Jill L. Wegrzyn

Butternut ( Juglans cinerea ) is a North American hardwood in rapid decline, driven largely by butternut canker disease (BCD). Within the genus, Juglans ailantifolia (Japanese walnut) is comparatively resistant and hybridizes readily with J. cinerea , yet the genomic basis of the difference is unresolved. The first chromosome-scale reference genome for J. ailantifolia is presented here, together with a second J. cinerea accession from the species’ primary range, with independent scaffolding and uniform annotation throughout. Gene family evolution was assessed across twelve Juglandaceae genomes, and a four accession pangenome contrasted the BCD resistant section Cardiocaryon ( J. ailantifolia , J. mandshurica ) with the BCD susceptible section Trachycaryon ( J. cinerea , Iowa and New Brunswick accessions). Across sections separated by approximately 30 My, most defense gene families differ in presence and absence rather than copy number; five surface receptor and protease families are overrepresented in the lineage specific complement of both sections, indicating rapid bidirectional turnover. Five families differ between sections in copy number while remaining stable between the conspecific accessions, all favoring the susceptible section. The smaller set includes chitinases and NB-LRR receptors biased toward the resistant section, and dehydrins, pectin-modifying enzymes, pathogenesis-related proteins and the CBF regulon toward the susceptible one. The largest copy number difference separates the two conspecific accessions at a senescence associated cysteine protease. The northern New Brunswick accession also retains lower heterozygosity, a distinct demographic trajectory, and unique gene content enriched for calcium transport, salt stress regulation and raffinose family oligosaccharide biosynthesis, consistent with freezing tolerance. Significance Statement: Juglans cinerea (butternut), a threatened North American walnut tree, is being lost to butternut canker disease, while Juglans ailantifolia (Japanese walnut) is resistant to the fungal pathogen. Chromosome-scale genomes and a pangenome place defense differences between resistant and susceptible lineages primarily in gene presence and absence. The pangenome and demographic modeling distinguish the northern J. cinerea accession by unique gene content consistent with cold tolerance and a distinct population history.

The guano of insectivorous bats holds ecological information that can be assessed non-invasively to characterize the gut microbiome and diet, alongside environmental microbes and pathogens of conservation concern. Despite this potential, how guano communities change during decomposition remains understudied, particularly inside anthropic roosts rather than caves. In this study, guano from little brown bat (Myotis lucifugus) colonies was sampled monthly across the summer maternity season from three sites across two locations in Connecticut, USA, at fresh deposition and at 4, 8, and 12 weeks following deposition. Resolving these cross-kingdom signals required five workflows: short-read 16S and ITS2 amplicon sequencing (Illumina) for bacterial and fungal profiling, long-read CO1 metabarcoding (Oxford Nanopore) for arthropod diet in fresh samples, long-read shotgun metagenomics for viral identification in aged samples, and targeted qPCR for organisms of bat, human, and forest-health concern. Fresh guano generated a consistent bacterial signal across sites, whereas fresh fungal communities differed by site. Responses to decomposition depended on roost setting: exterior sites lost fungal diversity and shifted toward environmental aerobes over time, while the interior roost retained the fresh sample profile. Dietary composition varied temporally, was dominated by Diptera, and included the invasive emerald ash borer (Agrilus planipennis). Pseudogymnoascus destructans, the causal agent of white-nose syndrome, occurred in fresh and aged samples at all three sites but persisted for 12 weeks only at the interior roost, where antifungal bacterial taxa were depleted. Long-read shotgun metagenomics of aged guano recovered roughly 100 viral species, predominantly bacteriophages, alongside non-bacteriophage mastadenoviruses associated with humans, bats, and other mammals. These results show that anthropic structures influence the trajectory of guano microbiome succession, and that maternity colony guano enables non-invasive assessment of environmental pathogens, bat diet, and bacterial and fungal communities.

Understanding the origin of new structures is a central goal of evolutionary biology. In many instances, novel phenotypes arise through heterotopy: the expression of a structure in a new location. Using bracken fern (Pteridium aquilinum) as a model, we combine genomics, transcriptomics and metabolomics to begin to explore the origin and developmental routes in the convergent evolution of ant-enticing nectaries. We observe that P. aquilinum does not exclusively express flowering plant ‘nectary genes’ during nectary development. Rather, this fern builds nectaries through co-option of stomata. Specifically, P. aquilinum heterotopically expresses canonical angiosperm stomatal regulatory genes, leading to stomatal development in novel positions along the petiole. These non-laminar stomata were co-opted for nectar secretion through the expression of putative sugar transport genes, forming secretory nectarostomata. This work provides two advances in our understanding of nectary evolution and the origin of complex structures. First, heterotopic expression of stomata, and later exaptation, represents one realized developmental mechanism for the evolution of nectar glands. Second, while there are many routes to nectary evolution, nectarostomata development is a repeatable path that has evolved in ferns and flowering plants, representing an impressive case of convergent evolution through the same developmental mechanism, despite over 400 million years of divergent history.

Steps for collecting tissue from American beech, Fagus grandifolia, for DNA analysis. The Plant Computational Genomics lab is conducting a landscape genomics study of American beech to assess population structure, genetic diversity, and climate adaptation across the range. This protocol is a step-by-step guide to collect a tissue sample, with metadata recorded in TreeSnap (https://treesnap.org). Trees must be wild/unplanted, but do not need to be disease-free.

Subspecies represent evolutionarily distinct lineages that preserve patterns of adaptive diversity and ecological specialization within species. Genomic tools can assist with subspecies delineation, and provide support for classifications based solely on morphological, geographic, or ecological traits. The American mink (Neogale vison), as semi-aquatic mustelid carnivore with a broad ecological range across North America, includes several putative subspecies of conservation concern. To investigate their evolutionary history and adaptive signatures, chromosome-scale genome assemblies were generated for six individuals representing three subspecies: N. vison evergladensis, N. vison vulgivaga, and N. vison lutensis. Genomes were assembled using Illumina short reads, scaffolded with Oxford Nanopore long reads, and aligned to the phased N. vison reference genome. The reference-free pangenome revealed an open architecture and presence/absence analysis was consistent with distinct adaptive profiles. Neogale vison evergladensis showed enrichment in traits related to reproduction and sensory function, N.v. vulgivaga in cytoskeletal remodeling and oxidative stress, and N. v. lutensis in neuronal development and synaptic plasticity. Mitochondrial analyses resolved N.v. lutensis as a distinct lineage, while nuclear data lacked fine-scale resolution. Our findings support N.v. evergladensis as a distinct subspecies, supported by both the mitogenome phylogeny and functional differentiation. Neogale vison evergladensis also exhibited multiple indicators of small population size, including high inbreeding estimates, and evidence of sustained population decline. As the first pangenome for Mustelidae, this study demonstrates the power of natural history specimens to detect signatures of adaptation and inform the management of threatened populations.

Climate change is threatening plant health and productivity at all spatial scales, and these impacts are further compounded by the rising incidence of invasive pests and pathogens. Effectively addressing these challenges requires a comprehensive understanding of plant demography as well as the mechanisms and drivers of adaptation. Achieving this understanding requires the integration of physiological, ecological, and genetic datasets. However, such integration is often hindered by disconnected data sources, inconsistent metadata standards, and limited tools to link, analyze, and visualize multi-dimensional datasets in a unified framework. Addressing these hurdles is critical to advancing the understanding of species responses to environmental change and developing informed strategies for conservation, restoration, and adaptive management. CartograPlant (https://cartograplant.org) is a web-based interactive application which facilitates the visualization and analysis of genotypic, phenotypic, and environmental data, as well as associated metadata, from georeferenced individuals. Developed as a Tripal module, CartograPlant addresses a critical gap in biological data integration by enabling users to explore complex eco-evolutionary patterns across space and time. Recent updates have expanded its data sources, improved interoperability, and introduced NextFlow pipelines alongside new tools for the integration and analysis of these data. CartograPlant offers a scaleable, flexible, and continually updated platform for researchers, conservationists, land managers, and plant breeders to better understand and mitigate the impacts of global change on plant biodiversity, accelerate resilience in breeding programs, and inform data-driven decisions in agriculture and ecosystem management.

Two invasive adelgids are associated with widespread damage to several North American conifer species. Adelges tsugae, hemlock woolly adelgid, was introduced from Japan and reproduces parthenogenetically in North America, where it has rapidly decimated Tsuga canadensis and Tsuga caroliniana (eastern and Carolina hemlocks, respectively). Adelges abietis, eastern spruce gall adelgid, introduced from Europe, forms distinctive pineapple-shaped galls on several native spruce species. While not considered a major forest pest, it weakens trees and increases susceptibility to additional stressors. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects. Whole-genome sequencing was performed on both species to aid in the development of targeted solutions that may minimize ecological impact. A. abietis was sequenced using barcoded linked-reads from 30 pooled individuals, with Hi-C scaffolding performed using data from a single individual collected from the same host plant. A. tsugae used long-read sequencing from pooled nymphs. The assembled A. tsugae and A. abietis genomes, pooled from several parthenogenetic females, are 220.75 and 253.16 Mb, respectively. Each consists of 8 autosomal chromosomes, as well as 2 sex chromosomes (X1/X2), supporting the XX-XO sex determination system. The genomes are over 96% complete based on BUSCO assessment. Genome annotation identified 11,424 and 12,060 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis of proteins across 31 hemipteran species and 14 arthropod outgroups identified 32,340 putative gene families. Gene family evolution analysis with CAFE revealed lineage-specific expansions in immune-related aminopeptidases (ERAP1) and juvenile hormone binding proteins (JHBP), contractions in juvenile hormone acid methyltransferases (JHAMT), and conservation of nicotinic acetylcholine receptors (nAChRs). These genes were explored as candidate families toward a long-term objective of developing adelgid-selective insecticides. Structural comparisons of proteins across 7 focal species (A. tsugae, A. abietis, Adelges cooleyi, Rhopalosiphum maidis, Apis mellifera, Danaus plexippus, and Drosophila melanogaster) revealed high conservation of nAChR and ERAP1, while JHAMT exhibited species-specific structural divergence. The potential of JHAMT as a lineage-specific target for pest control was explored through virtual screening of drugs and pesticides.

The American mink ( Neogale vison ), a semi-aquatic Mustelidae carnivoran with broad ecological range across North America, includes several putative subspecies of conservation concern. To investigate the evolutionary history and adaptive signatures of mink subspecies, chromosome-scale genome assemblies were generated for six individuals representing three southern subspecies: N. vison evergladensis , N. vison vulgivaga , and N. vison lutensis . Genomes were assembled using Illumina short reads, scaffolded with Oxford Nanopore long reads, and aligned to the phased N. vison reference genome. Assemblies ranged from 75.9% to 97.8% completeness, with five meeting thresholds for pangenome construction. A reference-free pangenome revealed an open architecture, highlighting considerable subspecies diversity. Subspecies-specific gene enrichment reflected adaptation: N. vison evergladensis showed enrichment in traits related to reproduction and sensory function; N. vison vulgivaga in cytoskeletal remodeling and oxidative stress; and N. vison lutensis in neuronal development, synaptic plasticity and cellular stress pathways. Assessment of the mitogenomes resolved N. vison lutensis as a distinct lineage, while nuclear data supported broader subspecies divergence but lacked fine scale resolution. N. vison evergladensis showed multiple signatures of small population size, including inbreeding coefficients (F _ROH ) above 0.5, and displayed consistent population decline over time via demographic inference. Our findings support evergladensis as a distinct subspecies, supported by both the mitogenome phylogeny, and significant functional differentiation. As the first pangenome for Mustelidae, this study demonstrates the power of integrating cross-platform sequencing with natural history specimens to improve the resolution on signatures of adaptation and inform conservation policy and management of threatened populations.

Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70–90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.