2025 Hyper Recent •CC0 1.0 Universal

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

Access Preprint From Server
April 1st, 2025
Version: 1
Indian Institute of Science Education and Research, Bhopal
genomics
biorxiv

Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss

Salve, B. G.Open in Google Scholar•Vijay, N.Open in Google Scholar

Gene loss shapes lineage-specific traits but is often overlooked in species survival. In this study, we investigate the role of ancestral gene loss using the extinction icon-thylacine (Thylacinus cynocephalus). While studies of neutral genetic variation indicate a population decline before extinction, the impact of thylacine-specific ancestral gene losses remains unexplored. The availability of a chromosomal-level genome of the extinct thylacine offers a unique opportunity for such comparative studies. Here, we leverage palaeogenomic data to compare gene presence/absence patterns between the Tasmanian devil and thylacine. We discovered ancestral (an interval of 13-1 Ma) loss of SAMD9L, HSD17B13, CUZD1 and VWA7 due to multiple gene-inactivating mutations, corroborated by short-read sequencing. The timing of gene loss mirrors the thylacine\'s shift toward hypercarnivory and increased body size. Our genome-wide analysis reveals olfactory receptor loss and relaxed selection, aligning with reduced olfactory lobes in the thylacine, indicating olfaction is not its primary hunting sense. By integrating palaeogenomic data with comparative genomics, our study sheds light on ancestral gene losses and their impact on species fitness while providing a foundation for selecting candidate species and genes for thylacine de-extinction. Our approach can be extended to other extinct/endangered species, helping to identify genetic factors for de-extinction efforts.

Similar Papers

biorxiv
Wed Apr 02 2025
Protocol for Extracting Circulating Cell-Free DNA from Murine Saliva: Insights into Oral and Systemic Disease Research
Circulating cell-free DNA (cfDNA) consists of small fragments of extracellular DNA from mammalian and bacterial cells found in bodily fluids such as blood and saliva, and it has been strongly recognized as a critical biomarker for various disease diagnoses, prognoses, and therapeutic monitoring. In this study, we present a reproducible protocol for efficiently isolating cfDNA from murine saliva us...
Elamin, I.
•
Rao, M. S.
•
Figliozzi, R. W.
•
Maahs, J. C.
...•
Fan, J.
biorxiv
Wed Apr 02 2025
Machine learning-predicted chromatin organization landscape across pediatric tumors
Structural variants (SVs) are increasingly recognized as important contributors to oncogenesis through their effects on 3D genome folding. Recent advances in whole-genome sequencing have enabled large-scale profiling of SVs across diverse tumors, yet experimental characterization of their individual impact on genome folding remains infeasible. Here, we leveraged a convolutional neural network, Aki...
Gjoni, K.
•
Zhang, S.
•
Yan, R. E.
•
Zhang, B.
...•
Pollard, K. S.
biorxiv
Wed Apr 02 2025
Predicting the DNA binding specificity of transcription factor mutants usingfamily-level biophysically interpretable machine learning
Sequence-specific interactions of transcription factors (TFs) with genomic DNA underlie many cellular processes. High-throughput in vitro binding assays coupled with machine learning have made it possible to accurately define such molecular recognition in a biophysically interpretable way for hundreds of TFs across many structural families, providing new avenues for predicting how the sequence pre...
Liu, S.
•
Gomez-Alcala, P.
•
Leemans, C.
•
Glassford, W. J.
...•
Bussemaker, H. J.
biorxiv
Wed Apr 02 2025
KhufuEnv, an auxiliary toolkit for building computational pipelines for plant and animal breeding
In the era of short and long read sequencing, vast amounts of DNA sequencing data are being generated. While a variety of tools exist for analyzing and manipulating genomics data, many have a finite number of tools, and thus, require users to depend on multiple sources for conducting analyses and processing data. An integrative environment of tools which is accessible to users of different computa...
Wright, H. C.
•
Davis, C. E. M.
•
Clevenger, J.
•
Korani, W.
biorxiv
Wed Apr 02 2025
A new genome assembly of the pea cultivar Cameor provides resources for functional genomics and genetics
Significant improvements in sequencing technologies have allowed the development of more contiguous genome assemblies in many plant species. The pea genome is characterized by its richness in repeated elements and its long and complex centromeres. This makes its assembly challenging. In this paper, we present an improved version of the genome sequence of the French cultivar Cameor. This sequence w...
Kreplak, J.
•
Novak, P.
•
Robledillo, L. A.
•
AUBERT, G.
...•
Burstin, J.
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.
biorxiv
Wed Apr 02 2025
Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina
Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell mu...
Yuan, Y.
•
Biswas, P.
•
Zemke, N.
•
Dang, K.
...•
Ren, B.
biorxiv
Wed Apr 02 2025
Female-biased vascular smooth muscle cell gene regulatory networks predict MYH9 as a key regulator of fibrous plaque phenotype
Atherosclerosis, a chronic inflammatory condition driving coronary artery disease (CAD), manifests in two primary plaque types: unstable atheromatous plaques and stable fibrous plaques. While significant research has focused on atheromatous plaques, recent studies emphasize the growing importance of fibrous plaques, particularly in females under 50 years of age, where erosion on fibrous plaques si...
Perry, R. N.
•
Lenert, G.
•
Benavente, E. D.
•
Ma, A.
...•
Civelek, M.
biorxiv
Wed Apr 02 2025
The information content of species: formal definitions of pangenome complexity track with bacterial lifestyle
The information content encoded in the genomes of species varies across the microbial tree of life. Bacterial lifestyle has been shown to drive this information diversity. Challenging environments are linked to information accrual. Pangenome fluidity is often invoked to provide a measure of this genomic diversity. Fluid pangenomes contain genes found only in subsets of species strains. Tighter pan...
Narechania, A.
•
Bobo, D.
•
Gilbert, T.
•
Gopalakrishnan, S.