Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.03.14.643328

Genomic resources for curimba Prochilodus lineatus reveal a fractal pattern of hierarchical genetic population structure in mixed stocks across fish segregated by dams.

Yazbeck, G. M.·Nascimento, G. A. S.·Carvalho, L. C.·Graciano, R. C. D.·Santos, R.·Oliveira, R. S.
View original source ↗Export metadata ↓

Abstract

Genomic resources, new microsatellite markers and a novel observation of a fractal pattern of the genetic population structure are presented for curimba Prochilodus lineatus, a suitable model organism for freshwater migratory species in South America. Our main goals were to investigate the presence of mixed fish stocks, the effects of isolation by dams and broodstocking over the genetic diversity for this species. We focused on the upper segment of the extremely fragmented Grande River, MG, Brazil, from the megadiverse continental La Plata Basin. Two main co-occurring genetically admixed stocks were identified by maximum likelihood estimation and iteratively unfolded with two further steps, through a hierarchical analysis of genetic structure. It consistently unveiled two newly defined internal groups, from the previously resolved clusters (23). We suggest this stratified pattern of mixed stocks from the main river channel may be attributed to the existence of different, well defined breeding grounds, nested within differential scales throughout this basin, arranged according to fractal geometry (1st order river, 2nd and 3rd order tributaries, and so on). This would imply in homing behaviour for this species. Our work also provides massive molecular data for this fish, including its first draft genome assembly and a valuable panel for the rapid and low-cost development of new microsatellite DNA markers. These findings will likely benefit researchers and environmental managers in tackling challenging issues regarding the conservation of Neotropical migratory fishes, as they support the hypothesis of the isolating effects of dams and broodstocking over genetic variability. More importantly, the results presented here point to the potential role of tributaries of different orders in harbouring genetically diverse populations of migratory freshwater fishes.

Source connections

Explore related subjects

geneticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Yazbeck, G. M., Nascimento, G. A. S., Carvalho, L. C., Graciano, R. C. D., Santos, R., Oliveira, R. S.. 2025-03-17. Genomic resources for curimba Prochilodus lineatus reveal a fractal pattern of hierarchical genetic population structure in mixed stocks across fish segregated by dams.. https://doi.org/10.1101/2025.03.14.643328

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Generation of a transgenic cephalopod

Coleoid cephalopods (cuttlefish, octopus, and squid) are marine mollusks with elaborate nervous systems that support a diverse repertoire of complex behaviors. These include the neural control of the color, pattern, and texture of the skin, facilitating both adaptive camouflage and innate patterning that may reflect internal state. The development of transgenic cephalopods expressing fluorescent proteins, optogenetic actuators, and reporters of neural activity would contribute a new and important technology to cephalopod biology. The generation of transgenic cephalopods, however, has remained a major challenge. Here, we report the development of stable transgenic dwarf cuttlefish (Ascarosepion bandense) expressing ubiquitous nuclear-localized mScarlet, a red fluorescent protein. We evaluated multiple strategies for transgenesis, and established cuttlefish lines using both CRISPR and the transposons Sleeping Beauty and Minos. The stable expression of transgenes enabled live imaging of cell dynamics during embryonic development. The Minos transposon emerged as the most efficient transgenesis strategy and is adaptable to promoters and transgenes of choice. These strategies now enable the generation of diverse genetic tools for mechanistic studies of cephalopod biology.

genetics↗
bioRxiv2026

Large language model-based bibliometric evaluation of population descriptors in human genetics

As the use of population descriptors such as race, ethnicity, and ancestry have become increasingly common in modern genetics research, there have been growing calls to critically examine their use. Most notably, in 2023, the National Academies of Science, Engineering, and Medicine (NASEM) published a report titled Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field, which included eight specific and actionable recommendations for researchers to implement the ethical and accurate use of population descriptors in genetic research. Here, we use the 2023 NASEM report as a benchmark to analyze the use of population descriptors in genome-wide association studies (GWAS). We develop a general toolkit for large language model-based bibliometrics, operationalize the report's recommendations into an evaluation framework, and apply this framework to evaluate all 4,007 papers from the GWAS Catalog published between 2007 and 2025 with full text available on PubMedCentral. We find significant improvements in adherence to NASEM report recommendations over time. However, most improvements predate the publication of the NASEM report itself, suggesting the report functioned primarily as a synthesis of existing best practices rather than a catalyst for change. We conclude by highlighting opportunities for growth in the field of human genetics.

genetics↗
bioRxiv2026

Mitigating biases of rescaling in forward-in-time population genetic simulations

Forward-in-time population genetic simulations are widely used in evolutionary analyses, but simulating large populations and long genomic regions remains computationally demanding. To reduce this cost, parameter rescaling is widely employed, in which the original evolutionary process is approximated by one with a smaller population size and fewer generations. Recently, several studies using the SLiM simulator have raised concerns about the accuracy of this rescaling approach. In this study, we show that many of the biases reported in these studies can be mitigated by using a different simulation algorithm. These results reveal that the accuracy of parameter rescaling depends on how well the simulation algorithm preserves diffusion-limit properties under rescaling.

genetics↗