Biology subjects

Myers, J. A.

Publications and source records attributed to Myers, J. A..

9 recordsLinked to original sources

bioRxiv2024

plantMASST - Community-driven chemotaxonomic digitization of plants

Understanding the distribution of hundreds of thousands of plant metabolites across the plant kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 plant extracts and developed the plantMASST reference database encompassing 246 botanical families, 1,469 genera, and 2,793 species. This taxonomically focused database facilitates the exploration of plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. This tool will aid in drug discovery, biosynthesis, (chemo)taxonomy, and the evolutionary ecology of herbivore interactions.

plant biology↗

bioRxiv2024

Pervasive but lagged responses in the composition of small mammal communities to a century of climate change

Climate change has widespread effects on the distribution, abundance, and behavior of species around the world, leading to the reshuffling of ecological communities. However, it remains unclear whether individual species range shifts scale up to result in communities whose rate of change lag, lead, or track the rate of climate change. We capitalized on a century-old data set originally collected by Joseph Grinnell and his students, plus modern resurveys, to measure long-term compositional responses of small mammal communities to climate change in historical and modern eras across three regions in the Sierra Nevada of California (Lassen, Yosemite, and Sequoia and Kings Canyon National Parks). Across this period, mean annual temperature in each region increased and mean annual precipitation decreased. We tested whether small mammal communities have shifted their composition in favor of species more adapted to hot and dry conditions, processes known as thermophilization and mesophilization respectively. We found positive thermophilization rates (communities composed of more warm-adapted species) in all three regions and negative mesophilization rates (communities composed of dry-adapted species) in one of the three regions. Importantly, thermophilization and mesophilization rates lagged behind corresponding rates of climate change on average by 0.90-1.2 {degrees}C and 26.5-111.0 mm, but the magnitude of lags was unrelated to region, amount of climate change, or their interaction. Previous work demonstrated high intraspecific variability in range shifts across the three regions in our study. Our results suggest that the net effects of climate change will be directional at the scale of the ecological community, despite variability in individual species responses to environmental change and the varied mechanisms that govern them. Communities, like many individual species, may already be out of equilibrium with ambient climate.

ecology↗

bioRxiv2024

Pawpaws prevent predictability: A locally-dominant tree alters understory beta-diversity and community assembly

While dominant species are known to be important in ecosystem functioning and community assembly, biodiversity responses to the presence of dominant species can be highly variable. Dominant species can increase the importance of deterministic community assembly by competitively excluding species in a consistent way across local communities, resulting in low site-to-site variation in community composition (beta-diversity) and non-random community structure. In contrast, dominant species could increase the importance of stochastic community assembly by reducing the total number of individuals in local communities (community size), resulting in high beta-diversity and more random community structure. We tested these hypotheses in a large, temperate oak-hickory forest plot containing a locally-dominant tree species, pawpaw (Asimina triloba; Annonaceae), an understory tree species that occurs in dense, clonal patches in forests throughout the east-central United States. We determined how the presence of pawpaw influences local species diversity, community size, and beta-diversity by measuring the abundance of all vascular plant species in 1x1-m plots both inside and outside pawpaw patches. To test whether the presence of pawpaw influences local assembly processes, we compared observed patterns of beta-diversity inside and outside patches to a null model of random assembly. We found lower local species diversity, lower community size, and higher observed beta-diversity inside pawpaw patches than outside pawpaw patches. Moreover, standardized effect sizes of beta-diversity from the null model were lower inside pawpaw patches than outside pawpaw patches, indicating more random community composition inside pawpaw patches. Together these results suggest that pawpaw increases the importance of stochastic relative to deterministic community assembly at local scales, likely by decreasing overall numbers of individuals, and increasing random local extinctions inside patches. Our findings provide insights into the ecological processes by which locally-dominant tree species shape the assembly and diversity of understory plant communities at different spatial scales.

ecology↗

bioRxiv2023

Ecological metabolomics of tropical tree communities across an elevational gradient: Implications for chemically-mediated biotic interactions and species diversity

Seminal hypotheses in ecology and evolution postulate that stronger and more specialized biotic interactions contribute to higher species diversity at lower elevations and latitudes. Plant-chemical defenses mediate biotic interactions between plants and their natural enemies and provide a highly dimensional trait space in which chemically mediated niches may facilitate plant species coexistence. However, the role of chemically mediated biotic interactions in shaping plant communities remains largely untested across large-scale ecological gradients. To test this hypothesis, we used ecological metabolomics to quantify the chemical dissimilarity of foliar metabolomes among 473 tree species (906 unique species-plot combinations) in 16 tropical tree communities along an elevational gradient in Madidi National Park, Bolivia. We predicted that chemical dissimilarity among co-occurring tree species would be greater, and chemical phylogenetic signal lower, in communities with greater tree species richness and warmer, wetter, and less-seasonal climates, as pressure from natural enemies is likely to be greater in these locales. Further, we predicted that these relationships should be especially pronounced for secondary metabolites derived from biosynthetic pathways known to include anti-herbivore and antimicrobial defenses than for primary metabolites. We found that median chemical dissimilarity among tree species with respect to all metabolites and secondary metabolites increased with tree species richness, decreased with elevation, and increased along a principal component of climatic variation that reflected increasing temperature and precipitation and decreasing seasonality. In contrast, median chemical dissimilarity among tree species with respect to primary metabolites was unrelated to tree species richness, elevation, or the principal component of climatic variation. Furthermore, phylogenetic signal of secondary and primary metabolites decreased with tree species richness. Among tree communities in moist forests, phylogenetic signal of secondary metabolites also increased with elevation and decreased with the temperature and precipitation. Our results support the hypothesis that chemically mediated biotic interactions shape elevational diversity gradients by imposing stronger selection for interspecific divergence in plant chemical defenses in warmer, wetter, and more stable climates. Our study also illustrates the promise of ecological metabolomics in the study of biogeography, community ecology, and complex species interactions in high-diversity ecosystems.

ecology↗

bioRxiv2023

Latitudinal scaling of aggregation with abundance and its consequences for coexistence in species rich forests

The search for simple principles underlying the complex spatial structure and dynamics of plant communities is a long-standing challenge in ecology1-6. In particular, the relationship between the spatial distribution of plants and species coexistence is challenging to resolve in species-rich communities7-9. Analysing the spatial patterns of tree species in 21 large forest plots, we find that rare species tend to be more spatially aggregated than common species, and a latitudinal gradient in the strength of this negative correlations that increases from tropical to temperate forests. Our analysis suggests that latitudinal gradients in animal seed dispersal10 and mycorrhizal associations11,12,13 may jointly generate this intriguing pattern. To assess the consequences of negative aggregation-abundance correlations for species coexistence, we present here a framework to incorporate the observed spatial patterns into population models8 along with an analytical solution for the local extinction risk14 of species invading from low abundances in dependence of spatial structure, demographic parameters, and immigration. For example, the stabilizing effect of the observed spatial patterns reduced the local extinction risk of species when rare almost by a factor of two. Our approach opens up new avenues for integrating observed spatial patterns into mathematical theory, and our findings demonstrate that spatial patterns, such as species aggregation and segregation, can contribute substantially to coexistence in species-rich communities. This underscores the need to understand the interactions between multiple ecological processes and spatial patterns in greater detail.

ecology↗

bioRxiv2022

Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers

Genes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are mutated in >20% of cancers. SWI/SNF complexes exist in three distinct families that each contribute to regulation of transcription, although the functional interactions between the families are not well understood. Rhabdoid tumors constitute an informative model system as these highly aggressive cancers are driven by inactivation of a single SWI/SNF subunit, SMARCB1, which is present in two SWI/SNF families (cBAF and PBAF) but not in the third (GBAF/ncBAF). We and others have shown that BRD9, a therapeutically targetable member of ncBAF, is essential specifically in SMARCB1-deficient cancers, suggesting key functional relationships between SMARCB1-containing complexes and BRD9/ncBAF. However, the mechanistic underpinnings of these relationships are poorly understood. Here, we demonstrate that genomic binding of BRD9 is largely dependent upon SMARCB1 such that the absence of SMARCB1 results in significantly reduced BRD9 binding. At select sites, however, we show that SMARCB1-loss results in gain of BRD9 binding and BRD9-dependent accessibility. We find that this gain is associated with expression of genes promoting cell migration. Our results define relationships between SWI/SNF complex families, elucidate mechanisms by which SMARCB1 loss drives oncogenesis, and provide mechanistic insight into the synthetic-lethal relationship between SMARCB1 and BRD9.

cancer biology↗

bioRxiv2020

The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades?

O_LIBiogeographic events occurring in the deep past can contribute to the structure of modern ecological communities. However, little is known about how the emergence of environmental gradients shape the evolution of species that underlie community assembly. In this study, we address how the creation of novel environments lead to community assembly via two non-mutually exclusive processes: 1) the immigration and ecological sorting of pre-adapted clades (ISPC), and 2) recent adaptive diversification (RAD). We study these processes in the context of the elevational gradient created by the uplift of the Central Andes. C_LIO_LIWe develop a novel approach and method based on the decomposition of species turnover into within- and among-clade components, where clades correspond to lineages that originated before mountain uplift. Effects of ISPC and RAD can be inferred from how components of turnover change with elevation. We test our approach using data from over 500 Andean forest plots. C_LIO_LIWe found that species turnover between communities at different elevations is dominated by the replacement of clades that originated before the uplift of the Central Andes. C_LIO_LIOur results suggest that immigration and sorting of clades pre-adapted to montane habitats is the primary mechanism shaping communities across elevations. C_LI

ecology↗

bioRxiv2020

Conspecific negative density dependence and why its study should not be abandoned

Recent studies showing bias in the measurement of density dependence have the potential to sow confusion in the field of ecology. We provide clarity by elucidating key conceptual and statistical errors with the null-model approach used in Detto et al. (2019). We show that neither their null model nor a more biologically-appropriate null model reproduces differences in density-dependent recruitment between forests, indicating that the latitudinal gradient in negative density dependence is not an artefact of statistical bias. Finally, we suggest a path forward that combines observational comparisons of density dependence in multiple fitness components across localities with mechanistic and geographically-replicated experiments.

ecology↗

bioRxiv2018

Tetracyclines Modify Translation By Targeting Key Human rRNA Substructures.

Apart from their antimicrobial properties, tetracyclines demonstrate clinically validated effects in the amelioration of pathological inflammation and human cancer. Delineation of the target(s) and mechanism(s) responsible for these effects, however, has remained elusive. Here, employing quantitative mass spectrometry-based proteomics, we identified human 80S ribosomes as targets of the tetracyclines Col-3 and doxycycline. We then developed in cell click selective crosslinking with RNA sequence profiling (icCL-Seq) to map binding sites for these tetracyclines on key human rRNA substructures at nucleotide resolution. Importantly, we found that structurally and phenotypically variant tetracycline analogs could chemically discriminate these rRNA binding sites. We also found that tetracyclines both subtly modify human ribosomal translation and selectively activate the cellular integrated stress response (ISR). Together, the data reveal that targeting of specific rRNA substructures, activation of the ISR, and inhibition of translation are correlated with the anti-proliferative properties of tetracyclines in human cancer cell lines.

cell biology↗