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Bayesian estimate of the cave bear phylogeny, drawn to a timescale. The horizontal time axis is in kiloyears before present. Numbers of samples are given in parentheses. The position of the root was estimated by molecular clock rooting.
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a b s t r a c t Cave bears are among the most well known extinct Pleistocene mammals. Their biogeography and taxonomy, along with the factors that led to their extinction, have been subject to long-standing con-troversy. Here, we reconstruct the phylogeography as well as the temporal and spatial population dy-namics of cave bears across their range...
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... Ursus rossicus and Ursus kudarensis (Table S1; Baryshnikov, 1998;Baryshnikov and Puzachenko, 2011). Our phylogenetic analyses of the samples confirmed genetic distinctiveness consistent with a taxonomic designation for U. spelaeus, U. ingressus, U. rossicus and U. kudarensis and the differentiation of these four groups was well supported (Fig. 3). U. s. eremus and U. s. ladinicus were also found to be genetically distinct from their closest relative U. s. spelaeus. How- ever, clades within the ladinicus/eremus complex were very poorly resolved by Bayesian and Neighbor-Joining approaches and topol- ogies differ significantly depending on the tree building approach ( Fig. 3; Fig. ...
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... well supported (Fig. 3). U. s. eremus and U. s. ladinicus were also found to be genetically distinct from their closest relative U. s. spelaeus. How- ever, clades within the ladinicus/eremus complex were very poorly resolved by Bayesian and Neighbor-Joining approaches and topol- ogies differ significantly depending on the tree building approach ( Fig. 3; Fig. S1). The cave bears from the Altai region, which had genetically been assigned to U. s. eremus ( Knapp et al., 2009) and the specimen from Baumann's cave in the Harz Mountains (Ger- many) formed a separate clade but the systematic assignment of the clade differs between both tree building approaches and is not well supported by either ...
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... S1). The cave bears from the Altai region, which had genetically been assigned to U. s. eremus ( Knapp et al., 2009) and the specimen from Baumann's cave in the Harz Mountains (Ger- many) formed a separate clade but the systematic assignment of the clade differs between both tree building approaches and is not well supported by either approach (Fig. 3; Fig. S1). Both Bayesian and Neighbor-Joining approaches confirmed the deep divergence of the Caucasus cave bears (U. kudarensis) from all other cave bears, as in Stiller et al. (2009), as well as their sister-group relationship to the single individual from the Siberian Yana River region as described by Knapp et al. ...
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... is unknown but morphological similarity of these small bears to U. rossicus from the Late Pleistocene suggests that they belonged to a single phylogenetic lineage. Our data set con- tains two U. rossicus individuals, both coming from Kizel cave in the Ural Mountains. Our phylogenetic analyses suggest that they form a sister group to U. ingressus (Fig. ...
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... with recent findings of Dabney et al. (2013), [our data suggest that the three main haplogroups found in Late Pleistocene cave bears (spelaeus, ingressus, kudarensis) were already present as early as the Middle Pleistocene (Fig. 3) and that initially their rep- resentatives were most likely widely distributed. Interestingly, we found ladinicus, eremus and rossicus haplotypes only in a few samples that were either quite old (eremus from Baumann's cave) or from mountain regions. In fact, in our data, there is very little temporal overlap between U. s. eremus and U. ...
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... The phylogenetic analyses performed on published data and data generated using the amplification-free protocol shows the same topology for the amplification-free and standard single-stranded libraries, and no apparent differences in branch lengths. We do note that in neither analysis the individual O34-16, identified as an ingressus cave bear based on morphology, clusters with the published ingressus genome, but rather with the spelaeus genome which can be considered a separate evolutionary lineage [39,40]. Further investigations of cave bear population structure is needed to resolve this apparent discrepancy. ...
In recent years, methodological advances have substantially improved our ability to recover DNA molecules from ancient samples, raising the possibility to sequence palaeogenomes without PCR amplification. Here we present an amplification-free library preparation method based on a benchmark library preparation protocol in palaeogenomics based on single-stranded DNA, and demonstrate suitability of the new method for a range of sample types. Furthermore, we use the method to generate the first amplification-free nuclear genome of a Pleistocene cave bear, and analyse the resulting data in the context of cave bear population genetics and phylogenetics using standard genomic clustering analyses. We find that the PCR-free adaptation provides endogenous DNA contents, GC contents and fragment lengths consistent with the standard protocol, although with reduced conversion efficiency, and shows no biases in downstream population clustering analyses. Our amplification-free library preparation method could find application in experimental designs where the original template molecule needs to be characterised more directly.
... Sexual size dimorphism has also been noted in the only extant species of short-faced bear, the spectacled bear (Tremarctos ornatus) (Vela-Vargas et al. 2021). Ancient DNA can be used to test hypotheses about sexual dimorphism (Pecnerova et al. 2017, Gower et al. 2019, taxonomic identification, morphology based phylogenetic systematics, and phylogeography (Barnes et al. 2002, Shapiro et al. 2004, Debruyne et al. 2008, Barnett et al. 2009, Palkopoulou et al. 2013, Stiller et al. 2014, Enk et al. 2016, Heintzman et al. 2016, Froese et al. 2017, Bover et al. 2018. For example, genetic sex assignment was used to confirm that size variation used to differentiate two extinct genera of North American muskoxen-Symbos and Bootherium-actually represented sexual dimorphism within a single species (Bover et al. 2018). ...
... First, to check the power of the relatively few dated samples to estimate the ages of the undated specimens, a leave-one-out cross-validation was performed using only the finite dated specimens (e.g. Stiller et al. 2014). Cross-validation runs were performed with a strict clock with a uniform prior on rate (0-10 -5 mutations per site per year), constant population coalescent tree prior with a 1/X distribution on population size, a uniform prior (0-500 000) on the age of the sequence being estimated, and run for 15 million steps with sampling every 1500 steps. ...
... Once all specimens had an associated date (whether estimated or radiocarbon), a date-randomization test was performed (Ramsden et al. 2009, Stiller et al. 2014. This involved randomly reassigning the ages of the sequences 20 times, using BEAST to analyse the randomized dataset, and comparing the resulting rates. ...
Giant short-faced bears (Arctodus simus) were the largest carnivoran of Pleistocene North America and are one of the most extensively studied extinct megafaunal species from the continent. Smaller and larger forms of A. simus have previously been recognized and are sometimes considered subspecies (A. s. simus and A. s. yukonensis, respectively). However, researchers have also proposed that this size variation is primarily the result of sexual dimorphism. We sequenced 31 mitogenomes of A. simus from locations ranging from Alaska to New Mexico. Our results revealed a lack of phylogeographic structure in A. simus, as well as low genetic diversity and relatively recent mitochondrial diversification. These observa-
tions may either represent population bottlenecks during the Late Pleistocene or simply a naturally low effective population size resulting from a dispersed population and low population density. We found no evidence for genetic differences among our samples, which were compatible with the previously proposed A. simus subspecies. In contrast, all large specimens to which we could assign a sex using genetic data were male, whereas the small specimens in our dataset were all female, supporting the hypothesis that A. simus size variation can be explained by sexual dimorphism.
... During the Late Pleistocene, five putative species/subspecies inhabited Europe, the Urals and the Caucasus -U. s. spelaeus, U. ingressus, U. kudarensis (Knapp et al., 2009;Stiller et al., 2014), U. spelaeus eremus, and U. kanivetz (Barlow et al., 2021). Some of these coexisted in the same region such as U. s. spelaeus and U. ingressus in eastern France (Gretzinger et al., 2019) and U. ingressus and U. s. eremus in the Alps (Rabeder et al., 2004). ...
... The taxonomy of cave bears has been addressed by several studies due to its geographic variability throughout the Pleistocene. Recent morphological and genetic studies have recognised distinct species, sub-species and multiple evolutionary lineages including: Ursus kudarensis, Ursus deningeri, Ursus rossicus, Ursus ladincus and Ursus spelaeus (Rabeder et al. 2004(Rabeder et al. , 2008(Rabeder et al. , 2010Valdiosera et al. 2008;Knapp et al. 2009;Baryshnikov and Puzachenko 2011;Dabney et al. 2013;Stiller et al. 2014). Their diet has also been a topic of great debate for many years, with recent research largely suggesting that species such as U. spelaeus were omnivorous but predominantly consumed plant material (Kurtén 1968;Bocherens et al. 1997Bocherens et al. , 2014Garsia 2003;Raia 2004;Figueirido et al. 2009;Peigné et al. 2009;Rabeder et al. 2010;Meloro 2011;Baryshnikov and Puzachenko 2011;Bocherens 2015Bocherens , 2019Charters et al. 2019Charters et al. , 2022Pérez-Ramos et al. 2019, 2020a, 2020bvan Heteren and Figueirido 2019). ...
... savini-rossicus. Based on the methods of paleoDNA analysis, many species of cave bears are currently separated (Hofreiter et al. 2007;Krause et al. 2008;Knapp et al. 2009;Stiller et al. 2014;Barlow et al. 2016Barlow et al. , 2018Barlow et al. , 2019Barlow et al. , 2020. By the reason that not all cave bears from the Late Pleistocene have been genetically studied, we suppose that it is possible to consider them as U. ex. ...
The present work describes the dentognathic remains of Ursus etruscus Cuvier, 1823 from the recently discovered Taurida cave in central Crimea at the north Black Sea area. The bone-bearing layer of Taurida cave corresponds to the Psekupsian Faunal Assemblage of Eastern Europe and to the Late Villafranchian of Western Europe (ca. 1.8–1.5 Ma). Here, we describe unpublished ursid material unearthed during the excavations performed at the cave in 2020–2021, further comparing it with coeval chronologic and geographic sites around Europe. Our anatomical and biometrical analyses suggest the inclusion of the studied specimens in the hypodigm of the Early Pleistocene medium-sized species Ursus etruscus. The finds of the U. etruscus from the southern part of Eastern Europe provide a link between the western and eastern parts of the species range. Therefore, the finds from Crimea are important for understanding of the morphological diversity and evolution of U. etruscus which is the putative ancestor of both cave bears and brown bears. Furthermore, the study of these remains is also important for understanding the processes of the forming of the large mammal assemblages in the late Early Pleistocene and its relationships with the dispersal of the genus Homo.
... The cave contains Upper Palaeolithic stone artefacts (Guslitser & Pavlov 1988). On the bear skull (ZIN 34991-6) and mandible (ZIN 34991-19) AMS dates of 45 150AE600 years BP (OxA-19568) and 42 000AE450 years BP (OxA-19608) were obtained, respectively (Stiller et al. 2014). The lower canines (ZIN 34756-102, 34756-10 and 34991-2; Fig. 3J, K, L) were assigned to U. kanivetz (Stiller et al. 2014). ...
... On the bear skull (ZIN 34991-6) and mandible (ZIN 34991-19) AMS dates of 45 150AE600 years BP (OxA-19568) and 42 000AE450 years BP (OxA-19608) were obtained, respectively (Stiller et al. 2014). The lower canines (ZIN 34756-102, 34756-10 and 34991-2; Fig. 3J, K, L) were assigned to U. kanivetz (Stiller et al. 2014). The crown shape of the canine (ZIN 34756-102) indicates post-breakage wearing, which occurred during the life of the animal after the canine had broken. ...
Cementum and dentine increment analysis was used for the first time to study the remains of cave bears from European Russia, the Urals and the Caucasus. This study analysed 12 canines belonging to 12 different individuals (five males and seven females) from genetically different lineages of cave bears. The increment analysis showed that all studied cave bears belong to the categories adults and old animals (from 10 to 32.5 years). The enamel crowns of all 12 canines were broken and/or had wear facets. Seven canines studied were severely broken (more than one‐third of a canine crown missing). Significant damage to dental crowns may indicate old age, conflict between males and/or high food abrasion. The absence of significant differences in the extent of canine breakage between the youngest and the oldest animals, as well as between the males and the females, may indicate a significant role of food abrasiveness in the process of the grinding of canines. Until now, the question of whether these animals visited caves year‐round or stayed there mainly for overwintering remained open. The increment analysis showed different seasons of the bears’ death. Six individuals died in the warm season and four individuals died in the cold season. In all of the studied caves (excluding Medvezhiya Cave) the animals died in the warm season as well as in the cold season. All of the studied females perished either during the cold season or at the very beginning of the warm season. On the contrary, almost all of the examined males perished in the warm season. Thus, the cave bears visited the caves year‐round. This study raises new questions in the study of the ecology of cave bears from different parts of their range.
... U. savini was chosen because there is no consensus among researchers about the taxonomic position of the small cave bear and the relationship with the U. deningeri group, in particular, with U. deningeroides (Mottl 1964). Currently, based on morphological and molecular data, many evolutionary lineages or even separate species are recognised (Knapp et al. 2009;Dabney et al. 2013;Stiller et al. 2014;Knapp 2018;Gretzinger et al. 2019; Barlow et al. 2021). Four main groups have been defined, that is, the U. deningeri group including U. deningeri von Reichenau 1904 and U. deningeroides Mottl (1964) and separately the Caucasian cave bear U. kudarensis Baryshnikov 1985, the small cave bear group with U. savini Andrews (1922) and U. rossicus Borissiak (1930), and the cave bear group with U. spelaeus Rosenmüller 1794 and U. kanivetz Vereshchagin 1973. ...
In the rich vertebrate fauna of Imanay Cave the abundant material of the small-sized cave bears was originally assigned to the taxon Ursus savini. Teeth and metapodials of statistical amounts were compared with other cave bear faunas and the taxonomic position was determined through morphological and metric analyses. The size of teeth and metapodial bones is significantly smaller in Imanay Cave bears compared to the typical U. deningeri from Mosbach and Hundsheim. Although the teeth are smaller, they reached higher evolutionary level than those from Mosbach or Hundsheim.The bear remains from Imanay Cave show great similarities to the fossils from Kizel Cave in the Ural Mountains described as Ursus rossicus Borissiak, 1930 but also to the remains of small-bodied cave bears of the Alps described as Ursus deningeroides Mottl, 1964. Remarkable are the differences in size of the front dentition: the incisors from Imanay Cave are on average >10% longer and wider than the corresponding teeth from U. deningeroides but also wider than the classic U. deningeri. Preliminary carbon and nitrogen stable isotope analyses suggest that the small cave bears from Imanay Cave were herbivorous.
... Вплоть до начала XXI в. считалось, что в позднем плейстоцене существовало два вида пещерных медведей: большой пещерный медведь Ursus spelaeus Rosenmüller, 1794 и малый пещерный медведь U. savini Andrews, 1922, или U. rossicus Borissiak, 1930(Kurtèn, 1995Барышников, 2007). В настоящее время по молекулярным данным (Barlow et al., 2021) в группе больших пещерных медведей различают три вида: U. spelaeus и U. eremus Rabeder, Hofreiter, Nagel et Withalm, 2004 (распространены в Западной Европе), а также U. kanivetz Vereshchagin, 1973 (распространен в Центральной и Восточной Европе и на Урале; Knapp et al., 2009;Rabeder et al., 2011;Stiller et al., 2014;Baryshnikov, Puzachenko, 2019, 2020. В группе малых пещерных медведей выделяют U. savini (Западная Европа) и U. rossicus (Северный Кавказ, Восточная Европа, Урал, Алтай, Западная и Восточная Сибирь) (Борисяк, 1930;Spassov et al., 2017;Baryshnikov, Puzachenko, 2019, 2020Barlow et al., 2021). ...
... и продолжается по настоящее время. В этот период активно используются молекулярно-генетические методы (Stiller et al., 2009(Stiller et al., , 2010(Stiller et al., , 2014Knapp et al., 2009;Gretzinger et al., 2019;Knapp, 2019;Barlow et al., 2021). В результате анализа ядерной ДНК установлена таксономическая самостоятельность и определено время дивергенции филетических линий малого и большого пещерных медведей Урала, а также оценено их морфологическое своеобразие. ...
... Изучение митохондриальной ДНК по образцам из пещеры Медвежья показало, что большой пещерный медведь с Северного Урала относится к гаплогруппе "ingressus" (Knapp et al., 2009;Stiller et al., 2009), представители которой ранее были выделены в самостоятельный вид U. ingressus Rabeder et al., 2004(Rabeder et al., 2004. Позднее это подтвердилось новыми исследованиями митохондриальной ДНК медведей (Stiller et al., 2014;Gretzinger et al., 2019). Пещера Медвежья представляет собой типовое местонахождение для U. spelaeus kanivetz Vereshchagin, 1973. ...
... Unlike massively parallel sequencing, Sanger sequencing provides only one read of a certain DNA sequence. Despite the rise of massively parallel sequencing, ancient mitogenomes are still studied by Sanger sequencing in many fields, such as the divergence of the extinct Indian cheetah (Rai et al., 2020), maternal genetic variation in Turkey (Yaka et al., 2018;Ottoni et al., 2015), haplogroup detection of the Avar-Slavic population (Šebest et al., 2018), maternal kinship from medieval cemetery (Biol et al., 2016), Viking mass grave in Sweden (Buś et al., 2019), or mitochondrial diversity of ancient bears throughout Eurasia (Stiller et al., 2014;Mizumachi et al., 2020;Mizumachi et al., 2021). ...
Working with ancient DNA is challenging and requires an authentication step. We analyzed eleven badly preserved samples from the Nitra culture with the influence of Únětice culture dated to the 4000 BP Bronze Age. We present estimated mitochondrial haplogroups of four samples based on Sanger sequencing of HVR1 and a part of HVR2.
Sanger sequencing has strong limitations in haplogroup prediction, especially when working with ancient DNA. However, Sanger sequencing in this study is featured as a control step to provide us with quality results of mitochondrial DNA and as a screening of present haplogroups. DNA quality estimation is further supported by sample concentration and fragment analysis. The presence of mitochondrial DNA is confirmed by PCR. However, the Sanger sequencing of mitochondrial DNA can confirm its presence in good quality for further sequencing. Therefore, only suitable samples were selected for further high-throughput sequencing of the whole mitogenome.
... Cave bear nuclear and mitochondrial relationships are highly incongruent Phylogenetic relationships among cave bear taxa have been largely guided by analysis of their mitochondrial DNA. 15,16 Our previous study on nuclear genomes did reveal one instance of mito-nuclear discordance among three Late Pleistocene taxa, 10 but the limited sampling of this study precluded a broader assessment of cave bear nuclear relationships. To investigate this further, we analyzed the Middle Pleistocene praekudarensis genome dataset alongside novel genome datasets of Late Pleistocene cave bears generated from their petrous bones, representing the taxa rossicus (Kizel Cave, Ural Mountains, Russia), kanivetz (Medvezhiya Cave, Ural Mountains, Russia), and kudarensis (Hovk 1 Cave, Armenia). ...
... This suggests a single increase in body size in their common ancestor, rather than two independent shifts as previously inferred from their mitochondrial relationships. 15 Moreover, the validity of the taxon kanivetz has itself been questioned by mitochondrial phylogeographic studies, 15 which show it to be nested within the wider ingressus mitochondrial clade. Nuclear genome analysis, however, supports its distinctiveness and position as sister to the European taxa spelaeus and ingressus. ...
... This suggests a single increase in body size in their common ancestor, rather than two independent shifts as previously inferred from their mitochondrial relationships. 15 Moreover, the validity of the taxon kanivetz has itself been questioned by mitochondrial phylogeographic studies, 15 which show it to be nested within the wider ingressus mitochondrial clade. Nuclear genome analysis, however, supports its distinctiveness and position as sister to the European taxa spelaeus and ingressus. ...
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.¹
• Hofreiter M.
• Paijmans J.L.A.
• Goodchild H.
• Speller C.F.
• Barlow A.
• Fortes G.G.
• Thomas J.A.
• Ludwig A.
• Collins M.J.
The future of ancient DNA: Technical advances and conceptual shifts.BioEssays. 2015; 37: 284-293
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As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
