Biology subjects

Johnson, R. A.

Publications and source records attributed to Johnson, R. A..

8 recordsLinked to original sources

bioRxiv2026

Understanding cryptic diversity within the honeypot ant species complex of Myrmecocystus mendax

Cryptic species diversity, overlooked due to extreme morphological similarity, is a common phenomenon among ants. The "honeypot ant" genus Myrmecocystus (Wesmael, 1838; Formicinae: Lasiini) likely features multiple cryptic species, as previously suggested by phylogenetic studies based on ultraconserved elements (UCEs). Here, this work is expanded upon by examining 140 specimens and 2,508 UCE loci, with a particular focus on the M. mendax species complex from the southwestern USA and northern Mexico. Phylogenomic and population genomic analyses revealed five distinct M. mendax-like lineages and identified two potential cases of cryptic species diversity, one within samples matching the morphology of M. mendax and another within samples conforming to M. placodops. Most specimens morphologically identified as M. mendax formed a well-supported monophyletic group sister to M. melliger assigned individuals, with evidence for ongoing hybridization between both species in the Madrean Sky Islands along the USA-Mexico border. Patterns in the main M. mendax clade also suggest adaptive divergence across ecological gradients, warranting further investigation. Overall, these findings highlight the power of UCE-based genomic data in phylogenetic reconstructions and population genetic analyses to better resolve cryptic species diversity, and clarify complex evolutionary histories shaped by introgression and incomplete lineage sorting.

genomics↗

bioRxiv2026

Evolution of neurometabolic frugality in harvester ants

Despite the importance of neurometabolic costs in brain size evolution, quantitative data on brain metabolic rates are lacking. We measured ex vivo brain metabolic rates among species of the ant genus Pogonomyrmex to differentiate the roles of sociality and body size in brain evolution in a phylogenetic context. Worker body size and colony size (a proxy for social complexity) vary significantly among Pogonomyrmex species and were positively correlated. However, sociality was not a determinant of brain energetics. Worker body size strongly affected brain metabolism: 38% of resting metabolic rate was attributable to brain metabolism in species with the smallest workers, compared to 6% in species with the largest workers. More derived species had strikingly lower mass-specific brain metabolic costs, suggesting that increases in worker body size have selected for neurometabolic frugality through reductions in brain mass-specific metabolic rate. Additionally, smaller worker body sizes may require higher brain mass-specific energetic costs to achieve comparable performance by absolutely smaller brains. Our study shows that the social brain hypothesis does not explain patterns of brain size in Pogonomyrmex, but body size and evolutionary history strongly influence brain evolution in regard to both size and metabolic cost.

zoology↗

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↗

bioRxiv2025

Integrated metabolomic and genomic insights into amino acid incorporation within the hybrid polyketide-alkaloid antibiotic TLN-05220

Actinobacteria are a rich source of bioactive compounds and unique biosynthetic chemistry. Micromonospora echinospora subsp. challisensis NRRL 12255 produces the aromatic polyketide TLN-05220, which exhibits nanomolar activity against antibiotic-resistant human pathogens including vancomycin-resistant Enterococcus faecalis and methicillin-resistant Staphylococcus aureus. The pentangular polyphenol core of TLN-05220 is decorated with a piperazinone moiety, yet the enzymes responsible for the construction of this uncommon modification from amino acid precursors are unknown. Synthetic piperazinone-containing molecules have diverse antimicrobial, antiviral, anticancer, and anti-inflammatory bioactivity profiles, and determining biosynthetic routes for the assembly of this heterocycle may enhance drug discovery and medicinal chemistry efforts. We identified a putative TLN-05220 biosynthetic gene cluster (BGC) in the commercially available strain M. echinospora ATCC 15837 containing both type-I and type-II polyketide synthases, two predicted asparagine synthetase-like enzymes, and two genes (tln1 and tln5) that putatively encode pyridoxal 5-phosphate (PLP)-dependent amino acid synthases. Stable isotopic feeding studies coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS), identified L-alanine, L-serine, and glycine as metabolic precursors of TLN-05220. Subsequent in vitro enzymology established that Tln1 is a PLP-dependent alanine racemase, while Tln5 performs a stereoselective {beta}-substitution reaction of O-phospho-L-serine with a preferential D-alanine nucleophile. Alanine racemization and Tln5 pseudodipeptide L-serine-C{beta}-N-D-alanine (D,L-PDP) incorporation into TLN-05220 were further supported using deuterated intermediates and mass spectrometry techniques. Establishing the enzymes that catalyze amino acid installation within TLN-05220 inspires further biosynthetic discovery and engineering while enabling the biocatalytic syntheses of novel amino acid-containing polyketide antibiotics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/685158v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@4402e8org.highwire.dtl.DTLVardef@11af789org.highwire.dtl.DTLVardef@1717c5borg.highwire.dtl.DTLVardef@19b6529_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2021

Color, activity period, and eye structure in four lineages of ants: pale, nocturnal species have evolved larger eyes and larger facets than their dark, diurnal congeners

The eyes of insects display an incredible diversity of adaptations to enhance vision across the gamut of light levels that they experience. One commonly studied contrast is the difference in eye structure between nocturnal and diurnal species, with nocturnal species typically having features that enhance eye sensitivity such as larger eyes, larger eye facets, and larger ocelli. In this study, we compared eye structure between workers of closely related nocturnal and diurnal above ground foraging ant species (family Formicidae) in four genera (Myrmecocystus, Aphaenogaster, Temnothorax, Veromessor). In all four genera, nocturnal species tend to have little cuticular pigment (pale), while diurnal species are fully pigmented (dark), hence we could use cuticle coloration as a surrogate for activity pattern. Across three genera (Myrmecocystus, Aphaenogaster, Temnothorax), pale species, as expected for nocturnally active animals had larger eyes, larger facet diameters, and larger visual spans compared to their dark, more day active congeners. This same pattern occurred for one pale species of Veromessor, but not the other. There were no consistent differences between nocturnal and diurnal species in interommatidial angles and eye parameters both within and among genera. Hence, the evolution of eye features that enhance sensitivity in low light levels do not appear to have consistent correlated effects on features related to visual acuity. A survey across several additional ant genera found numerous other pale species with enlarged eyes, suggesting these traits evolved multiple times within and across genera. We also compared size of the anterior ocellus in workers of pale versus dark species of Myrmecocystus. In species with larger workers, the anterior ocellus was smaller in pale than in dark species, but this difference mostly disappeared for species with smaller workers. Presence of the anterior ocellus also was size-dependent in the two largest pale species.

evolutionary biology↗

bioRxiv2020

Urbanization alters ecological and evolutionary interaction between Darwin's Finches and Tribulus cistoides on the Galapagos Islands

Emerging evidence suggests that urbanization shapes the ecology and evolution of species interactions. Islands are particularly susceptible to urbanization due to the fragility of their ecosystems; however, few studies have examined the effects of urbanization on species interactions on islands. To address this gap, we studied the effects of urbanization on interactions between Darwins finches and its key food resource, Tribulus cistoides, in three towns on the Galapagos Islands. We assessed the effects of urbanization on seed and mericarp removal, mericarp morphology, and finch community composition using natural population surveys, experimental manipulations, and finch observations. We found that both seed and fruit removal rates were higher in urban compared to non-urban populations in the natural and experimental populations, and that urbanization modified selection on mericarp size and defense. Urban environments supported smaller and less diverse finch communities than non-urban environments. Together, our results suggest that urbanization can dramatically alter ecological interactions between Darwins finches and T. cistoides, leading to modified selection on T. cistoides populations. Our study demonstrates that urban development on islands can have profound effects on the ecology and evolution of trophic interactions.

evolutionary biology↗

bioRxiv2020

Polygenic Scores for Plasticity: A New Tool for Studying Gene-Environment Interplay

Outcomes of interest to demographers--fertility; health; education--are the product of both an individuals genetic makeup and his or her social environment. Yet Gene x Environment research (GxE) currently deploys a limited toolkit on the genetic side to study gene-environment interplay: polygenic scores (PGS, or what we call mPGS) that reflect the influence of genetics on levels of an outcome. The purpose of the present paper is to develop a genetic summary measure better suited for GxE research. We develop what we call variance polygenic scores (vPGS), or polygenic scores that reflect genetic contributions to plasticity in outcomes. The first part of the analysis uses the UK Biobank (N ~ 326,000 in the training set) and the Health and Retirement Study (HRS) to compare four approaches for constructing polygenic scores for plasticity. The results show that widely-used methods for discovering which genetic variants affect outcome variability fail to serve as distinctive new tools for GxE. Then, using the polygenic scores that do capture distinctive genetic contributions to plasticity, we analyze heterogeneous effects of a UK education reform on health and educational attainment. The results show the properties of a new tool useful for population scientists studying the interplay of nature and nurture and for population-based studies that are releasing polygenic scores to applied researchers.

genetics↗

bioRxiv2020

Alterations in the human plasma lipidome in response to Tularemia vaccination

Tularemia is a rare but highly contagious and potentially fatal disease caused by bacteria Francisella tularensis where as few as ten inhaled organisms can lead to an infection, making it one of the most infectious microorganisms known and a potential bioweapon. To better understand the response to a live, attenuated tularemia vaccine and the biological pathways altered post-vaccination, healthy adults were vaccinated by scarification and plasma was collected pre- and post-vaccination for longitudinal lipidomics studies. Using tandem mass spectrometry, we identified and quantified individual lipid molecular species within representative lipid classes in plasma to characterize alterations in the plasma lipidome during the vaccine response. Separately, we targeted oxylipins, a subset of lipid mediators involved in inflammatory pathways. We identified 14 differentially abundant lipid species from eight lipid classes. These included 5-Hydroxyeicosatetraenoic acid (5-HETE), an eicosanoid produced following arachidonic acid liberation and epoxygenation, which is indicative of lipoxygenase activity and, subsequently, inflammation. Results suggest that 5-HETE was metabolized to a dihydroxyeicosatrienoic acid (DHET) by Day 7 post-vaccination, shedding light on the kinetics of the 5-HETE-mediated inflammatory response. In addition to 5-HETE and DHET, we observed pronounced changes in 34:1 phosphatidylinositol, anandamide, oleamide, ceramides, 16:1 cholesteryl ester, and several glycerophospholipids, several of these changes in abundance were correlated with serum cytokines and T cell activation. These data provide new insights into alterations in plasma lipidome post tularemia vaccination, potentially identifying key mediators and pathways involved in vaccine response and efficacy.

biochemistry↗