• Energy Research

Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears (Ursus maritimus) into Alaskan brown bears (Ursus arctos), with some analyses suggesting a link between climate change and genomic introgression. However, because it has mainly been possible to sample bears from the present day, the timing, frequency, and evolutionary significance of this admixture remains unknown. Here, we analyze genomic DNA from three additional and geographically distinct brown bear populations, including two that lived temporally close to the peak of the last ice age. We find evidence of admixture in all three populations, suggesting that admixture between these species has been common in their recent evolutionary history. In addition, analyses of ten fossil bears from the now-extinct Irish population indicate that admixture peaked during the last ice age, whereas brown bear and polar bear ranges overlapped. Following this peak, the proportion of polar bear ancestry in Irish brown bears declined rapidly until their extinction. Our results support a model in which ice age climate change created geographically widespread conditions conducive to admixture between polar bears and brown bears, as is again occurring today. We postulate that this model will be informative for many admixing species pairs impacted by climate change. Our results highlight the power of paleogenomics to reveal patterns of evolutionary change that are otherwise masked in contemporary data.

Disentangling the effects of glaciers and climate on vegetation is complicated by the confounding role that climate plays in both systems. We reconstructed changes in vegetation occurring over the Holocene at Jøkelvatnet, a lake located directly downstream from the Langfjordjøkel glacier in northern Norway. We used a sedimentary ancient DNA (sedaDNA) metabarcoding dataset of 38 samples from a lake sediment core spanning 10,400 years using primers targeting the P6 loop of the trnL (UAA) intron. A total of 193 plant taxa were identified revealing a pattern of continually increasing richness over the time period. Vegetation surveys conducted around Jøkelvatnet show a high concordance with the taxa identified through sedaDNA metabarcoding. We identified four distinct vegetation assemblage zones with transitions at ca. 9.7, 8.4 and 4.3 ka with the first and last mirroring climatic shifts recorded by the Langfjordjøkel glacier. Soil disturbance trait values of the vegetation increased with glacial activity, suggesting that the glacier had a direct impact on plants growing in the catchment. Temperature optimum and moisture trait values correlated with both glacial activity and reconstructed climatic variables showing direct and indirect effects of climate change on the vegetation. In contrast to other catchments without an active glacier, the vegetation at Jøkelvatnet has displayed an increased sensitivity to climate change throughout the Middle and Late Holocene. Beyond the direct impact of climate change on arctic and alpine vegetation, our results suggest the ongoing disappearance of glaciers will have an additional effect on plant communities.

Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In this study, we sequenced two woolly mammoth genomes and combined these with previously sequenced mammoth and elephant genomes to conduct a survey of mammoth-specific deletions and indels. We find that deletions are highly enriched in non-coding regions, suggesting selection against structural variants that affect protein sequences. Nonetheless, at least 87 woolly mammoth genes contain deletions or indels that modify the coding sequence, including genes involved in skeletal morphology and hair growth. These results suggest that deletions and indels contributed to the unique phenotypic adaptations of the woolly mammoth, and were potentially critical to surviving in its natural environment.

Abstract In the face of human land use and climate dynamics, it is essential to know the key drivers of plant species diversity in montane regions. However, the relative roles of climate and ungulates in alpine ecosystem change is an open question. Neither observational data nor traditional palaeoecological data have the power to resolve this issue over decadal to centennial timescales, but sedimentary ancient DNA (sedaDNA) does. Here we record 603 plant taxa, as well as 5 wild, and 6 domesticated mammals from 14 lake sediment records over the last 14,000 years in the European Alps. Sheep were the first domesticated animals detected (at 5.8 ka), with cattle appearing at the early Bronze Age (4.2 ka) and goats arriving later (3.5 ka). While sheep had an impact similar to wild ungulates, cattle have been associated with increased plant diversity over the last 2 ka by promoting the diversity of forbs and graminoids. Modelling of the sedaDNA data revealed a significantly larger effect of cattle and wild ungulates than temperature on plant diversity. Our findings highlight the significant alteration of alpine vegetation and the entire ecosystem in the Alps by wild and domesticated herbivores. This study has immediate implications for the maintenance and management of high plant species diversity in the face of ongoing anthropogenic changes in the land use of montane regions.

AbstractThe European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.