Biology subjects

Camenisch, G.

Publications and source records attributed to Camenisch, G..

3 recordsLinked to original sources

bioRxiv2024

A highly contiguous reference genome for the Alpine ibex (Capra ibex)

Species conservation efforts can be threatened by deleterious mutation accumulation following population contractions. In addition to de novo mutations, a significant source of genetic load could be deleterious variants introduced into a population through hybridization. Hence, even successfully restored species may face deleterious mutation swamping due to hybridization with an abundant and closely related species. The outcomes of such hybridization events are poorly understood given the complex interplay of introduced adaptive and maladaptive variation. Here, we analyze this potential risk for Alpine ibex (Capra ibex), a flagship species of large mammal restoration in the Alps. Near-extinction two centuries ago resulted in exceptionally low genome-wide diversity and increased inbreeding, which facilitated the purging of severe deleterious mutations but accumulation of less severe ones. We produced a highly contiguous chromosome-level genome assembly of the Alpine ibex capturing structural divergence from its closest domestic species, the domestic goat (Capra hircus) known to hybridize with Alpine ibex Genome sequencing of eight recent ibex-goat hybrids and backcrosses from two hybrid swarms in Northern Italy revealed highly diverse recombinants and an average of 30 masked, predicted loss-of-function (LOF) mutations per hybrid compared to 10 in non-hybrid Alpine ibex. This exposes Alpine ibex to further backcrosses, exposing their vulnerable gene pool to an influx of hybridization load. Individual-based genomic simulations suggest that such LOF load would return to pre- hybridization levels with a lag of over 100 generations after gene flow subsides. Hybridization could also disrupt local adaptation in the recipient species. Our work provides a direct estimate of hybridization load and, by this, informs on the complexity of managing endangered gene pools in the face of hybridization.

evolutionary biology↗

bioRxiv2023

Morphometry and mechanical instability at the onset of epithelial bladder cancer

Malignancies of epithelial tissues, called carcinomas, account for the majority of cancer cases. Much cancer research has focused on genetic alterations and their relation to different carcinoma phenotypes. Besides a rewiring in the signalling networks, carcinoma progression is accompanied by mechanical changes in the epithelial cells and the extracellular matrix. Here, we reveal intricate morphologies in the basement membrane at the onset of bladder cancer, and propose that they emerge from a mechanical buckling instability upon epithelial overgrowth. Using a combination of microscopy imaging of the mouse and human bladder tissue, elasticity theory, and numerical simulations of differential growth in the bladder mucosa, we find that aberrant tissue morphologies can emerge through stiffness changes in the different mucosa layers. The resulting thickening, wrinkles and folds exhibit qualitative and quantitative similarity with imaged early papillary tumors and carcinomas in situ. Atomic force microscopy indeed reveals local stiffness changes in the pathological basement membrane. Our findings suggest a mechanical origin of the different carcinoma subtypes in the bladder, which have vastly different clinical prognosis. They might provide the basis for a new line of attack in medical carcinoma treatment and prophylaxis.

cancer biology↗

bioRxiv2020

A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics

Genetic variation is a major factor determining susceptibility to diseases. Polymorphism at the major histocompatibility complex (MHC) and other immune function loci can underlie health and reproductive success of individuals. Endangered species of low population size could be severely compromised to evolve disease resistance due to reduced adaptive variation. A major impediment to screen adaptive genetic variation in wild species is the difficulty to comprehensively genotype immune-related loci based on low input material. Here, we design and validate a targeted amplicon sequencing assay to parallelize the analysis of a thousand loci of the MHC, other immunity-related genes, and genome-wide markers for the assessment of population structure. We apply the approach to Alpine ibex, one of the most successful examples of restoration of a large mammal in Europe. We used 51 whole genome sequenced individuals to select representative target SNPs. We integrated SNP call data from four related species for amplification robustness and genotyped 158 Alpine ibex individuals for validation. We show that the genome-wide markers perform equally well at resolving population structure as RAD-seq or low-coverage genome sequencing datasets with orders of magnitude more markers. The targeted amplicon sequencing assay is robust to >100-fold variation in input DNA quantity and generates useful genotype information from fecal samples. The amplicon marker set also identified recent species hybridization events with domestic goats. The immune loci show unexpectedly high degrees of differentiation within the species. Our assay strategy can realistically be implemented into population genetic surveys of a large range of species.

genomics↗