Biology subjects

Peck, L. D.

Publications and source records attributed to Peck, L. D..

5 recordsLinked to original sources

bioRxiv2026

Is epigenetics Lamarck's revenge? The evolutionary and ecological impacts of DNA methylation in a California oak

DNA methylation, an epigenetic mechanism, has been proposed as a basis for Lamarckian inheritance of acquired characteristics. This hypothesis raises questions about environmental induction of DNA methylation, its persistence across generations, and associations with gene expression. We investigated these processes in the California oak, Quercus lobata. Based on 40 range-wide adult trees and their progeny grown in two common gardens, we tested four predictions: (i) DNA methylation is environmentally induced; (ii) methylation shows parent-offspring correspondence; (iii) environmentally induced patterns remain stable after transmission; and (iv) DNA methylation is associated with gene expression, varying by sequence context and TE proximity. Using methylomes and transcriptomes, we found support for all predictions except the third: CHH methylation was environmentally induced, but rarely showed parent/offspring correspondence, whereas CG methylation showed the opposite pattern. DNA methylation was associated with gene expression, depending on the sequence context and proximity to TEs. We identified one stress-associated gene with environmentally responsive CHH methylation that showed parent offspring correspondence in two common gardens in both gardens. Still, overall evidence for Lamarckian like evolution is not compelling. Nevertheless, DNA methylation was environmentally responsive, showed parent offspring correspondence, and was associated with gene expression, highlighting its potential importance for the ecological and evolutionary responses of long-lived trees to environmental change.

evolutionary biology↗

bioRxiv2026

Cheese adaptation beyond Penicillium: contrasting genomic trajectories in the distantly related Nectriaceae molds

Fungal domestication provides a powerful framework for understanding adaptation to human-made environments, yet genomic studies of cheese-associated fungi have largely focused on Penicillium molds. Here, we investigated cheese-associated Nectriaceae, a phylogenetically distant fungal lineage of ascomycetes, by comparing genomes of nine cheese isolates, belonging to five species, with 22 relatives from other environments. Comparative genomic analyses revealed strikingly contrasting evolutionary trajectories in the two cheese-associated genera. Longinectria showed extensive gene family expansions and duplications, particularly affecting nutrient transport, specialised metabolism and fungal recognition, whereas cheese-associated Bisifusarium exhibited genome reduction and contraction of many of the same functional systems. In Bisifusarium domesticum, these reductions extended to biosynthetic gene clusters, carbohydrate-active enzymes and peptidases, consistent with ecological specialisation. We further identified a 75-kb region with >98% nucleotide identity between two cheese-associated Bisifusarium species, strongly supporting recent horizontal transfer. This region contains several genes involved in ion transport and salt tolerance, including functions previously identified in horizontally transferred regions of cheese-associated Penicillium populations. Together, our results reveal multiple genomic routes to cheese association and highlight gene-family turnover, adaptive protein evolution and horizontal gene transfer as complementary mechanisms shaping fungal evolution in anthropogenic environments.

evolutionary biology↗

bioRxiv2026

CHH methylation is recruited to gene-proximal transposable elements during repeated drought stress

Long-lived trees must continually adjust to environmental change and face sustained climatic shifts over their lifetimes. One increasingly important challenge is the rising frequency of drought caused by climate change. Environmentally responsive DNA methylation is widespread in plants, but whether it contributes to gene expression during environmental stress remains unclear, particularly in long-lived trees. Here, we integrated long read methylomes and transcriptomes from valley oak (Quercus lobata) seedlings exposed to repeated drought and well-watered treatments. Repeated drought induced a reproducible DNA methylation response that repeatedly targeted the same genomic regions despite turnover of individual methylated sites. These repeatedly targeted regions were transposable elements (TEs) located near genes. Genes adjacent to CHH-methylated TEs were enriched for core drought-response pathways, including abscisic acid signaling, osmotic adjustment and cell-wall remodeling, and remained transcriptionally activated under drought. However, higher CHH methylation levels were associated with progressively smaller transcriptional responses, suggesting that environmentally responsive DNA methylation influences how strongly drought-response genes are activated rather than simply switching them on or off. At the same time, greater CHH methylation was associated with continued repression of nearby TEs, suggesting that this response may simultaneously regulate gene activity while maintaining genome stability. Together, these findings identify a reproducible genome-regulatory response associated with repeated environmental stress in a long-lived tree. By repeatedly targeting the same genomic regions despite turnover of individual sites, this response provides a framework for how long-lived trees repeatedly adjust gene expression while maintaining genome stability during environmental change.

evolutionary biology↗

bioRxiv2025

Drought-associated genes exhibit high constitutive expression in Quercus douglasii, a drought tolerant California oak

Drought stress is a strong selective pressure for all plant species. Plants can respond to water shortage through various strategies that confer drought tolerance, but with a potential cost for growth. These strategies may be plastic responses that occur with the onset of stress or may comprise continuously-expressed (constitutive) traits regardless of water availability. Here, we used RNA-Seq to characterize transcriptional responses to dehydration in seedlings of a drought tolerant oak, Quercus douglasii, from a population in the Sierra Nevada Foothills in California. In the greenhouse, we subjected 24 seedlings from six maternal families to dry-down or well-watered treatments and prepared RNA libraries from tissue collected before and after each treatment (48 libraries). Our goals were to characterize the pattern of up- and down-regulated genes in response to dehydration and to assess the extent to which this drought tolerant species shows differential versus constitutive expression as a drought response strategy. We identified few differentially expressed genes in response to dehydration. Up-regulated genes were related to known drought response functions, while down-regulated genes were enriched for gene ontology terms related to growth and carbohydrate metabolism. We discovered high constitutive expression of many putatively drought-responsive genes that had been found to exhibit gene expression plasticity in a drought sensitive oak, which a novel finding for drought tolerance strategies in tree species. We conclude that the drought tolerant strategy of Q. douglasii incorporates high constitutive expression levels of drought-responsive genes, as well as some plasticity in its response once environmental stress is experienced.

plant biology↗

bioRxiv2023

Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease

Outbreaks of fungal disease have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogen Fusarium xylarioides severely impacted coffee production across sub-Saharan Africa. To improve the disease management of such pathogens, it is crucial to understand their genetic structure and evolutionary potential. We compared the genomes of 13 historic strains spanning six decades and multiple disease outbreaks to investigate population structure and host specialisation. We found F. xylarioides comprises at least four distinct lineages: one host-specific to Coffea arabica, one to C. canephora var. robusta, and two historic lineages isolated from various Coffea species. Mapping variation onto a new long-read reference genome showed that host-specificity appears to be acquired through horizontal transfer of effector genes from members of the F. oxysporum species complex. This species complex is known to cause wilt disease in over 100 plant species. Multiple transfers into the F. xylarioides populations matched to different parts of the F. oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons. Effector genes in this region and other horizontally transferred carbohydrate-active enzymes important in the breakdown of plant cell walls were shown by transcriptomics to be highly expressed during infection of C. arabica by the fungal arabica strains. Widespread sharing of specific transposons between F. xylarioides and F. oxysporum, and the presence of large Starship elements, indicate that transposons were involved in horizontal transfers. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of this fungal disease.

evolutionary biology↗