bioRxiv Science⌕ Search

bioRxiv · 10.64898/2025.12.10.693505

TWO STEPS AWAY FROM EXTINCTION: DO YOU BELIEVE?

Abstract

Forest fragmentation can have detrimental effects on plant populations, reducing population sizes and depleting genetic diversity, as a consequence. As a matter of urgency, it is crucial to assess the effects of forest fragmentation on genetics and ecological processes, particularly for threatened species on the brink of extinction. Here, we examined the responses of Dinizia jueirana-facao G. P. Lewis & G. S. Siqueira (Fabaceae, Caesalpinioideae) - a rare and critically endangered tree species endemic to the Brazilian Atlantic Forest-, to forest fragmentation. Based on theoretical predictions for barochory plant species with small population sizes, we hypothesized that forest fragmentation would reduce gene flow, erode genetic diversity, and negatively impact demography. Using neutral SNPs (Single Nucleotide Polymorphisms) derived from ddRADSeq (double-digest restriction site-associated DNA sequencing), we found that pollen dispersal occurred within short distances, with the majority of outcrossed pollination events occurring locally. Furthermore, contemporary estimates of gene dispersal distances were lower than historical ones, indicating a seasonal shift in the scale of gene flow due to recent forest fragmentation. Our results also indicated no evidence of inbreeding and loss of genetic diversity. In terms of ecological process, the demographic structure of fragmented populations of D. jueirana-facao followed a reverse J-shaped size class distribution, with more than 45% of plants found in small diameter classes. While a more in-depth understanding of ecological and evolutionary processes at fine-scale is still needed to safeguard this unique plant species, our infant study plays a crucial role to help keep the evolutionary potential of D. jueirana-facao. We stress that the approach used here would be useful to guide conservation and management efforts for species on the brink of extinction.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

de Padua, K. A. S., Teixeira, T. M., Nazareno, A. G.. 2025-12-14. TWO STEPS AWAY FROM EXTINCTION: DO YOU BELIEVE?. https://doi.org/10.64898/2025.12.10.693505

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗