A palaeogenomic 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 centuries. 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 and historical 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 followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already 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.

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

Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the 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 recolonizations 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 recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized 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 recolonization 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.

Rapid localization of bone fragments on surfaces using back-projection and hyperspectral imaging.

Manual localization of bone fragments on the ground or on complex surfaces in relation to accidents or criminal activity may be time-consuming and challenging. It is here investigated whether combining a near-infrared hyperspectral camera and chemometric modeling with false color back-projection can be used for rapid localization of bone fragments. The approach is noninvasive and highlights the spatial distribution of various compounds/properties to facilitate manual inspection of surfaces. Discriminant partial least squares regression is used to classify between bone and nonbone spectra from the hyperspectral camera. A predictive model (>95% prediction ability) is constructed from raw chicken bones mixed with stone, sand, leaves, moss, and wood. The model uses features in the near-infrared spectrum which may be selective for bones in general and is able to identify a wide variety of bones from different animals and contexts, including aged and weathered bone.

Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA.

BACKGROUND: Red deer (Cervus elaphus) have been an important human resource for millennia, experiencing intensive human influence through habitat alterations, hunting and translocation of animals. In this study we investigate a time series of ancient and contemporary DNA from Norwegian red deer spanning about 7,000 years. Our main aim was to investigate how increasing agricultural land use, hunting pressure and possibly human mediated translocation of animals have affected the genetic diversity on a long-term scale. RESULTS: We obtained mtDNA (D-loop) sequences from 73 ancient specimens. These show higher genetic diversity in ancient compared to extant samples, with the highest diversity preceding the onset of agricultural intensification in the Early Iron Age. Using standard diversity indices, Bayesian skyline plot and approximate Bayesian computation, we detected a population reduction which was more prolonged than, but not as severe as, historic documents indicate. There are signs of substantial changes in haplotype frequencies primarily due to loss of haplotypes through genetic drift. There is no indication of human mediated translocations into the Norwegian population. All the Norwegian sequences show a western European origin, from which the Norwegian lineage diverged approximately 15,000 years ago. CONCLUSIONS: Our results provide direct insight into the effects of increasing habitat fragmentation and human hunting pressure on genetic diversity and structure of red deer populations. They also shed light on the northward post-glacial colonisation process of red deer in Europe and suggest increased precision in inferring past demographic events when including both ancient and contemporary DNA.