenetic placement. Even if the scalability of joint species distribution models to large communities has greatly advanced, incorporating hundreds of thousands of species has not been feasible to date, leading to compromised analyses. Here we present a novel "common to rare transfer learning" approach (CORAL), based on borrowing information from the common species to enable statistically and computationally efficient modelling of both common and rare species. We illustrate that CORAL leads to much improved prediction and inference in the context of DNA metabarcoding data from Madagascar, comprising 255,188 arthropod species detected in 2874 samples.

ecology↗

bioRxiv2024

Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants

While some relationships in phylogenomic studies have remained stable since the era of Sanger sequencing, many challenging nodes elude resolution, even with genome-scale data. As early studies grappled with random error and insufficient information, incongruence or lack of resolution in phylogenomics is generally associated with inadequate modeling of biological phenomena combined with analytical issues leading to systematic biases. Few phylogenomic studies, however, explore the potential for random error or establish an expectation of what level of resolution should be expected from a given empirical dataset. In presenting incongruent results, phylogeneticists face a choice of providing a diverse array of results from different approaches or a single preferred tree, with few attempting to integrate uncertainties across methods. Recent phylogenetic work has uncovered many well-supported and often novel relationships, as well as more contentious findings, across the phylogeny of ants. Ants are the most species-rich lineage of social insects and among the most ecologically important terrestrial animals. As a result, they have attracted much research, including regarding systematics. To date, however, there has been no comprehensive genus-level phylogeny of the ants inferred using genomic data combined with an effort to evaluate signal and incongruence throughout. Here we provide deeper insight into and quantify uncertainty across the ant tree of life. We accomplish this with the most taxonomically comprehensive Ultraconserved Elements dataset to date, including 277 (81%) of recognized ant genera from all 16 extant subfamilies, representing over 98% of described species-level diversity. We use simulations to establish expectations for resolution, identify branches with less-than-expected concordance, and dissect the effects of data and model selection on recalcitrant nodes. We also construct a consensus tree integrating uncertainty from multiple analyses. Simulations show that hundreds of loci are needed to resolve recalcitrant nodes on our genus-level ant phylogeny, even under a best-case scenario of known model parameters and without systematic bias. This demonstrates that random error continues to play a role in phylogenomics. Our analyses provide a comprehensive picture of support and incongruence across the ant phylogeny, and our consensus topology is congruent with a recent phylogenomic study on the subfamily-level, while rendering a more realistic picture of uncertainty and significantly expanding generic sampling. We use this topology for divergence dating and find that assumptions about root age have significant impact on the dates inferred. Our results suggest that improved understanding of ant phylogeny will require both more data and better phylogenetic models. We also provide a workflow to identify under-supported nodes in concatenation analyses, outline a pragmatic way to reconcile conflicting results in phylogenomics, and introduce a user-friendly locus selection tool for divergence dating.

evolutionary biology↗

bioRxiv2024

Biotic and abiotic drivers of ecosystem functioning differ between a temperate and a tropical region

Any single ecosystem will provide many ecosystem functions. Whether these functions tend to increase in concert or trade off against each other is a question of much current interest. Equally topical are the drivers behind ecosystem function rates. Yet, we lack large-scale systematic studies that investigate how abiotic factors can directly or indirectly -- via effects on biodiversity -- drive ecosystem functioning. In this study, we assessed the impact of climate, landscape and biotic community on ecosystem functioning and multifunctioning in the temperate and tropical zone, and investigated potential trade-offs among ecosystem functions in both zones. To achieve this, we measured a diverse set of insect-related ecosystem functions -- including herbivory, seed dispersal, predation, decomposition and pollination -- at 50 sites across Madagascar and 171 sites across Sweden, and characterized the insect community at each site using Malaise traps. We used structural equations models to infer causality of the effects of climate, landscape, and biodiversity on ecosystem functioning. For the temperate zone, we found that abiotic factors were more important than biotic factors in driving ecosystem functioning, while in the tropical zone, effects of biotic drivers were most pronounced. In terms of trade-offs among functions, in the temperate zone, only seed dispersal and predation were positively correlated, while all other functions were uncorrelated. By contrast, in the tropical zone, most ecosystem functions increased in concert, highlighting that tropical ecosystems can simultaneously provide a diverse set of functions. These correlated functions in Madagascar could for the most part be explained by similar responses to local climate, landscape, and biota. Our study suggests that the functioning of temperate and tropical ecosystems differs fundamentally in patterns and drivers. Without a better understanding of these differences, it will be impossible to correctly predict shifts in ecosystem functioning in response to environmental disturbances. To identify global patterns and drivers of ecosystem functioning, we will next need replicate sampling across biomes - as here achieved for two regions, thus paving the road and setting the baseline expectations.

ecology↗

bioRxiv2017

Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants

Knowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the worlds most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Here we assemble a new data set to attempt a resolution of these two problems and carry out divergence dating, focusing on the age of the root node of crown Formicidae. For the phylogenetic analyses we included data from 110 ant species, including the key species Martialis heureka. We focused taxon sampling on non-formicoid lineages of ants to gain insight about deep nodes in the ant phylogeny. For divergence dating we retained a subset of 62 extant taxa and 42 fossils in order to approximate diversified sampling in the context of the fossilized birth-death process. We sequenced 11 nuclear gene fragments for a total of ~7.5 kb and investigated the DNA sequence data for the presence of among-taxon compositional heterogeneity, a property known to mislead phylogenetic inference, and for its potential to affect the rooting of the ant phylogeny. We found sequences of the Leptanillinae and several outgroup taxa to be rich in adenine and thymine (51% average AT content) compared to the remaining ants (45% average). To investigate whether this heterogeneity could bias phylogenetic inference we performed outgroup removal experiments, analysis of compositionally homogeneous sites, and a simulation study. We found that compositional heterogeneity indeed appears to affect the placement of the root of the ant tree but has limited impact on more recent nodes. We put forward a novel hypothesis regarding the rooting of the ant phylogeny, in which Martialis and the Leptanillinae together constitute a clade that is sister to all other ants. After correcting for compositional heterogeneity this emerges as the best-supported hypothesis of relationships at deep nodes in the ant tree. The results of our divergence dating under the fossilized birth-death process and diversified sampling suggest that the crown Formicidae originated during the Albian or Aptian ages of the Lower Cretaceous (103-124 Ma). In addition, we found support for monophyletic poneroids comprising the subfamilies Agroecomyrmecinae, Amblyoponinae, Apomyrminae, Paraponerinae, Ponerinae, and Proceratiinae, and well-supported relationships among these subfamilies except for the placement of Proceratiinae and (Amblyoponinae + Apomyrminae). Our phylogeny also highlights the non-monophyly of several ant genera, including Protanilla and Leptanilla in the Leptanillinae, Proceratium in the Proceratiinae, and Cryptopone, Euponera, and Mesoponera within the Ponerinae.

evolutionary biology↗