Biology subjects

Bever, J. D.

Publications and source records attributed to Bever, J. D..

4 recordsLinked to original sources

bioRxiv2023

RenSeq of Silphium integrifolium Reveals a Biotic Gradient for Disease Resistance

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plants source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

evolutionary biology↗

bioRxiv2023

Purifying Selection and Persistent Polymorphism among Nuclei in the Multinucleate Arbuscular Mycorrhizal (AM) Fungi

Arbuscular mycorrhizal (AM) fungi form obligate symbiosis with the roots of the majority of land plants and are found in all terrestrial ecosystems. The source and structure of genetic variation in AM fungi has remained an enigma due to difficulties in the axenic cultivation and generation of high-quality genome assemblies from most species. Furthermore, how AM fungi survives long-term without a single nuclear stage per cell life history is puzzling, prompting hypotheses on selection at the nuclear level which functions to purge deleterious mutations. In this study, we aimed to characterize both intra- and inter-organismal genetic variation in AM fungi by analyzing genomic information from individual nuclei of three strains from two species of the genus Claroideoglomus. We observed overall low levels of genetic variation within the strains, most of which represent rare variants likely kept at low frequency by purifying selection. We also observed variants that have been maintained as polymorphic across both strains and species. The results in this study affirm our conceptual understanding that nuclei in AM fungal strains function as populations of asexually reproducing units. Further, we propose that selection acts on different levels within the organism, with strong signals of purifying selection on nuclei within strain.

evolutionary biology↗

bioRxiv2021

In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies

O_LIMorphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the phylogeny and evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. C_LIO_LITo circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates high-quality genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. C_LIO_LIBased on analyses of sets of orthologous genes, we highlight three alternative topologies among families of AM fungi. In the main topology, Glomerales is polyphyletic and Claroideoglomeraceae, is the basal sister group to Glomeraceae and Diversisporales. C_LIO_LIOur results support family level classification from previous phylogenetic studies. New evolutionary relationships among families where highlighted with phylogenomic analysis using the hitherto most extensive taxon sampling for AM fungi. C_LI

genomics↗

bioRxiv2019

Copulas reveal complex and informative dependencies propagating throughout ecology

All branches of ecology study relationships among and between environmental and biological variables. However, standard approaches to studying such relationships, based on correlation and regression, provide only a small slice of the complex information contained in the relationships. Other statistical approaches exist that provide a complete description of relationships between variables, based on the concept of the copula; they are applied in finance, neuroscience and other fields, but rarely in ecology. We here explore the concepts that underpin copulas and examine the potential for those concepts to improve our understanding of ecology. We find that informative copula structure in dependencies between variables is common across all the environmental, species-trait, phenological, population, community, and ecosystem functioning datasets we considered. Many datasets exhibited asymmetric tail associations, whereby two variables were more strongly related in their left compared to right tails, or vice versa. We describe mechanisms by which observed copula structure and asymmetric tail associations can arise in ecological data, including a Moran-like effect whereby dependence structures between environmental variables are inherited by ecological variables; and asymmetric or nonlinear influences of environments on ecological variables, such as under Liebigs law of the minimum. We also describe consequences of copula structure for ecological phenomena, including impacts on extinction risk, Taylors law, and the stability through time of ecosystem services. By documenting the importance of a complete description of dependence between variables, advancing conceptual frameworks, and demonstrating a powerful approach, we aim to encourage widespread use of copulas in ecology, which we believe can benefit the discipline.

ecology↗