Biology subjects

Howe, D. K.

Publications and source records attributed to Howe, D. K..

5 recordsLinked to original sources

bioRxiv2026

Population Genetic Structure of Ariolimax columbianus around Corvallis, Oregon, USA

Urbanization has been previously shown to affect evolution of plants and animals by restricting gene flow, increasing genetic drift, and causing divergent selection between rural and urban populations, however, the effect of urbanization on terrestrial gastropod evolution has only been minimally researched. Most research on terrestrial gastropods primarily focusing on invasive pest species, and little attention is given to native species like Ariolimax columbianus (Pacific banana slug). There is no current published research on the phylogeography of A. columbianus. In this study, surface epithelial cells from 66 Ariolimax columbianus individuals were collected from 11 locations around Corvallis, Oregon, and one site in northern California. These samples were amplified and sequenced at two loci: cytochrome oxidase 1 (CO1) and the internal transcribed spacer 2 (ITS-2). This data was used to generate maximum-likelihood phylogenetic trees to better understand the population genetics of these local native gastropods. The CO1 phylogenetic analysis showed two major haplotypes around the city of Corvallis - northwestern and southern, while the ITS-2 phylogenetic analysis showed three general haplotypes around the city - northern, western, and southern. The results in this study show the presence of genetic breaks between many of these populations, possibly due to a combination of factors including anthropogenic fragmentation, natural barriers, and the low active dispersal ability of A. columbianus. However, the extent that each of those factors has on disrupting gene flow and explaining patterns of genetic variation in this species requires further research. The present study acts as a foundation for the development of future research on banana slug phylogenetics and population genetic structure.

genetics↗

bioRxiv2026

Comparative genomic and transcriptomic analyses of Strongylus vulgaris reveal developmental and evolutionary deployment of parasitism in a migratory equine nematode

BackgroundStrongylus vulgaris is a highly pathogenic equine strongyle whose larval stages migrate through the mesenteric arterial system, yet the molecular basis of its development, host association, and evolutionary biology remains poorly resolved. We generated an integrated genomic and transcriptomic resource to characterize genome structure, gene annotation, stage-associated expression, candidate secreted proteins, isoform diversity, gene-family evolution, putative horizontal gene transfer, and drug resistance-associated homologs in S. vulgaris. ResultsPacBio HiFi sequencing produced a 329.0 Mb genome assembly comprising 3,913 contigs, with a contig N50 of 147 kb and 94.8% BUSCO completeness, substantially improving the prior fragmented draft. Repeat annotation identified 127.5 Mb of repetitive sequence, representing 38.72% of the genome and dominated by unclassified repeats. Integration of RNA-seq-guided annotation with PacBio Iso-Seq evidence refined 16,387 loci and 24,546 transcripts, generating an isoform-retaining discovery proteome of 23,363 predicted proteins. Functional annotation supported 93.5% of predicted proteins and identified 1,530 unknown or weakly annotated candidates. Consensus secretome prediction identified 2,210 high-confidence putative secreted proteins. Stage-associated transcriptomics showed that development was the dominant axis of expression variation, with 5,299 genes differentially expressed between larvae and adults and strong adult sex-associated divergence. Isoform analysis identified 490 high-confidence isoform switches, concentrated primarily in the ML5 female-to-adult female transition. Comparative genomics identified 27,641 orthogroups, 201 S. vulgaris-specific orthogroups, and, after repeat-aware filtering, 48 expanded and 250 contracted gene families. Structure-guided annotation prioritized migratory-stage-enriched secreted candidates, including Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 (CAP), Sperm-coating protein (SCP) Tpx-1/Ag5/PR-1/Sc7 protein superfamily (TAPS) -like, von Willebrand factor type A (VWA) - domain, lipid-binding-like, DNase II-like, and peptidase-like proteins. Conservative screening retained 17 putative horizontal gene transfer (HGT) candidates, and drug resistance-homolog analysis recovered 18 nonredundant S. vulgaris homologs without canonical {beta}-tubulin benzimidazole-resistance substitutions. ConclusionsThese results establish the first integrated, high-quality molecular framework for S. vulgaris and show that its parasitic biology is developmentally structured, isoform-rich, and shaped by both conserved strongylid features and lineage-specific gene-family change. This resource provides a foundation for future studies of interhost migration, host interaction, parasite evolution, and genomic surveillance.

genomics↗

bioRxiv2026

Two Pellioditis biocontrol nematode species infect Ariolimax columbianus, the Pacific banana slug, and increase mortality in laboratory infectivity trials

Gastropods are a highly diverse and often overlooked taxonomic group of significant ecological and economic importance. Some terrestrial gastropods are critical pests of commercial agriculture and home gardens worldwide. Malacopathogenic nematodes offer an effective biological control method of managing pest slugs and snails as a natural enemy. Pellioditis (syn. Phasmarhabditis) hermaphrodita and Pellioditis (syn. Phasmarhabditis) californica are two species of biocontrol nematodes that have been commercialized, sold as Nemaslug(R) and Nemaslug(R) 2.0 respectively on three continents. Although there is interest in bringing Nemaslug(R) products to the US, they are currently not permitted due to limited knowledge on their North American distribution and effects on non-target and native species. In this study, we investigated the impact of P. hermaphrodita and P. californica on Ariolimax columbianus across two slug-host life stages, in laboratory infectivity assays. The objectives were to 1. determine whether P. hermaphrodita and P. californica nematodes impact survival of A. columbianus, and 2. evaluate whether there are differential effects on survival in juvenile and adult life stages of A. columbianus, in laboratory infectivity trials. We found that P. hermaphrodita caused significant mortality in A. columbianus with 100% mortality observed in both juvenile and adult slug hosts. The P. californica treatment had significant effects on the juvenile A. columbianus group only, with 80% mortality. By contrast, only 16% of unexposed control juveniles and 4% of control adult slugs died during the experiment. These results indicate that P. hermaphrodita and P. californica are lethal to the native, non-target Pacific banana slug (A. columbianus) under laboratory conditions, with mortality differing between juvenile and adult host life stages. Given the ecological importance of A. columbianus, these findings raise concerns for potential non-target effects of P. californica and P. hermaphrodita on terrestrial gastropod communities and emphasize the need for testing biocontrol agents against multiple life stages.

zoology↗

bioRxiv2025

Microbiome dynamics associated with the infection of grey field slugs by the biocontrol nematode Phasmarhabditis hermaphrodita

The facultative-parasitic nematode Phasmarhabditis hermaphrodita has been used for many years as a biological control agent targeting slug pests. During the nematodes infection process, the presence of certain bacteria has been suggested to affect the pathogenicity and efficiency of the nematodes in killing slugs, though the potential roles of different bacteria in affecting host-infection by nematodes remains unclear. In this study, we examined three experimental P. hermaphrodita populations cultured with three different bacteria: 1) Escherichia coli (EC), 2) a newly isolated Pseudomonas sp. Strain (PS) that co-cultured with a P. hermaphrodita strain found in Oregon, USA, and 3) the original complex bacterial community (BC) associated with the nematode. For each of the three treatments, we evaluated the pathogenicity of P. hermaphrodita at a low and high concentration towards adult Deroceras reticulatum (Mollusca: Gastropoda) and investigated the changes in the nematode microbiome structure before and after slug infection. Slugs exposed to EC low treatments (LT50: 8.61 days) and EC high treatments (LT50: 7.74 days) survived significantly longer than slugs exposed to PS high (LT 50: 5.68 days) and BC high (LT50: 5.92 days). Slugs in the BC low treatment (LT50: 6.77 days) survived significantly longer when compared to BC high, but survival was significantly shorter when compared to EC high. We identified a wide variety of taxa components (82 genera) in the community associated with the nematode pre-infection, most of which are of low abundance. In all bacterial treatments post-infection, the number of genera almost quadrupled and those taxas abundance changed remarkably, although the taxa with the highest abundance remained stable. We also observed four Pseudomonas amplicon sequence variants (ASVs) that increased in abundance after slug infection in the Pseudomonas treatment, which may suggest a role of the taxa in the infection process.

microbiology↗

bioRxiv2020

Fussing about fission: defining variety among mainstream and exotic apicomplexan cell division modes

Cellular reproduction defines life, yet our textbook-level understanding of cell division is limited to a small number of model organisms centered around humans. The horizon on cell division variants is expanded here by advancing insights on the fascinating cell division modes found in the Apicomplexa, a key group of protozoan parasites. The Apicomplexa display remarkable variation in offspring number, whether karyokinesis follows each S/M-phase or not, and whether daughter cells bud in the cytoplasm or bud from the cortex. We find that the terminology used to describe the various manifestations of asexual apicomplexan cell division emphasizes either the number of offspring or site of budding, which are not directly comparable features and has led to confusion in the literature. Division modes have been primarily studied in two human pathogenic Apicomplexa, malaria-causing Plasmodium spp. and Toxoplasma gondii, a major cause of opportunistic infections. Plasmodium spp. divide asexually by schizogony, producing multiple daughters per division round through a cortical budding process, though at several life-cycle nuclear amplifications are not followed by karyokinesis. T. gondii divides by endodyogeny producing two internally budding daughters per division round. Here we add to this diversity in replication mechanisms by considering the cattle parasite Babesia bigemina and the pig parasite Cystoisospora suis. B. bigemina produces two daughters per division round by a binary fission mechanism whereas C. suis produces daughters through both endodyogeny and multiple internal budding known as endopolygeny. In addition, we provide new data from the causative agent of equine protozoal myeloencephalitis (EPM), Sarcocystis neurona, which also undergoes endopolygeny but differs from C. suis by maintaining a single multiploid nucleus. Overall, we operationally define two principally different division modes: internal budding found in cyst-forming Coccidia (comprising endodyogeny and two forms of endopolygeny) and external budding found in the other parasites studied (comprising the two forms of schizogony, binary fission and multiple fission). Progressive insights into the principles defining the molecular and cellular requirements for internal versus external budding, as well as variations encountered in sexual stages are discussed. The evolutionary pressures and mechanisms underlying apicomplexan cell division diversification carries relevance across Eukaryota. Contribution to the FieldMechanisms of cell division vary dramatically across the Tree of Life, but the mechanistic basis has only been mapped for several model organisms. Here we present cell division strategies across Apicomplexa, a group of obligate intracellular parasites with significant impact on humans and domesticated animals. Asexual apicomplexan cell division is organized around assembly of daughter buds, but division forms differ in the cellular site of budding, number of offspring per division round, whether each S-phase follows karyokinesis and if mitotic rounds progress synchronously. This varies not just between parasites, but also between different life-cycle stages of a given species. We discuss the historical context of terminology describing division modes, which has led to confusion on how different modes relate to each other. Innovations in cell culture and genetics together with light microscopy advances have opened up cell biological studies that can shed light on this puzzle. We present new data for three division modes barely studied before. Together with existing data, we show how division modes are organized along phylogenetic lines and differentiate along external and internal budding mechanisms. We also discuss new insights into how the variations in division mode are regulated at the molecular level, and possess unique cell biological requirements.

microbiology↗