From a molecules’ perspective – contributions of ancient DNA research to understanding cave bear biology

Abstract

Few members of the Pleistocene megafauna have been as extensively studied as cave bears. Multidisciplinary research into cave bears has provided insights into their morphology, ecology, and evolution. Genetic studies have profited from the availability of large numbers of well-preserved remains. As a result, ‘ancient DNA (aDNA)’ from cave bears has provided significant insights into cave bear ecology, phylogeography and even potential causes of their extinction. Here I review the contributions that genetic research has made to our understanding of cave bear biology and evaluate the potential that new, genomic tools provide to shed further light onto how these iconic representatives of the Pleistocene megafauna lived and died.     

Determination of the evolutionary mode of Austrian alpine cave bears by uranium series dating

Middle and Late Pleistocene sediments in many caves in Central and South Europe contain large numbers of bones and teeth of the cave bear (Ursus spelaeus). The cave bear differs in many characteristics from the recent brown bear and shows a rapid evolution especially in the changes of the teeth due to adaptation to pure herbivorous nutrition. The shifts of the morphotype frequencies of the fourth premolar from the upper jaw were used as a measure of the evolution. The uranium series method is the only suitable tool for the absolute age determination of the fossil bones with ages beyond the time range accessible to the radiocarbon method. By applying this method to the Herdengel cave profile the evolutionary rate of the cave bears was determined. Uranium series data from the fossil bones were partly verified by an independent carbonate speleothem age. For both, bone layers and carbonate formation found in stratigraphic relation, the determined ages correspond to a normal time sequence. According to the relatively fine time scale obtained by absolute dating, the evolutionary mode of the cave bears was determined as gradual. The main novelty of this study is the dating of the successive layers of the Herdengel cave and the determination of evolutionary stages of the cave bear in them.     

Upper Pleistocene Panthera leo spelaea (Goldfuss, 1810) remains from the Bilstein Caves (Sauerland Karst) and contribution to the steppe lion taphonomy,palaeobiology and sexual dimorphism

Remains of the steppe lion Panthera leo spelaea (Goldfuss) from historical digs in the Bilstein Caves of Warstein (Sauerland, NW Germany) are described. Their age seems to be from the Early Weichselian periods (Upper Pleistocene). Whereas the Bilstein cave was inhabited by cave bears at that time only a few hyena prey remains, were most likely imported into the cave entrance by hyenas. Bite and crush marks on a few bones of Bison priscus, Bos primigenius, Cervus elaphus, a rhinoceros Coelodonta antiquitatis vertebra and even several chewed cave bear bones prove the hyena presence which is similar to other caves in the Sauerland hyena den cave rich region. Additionally some larger wolves subspecies Canis lupusspelaeus bones were found, but only few Crocuta crocuta spelaea remains are present. After taphonomic comparisons to six other hyena and cave bear den caves of northern Germany, this cave can be classified as a cave bear den, which was briefly used by hyenas only for food storage or commuting or cave bear predation site in one part of the Cave. The lion material refers at least to one young adult lioness, one more adult female and two male lions; therefore, at minimum, the remains of four adult individuals are represented. The absence of juvenile lion material, in contrast to cave bear cub remains in the Bilstein Caves, proves that P. leo spelaea did not use this and all other caves in the region to raise their cubs. The bone material from the Bilstein Caves would prove the same hyena-lion antagonism conflict being recently proven for the Perick Caves, Balve Cave or Martins Cave well. Other situations in caves such as the Keppler Cave and the Bilstein Cave initially show the more complex taphonomic situation of lion remains in European caves, especially in cave bear dens, where they seem to have hunted periodically cave bears, such as it is already proven for hyenas in the Sauerland Karst and other caves of Europe.     

Limb bone proportions and body mass of the cave bear (Ursus spelaeus)

The European cave bear evolved during the Middle Pleistocene and adapted to mountain environments. Earlier workers have described the cave bear as a robust bear. In this study the cave bears limb bone morphology is compared to the limb bone morphology of extant bears. Body mass estimates for the cave bear are made both based on different limb bone characters and based on dental and cranial characters. The shafts are wider in the cave bear limb bones than in the extant bear limb bones, and consequently the shaft widths give higher weight estimates to the cave bear than the other dimensions. The widened shafts are suggested to be a special adaptation (of presently unknown significance) rather than an indicator of an increased body mass.     

First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns

Until recently, cave bears were believed to have only inhabited Europe. However, recent morphological evidence suggests that cave bears' geographic range extended as far east as Transbaikalia, Eastern Siberia. These Asian cave bears were morphologically distinct from European cave bears. However, how they related to European lineages remains unclear, stressing the need to assess the phylogenetic and phylogeographic relationship between Asian cave bears and their European relatives. In this work, we address this issue using a 227 base-pair fragment of the mitochondrial control region obtained from nine fossil bone samples from eight sites from the Urals, Caucasus, Altai Mountains, Ukraine and Yana River region in Eastern Siberia. Results of the phylogenetic analyses indicate that (i) the cave bear from the Yana River is most closely related to cave bears from the Caucasus region; (ii) the Caucasus/Yana group of bears is genetically very distinct from both European cave bears and brown bears, suggesting that these bears could represent an independent species; and (iii) the Western European cave bear lineage reached at least temporarily to the Altai Mountains, 7000 km east of their known centre of distribution. These results suggest that the diversity of cave bears was greater than previously believed, and that they could survive in a much wider range of ecological conditions than previously assumed. They also agree with recent studies on other extinct and extant species, such as wolves, hyenas and steppe bison, which have also revealed higher genetic and ecological diversity in Pleistocene populations than previously known.     

An Overview of the Ichnological and Ethological Studies in the Cave Bear Den in Urşilor Cave (Western Carpathians,Romania)

This paper presents a preliminary investigation of late Pleistocene cave bear traces from Ur?ilor Cave in the western Carpathians, Romania. The bears left thousands of traces on the walls, plateaus, and slopes of the cave interior. Some areas in the cave have been heavily trampled, leaving more than 140 hibernation beds as well as fur impressions. The footprints of cave bears are assigned to Ursichnus europaeus nov. ichnogen. and nov. ichnosp. and the cave bear-beds to Ursalveolus carpathicus nov. ichnogen. and nov. ichnosp. as behavioral traces. Tens of thousands of scratch marks on the slopes and top of a clay plateau are the result of bears moving from the hibernation area down to a stream and back. These traces reveal that the cave bears had short claws, similar to those of modern, primarily herbivorous black bears. Deep within the cave, three weathered, articulated cave bear skeletons still lie in their hibernation beds on the clay plateaus or a natural cave corner. One of these bears was a one-year-old male cub that did not survive its first hibernation; a second skeleton close was an adult female. The third, a young male, was found close to the end of the cave system. The bears of Ur?ilor Cave would have felt well protected against carnivores during their hibernation because their sleeping places were so deep within the cave. Their strategy may well have been to avoid any conflict with hyenas and lions during hibernation.     

The largest European lion Panthera leo spelaea (Goldfuss 1810) population from the Zoolithen Cave,Germany: specialised cave bear predators of Europe

Remains of 13 individuals with 3/1 male/female ratio of the extinct Upper Pleistocene lion Panthera leo spelaea (Goldfuss, 1810) from the Zoolithen Cave near Burggeilenreuth (Bavaria, Germany) include the holotype skull and all paratype material. The highest mortality rate for the Zoolithen Cave lions is in their reproductive adult ages. Bite marks on lion bones or skulls are results of hyena activities, or rare cannibalism of lions under stress situations. Lions were possibly also killed in battles with cave bears during predation on hibernating bears in winter times. This cave bear hunt specialisation in caves overlaps with the ecological behaviour of cave bear feeding by Ice Age-spotted hyenas. Both largest Ice Age predators, lions and hyenas, had to specialise on feeding herbivorous cave bears in boreal forest mountainous cave rich regions, where the mammoth steppe megafauna prey was absent. This cave bear hunt by felids, and scavenging by hyenas and other large carnivores such as leopards and wolves explains why cave bears hibernated deep in to the European caves, for protection reasons against predators. Within such lion–cave bear and even lion–hyena conflicts in the caves lions must have been killed sometimes, explaining mainly the skeleton occurrences in different European caves.     

Isotopic insights on cave bear palaeodiet

Abstract

More than 300 cave bear bones from all over Europe have carbon and nitrogen isotopic composition that match overwhelmingly a diet based on plants, except for samples from two caves in Romania, for which high nitrogen-15 amounts have been interpreted as reflecting an omnivorous diet. This paper aims at deciphering the various factors influencing the carbon and nitrogen isotopic composition of a potential omnivorous species like cave bear, those linked to trophic levels and variations among plants and those caused by physiological factors. The comparison of European cave bears with coeval Late Pleistocene large mammals with different diets clearly shows that all the cave bear populations, including those from Romania, present isotopic values overlapping with herbivores, not with carnivores. Therefore omnivory is very unlikely for cave bears. Consumption of plants with high δ¹⁵N values, such as graminoids, forbs and possibly fungi, could explain in part the observed isotopic pattern. In addition, the variations in δ¹⁵N values through ontogeny support the hypothesis of a different hibernation pattern for the Romanian cave bears with high δ¹⁵N values. Future investigations using new isotopic approaches, especially nitrogen isotopic composition of collagen amino acids, should contribute to decipher the paleoecology of these Romanian cave bears.     

A three-dimensional analysis of tooth-root morphology in living bears and implications for feeding behaviour in the extinct cave bear

ABSTRACT

The morphology of both crowns and tooth-roots reflects dietary specialisation in mammalian carnivores. In this article, we analyse the tooth-root morphology of maxillary teeth from CT scans of living bears (Ursus arctos, Ursus americanus, Ursus maritimus, Ursus thibetanus, Melursus ursinus, Helarctos malayanus, Tremarctos ornatus and Ailuropoda melanoleuca) in order to make inferences about the diet and feeding behaviour of the extinct cave bear (Ursus spelaeus sensu lato). Specifically, we investigate two major mitochondrial clades of extinct cave bears recognized by previous authors: Ursus ingressus and Ursus spelaeus (U. spelaeus spelaeus, U. spelaeus ladinicus, U. spelaeus eremus). Our results indicate a close association between tooth-root surface area and feeding behaviour in all living bear species. Tooth-root surface area values of cave bears suggest that they relied more on vegetative matter than living brown bears (Ursus arctos) but subtle differences between these species/subspecies could also indicate different feeding strategies among the members of cave bear complex.     

Longevity and life history of cave bears – a review and novel data from tooth cementum and relative emergence of permanent dentition

Abstract

Longevity and other life history variables are key to understanding evolutionary processes and the biology of extinct animals. For the past 20 years, the lifespan of cave bears received an increased interest. Studies focusing on incremental lines of tooth cementum resulted in detailed mortality patterns from different localities. In this review, we summarise literature on age estimation as well as mortality of different European cave bear localities and present novel data on longevity from 94 teeth originating from 20 European localities. Additionally, the relative tooth emergence pattern of the permanent dentition is investigated under the Schultz’s rule framework of possible life history implications. For this, the known sequences of extant bear species are compared with the one of cave bears. Our results suggest that the typical duration of the life of cave bears was 19 years but data from literature show that in rare cases ages of up to 30–32 years were achieved. Additionally, we present the oldest known age for the Middle Pleistocene cave bear Ursus deningeri, 29 years. The tooth eruption pattern of cave bears exhibits a heterochronic shift that implies, under the assumption of Schulz’ rule, a slightly faster life history than closely related species.     

Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages

The cave bear, Ursus spelaeus, represents one of the most frequently found paleontological remains from the Pleistocene in Europe. The species has always been confined to Europe and was contemporary with the brown bear, Ursus arctos. Relationships between the cave bear and the two lineages of brown bears defined in Europe, as well as the origins of the two species, remain controversial, mainly due to the wide morphological diversity of the fossil remains, which makes interpretation difficult [1, 2]. Sequence analysis of ancient DNA is a useful tool for resolving such problems because it provides an independent source of data [3]. We previously amplified a short DNA fragment of the mitochondrial DNA control region (mt control region) of a 40,000-year-old Ursus spelaeus sample [4]. In this paper, we describe the DNA analysis of two mtDNA regions, the control region and the cytochrome b gene. Control region sequences were obtained from ten samples of cave bears ranging from 130,000 to 20,000 years BP, and one particularly well-conserved sample gave a complete cyt b sequence. Our data demonstrate that cave bears split largely before the lineages of brown bears around 1.2 million years ago. Given its abundance, its wide distribution in space and time, and its large morphological diversity, the cave bear is a promising model for direct observation of the evolution of sequences throughout time, extinction periods, and the differentiation of populations shaped by climatic fluctuations during the Pleistocene.     

Was the European cave bear an occasional scavenger?

Rabal‐Garcés, R., Cuenca‐Bescós, G., Canudo, J.I. & de Torres, T. 2011: Was the European cave bear an occasional scavenger? Lethaia, Vol. 45, pp. 96–108. The cave bear Ursus spelaeus fossils remains are quite abundant in the Late Pleistocene site of Coro Tracito (Huesca, Spain). The site constitutes the highest mountain record of cave bears in the Iberian Peninsula. Being a monospecific locality, it permits the study of the biology and dietary habits of this species. The study of the limb bones established first, the mortality pattern of this population of Ursus spelaeus and, second, the alteration pattern due to carnivore tooth‐marks. Some authors have performed similar analyses in the same kind of skeletal elements in other cave bear localities all over Europe and, therefore it has been possible to compare our results with those from other sites. The tooth‐marks found in the bones of cave bears, especially in monospecific sites, have been attributed to a scavenging behaviour. In agreement with the authors, our analysis presented here supports the hypothesis of scavenging behaviour for cave bears. □Behaviour, Late Pleistocene, Spain, taphonomy, tooth‐marks, Ursus spelaeus.     

Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late pleistocene cave bears

Cave bears (Ursus spelaeus) existed in Europe and western Asiauntil the end of the last glaciation some 10,000 years ago.To investigate the genetic diversity, population history, andrelationship among different cave bear populations, we havedetermined mitochondrial DNA sequences from 12 cave bears thatrange in age from about 26,500 to at least 49,000 years andoriginate from nine caves. The samples include one individualfrom the type specimen population, as well as two small-sizedhigh-Alpine bears. The results show that about 49,000 yearsago, the mtDNA diversity among cave bears was about 1.8-foldlower than the current species-wide diversity of brown bears(Ursus arctos). However, the current brown bear mtDNA gene poolconsists of three clades, and cave bear mtDNA diversity is similarto the diversity observed within each of these clades. The resultsalso show that geographically separated populations of the high-Alpinecave bear form were polyphyletic with respect to their mtDNA.This suggests that small size may have been an ancestral traitin cave bears and that large size evolved at least twice independently.     

Diet reconstruction in cave bears from craniodental morphology: past evidences,new results and future directions

ABSTRACT

The diet of the cave bear (Ursus spelaeus) is a controversial topic, as different paleobiological approaches (e.g. dental wear, isotopic biochemistry, skull morphometrics) result in different dietary inferences for the cave bear, ranging from carnivory to pure herbivory. Here, we review the main results obtained from these approaches, with special emphasis on those obtained from the morphometric analyses of the cave bear craniodental skeleton. Then, we compute a between-group Principal Components Analysis from a set of 3D-landmarks digitized on 103 mandibles of living bears and extinct cave bears and using a phylomorphospace approach. Moreover, we also reconstructed the evolutionary trajectory of the cave bear mandible from the hypothetical shape of its inferred ancestor. Our results indicate that the mandible of the cave bear possess specific traits indicative of a highly-herbivorous diet or, at least, more herbivorous than their closest living relative, the brown bear (Ursus arctos). Moreover, we also propose new directions for future research to obtain more detailed inferences on the potential food resources consumed by the cave bear being crucial to understand the ‘life and death’ of this vanished animal.     

Chronological and Isotopic data support a revision for the timing of cave bear extinction in Mediterranean Europe

Abstract

The Cave Bear, Ursus spelaeus (sensu lato), was one of many megafaunal species that became extinct during the Late Pleistocene in Europe. With new data we revisit the debate about the extinction and paleoecology of this species by presenting new chronometric, isotopic and taphonomic evidence from two Palaeolithic cave bear sites in northeastern Italy: Paina Cave and Trene Cave. Two direct radiocarbon dates on well-preserved collagen have yielded ages around 24,200–23,500 cal yr BP, which make them the latest known representatives of the species in Europe. The carbon (δ¹³C) and nitrogen (δ¹⁵N) isotopic values of bone collagen exhibit values similar to those of older cave bears from Swabian Jura and France, suggesting that the feedings preferences of cave bears remained unchanged until the disappearance of this species in Europe. Several bear remains preserved traces of human modification such as cut marks, which enables a reconstruction of the main steps of fur recovery and the butchering process. The broad range of plant types available and the favorable location of Berici Hills may have played an important role in the range expansion of cave bears and their interaction with the Paleolithic hunters settled the same area.     

Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA

The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands.This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene, and it supports our new evolutionary hypothesis of the Japanese black bear.     

The cave bear’s hibernation: reconstructing the physiology and behaviour of an extinct animal

Abstract

When studying an extinct species such as the cave bear (Ursus spelaeus ROSENMÜLLER 1794), it is possible to apply a variety of molecular biology techniques such as the study of stable isotopes or mitochondrial DNA (mDNA) to infer patterns of behaviour or physiology that would otherwise remain concealed. Throughout Europe and along time, differences in the isotopic values (δ¹³C and δ¹⁵N) of cave bears arise from environmental differences and the Pleistocene climatic evolution. The climate determines the hibernation length, during which the cave bears undergo a particular physiology that can be related to an increase in δ¹⁵N during climate cooling. In order to verify whether hibernation affected the isotopic values, we compared cave bears in different ontogenetic stages. The results show that perinatal values reflect the values for mothers during hibernation, while juveniles show differences in maternal investment. A previous study in the literature based on complete mitochondrial DNA sequences of several individuals collected from closely situated caves showed that each cave housed, almost exclusively, a single lineage of haplotypes. This pattern suggests extreme fidelity to the birth site, or homing behaviour, and that cave bears formed stable maternal social groups, at least for the purpose of hibernation. Studies of this type offer unexpected data on the palaeobiology of this extinct animal.     

Sex-ratio et analyse des mélanges d'Ursus spelaeus (Carnivora,Ursidae) du gisement pléistocène supérieur de Fate (Ligurie,Italie). Implications paléobiologiques

Determination of the sex-ratio of a fossil population is essential for understanding the palaeoethology of a taxon, and this is especially true for the cave bear (Ursus spelaeus). Classical methods for determining sex-ratios such as analyses using uni and bivariate plots are based on an arbitrary fixing of the limit between the sexes. Therefore, a more robust statistical method termed mixture analysis has been applied in this study to test all the postcranial remains of cave bear (essentially carpals, tarsals and metapodials) derived from the Upper Pleistocene site of Fate (Liguria, Italy).Results give a sex-ratio of about 35% female individuals and show a clear predominance of males. Mixture analysis appears to be a reliable method for sex-ratio determination in U. spelaeus. In this study, few dimensions have been excluded because of a significant error in sex classification. The numerous measurements identified as good predictors of sexual dimorphism in the cave bear are probably linked to the marked sexual differences in the body mass of the animal. Palaeobiological interpretations suggest that there are no available hypotheses to explain the high variability of sex-ratios documented for the cave bear in Palaeolithic sites. The individual animal behaviour appears to be the only criteria in determining their choice of a winter den. But trophic and social regulations on living populations may have influenced this choice.The association between mortality profiles and sex-ratios appears to be related to the general function of a den. The thanatocenosis of cave bears in the Fate assemblage indicates the presence of a high number of juveniles and male individuals, such that the site may have served either as a nursery or and as a male den.     

Could brown bears (Ursus arctos) have survived in Ireland during the Last Glacial Maximum?

Brown bears are recorded from Ireland during both the Late Pleistocene and early–mid Holocene. Although most of the Irish landmass was covered by an ice sheet during the Last Glacial Maximum (LGM), Irish brown bears are known to have hybridized with polar bears during the Late Pleistocene, and it is suggested that the Irish brown bear population did not become extinct but instead persisted in situ through the LGM in a southwestern ice-free refugium. We use historical population modelling to demonstrate that brown bears are highly unlikely to have survived through the LGM in Ireland under any combination of life-history parameters shown by living bear populations, but instead would have rapidly become extinct following advance of the British–Irish ice sheet, and probably recolonized Ireland during the end-Pleistocene Woodgrange Interstadial from a closely related nearby source population. The time available for brown bear–polar bear hybridization was therefore restricted to narrow periods at the beginning or end of the LGM. Brown bears would have been extremely vulnerable to extinction in Quaternary habitat refugia and required areas substantially larger than southwestern Ireland to survive adverse glacial conditions.