Biology subjects

Fleck, S. J.

Publications and source records attributed to Fleck, S. J..

4 recordsLinked to original sources

bioRxiv2026

A Lake Charr Pangenome Reveals Highly Conserved Ohnologs as Drivers of Phenotypic Diversity

Whole-genome duplication (WGD) is hypothesized to spur evolutionary diversification by producing genome-wide duplicate gene sets (Ohnologs) that are initially functionally redundant but can diverge markedly as the effects of relaxed selection accumulate over time. However, the underlying mechanisms remain unclear, in part because genomic studies often reconstruct Ohnolog evolution over millions of years, during which subsequent mutations can obscure deep-time signals. Investigating the relationship between Ohnolog evolution and diversification on a contemporary timescale offers clearer insights. We explore this relationship in Lake Charr (Salvelinus namaycush), where [~]10% of genes are retained highly conserved polyploid duplicates following the Salmonid-Specific Fourth Round WGD. Using 31 chromosome-level assemblies of Lake Charr from morphologically and ecologically diverse populations, joined into a pangenome graph, we characterized 189,555 structural variants (SVs) that were significantly less likely to affect genes retained as sequence-conserved Ohnolog pairs, nuancing the hypothesis that gene redundancy, relaxed selection, and functional diversification are intertwined. However, we found that SVs affecting such conserved Ohnologs may be potent drivers of adaptive evolution. Notably, we identified a putative 938-Kb interchromosomal translocation containing 25 genes with highly conserved Ohnologs in a paralogous (but untranslocated) genomic block. This putative translocation appears to have facilitated Ohnolog divergence in ankrd11 and hp, genes putatively linked to craniofacial and lipid metabolic diversity in sympatric Lake Superior morphs. This research reveals that conserved Ohnologs previously presumed to be redundant remain a reservoir for adaptive change.

genomics↗

bioRxiv2026

Genomic Structural Variation Rescues a Classic Biological Invader from a Population Bottleneck

Invasion genetics presents a classic paradox: how do species successfully spread despite severe population bottlenecks? The brown treesnake (Boiga irregularis) in Guam represents a striking example of this phenomenon, having been introduced with only a handful of individuals. We show that the population endured an extreme bottleneck, with roughly half of the genome exhibiting runs of homozygosity, comparable to species of conservation concern. Despite this, we uncovered extensive diversity in the form of nearly 19,000 genomic structural variants, which affect almost eight times more of the genome than single-nucleotide variants and provide material for rescuing the population from inbreeding-driven declines. Structural variant density was highest in gene promoters, where recombination and DNA repair often occur, providing a mechanism for rapid evolution of gene-linked diversity. This diversity is enriched in genes vital for adaptive immunity and olfaction, suggesting genomic diversity in key chromosomal regions can rescue populations from inbreeding. This work has critical implications for invasion biology and conservation genetics practitioners. TEASERGenomic structural variants rescue a textbook biological invader from a population bottleneck and inbreeding

genomics↗

bioRxiv2025

Genomic Insights into the Evolution of Carnivory in the Giant Butterwort, Pinguicula gigantea: Chromosome-Level Assembly and Phylogenomic Analysis

Carnivorous plants provide a powerful system for studying plant morphological and physiological evolution. These plants capture and digest prey for nutrients and this rare trait has evolved independently at least eleven times in thirteen families within six orders. Among these are the butterworts in the genus Pinguicula. This group of plants captures prey on a basal rosette of sticky leaves where the prey is broken down and digested. Here we present the chromosome-level reference assembly of the carnivorous giant butterwort, Pinguicula gigantea. An additional two assemblies were generated for this study, primarily from long-read sequencing data. In this study, we focus on the genome evolution of Pinguicula, including confirming at least two whole genome duplications since the gamma hexaploidy event at the base of the core eudicots. We provide evidence from full-genome data that the carnivorous family that Pinguicula belongs to, the Lentibulariaceae, is most closely related to the Acanthaceae. We also report multiple tandem duplications of candidate digestive enzyme genes, including a putative tandem duplication of cysteine proteases that is syntenic with two cysteine protease tandem duplication in Utricularia gibba that contain genes with trap specific expression. We also show evidence that these tandem duplications evolved independently in both Pinguicula and Utricularia gibbaUtricularia gibba and were potentially facilitated by different repeat element families.

genomics↗

bioRxiv2025

Ancient gene clusters initiate monoterpene indole alkaloid biosynthesis and C-3 stereochemistry inversion

The inversion of C3 stereochemistry in monoterpenoid indole alkaloids (MIAs), derived from the central precursor strictosidine (3S), is a critical step for the biosynthesis of numerous 3R MIAs and spirooxindoles, including the antihypertensive drug reserpine. While early MIA biosynthesis preserves the 3S configuration, the mechanism underlying C3 inversion has remained unresolved. Here, we identify and biochemically characterize a conserved oxidase-reductase pair in the Gentianales order: the heteroyohimbine/yohimbine/corynanthe C3-oxidase (HYC3O) and C3-reductase (HYC3R), which together invert the 3S stereochemistry to 3R across diverse substrates. Notably, HYC3O and HYC3R reside in gene clusters in Rauvolfia tetraphylla and Catharanthus roseus, homologous to an elusive geissoschizine synthase (GS) cluster we also uncovered. In R. tetraphylla, these clusters are in tandem on a single chromosome, likely derived from segmental duplication, whereas in C. roseus they reside on separate chromosomes due to translocation. Comparative genomics indicate the GS cluster originated at the base of Gentianales ([~]135 Mya), coinciding with the evolution of the strictosidine synthase cluster, while the reserpine cluster arose later in rauvolfioid Apocynaceae. Together, these findings uncover the genomic and biochemical basis for key events in MIA evolution and diversification, providing insights beyond the canonical vinblastine and ajmaline biosynthetic pathways.

biochemistry↗