52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms.

The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.

Elucidating the sustainability of 700 y of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada.

Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remain unknown. Here, we integrate paleogenomics, genetic simulations, and stable δ13C and δ15N isotope analysis to investigate 700 y of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which is based on radiocarbon dating, span three time periods (1290 to 1440 CE; 1450 to 1650 CE; 1800 to 1870 CE), indicates shifts across time in the sex ratio of the harvested belugas. The equal number of females and males harvested in 1450 to 1650 CE versus more males harvested in the two other time periods may reflect changes in hunting practices or temporal shifts in beluga availability. We find temporal shifts and sex-based differences in δ13C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. We uncovered distinct mitochondrial diversity unique to the Mackenzie Delta belugas, but found no changes in nuclear genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 y surveyed, indicating the impact of Inuvialuit subsistence harvests on the genetic diversity of contemporary beluga individuals has been negligible.

The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations.

The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent.

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.