Biology subjects

Hernandez, D. J.

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

6 recordsLinked to original sources

bioRxiv2026

The genetic basis of extra-lobed leaves in ivyleaf morning glory (Ipomoea hederacea)

Intraspecific leaf shape variation is common among angiosperms. Ivyleaf morning glory (Ipomoea hederacea) has become a useful system for studying the genetics and ecology of leaf shape variation as this species exhibits two leaf shapes: leaves with entire margins, and 3-lobed leaves. It is known that these phenotypes are controlled by a single locus, and differ in their ecophysiology, geographic distribution, ecology, and fitness. However, individuals producing leaves with 1-2 extra lobes have also been observed, but the genetic basis of these phenotypes have not been described. To investigate the genetic basis of extra-lobing, we compared phenotypic distributions of leaf shapes of an F2 generation to Mendelian ratios for a single locus trait, and conducted a bulked segregant analysis to uncover quantitative trait loci. Our results suggest that producing extra-lobed leaves has a complex genetic basis and that there are multiple QTLs underlying this phenotype containing potential candidate genes involved with auxin distribution and leaf development. Whether these extra-lobed phenotypes also differ in terms of their physiology and ecology remains unexplored.

plant biology↗

bioRxiv2026

A rare deletion of BZ1 in the ivy-leaf morning glory eliminates anthocyanin-based pigmentation.

Anthocyanin biosynthesis is a highly branched network with upstream mutations leading to the loss of many other branches beyond just anthocyanins like flavonols, isoflavonoids, and proanthocyanidins. Consequently, disentangling the specific effects of anthocyanins on plant fitness from those of other branches is difficult unless a mutant impacting the terminal step of anthocyanin biosynthesis can be found. We discovered an Ipomoea hederacea plant (ivy-leaf morning glory) lacking anthocyanins due to a genetic deletion in the terminal step of the anthocyanin biosynthetic pathway. Anthocyanin loss follows a recessive, Mendelian inheritance pattern. Anthocyanin loss is perfectly correlated with a lack of expression of the anthocyanin biosynthesis gene IhUF3GT1 (anthocyanidin-3-O-glucosyltransferase). IhUF3GT1 is the gene most strongly and consistently differentially expressed between unpigmented and pigmented flowers in F2 siblings. A deletion of half of the IhUF3GT1 gene which includes the start codon is the genetic basis underlying a loss of IhUF3GT1 expression and, consequently, anthocyanins in unpigmented plants. The IhUF3GT1 deletion is rare and unique to the unpigmented line. Genome coverage analyses demonstrate that no other pigmented I. hederacea line (of 123 screened) has a loss-of-function mutation in IhUF3GT1. Furthermore, we confirm cosegregation of the IhUF3GT1 deletion with the unpigmented phenotype in F3 progeny from a cross where all unpigmented plants are homozygous for the IhUF3GT1 deletion. Taken together, we describe the genetic basis of a novel unpigmented mutant in I. hederacea, creating a potentially important model for studying the fitness effects of anthocyanin loss.

evolutionary biology↗

bioRxiv2025

Single-cell, Spatially-Resolved TCR Profiling Links T Cell Phenotype and Clonality in Human Tumors

Despite remarkable success in melanoma and other cancers, immune checkpoint blockade has shown limited efficacy in head and neck squamous cell carcinoma (HNSCC), with durable responses in only [~]10% of patients. This is paradoxical given the abundant infiltration of CD8 T cells in HNSCC, suggesting that current T cell profiling methods fail to fully capture functional anti-tumor immunity and that key immunosuppressive mechanisms remain poorly understood. To uncover mechanisms regulating T cell function in situ, we developed a multimodal profiling framework integrating high-dimensional flow cytometry, single-cell RNA- and TCR-sequencing, and spatial transcriptomics, including spatially-resolved TCR profiling at single-cell resolution. Applying this approach to paired blood and tumor samples from 27 HNSCC patients enabled single-cell resolution mapping of T cell clonality, transcriptional state, and spatial localization within intact tumors. Tumors with similar clinical features and immune profiles by flow cytometry and scRNA-seq exhibited markedly different spatial immune architectures. Within the T cell compartment, stem- and memory-like T cells localized within immune-rich niches, while exhausted cells were broadly dispersed in tumor-rich regions. Targeted spatial TCR mapping revealed that tumor-enriched TCR clones were distributed throughout the tumor yet adopted distinct, location-dependent phenotypes, indicating that both antigen specificity and spatial cues shape T cell differentiation and function in human tumors. These findings reveal fundamental principles of T cell organization in solid tumors and establish a versatile platform for spatially-resolved, antigen-specific T cell profiling.

immunology↗

bioRxiv2024

Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis.

As environments worldwide change at unprecedented rates during the Anthropocene, understanding context-dependency - how species regulate interactions to match changing environments - is crucial. However, generalizable molecular mechanisms underpinning context-dependency remain elusive. Combining comparative genomics across 42 angiosperms with transcriptomics, genome-wide association mapping, and gene duplication origin analyses, we show for the first time that gene family expansions undergird context-dependent regulation of species interactions. Gene families expanded in mycorrhizal fungi-associating plants display up to 200% more context-dependent gene expression and double the genetic variation associated with mycorrhizal benefits to plant fitness. Moreover, we discover these gene family expansions arise primarily from tandem duplications with >2-times more tandem duplications genome-wide, indicating gene family expansions continuously supply genetic variation allowing fine-tuning of context-dependency in species interactions throughout plant evolution. One-Sentence SummaryGene family expansions arising from tandem duplications underpin genetic regulation and fitness effects of context-dependency

evolutionary biology↗

bioRxiv2023

Multidimensional specialization and generalization are pervasive in soil prokaryotes with generalists dominating communities and specialists more central in networks

Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analyzed 236 prokaryotic communities across the United States demonstrating for the first time that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had a wide range of ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with [~]220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities likely stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance, and community roles. One-Sentence SummaryPervasive multidimensional specialization and generalization impacts evolutionary trajectories, microbial dominance, and community roles.

microbiology↗

bioRxiv2023

Hub taxa are keystone microbes during early succession

Microorganisms underpin numerous ecosystem processes and support biodiversity globally, yet we understand surprisingly little about what structures environmental microbiomes themselves. Combining culturing, sequencing, and microbial networks, we identified central (highly-connected, hub taxa), intermediate (moderately-connected), and peripheral (weakly/un-connected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession. Our results demonstrate central early colonizers significantly (1) enhanced biodiversity, (2) increased recruitment of additional influential, hub taxa, and (3) shaped microbiome assembly trajectories. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central, hub microbes are keystones.

microbiology↗