Biology subjects

Pelosi, J. A.

Publications and source records attributed to Pelosi, J. A..

5 recordsLinked to original sources

bioRxiv2026

Temporal changes in genetic variation during the invasion of Lygodium japonicum in North America

Premise of the study. Invasive species are now widespread and have detrimental ecological and economic impacts. They also offer opportunities to investigate rapid evolution in colonizing populations. Here, we leverage nuclear DNA from herbarium specimens of Lygodium japonicum, an invasive fern to 1) identify the putative source(s) of its invasion, 2) test for climate adaptation in its invaded range, and 3) characterize the effects of genetic bottlenecks on adaptive and neutral variation during its establishment. Methods. We use low-coverage genome skimming data from specimens spanning 1905 through 2017 to identify the source region(s) of the L. japonicum invasion of North America. We use a genotype-environment analysis of invaded range samples to identify genomic regions associated with local adaptation to variation in five bioclimatic variables. Finally, we compare heterozygosity between native and invasive individuals and their changes through time in non-coding, coding, and putatively adaptive loci. Key results. We identify mainland Asia as the most likely source region for this invasion. Our genotype-environment analysis found 144 candidate SNPs significantly associated with climatic variation in the invaded range, with precipitation of the driest month associated with the greatest number of SNPs, suggesting rapid genomic adaptation in the invaded range. Finally, we found conflicting trends in individual-level heterozygosity over time when analyzing different types of genetic variation: in non-coding loci, there was a small, yet significant decrease in genetic diversity, but in putatively adaptive loci we did not find evidence of a genetic bottleneck. Conclusions. Natural history collections provide exceptional opportunities to explore evolutionary processes, by capturing genomic sequences across time. Here, herbarium specimens reveal rapid evolution, maintenance of adaptative variation, and accumulation of noncoding diversity in the Lygodium japonicum invasion, highlighting the potential for adaptative variation to fuel the success of invasive species.

evolutionary biology↗

bioRxiv2026

Mite Genome Miniaturization: Assembly of the biological control agent Floracarus perrepae reveals dynamic genome evolution in eriophyoid mites

The eriophyoid mites (Acari: Eriophyoidea) represent an extreme case of genome streamlining, with genomes averaging just 32Mb, among the smallest of all animals. This clade of mites is highly diverse with more than 4000 species. Their morphologies are specialized for feeding on their host plants, including a simplified worm-like body plan with just two pairs of legs and modified mouth parts that can induce the formation of galls or plant deformities during feeding. Their generally strong host affinities make eriophyoid mites appealing for use as biological control agents, although their short generation times and small genomes could facilitate rapid evolution and impact their efficacy in management programs. Here, we sequenced the genome of the biological control mite Floracarus perrepae, producing a highly contiguous genome totalling just 23.1 Mb, among the smallest of all animals. We also assembled another non-eriophyid mite genome from accidental DNA bycatch (69.4Mb). We placed this new genomic resource in a phylogenetic context to reveal that mites have highly dynamic genome evolution, with a significant trend in genome downsizing in the eriophyoids. Our results suggest that this streamlining is associated with non-genic elements such as the suppression or excision of retrotransposons and purging of introns. As new sequencing techniques become available, novel genomic resources for tiny organisms such as F. perrepae will be more readily accessible, facilitating both fundamental genome evolutionary biology and applied sciences such as biological control programs which use eriophyoid mites for the management of invasive species.

evolutionary biology↗

bioRxiv2025

Microsynteny Analysis Clarifies the Early Diversification of Cypriniform Fishes

While genomic data are powerfully informative for phylogenetic inference, traditional sequence-based analyses can be confounded by issues like homoplasy and incomplete lineage sorting, leaving deep nodes unresolved. Synteny, the conservation of gene order along a chromosome, presents a promising alternative source of phylogenetic information that is potentially less prone to these issues. Here we compare sequence and synteny phylogenetic phylogenomic approaches to unravel the evolutionary history of Cypriniformes, one of the most species-rich lineages of freshwater fishes. This clade has been plagued by uncertainty, particularly concerning the phylogenetic relationships between its four major subclades: Gyrinocheilidae (algae eaters), Catostomidae (suckers), Cobitoidei (loaches), and Cyprinoidei (minnows and carps). Phylogenomic approaches require high-quality genomic resources, which have been lacking for the family Gyrinocheilidae, a key lineage for understanding cypriniform evolution. To address this, we generated the first chromosome-level genome assembly and annotation for the Chinese Algae Eater (Gyrinocheilus aymonieri). We utilized this new genome along with 42 other fish genomes to conduct comprehensive phylogenomic analyses and compare results from sequence-based methods with a microsynteny-based approach. Although chromosome-level macrosynteny is broadly conserved among cypriniforms, we demonstrate that microsynteny has impressive power to resolve deep phylogenetic nodes. Both sequence-based and microsynteny-based analyses find that Gyrinocheilidae is the sister lineage to all other cypriniforms, resolving a long-standing phylogenetic point of contention. However, while sequence-based analyses provided weak support for the relationships among the remaining subclades, our microsynteny analysis revealed a novel and strongly supported sister relationship between Catostomidae and Cyprinoidei. This conclusion is supported by a 3- to 12-fold greater number of shared microsynteny clusters (synapomorphies) compared to the alternative topologies. We also demonstrate that microsynteny synapomorphies often arise from gene family expansions. Conservation of synteny concentrated in specific genomic regions may harbor the genomic underpinnings of the unique aspects of these clades and have played an important role in the evolutionary history of these taxa. Together, these results provide a robust phylogenomic backbone for Cypriniformes. More broadly, our findings highlight the power of microsynteny to resolve recalcitrant phylogenetic nodes where sequence data is uninformative, while also underscoring the critical importance of high-quality reference genomes, as our work also shows that including fragmented assemblies can lead to spurious results. Beyond phylogenomics, our results also provide a functional genomics glimpse into how conserved, clade-specific blocks of collinear genes (synteny synapomorphies) might contribute to what makes this hyperdiverse clade so unique and evolutionarily successful.

evolutionary biology↗

bioRxiv2024

Chromosome-scale reference genome of Pectocarya recurvata, a species with one of the smallest genome sizes in Boraginaceae

PremisePectocarya recurvata (Boraginaceae), a native species of the Sonoran Desert, has served as an important model system for a suite of ecological and evolutionary studies. Despite its relevance as an eco-evolutionary model, no reference genome assemblies in the Cynoglossoideae subfamily have been published. MethodsUsing PacBio HiFi sequencing, we assembled a reference genome for P. recurvata and annotated coding regions with full-length transcripts from an Iso-Seq transcriptome library. We assessed genome completeness with BUSCO and used flow cytometry and K-mer analysis to estimate the genome size of P. recurvata. ResultsThe chromosome-scale reference genome assembly for P. recurvata was 216.0 Mbp long with a contig N50 of 12.1 Mbp. Our assembly included 12 primary contigs bounded by telomeres at all ends but one, consistent with the 12 chromosomes documented for the species. The chromosomes covered 158.3 Mbp and contained 30,655 predicted genes. Our measured haploid genome size from the same population was 386.5 Mbp, among the smallest for Boraginaceae. Genomic analyses suggested that this may reflect a recent autotetraploid, such that predicted diploid genome size would be even smaller and similar to the assembly size. DiscussionThe P. recurvata assembly and annotation provide a high-quality genomic resource in a sparsely represented area of the Angiosperm phylogeny. Our new genome will enable future ecophysiology, biogeography, and phylogenetics research.

genomics↗

bioRxiv2020

Thermally tolerant symbionts may explain Caribbean octocoral resilience to heat stress

Coral reef ecosystems are under threat from the frequent and severe impacts of anthropogenic climate change, particularly rising sea surface temperatures. The effects of thermal stress may be ameliorated by adaptation and/or acclimation of the host, symbiont, or holobiont (host + symbiont) to increased temperatures. We examined the role of the symbiont in promoting thermal tolerance of the holobiont, using Antillogorgia bipinnata (octocoral host) and Breviolum antillogorgium (symbiont) as a model system. We identified five distinct genotypes of B. antillogorgium from symbiont populations isolated from Antillogorgia colonies in the Florida Keys. Three symbiont genotypes were cultured and maintained at 26{degrees}C (ambient historical temperature) and two were cultured and maintained at 30{degrees}C (elevated historical temperature) for two years. Following culturing, we analyzed the growth rate and carrying capacity of each symbiont genotype at both ambient and elevated temperatures in culture (in vitro). All genotypes grew well at both temperatures, indicating thermal tolerance among these B. antillogorgium cultures. Prior culturing at the elevated temperature, however, did not result in increased thermal tolerance. We then inoculated juvenile A. bipinnata polyps with each of the five symbiont genotypes, and reared these polyps at both ambient and elevated temperatures (in hospite experiment). All genotypes were able to establish symbioses with polyps in both temperature treatments. Survivorship of polyps at 30{degrees}C was significantly lower than survivorship at 26{degrees}C, but all treatments had surviving polyps at 56 days post-infection, suggestive of broad thermal tolerance in B. antillogorgium, which may play a part in the increased resilience of Caribbean octocorals during heat stress events.

evolutionary biology↗