Retreat and extinction of the Late Pleistocene cave bear (Ursus spelaeus sensu lato)

Fate and preservation of the late pleistocene cave bears from Niedźwiedzia Cave in Poland, through taphonomy, pathology, and geochemistry

This comprehensive study examines fossil remains from Niedźwiedzia Cave in the Eastern Sudetes, offering detailed insights into the palaeobiology and adversities encountered by the Pleistocene cave bear Ursus spelaeus ingressus. Emphasising habitual cave use for hibernation and a primarily herbivorous diet, the findings attribute mortality to resource scarcity during hibernation and habitat fragmentation amid climate shifts. Taphonomic analysis indicates that the cave was extensively used by successive generations of bears, virtually unexposed to the impact of predators. The study also reveals that alkaline conditions developed in the cave during the post-depositional taphonomic processes. Mortality patterns, notably among juveniles, imply dwindling resources, indicative of environmental instability. Skeletal examination reveals a high incidence of forelimb fractures, indicating risks during activities like digging or confrontations. Palaeopathological evidence unveils vulnerabilities to tuberculosis, abscesses, rickets, and injuries, elucidating mobility challenges. The cave's silts exhibit a high zinc concentration, potentially derived from successive bear generations consuming zinc-rich plants. This study illuminates the lives of late cave bears, elucidating unique environmental hurdles faced near their species' end.

A 41,500 year-old decorated ivory pendant from Stajnia Cave (Poland)

Evidence of mobiliary art and body augmentation are associated with the cultural innovations introduced by Homo sapiens at the beginning of the Upper Paleolithic. Here, we report the discovery of the oldest known human-modified punctate ornament, a decorated ivory pendant from the Paleolithic layers at Stajnia Cave in Poland. We describe the features of this unique piece, as well as the stratigraphic context and the details of its chronometric dating. The Stajnia Cave plate is a personal 'jewellery' object that was created 41,500 calendar years ago (directly radiocarbon dated). It is the oldest known of its kind in Eurasia and it establishes a new starting date for a tradition directly connected to the spread of modern Homo sapiens in Europe.

Three-dimensional dental topography and feeding ecology in the extinct cave bear

The cave bear (Ursus spelaeus s.l.) was an iconic extinct bear that inhabited the Pleistocene of Eurasia. The cause of extinction of this species is unclear and to identify the actual factors, it is crucial to understand its feeding preferences. Here, we quantified the shape descriptor metrics in three-dimensional (3D) models of the upper teeth (P⁴-M²) of the cave bear to make inferences about its controversial feeding behaviour. We used comparative samples, including representatives of all living bear species with known diets, as a template. Our topographic analyses show that the complexity of upper tooth rows in living bears is more clearly associated with the mechanical properties of the items consumed than with the type of food. Cave bears exhibit intermediate values on topographic metrics compared with the bamboo-feeder giant panda (Ailuropoda melanoleuca) and specialists in hard mast consumption (Ursus arctos and Ursus thibetanus). The crown topography of cave bear upper teeth suggests that they could chew on tough vegetal resources of low quality with high efficiency, a characteristic that no living bear currently displays. Our results align with a climate-driven hypothesis to explain the extinction of cave bear populations during the Late Pleistocene.

Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis

Heavy reliance on plants is rare in Carnivora and mostly limited to relatively small species in subtropical settings. The feeding behaviors of extinct cave bears living during Pleistocene cold periods at middle latitudes have been intensely studied using various approaches including isotopic analyses of fossil collagen. In contrast to cave bears from all other regions in Europe, some individuals from Romania show exceptionally high δ15N values that might be indicative of meat consumption. Herbivory on plants with high δ15N values cannot be ruled out based on this method, however. Here we apply an approach using the δ15N values of individual amino acids from collagen that offsets the baseline δ15N variation among environments. The analysis yielded strong signals of reliance on plants for Romanian cave bears based on the δ15N values of glutamate and phenylalanine. These results could suggest that the high variability in bulk collagen δ15N values observed among cave bears in Romania reflects niche partitioning but in a general trophic context of herbivory.

Biomechanical simulations reveal a trade-off between adaptation to glacial climate and dietary niche versatility in European cave bears

The cave bear is one of the best known extinct large mammals that inhabited Europe during the "Ice Age," becoming extinct ≈24,000 years ago along with other members of the Pleistocene megafauna. Long-standing hypotheses speculate that many cave bears died during their long hibernation periods, which were necessary to overcome the severe and prolonged winters of the Last Glacial. Here, we investigate how long hibernation periods in cave bears would have directly affected their feeding biomechanics using CT-based biomechanical simulations of skulls of cave and extant bears. Our results demonstrate that although large paranasal sinuses were necessary for, and consistent with, long hibernation periods, trade-offs in sinus-associated cranial biomechanical traits restricted cave bears to feed exclusively on low energetic vegetal resources during the predormancy period. This biomechanical trade-off constitutes a new key factor to mechanistically explain the demise of this dominant Pleistocene megafaunal species as a direct consequence of climate cooling.

Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear

The cave bear (Ursus spelaeus) is one of the Late Pleistocene megafauna species that faced extinction at the end of the last ice age. Although it is represented by one of the largest fossil records in Europe and has been subject to several interdisciplinary studies including palaeogenetic research, its fate remains highly controversial. Here, we used a combination of hybridisation capture and next generation sequencing to reconstruct 59 new complete cave bear mitochondrial genomes (mtDNA) from 14 sites in Western, Central and Eastern Europe. In a Bayesian phylogenetic analysis, we compared them to 64 published cave bear mtDNA sequences to reconstruct the population dynamics and phylogeography during the Late Pleistocene. We found five major mitochondrial DNA lineages resulting in a noticeably more complex biogeography of the European lineages during the last 50,000 years than previously assumed. Furthermore, our calculated effective female population sizes suggest a drastic cave bear population decline starting around 40,000 years ago at the onset of the Aurignacian, coinciding with the spread of anatomically modern humans in Europe. Thus, our study supports a potential significant human role in the general extinction and local extirpation of the European cave bear and illuminates the fate of this megafauna species.

Microwear and isotopic analyses on cave bear remains from Toll Cave reveal both short-term and long-term dietary habits

Dietary habits of the extinct Ursus spelaeus have always been a controversial topic in paleontological studies. In this work, we investigate carbon and nitrogen values in the bone collagen and dental microwear of U. spelaeus specimens recovered in Level 4 from Toll Cave (Moià, Catalonia, NE Iberian Peninsula). These remains have been dated to > 49,000 ¹⁴C BP. The ability of both proxies to provide data on the diet of U. spelaeus at different times in the life-history (isotopes: average diet of life; microwear: last days/weeks before death), allows us to generate high-resolution and complementary data. Our results show lower values (δ¹³C & δ¹⁵N) in cave bears than in strict herbivores (i.e. Cervus elaphus) recovered from the same level of Toll Cave. On the other hand, 12 lower molars (m1) were analysed through low-magnification microwear technique. The cave bears from Toll Cave show a microwear pattern like that of extant bears with omnivorous and carnivorous diets. These data are discussed in the framework of all available data in Europe and add new information about the plasticity of the dietary habits of this species at the southern latitudes of Europe during Late Pleistocene periods.

The Promise of Paleogenomics Beyond Our Own Species

Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

Background

Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?

Results

In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these.

Conclusions

The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1268-0) contains supplementary material, which is available to authorized users.

Partial genomic survival of cave bears in living brown bears

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

Frequency of appearance of transverse (Harris) lines reflects living conditions of the Pleistocene bear-Ursus ingressus-(Sudety Mts., Poland)

Transverse lines, called Harris Lines (HL), osteological markers of recovery from growth arrest episodes, are visible in radiograms of recent and Pleistocene fossil bones. Since on the one hand they mark stressful episodes in life, and on the other are mainly used to trace health fluctuations in prehistoric human communities, I used a cave bear population to check if the processes that could affect the specie' condition were in any way reflected in the bone structure. 392 bear bones from Bear Cave in Kletno (collection: Department of Palaeozoology, University of Wrocław), dated as 32 100 ±1300 to >49 000 years BP, were radiologically examined. The bones were found in a non-anatomical position; morphological analysis indicated that they belonged to different individuals. HL shadows were observed on 9 tibiae and 3 radii: 8.8% out of the 59 tibiae and 77 radii and 3.1% of all the bones. At least 3 transverse lines were recognised in those cases; the specimens were histologically examined. The bear individuals in question experienced regular malnutrition periods during their ontogeny. Starvation resulting in growth inhibition involved young individuals, aged 1 to 4 years. Juveniles aged 6 months, i.e. before weaning, or younger, showed no signs of nutritional stress. Starvation periods associated with seasonal food deficit were not long or common and had no significant effect on the development and welfare of the species. This is the first description of the occurrence of transverse lines in the Pleistocene bear.

The effect of body size evolution and ecology on encephalization in cave bears and extant relatives

BACKGROUND

The evolution of larger brain volumes relative to body size in Mammalia is the subject of an extensive amount of research. Early on palaeontologists were interested in the brain of cave bears, Ursus spelaeus, and described its morphology and size. However, until now, it was not possible to compare the absolute or relative brain size in a phylogenetic context due to the lack of an established phylogeny, comparative material, and phylogenetic comparative methods. In recent years, many tools for comparing traits within phylogenies were developed and the phylogenetic position of cave bears was resolved based on nuclear as well as mtDNA.

RESULTS

Cave bears exhibit significantly lower encephalization compared to their contemporary relatives and intraspecific brain mass variation remained rather small. Encephalization was correlated with the combined dormancy-diet score. Body size evolution was a main driver in the degree of encephalization in cave bears as it increased in a much higher pace than brain size. In Ursus spelaeus, brain and body size increase over time albeit differently paced. This rate pattern is different in the highest encephalized bear species within the dataset, Ursus malayanus. The brain size in this species increased while body size heavily decreased compared to its ancestral stage.

CONCLUSIONS

Early on in the evolution of cave bears encephalization decreased making it one of the least encephalized bear species compared to extant and extinct members of Ursidae. The results give reason to suspect that as herbivorous animals, cave bears might have exhibited a physiological buffer strategy to survive the strong seasonality of their environment. Thus, brain size was probably affected by the negative trade-off with adipose tissue as well as diet. The decrease of relative brain size in the herbivorous Ursus spelaeus is the result of a considerable increase in body size possibly in combination with environmental conditions forcing them to rest during winters.