Biology subjects

Grant, V.

Publications and source records attributed to Grant, V..

3 recordsLinked to original sources

bioRxiv2026

Dog-assisted scat sampling reveals genetic diversity, structure, and relatedness in black-footed cats (Felis nigripes)

Advances in molecular techniques for non-invasive genetic sampling have strengthened wildlife genetics, enabling researchers to study elusive and difficult-to-study species with minimal disturbance, and conservation detection dogs can greatly increase sample numbers and the area covered. However, this combination is rarely used in Africa and has perhaps never been applied to a small carnivore on the continent. Here we use dog-assisted scat surveys to carry out the first fine-scale population genetic study of the black-footed cat (Felis nigripes), Africa's smallest and most range-restricted endemic felid, and a threatened species for which conventional survey methods are largely ineffective. Using 130 successfully genotyped scat samples (nine microsatellite loci) from two populations about 650 km apart, we identified 65 individuals and assessed genetic diversity and fine-scale relatedness to explore aspects of dispersal and reproductive ecology. Both populations exhibited similar observed heterozygosity (Ho = 0.67-0.69) and allelic richness, with no heterozygote deficit (FIS = -0.02 to -0.08). Differentiation between the southern Namibia and central South Africa sites was low but detectable (FST = 0.03-0.05). We used pairwise relatedness and candidate pedigree results to explore hypotheses about sex-specific relatedness patterns. Female-female dyads were more related than male-male dyads at the shortest distance class (0-2 km), a pattern compatible with female philopatry. There were more half-sibling than full-sibling assignments and uneven representation of candidate fathers, which may indicate polygamy and reproductive skew. These results provide baseline genetic data for a Vulnerable species and show that this approach is feasible for Africa's small, elusive carnivores, whose dispersal, mating systems and population structure remain largely unknown. Broader spatial and temporal sampling could help assess population connectivity and reveal how threats and changing land use impact genetic diversity and structure.

ecology↗

bioRxiv2022

Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering

Extrachromosomal DNA (ecDNA) are frequently observed in human cancers and are responsible for high levels of oncogene expression. In glioblastoma (GBM), ecDNA copy number correlates with poor prognosis. It is hypothesized that their copy number, size and chromatin accessibility facilitate clustering of ecDNA and colocalization with transcriptional condensates, and that this underpins their elevated transcriptional activity. Here, we use super-resolution imaging and quantitative image analysis to evaluate GBM stem cells harboring distinct ecDNA species (EGFR, MYC, PDGFR). We found no evidence that ecDNA cluster with one another or closely interact with transcriptional condensates. Cells with EGFR-containing ecDNA have increased EGFR transcriptional output, but transcription per gene copy was similar in ecDNA compared to the endogenous chromosomal locus. These data suggest that is the increased copy number of oncogene-harbouring ecDNA that primarily drives high levels of oncogene transcription, rather than specific interactions of ecDNA with the cellular transcriptional machinery.

genetics↗

bioRxiv2021

Genomic insights into variation in thermotolerance between hybridizing swordtail fishes

Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.

evolutionary biology↗