Biology subjects

Johnson, M. G.

Publications and source records attributed to Johnson, M. G..

17 recordsLinked to original sources

bioRxiv2026

Evolutionary reconstruction of bat influenza A viruses reveals segment-specific histories and host-associated selection

Influenza A (IAV) is a major zoonotic pathogen infecting a broad range of vertebrate hosts. In this study, we focus on inferring the evolutionary history of a subset of novel IAV, isolated from New World bats, which use a non-canonical host receptor and infer their relationship to sialic-acid-binding IAV. Little is known about when these novel subtypes emerged and how selection has acted upon them compared to sialic-acid-binding circulating strains. The current state of the field is split on whether bats are natural reservoirs for a distinct yet low abundance IAV lineage, or if influenza underwent rapid evolution after a recent spillover from a species within its standard host range. By analyzing segment-specific phylogenies, we hope to clarify the evolutionary history of bat IAV. Our objectives are to infer the date of divergence of non-canonical bat IAV from sialic-acid binding IAV, identify patterns of selection acting on bat IAV compared to representative samples of sialic-acid-binding IAV to identify potential signatures of genome-wide adaptation, and finally to reconstruct ancestral state transitions to infer which host taxa preceded spillover into bats. To accomplish this, we analyzed each IAV genome segment independently using least-squares molecular dating, Bayesian discrete-trait ancestral host reconstruction, and branch-site selection tests. Our results suggest that non-canonical bat IAV diverged from major IAV lineages 100-200 years ago, supporting a deeper evolutionary history rather than a very recent spillover event. However, discordance among genome segments in inferred divergence times, selective pressures, and ancestral hosts indicates that bat IAV experienced segment-specific evolutionary histories. Together, these findings suggest that non-canonical bat IAV represents a deeply divergent lineage with a complex evolutionary history involving segment-specific selection and host-transition dynamics.

microbiology↗

bioRxiv2026

First Plant sedaDNA assemblage from California reveals ecological stability throughout 10,000 years of human presence at Lake Elsinore

As we face the sixth mass extinction, understanding how ecosystems have persisted--or collapsed--through millennia of changing climates and human activity is critical for preventing biodiversity loss. We bolstered the past 24,000 years of plant and mammal records using targeted capture of ancient sedimentary DNA (sedaDNA) from Southern Californias Lake Elsinore, a cultural center for the Payomkawichum (Luiseno), Cahuilla, and other Peoples. Our sedaDNA approach generated a diverse dataset that included 18 plant orders not previously documented from Lake Elsinore. We paired these records with local measurements and paleo evidence of fire regimes, climate, demographic history, and ethnobotanical knowledge. We find that ecological stability persisted for 10,000 years of continuous human presence, reflecting ecosystem resilience through major climatic shifts, altered fire regimes, and varying intensities of Indigenous land use. SedaDNA revealed increased availability of food, medicinal, and utilitarian plant taxa during this period of botanical stability, shedding light on ancient fire-environment-human interactions that can inform contemporary management strategies.

paleontology↗

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

Fun-Sized Library Prep: Miniaturization is a valid method for per-sample cost reduction in targeted sequencing of angiosperm DNA

PremiseGenomic analysis of population structure is important to the conservation of plant species of concern. A limitation of using genetic information in conservation is the cost of obtaining large datasets. Targeted sequencing and low-volume robotic liquid handlers can reduce library preparation reaction volumes and costs. MethodsWe used targeted sequencing via Angiosperms353 to obtain data for 768 samples, 18 of which were identical, at 0.5X and 0.1X reaction volumes. We calculated quality and quantity control statistics to compare the effects of tissue age and library reaction volume on sequencing results for on-target nuclear and off-target plastid genes. ResultsLibrary miniaturization to 0.1X reduces costs and generally performs comparably to 0.5X libraries. In the full dataset, Tenth-Volume Only libraries showed smaller insert sizes and fewer genes with mapped sequences, but no reduction in mapped reads. In the Overlap Set, 0.1X had equal or improved performance with no significant decrease in sequencing efficiency. Differences by tissue type likely reflected sampling variation. ConclusionsMiniaturization to 0.1X substantially reduces per-sample costs while maintaining comparable sequencing quality across fresh and herbarium angiosperm DNA. Overall, miniaturization provides a reliable, cost-effective approach for targeted sequencing, increasing the feasibility of using herbarium collections and enabling broader access to population-level genomic studies.

plant biology↗

bioRxiv2023

Phylogenomics reveals patterns of ancient hybridization and differential diversification contributing to phylogenetic conflict in Populus L. and Salix L.

Despite the economic, ecological, and scientific importance of the genera Populus L. (poplars, cottonwoods, and aspens) and Salix L. Salicaceae (willows), we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a spectacular failure due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an fbranch analysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Populus and Salix have played important roles in the diversification and diversity in these two genera. Supplementary data files will be provided by request to matt.olson@ttu.edu

evolutionary biology↗

bioRxiv2022

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We find that while mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly LINEs, drive increases in genome size while DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TE at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals. One-Sentence SummaryA de novo assessment of TE content in 248 mammals finds informative trends in mammalian genome evolution.

genomics↗

bioRxiv2022

Including Phylogenetic Conservatism of Shortgrass Prairie Restoration Desired Species Does Not Improve Species Germination Prediction

PREMISEWe investigated whether phylogenetic conservatism can improve the performance of seed germinability prediction models. Previous studies in tallgrass prairie and alpine meadow revealed that seed morphological traits demonstrate phylogenetic conservatism. We hypothesized that phylogenetic conservatism in seed traits could help predict the seed germinability, under the assumption that seed traits contain phylogenetic signals. METHODSWe measured seed germination percentage and seed morphological traits (seed mass, seed height, and seed surface area) on 34 native species from shortgrass prairie in North America. We supplemented these data with similar data from the literature on 11 more species. We calculated the robustness of the phylogenetic signal of each trait to the number of species sampled. We also compressed the phylogenetic distance matrix to a two-dimensional space, and applied the Akaike information criterion to evaluate the effects of phylogeny on seed germinability prediction models. KEY RESULTSWe found weak but significant phylogenetic signals in seed mass and seed height in the full data set. These phylogenetic signals were not able to improve seed germinability prediction model performance among shortgrass prairie species. Our robustness tests of phylogenetic signals using random sub-sampling showed that the detection rate of phylogenetic signals in seed mass was increased along with the expansion of species pool, and nearly 100% at 40 species. However, the detection rate of phylogenetic signals in seed height was constantly low, around 20%. CONCLUSIONSWhen the phylogenetic signals are weak, the phylogenetic position does not improve germinability prediction model performance. Therefore, phylogenetic signals detected during a single species pool calculation may not accurately reflect the phylogenetic conservatism of the trait in a plant community. We suggest testing for robustness of phylogenetic signals using random sub-sampling tests.

ecology↗

bioRxiv2022

Don't get a big head: Centris pallida (Hymenoptera: Apidae) male head widths decrease across five decades

Historical data suggest that many bee species have declined in body size. Larger-bodied bees with narrow phenological and dietary breadth are most prone to declines in body size over time. This may be especially true in solitary, desert-adapted species that are vulnerable to climate change - such as Centris pallida (Hymenoptera: Apidae). In addition, body size changes in species with size-linked behaviors could threaten the prevalence of certain behavioral phenotypes long-term. C. pallida solitary bees are found in the Sonoran Desert. Males use alternative reproductive tactics (ARTs) and are dimorphic in both morphology and behavior. C. pallida male body size has been studied since the 1970s in the same population. We collected body size data in 2022 and combined it with published records from 1974-2022. We find a persistent decline in the mean head width of patrolling males, and shifts towards smaller body sizes in the populations of males found foraging and hovering. Both morphs declined in average body size, and the proportion of large-morph males in the population decreased by 8%. Mating males did not decline in mean body size over the last five decades. We discuss hypotheses related to the decline in C. pallida male head width. Finally, we advocate for C. pallida as an excellent study system for understanding the stability of ARTs with size-linked behavioral phenotypes.

ecology↗

bioRxiv2021

Target enrichment and extensive population sampling help untangle the recent, rapid radiation of Oenothera sect. Calylophus

Oenothera sect. Calylophus is a North American group of 13 recognized taxa in the evening primrose family (Onagraceae) with an evolutionary history that may include independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. Like other groups that radiated relatively recently and rapidly, taxon boundaries within Oenothera sect. Calylophus have remained challenging to circumscribe. In this study, we used target enrichment, flanking non-coding regions, summary coalescent methods, tests for gene flow modified for target-enrichment data, and morphometric analysis to reconstruct phylogenetic hypotheses, evaluate current taxon circumscriptions, and examine character evolution in Oenothera sect. Calylophus. Because sect. Calylophus comprises a clade with a relatively restricted geographic range, we were able to extensively sample across the range of geographic and morphological diversity in the group. We found that the combination of exons and flanking non-coding regions led to improved support for species relationships. We reconstructed potential hybrid origins of some accessions and note that if processes such as hybridization are not taken into account, the number of inferred evolutionary transitions may be artificially inflated. We recovered strong evidence for multiple origins of the evolution of bee pollination from ancestral hawkmoth pollination, the evolution of edaphic specialization on gypsum, and permanent translocation heterozygosity. This study applies newly emerging techniques alongside dense infraspecific sampling and morphological analyses to effectively address a relatively common but recalcitrant problem in evolutionary biology.

evolutionary biology↗

bioRxiv2021

Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)

BackgroundPlant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool-plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six different Oenothera harringtonii tissues from each of three linalool+ and linalool-plants. ResultsThree clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts in Oenothera harringtonii, a single allele of which is found exclusively in linalool+ plants. ConclusionsBy using a naturally occurring polymorphism and comparing different tissues, we were able to identify genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool-plants suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.

evolutionary biology↗

bioRxiv2021

Is Palmer's elm leaf goldenrod real? The Angiosperms353 kit provides within-species signal in Solidago ulmifolia s.l.

The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri, a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia. Solidago ulmifolia var. palmeris status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the "Angiosperms353" probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded. The status of Solidago delicatula (formerly known as Solidago ulmifolia var. microphylla) was also assessed. Both morphological and phylogenic analyses supported the species status of S. delicatula and we suggest maintaining this species at its current rank. These results highlight the utility of the Angiosperms353 probe kit, both with herbarium tissue and at lower taxonomic levels. Indeed, this is the first study to utilize this kit to identify genetic groups within a species.

evolutionary biology↗

bioRxiv2020

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

biochemistry↗

bioRxiv2020

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

SummaryO_LIOrganisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference and other analyses since it is not apparent which gene copies from different loci are from the same subgenome and thus share an evolutionary history. C_LIO_LIHere we introduce homologizer, a flexible Bayesian approach that uses a phylogenetic framework to infer the phasing of gene copies across loci into their respective subgenomes. C_LIO_LIThrough the use of simulation tests we demonstrate that homologizer is robust to a wide range of factors, such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data, by analyzing a multilocus dataset consisting of nine diploids and 19 tetraploids from the fern family Cystopteridaceae. C_LIO_LIFinally, we describe how homologizer may potentially be used beyond its core phasing functionality to identify non-homologous sequences, such as hidden paralogs or contaminants. C_LI

evolutionary biology↗

bioRxiv2020

On the potential of Angiosperms353 for population genomics.

Targeted sequencing using Angiosperms353 has emerged as a low-cost tool for phylogenetics, with early results spanning scales from all flowering plants to within genera. The use of universal markers at narrower scales--within populations-- would eliminate the need for specific marker development while retaining the benefits of full-gene sequences. However, it is unclear whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters. Using herbarium specimens from a 50-year-old floristic survey of Guadalupe Mountains National Park, we sequenced 95 samples from 24 species using Angiosperms353. We adapted a data workflow to process targeted sequencing data that calls variants within each species and prepares data for population genetic analysis. We calculated genetic diversity using standard metrics (e.g. heterozygosity, Tajimas D). Angiosperms353 gene recovery was associated with genomic library concentration, with limited phylogenetic bias. We identified over 1000 segregating variants with zero missing data within 22 of 24 species. A subset of these variants, which were filtered to remove linked SNPs, revealed high heterozygosity in many species. Tajimas D calculated within each species indicated a moderate number of markers potentially under selection and identified evidence of population bottlenecks in some species. Despite sequencing few individuals per species, the Angiosperms353 markers contained sufficient variation calculate demographic parameters. Larger sampling within species will allow for estimating gene flow and population dynamics in any angiosperm. Our study will benefit conservation genetics, where Angiosperms353 provides universal repeatable markers, low missing data, and haplotype information.

evolutionary biology↗

bioRxiv2020

Chromosome fusions shape an ancient UV sex chromosome system

Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration1,2. The correlation between suppressed recombination and degeneration is clear in animal XY systems1,2, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions3,4. Here we test for degeneration in the bryophyte UV sex chromosome system through genomic comparisons with new female and male chromosome-scale reference genomes of the moss Ceratodon purpureus. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.

evolutionary biology↗

bioRxiv2019

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.

evolutionary biology↗

bioRxiv2019

A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae

Crocodilians are an economically, culturally, and biologically important group. To improve researchers ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple non-coding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, ten in C. porosus and six in A. mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.

genomics↗