2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
April 2nd, 2025
Version: 1
Swiss Federal Institute of Aquatic Science and Technology (Eawag)
genomics
biorxiv

Beyond genetic indicators: how reproductive mode and hybridization challenge freshwater mussel conservation

Faust, E.Open in Google Scholar•Conrads, J.Open in Google Scholar•Giulio, M.Open in Google Scholar•Ciofi, C.Open in Google Scholar•Natali, C.Open in Google Scholar•Feulner, P. G.Open in Google Scholar•Weber, A. A.-T.Open in Google Scholar

Genetic diversity is a fundamental component of biodiversity that should be monitored and preserved. Unionid freshwater mussels provide essential ecosystem services but are among the most imperilled aquatic organisms worldwide. Here, we assess key genetic Essential Biodiversity Variables (EBVs) - genetic diversity, genetic differentiation, inbreeding, and effective population size - in all Anodonta species in Switzerland. After generating draft genomes for Anodonta cygnea and Anodonta anatina, we performed whole-genome resequencing of 421 individuals (243 A. anatina, 151 A. cygnea, 17 A. exulcerata and 10 Anodonta sp.) from 31 populations. While A. anatina populations followed a metapopulation structure shaped by catchment areas, genetic diversity correlated positively with waterbody size, suggesting greater vulnerability in small ponds compared with large lakes. Inbreeding levels were low, however effective population sizes were consistently below 100, indicating serious extinction risks. We also detected hybridization between A. cygnea and A. exulcerata, indicating genomic permeability between these species. Furthermore, genomic data suggested facultative selfing in A. cygnea, leading to a marked reduction in genetic diversity, increased population structure and inbreeding, and a decline in effective population size compared to the outcrossing A. anatina, emphasizing that A. cygnea faces a particularly high risk of extinction due to its reproductive strategy. Our study reveals the vulnerability of freshwater mussels and emphasizes the need for genetic indicators to reflect species-specific reproductive strategies. More broadly, it calls for conservation policies to integrate genetic monitoring and consider reproductive modes to tailor conservation efforts and better assess extinction risks.

Similar Papers

biorxiv
Thu Apr 03 2025
Trypanosoma cruzi Has 32 Chromosomes: A Telomere-to-Telomere Assembly Defines Its Karyotype.
Trypanosoma cruzi, the causative agent of Chagas disease, exhibits remarkable genomic plasticity and possesses an expanded genome rich in multigene families. However, its precise chromosomal composition has remained elusive due to challenges in resolving repetitive regions. Using PacBio HiFi long-read sequencing, we assembled the complete nuclear genome of the Dm28c strain into 32 telomere-to-telo...
Greif, G.
•
Diaz-Viraque, F.
•
Chiribao, M. L.
•
Sanz-Rodriguez, C.
•
Robello, C.
biorxiv
Thu Apr 03 2025
Improving interpretability of transcription factor binding models with DNA shape features
Deep learning models in genomics that predict molecular phenotypes from DNA sequence traditionally focus on one-hot encoded representations. Here, we develop a novel model that extends this approach by incorporating DNA structural attributes indicative of local shape alongside canonical sequence inputs. This augmentation provides an additional axis for model interpretability and aids in identifyin...
Keivanfar, R. L.
•
Yang, F.
•
Pollard, K. S.
•
Ioannidis, N. M.
biorxiv
Thu Apr 03 2025
Expression spectrum of TE-derived transcripts in human adult tissues
Abstract Transposable elements (TEs) are vital components of eukaryotic genomes and have played a critical role in genome evolution. Although most TEs are silenced in the mammalian genome, increasing evidence suggests that certain TEs are actively involved in gene regulation during early developmental stages. However, the extent to which human TEs drive gene transcription in adult tissues remains ...
Miao, B.
•
Zhang, B.
•
WU, T. P.
•
Luo, X.
...•
Yang, Y.
biorxiv
Thu Apr 03 2025
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species
Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at deciphering sequence features and grammar that underlie their spatiotemporal activity. To enable end-to-end enhancer modeling and design, we developed a software and modeling package, called CREsted. It combi...
Kempynck, N.
•
De Winter, S.
•
Blaauw, C. H.
•
Konstantakos, V.
...•
Aerts, S.
biorxiv
Thu Apr 03 2025
Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones
Structural variation is increasingly recognized as a pivotal contributor to genomic diversity in marine invertebrates, yet its extent and evolutionary significance remain poorly characterized in many species. Haplotype-phased genome assembly is an excellent method for studying such variations by comparing homologous chromosomes. In this study, we constructed a haplotype-phased genome assembly for ...
Hirase, S.
•
Makino, T.
•
Takeuchi, T.
•
Kadota, M.
...•
Kikuchi, K.
biorxiv
Thu Apr 03 2025
Entry and exit of Fragilariopsis cylindrus diatoms from the polar night: evidence for chromatin-mediated genome control
Regulation of the epigenome landscape plays a crucial role in adaptation to environmental changes. However, the molecular mechanisms by which epigenome landscapes are established and tuned to adjust the cellular status to environmental cues remain poorly understood, especially in unicellular photosynthetic eukaryotes. Polar microalgae must adapt to extreme variations in light and temperature for s...
Joli, N.
•
Bourbousse, C.
•
Leduque, B.
•
Tirichine Delacour, L.
...•
Bowler, C.
biorxiv
Thu Apr 03 2025
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus
Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates treatment of S. aureus infections. Understanding S. aureus population structure and the distribution of genetic lineages is central to understanding the biology, epidemiology, and pathogenesis of this organism. This study exploited a large, publicly available dataset of ...
Hadjirin, N. F.
•
Yassine, I.
•
Bray, J. E.
•
Maiden, M. C. J.
...•
Brueggemann, A. B.
biorxiv
Thu Apr 03 2025
Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature
Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to identify N. gonorrhoeae lineages in a consistent manner is essential for surveillance of this increasingly antimicrobial resistant organism, and to facilitate efficient...
Unitt, A.
•
Krisna, M. A.
•
Parfitt, K. M.
•
Jolley, K. A.
...•
Harrison, O. B.
biorxiv
Wed Apr 02 2025
UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions
Interactions between enhancers and gene promoters provide insights into gene regulation. Experimental techniques, including Hi-C, that map these enhancer-promoter interactions (EPIs), have high costs and labor requirements, which limits their use. Therefore, in silico methods have been developed to predict EPIs computationally, but there are challenges with the generalizability and accuracy of exi...
Grover, A.
•
Zhang, L.
•
Muser, T.
•
Häfliger, S.
...•
Boeva, V.
biorxiv
Wed Apr 02 2025
Response to Tabin et al-Concerns about ancient DNA sequences reported from a Late Pleistocene individual from Southeast Asia
Tabin et al suspect a high error rate and abnormal error content in the MZR genome data from our published study, from which they raised concerns about the reliability and useability of our published sequences. Given the poor environmental conditions (such as warm climate and acidic soil in the low latitude area of Southwest China), as well as the non-ideal fossil material (cranium) for DNA extrac...
Zhang, X.
•
He, Y.
•
Ji, X.
•
Su, B.