Biology subjects

Burnett, H. A.

Publications and source records attributed to Burnett, H. A..

4 recordsLinked to original sources

bioRxiv2025

How Accurate is Genomic Prediction Across Wild Populations?

Evolutionary ecology seeks to understand causes and consequences of evolutionary changes across time and space, and genomic data present novel opportunities to investigate these processes. Genomic prediction - that is, predicting individual genetic values from high-density marker data - has revolutionized breeding programs and medical genetics. In wild populations, however, genomic prediction has been used in only a handful of studies, and only within populations. There is still a lack of applications that predict across wild populations, which could provide answers to questions related to spatially varying evolutionary processes, such as local adaptation. A severe challenge for across-population genomic prediction, however, is the decrease in accuracy when models are trained on data from one population and predict genetic values in another. Here, we used genomic prediction to predict across wild house sparrow populations, and compared the accuracy to within-population prediction. Predictions across populations were less accurate and more variable than within populations. We also highlighted limitations of the current theory for general genomic prediction accuracy, and related across-population accuracy to several population differentiation measures. Our results underline the necessity of understanding why genomic prediction currently performs poorly across populations, and of developing methods that exploit genomic data in novel ways.

evolutionary biology↗

bioRxiv2024

Rapid loss of genetic variation and increased inbreeding in small and isolated populations of Norwegian wild reindeer

Wildlife responses to habitat loss and fragmentation are a central concern in the management and conservation of biodiversity. Small and isolated populations are vulnerable, both due to demographic and genetic mechanisms, which are often linked. Thus, understanding how (changes in) genetic diversity, effective population sizes, and levels of inbreeding relate to population size and degree of isolation is key for developing effective conservation strategies. High-density Single Nucleotide Polymorphism (SNP) arrays represent an increasingly cost-efficient tool to achieve the data needed for such analysis. Here, we present the development of a novel 625k SNP array for reindeer Rangifer tarandus and apply this array to assess conservation genetic issues across thirteen Norwegian wild reindeer populations of varying size, isolation, and genetic origin (i.e., semi-domesticated reindeer origin or a mix of wild reindeer and semi-domesticated reindeer origins). Many of these populations are currently completely isolated, with no gene flow from other populations. We genotyped n = 510 individuals sampled by hunters and found that variation in population size across the populations largely predicted their (recent loss of) genetic variation (observed heterozygosity, Ho), as well as effective population size (Ne) and (change in) level of recent inbreeding. For the smallest and most isolated populations, with total population sizes of <50-100 individuals and a high and increasing level of recent inbreeding, estimated loss of genetic variation was as high as 3-10% over the time span of a generation or less, and estimated Ne was as low as six individuals. With the current level of isolation and associated lack of gene flow, and considering their already low genetic diversity, these populations are hardly viable - neither demographically nor genetically - in the long term. These results have direct relevance for the management of Norwegian wild reindeer, recently red-listed as Near Threatened. Yet, these genetic challenges, characterizing many of the small wild reindeer populations in Norway, have been largely ignored by management thus far. Mitigation efforts such as reducing barriers would introduce substantial conservation dilemma due to the aim of avoiding further spread of chronic wasting disease (CWD), as well as potential further domestic introgression into populations with genetically wild reindeer (or mixed) origin. Nevertheless, our cost-efficient and high-density SNP array especially designed for reindeer and caribou offers a powerful genetic tool to include in future monitoring, providing important contributions to management and conservation decisions.

genetics↗

bioRxiv2023

A paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies

Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-Arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th century. Here we investigate changes in genetic diversity, population structure and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90), to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation and 400 years of genetic drift have altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long- term interplay of past, current, and future stressors in wildlife conservation.

genomics↗

bioRxiv2022

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer

Anthropogenic reintroduction can supplement natural recolonisation in reestablishing a species distribution and abundance. However, both reintroductions and recolonisations can give rise to population bottlenecks that reduce genetic diversity and increase inbreeding, potentially causing accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonisations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonised populations without admixture possessed much lower heterozygosity, higher inbreeding, and longer runs of homozygosity, possibly caused by serial population bottlenecks and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonised populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonisation in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.

genomics↗