Biology subjects

Johnson, S. E.

Publications and source records attributed to Johnson, S. E..

9 recordsLinked to original sources

bioRxiv2026

The Dynamics of Long Terminal Repeat Proliferation in the Hesperis matronalis Genome

Genome sizes vary across four orders of magnitude in flowering plants, with consequences for evolution. Much of this variation is due to differences in transposable element content, particularly in long terminal repeat (LTR) retrotransposons. Despite their importance in plant genome evolution, LTRs have long been challenging to characterize because of their repetitive nature, but recent advances in sequencing allow more detailed explorations of their behavior. They are now known to occupy distinct genomic niches, and to evolve and proliferate over time as they escape host controls. In this study, we present a new genome sequence of the largest Brassicaceae genome, Hesperis matronalis, and describe its transposable element complement and how LTRs contributed to its genome expansion. We find evidence for both early proliferation of Ty3 elements and rapid recent expansion of Ty1-copia elements. In addition, we place the H. matronalis LTRs in a broader context of LTR evolution in the Brassicaceae, showing that the dominant copia families are part of an evolutionary radiation endemic to Hesperis. Finally, we describe differences in LTR age, proximity to genes, and apparent removal rate which suggest consistent genomic niches over the lifespan of a TE family. These results shed light on how LTRs evolve dynamically with host genomes, and have contributed to the expansion of the largest genome in the Brassicaceae. Significance StatementOrganisms differ in many ways, including the size of their genomes. Genome size, in turn, can affect many aspects of evolution, such as what kinds of mutations are available to natural selection and how effectively natural selection can act. The "complexity" of an organism does not predict its genome size; rather, much of this variation is explained by the amount of transposable elements, or "jumping genes," that inhabit a genome. This study describes the evolutionary history of the transposable elements in dames rocket (Hesperis matronalis), which has the largest genome of any plant in the mustard family (Brassicaceae). We find that the genome inflation in Hesperis is due to transposable elements that are not found elsewhere in the Brassicaceae, and likely diversified within Hesperis. Characterizing the evolution and behavior of transposable elements in this genome offers a better understanding of the forces that determine genome size and ultimately affect the evolution of life on earth.

genomics↗

bioRxiv2025

Color, size, shape: The drivers of floral variation in Hesperis matronalis (Dames Rocket)

Evolutionary biologists have long been intrigued by the factors that sustain genetic and phenotypic variation within and among natural populations. Polymorphisms underlying components of floral display - such as floral color, size, and shape - are uniquely of interest since variation in these traits impact pollinator attraction, rates of visitation, and pollinator efficiency, which ultimately influence patterns of plant reproduction and therefore fitness. We leverage existing floral variation present within and among populations of Hesperis matronalis (Dames Rocket) to disentangle the relative influence of natural selection and genetic drift in shaping floral trait variation. We employ a multi-tiered approach: we determine if variation in floral traits (color, size, and petal shape) is influenced by geography or environmental variables such as temperature and precipitation, we evaluate whether selection underlies trait variation by comparing phenotypic divergence (PST) with neutral genetic structure (FST), and we perform a Lande-Arnold selection analysis to explore the relationship between fitness and floral trait variation within natural populations. We find that selection underlies the divergence of floral color, floral size, and petal width among H. matronalis populations, with PST > FST for each trait. We find no indication, however, that variation in size in this species is influenced by the environment, but some evidence that variation in floral color and petal shape may be influenced by temperature. Finally, selection analyses of contemporary populations indicate divergent selection affecting combinations of color, petal shape, and plant size. These results suggest that the variation in floral shape in this species may be maintained due to environmental pressures, whereas floral color is influenced by pollinator visibility and the presence of different pollinator groups.

evolutionary biology↗

bioRxiv2025

Predictors of extinction risk in large tropical forest mammals: from global to local

Studies can only guide conservation if their findings are informative at the scales at which practitioners and policymakers operate. Yet, it is rarely tested whether large-scale studies reach similar conclusions to the smaller-scale studies on which conservation traditionally relies. We examine whether predictors of extinction risk are consistent across global, regional, and local scales, for 210 tropical forest mammal species ([≥] 1 kg) that existed during the last 130,000 years, in 64 tropical forests, across three biogeographical realms. We found consistent predictors of extinction risk (body mass, generation length, diet, brain volume and scansoriality) when analyses differed only in their spatial resolution. However, predictors differed when analyses also varied in their temporal extent. Macroecological findings about extinction risk can, thus, inform conservation at smaller scales, but they risk misidentifying threatened species if differences in temporal extent are not recognised.

ecology↗

bioRxiv2024

The moon's influence on the activity of tropical forest mammals

Changes in lunar illumination alter the balance of risks and opportunities for animals at night, influencing activity patterns and species interactions. Our knowledge about behavioral responses to moonlight is incomplete, yet it can serve to assess and predict how species respond to environmental changes such as light pollution or loss of canopy cover. As a baseline, we wish to examine if and how wildlife responds to the lunar cycle in some of the darkest places inhabited by terrestrial mammals: the floors of tropical forests. We quantified the prevalence and direction of activity responses to the moon in tropical forest mammal communities. Using custom Bayesian multinomial logistic regression models, we analyzed long-term camera trapping data on 88 mammal species from 17 protected forests on three continents. We also tested the hypothesis that nocturnal species are more prone to avoiding moonlight, as well as quantified diel activity shifts in response to moonlight. We found that, apparent avoidance of moonlight (lunar phobia, 16% of species) is more common than apparent attraction (lunar philia, 3% of species). The three species exhibiting lunar philia followed diurnal or diurnal-crepuscular activity patterns. Lunar phobia, detected in 14 species, is more pronounced with higher degree of nocturnality, and is disproportionately common among rodents. Strongly lunar phobic species were less active during moonlit nights, which in most cases also decreases their total daily activity. Our findings indicate that moonlight influences animal behavior even beneath the forest canopy. This suggests that such impacts may be exacerbated in degraded and fragmented forests. Additionally, the effect of artificial light on wild communities is becoming increasingly apparent. Our study offers empirical data from protected tropical forests as a baseline for comparison with more disturbed areas, together with a robust approach for detecting activity shifts in response to environmental change. Open Research statement: The data and code for performing the analyses described in this article are available at https://github.com/richbi/TropicalMoon.

ecology↗

bioRxiv2023

Functional traits fail to predict long-term responses to climate change

AimEnvironmental conditions strongly affect the distribution and abundance of species via complex forces. Shifts in environmental conditions and differences in the speed and scale of these effects complicate our efforts to infer how species will respond to future environmental change. We test how 18 functional traits affect plant species responses to gradients in environmental conditions and 50-year shifts in climate. LocationWe analyzed 50-year shifts in the distribution and abundance of 153 plant species distributed across 284 sites in Wisconsin, USA. Time period1950s to 2000s. Major taxa studiedVascular plants (much of the flora of NE North America). MethodsWe used random forest and integrated hierarchical mixed models to test how plant abundances (and 50-year changes in abundance) track gradients in overstory, soil, and climatic conditions. ResultsWithin study periods, plant abundances reflect gradients in environmental conditions. Leaf traits affected local abundance (both directly and via trait-environment interactions) in the 1950s and 2000s. Strong soil and temperature effects in the 1950s have weakened while precipitation effects have strengthened. Although we expected these models to also predict how plants would respond to shifts in climate, they did not. Main conclusionsLags in species responses, increases in the stochastic forces affecting community assembly, and other forces limit the ability of models fitted to static data (e.g., space-for-time substitutions) to predict how plant species will respond to long-term shifts in environmental conditions. We must therefore be cautious about applying trait-based species distribution models to predict how climate change will affect species distributions and community structure.

ecology↗

bioRxiv2021

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

genetics↗

bioRxiv2020

Asymmetrical pegs in square holes? Functional and phylogenetic determinants of plant community assembly in temperate forest understories

Despite advances in community assembly theory, uncertainties remain regarding how ecological and evolutionary processes shape species distributions and communities. We analyzed patterns of occurrence for 139 herbaceous plant species across 257 forest stands in Wisconsin (USA) to test predictions from community assembly theory. Specifically, we applied Bayesian phylogenetic linear mixed effects models (PGLMMs) to examine how functional traits and phylogenetic relationships influence plant distributions along environmental gradients and how functional similarity and phylogenetic relatedness affect local species co-occurrence. Leaf height, specific leaf area, and seed mass mediate species distributions along edaphic, climatic, and light gradients. In contrast, functional trait similarity and phylogenetic relationships only weakly affect patterns of local co-occurrence. These results confirm that broad-scale plant distributions are largely shaped by ecological sorting along environmental gradients but suggest deterministic assembly rules based on niche differentiation and complementary resource use may not govern local species co-occurrence in homogeneous environments. Statement of authorshipJB conceived the idea for the study. DL, SJ, and DR collected the vegetation and functional trait data. JB analyzed the data with assistance from DL. KC, KS, TG, and DW secured funding for research and oversaw data collection. JB wrote the first draft of the manuscript, all authors contributed to manuscript revisions. Data accessibility statementUpon acceptance, data will be archived at Figshare (https://figshare.com/) and scripts used to analyze the data will be shared on Github (https://github.com/jaredjbeck/).

ecology↗

bioRxiv2019

In vitro characterization of the colibactin-activating peptidase ClbP enables development of a fluorogenic activity probe

The gut bacterial genotoxin colibactin has been linked to the development of colorectal cancer. In the final stages of colibactins biosynthesis, an inactive precursor (pre-colibactin) undergoes proteolytic cleavage by ClbP, an unusual inner-membrane-bound periplasmic peptidase, to generate the active genotoxin. This enzyme presents an opportunity to monitor and modulate colibactin biosynthesis, but its active form has not been studied in vitro and limited tools exist to measure its activity. Here, we describe the in vitro biochemical characterization of catalytically active, full-length ClbP. We elucidate its substrate preferences and use this information to develop a fluorogenic activity probe. This tool will enable the discovery of ClbP inhibitors and streamline identification of colibactin-producing bacteria.

biochemistry↗

bioRxiv2018

A novel environmental DNA (eDNA) sampling method for aye-ayes from their feeding traces

Non-invasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal, facilitates the genetic analysis of cryptic and threatened species. One method that has been applied to these types of sample is target capture and enrichment which overcomes the issue of high proportions of exogenous (non-host) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of wild aye-ayes would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood from feeding traces where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-ayes mitochondrial genome and used these to isolate aye-aye DNA from other non-target DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-ayes geographic range that had not been sampled previously. This method can likely be applied to alternative foraged remains to sample species other than aye-ayes. Our method demonstrates the application to next-generation molecular techniques to species of conservation concern.

molecular biology↗