Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times

The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.     

Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa

Aim  Middle East brown bears ( Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species.
Location  Middle East region of south-western Asia.
Methods  We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed.
Results  Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals.
Main conclusion  This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations.     

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction.     

青藏高原可可西里地区藏棕熊暖季食性及采食行为模式

藏棕熊(Ursus arctos pruinosus)是青藏高原特有的棕熊亚种,作者曾对该地区藏棕熊夏季食性进行了初步报道(Xu et al,2006),然而,藏棕熊的采食行为模式一直未见报道。2009年7-8月,作者又对可可西里地区藏棕熊食性及采食行为模式做了补充调查研究,对两次考察所获得的数据进行了整合分析,研究结果表明,该地区藏棕熊主要以动物性食物为主,其中,高原鼠兔(Ochotona curzoniae)的相对频次为37.3%和干物质量为44.7%,下同);野牦牛(Bos grunniens)分别为18.7%和30.2%;藏羚(Pantholops hodgsoni)分别为15.0%和16.2%。藏棕熊在可可西里地区有两种采食行为模式:主动捕食高原鼠兔和采食藏羚、藏原羚和野牦牛尸体。观察期间藏棕熊约用10%的时间挖掘高原鼠兔的洞穴捕捉高原鼠兔,但未见藏棕熊主动捕食大型哺乳动物。粪样分析结果发现,藏棕熊主动捕食的高原鼠兔和喜马拉雅旱獭(Marmota himalayana)和通过食腐方式获得的藏羚、藏原羚和野牦牛的生物量基本相等。     

Introgressive hybridization: brown bears as vectors for polar bear alleles

The dynamics and consequences of introgression can inform about numerous evolutionary processes. Biologists have therefore long been interested in hybridization. One challenge, however, lies in the identification of nonadmixed genotypes that can serve as a baseline for accurate quantification of admixture. In this issue of Molecular Ecology, Cahill et al. (2015) analyse a genomic data set of 28 polar bears, eight brown bears and one American black bear. Polar bear alleles are found to be introgressed into brown bears not only near a previously identified admixture zone on the Alaskan Admiralty, Baranof and Chichagof (ABC) Islands, but also far into the North American mainland. Elegantly contrasting admixture levels at autosomal and X chromosomal markers, Cahill and colleagues infer that male‐biased dispersal has spread these introgressed alleles away from the Late Pleistocene contact zone. Compared to a previous study on the ABC Island population in which an Alaskan brown bear served as a putatively admixture‐free reference, Cahill et al. (2015) utilize a newly sequenced Swedish brown bear as admixture baseline. This approach reveals that brown bears have been impacted by introgression from polar bears to a larger extent (up to 8.8% of their genome), than previously known, including the bear that had previously served as admixture baseline. No evidence for introgression of brown bear into polar bear is found, which the authors argue could be a consequence of selection. Besides adding new exciting pieces to the puzzle of polar/brown bear evolutionary history, the study by Cahill and colleagues highlights that wildlife genomics is moving from analysing single genomes towards a landscape genomics approach.     

Ancestral Polymorphisms and Sex-Biased Migration Shaped the Demographic History of Brown Bears and Polar Bears

Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.     

Quality of frozen-thawed semen in brown bear is not affected by timing of glycerol addition

We have tested several freezing protocols for brown bear semen, modifying the time when glycerol was added (before and after cooling to 5 °C). No differences were found among protocols, indicating a good tolerance of brown bear semen to glycerol. This finding indicates that freezing protocols for brown bear semen could be modified to fit practical solutions which would facilitate preparation of the seminal samples in the field with the addition of glycerol at ambient temperature.     

Cranometric Variability in Brown Bears of the Russian Far East

Morphometric analysis of 282 skulls of the brown bear Ursus arctos from the Far Eastern part of the range was carried out. The presence of two morphological clusters for both males and females is shown. Samples from two clusters were compared with their geographical location and subspecies. It was found that one cluster or another had no specific reference to the particular region or subspecies of a particular cluster, only the superiority of one over the other in a cluster of different subspecies and regions was changed. A comparison with the spread of brown bear genetic lines in the Far East of Russia is made. It was noted that the precise distribution of a particular cluster to a specific genetic line of haplotypes was not found.     

Fallot's tetralogy in a European brown bear (Ursus arctos)

A congenital heart malformation was diagnosed in a free-ranging adult female European brown bear (Ursus arctos) found dead due to intraspecific violence. At necropsy, the heart had all four features of Fallot's tetralogy. No further malformations were identified in the animal, which was of normal size and weight for its age, in normal body condition, and had probably borne young. The heart condition was considered to have contributed to death during an attack by another bear.     

Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution

Despite extensive genetic analysis, the evolutionary relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) remains unclear. The two most recent comprehensive reports indicate a recent divergence with little subsequent admixture or a much more ancient divergence followed by extensive admixture. At the center of this controversy are the Alaskan ABC Islands brown bears that show evidence of shared ancestry with polar bears. We present an analysis of genome-wide sequence data for seven polar bears, one ABC Islands brown bear, one mainland Alaskan brown bear, and a black bear (U. americanus), plus recently published datasets from other bears. Surprisingly, we find clear evidence for gene flow from polar bears into ABC Islands brown bears but no evidence of gene flow from brown bears into polar bears. Importantly, while polar bears contributed <1% of the autosomal genome of the ABC Islands brown bear, they contributed 6.5% of the X chromosome. The magnitude of sex-biased polar bear ancestry and the clear direction of gene flow suggest a model wherein the enigmatic ABC Island brown bears are the descendants of a polar bear population that was gradually converted into brown bears via male-dominated brown bear admixture. We present a model that reconciles heretofore conflicting genetic observations. We posit that the enigmatic ABC Islands brown bears derive from a population of polar bears likely stranded by the receding ice at the end of the last glacial period. Since then, male brown bear migration onto the island has gradually converted these bears into an admixed population whose phenotype and genotype are principally brown bear, except at mtDNA and X-linked loci. This process of genome erosion and conversion may be a common outcome when climate change or other forces cause a population to become isolated and then overrun by species with which it can hybridize.     

The mating system of the brown bear Ursus arctos

• 1 Research on mating systems and reproductive strategies is valuable for providing ethological knowledge, important for the management and conservation of a species, and in a broader sense, important for biodiversity conservation.
• 2 We reviewed the literature to document the mating system of the brown bear Ursus arctos. We determined that many aspects of the reproduction of the brown bear remain unclear, including (i) biological aspects, such as hormone and oestrous cycling, sperm competition, mate choice, sexually selected infanticide, etc. and (ii) human impacts on the mating system, occurring when humans alter population size and structure, through, for example, hunting or habitat degradation.
• 3 We considered three mating system classification frameworks from the literature ( Emlen & Oring 1977 , Clutton‐Brock 1989 , Shuster & Wade 2003 ) and applied various brown bear populations to them. We did this (i) to document the plasticity of the mating system of the brown bear, and (ii) to find commonalities among the reported mating system classifications in order to provide a general and common classification of the brown bear's mating system.
• 4 The mating system of the brown bear can, in general, be classed as ‘polygamous’. Subclassifications can nevertheless be valuable on smaller spatial scales.
• 5 Within the polygamous mating system of the brown bear, biological aspects and human impacts can influence reproductive strategies at the individual and population level. Mating system classification frameworks often lack a common terminology, which contributes to the variety of published classifications of the mating system of the brown bear.

     

Biomechanical consequences of rapid evolution in the polar bear lineage

The polar bear is the only living ursid with a fully carnivorous diet. Despite a number of well-documented craniodental adaptations for a diet of seal flesh and blubber, molecular and paleontological data indicate that this morphologically distinct species evolved less than a million years ago from the omnivorous brown bear. To better understand the evolution of this dietary specialization, we used phylogenetic tests to estimate the rate of morphological specialization in polar bears. We then used finite element analysis (FEA) to compare the limits of feeding performance in the polar bear skull to that of the phylogenetically and geographically close brown bear. Results indicate that extremely rapid evolution of semi-aquatic adaptations and dietary specialization in the polar bear lineage produced a cranial morphology that is weaker than that of brown bears and less suited to processing tough omnivorous or herbivorous diets. Our results suggest that continuation of current climate trends could affect polar bears by not only eliminating their primary food source, but also through competition with northward advancing, generalized brown populations for resources that they are ill-equipped to utilize.     

Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

The brown bear has proved a useful model for studying Late Quaternary mammalian phylogeography. However, information is lacking from northern continental Eurasia, which constitutes a large part of the species' current distribution. We analysed mitochondrial DNA sequences (totalling 1943 bp) from 205 bears from northeast Europe and Russia in order to characterize the maternal phylogeography of bears in this region. We also estimated the formation times of the sampled brown bear lineages and those of its extinct relative, the cave bear.
Four closely related haplogroups belonging to a single mitochondrial subclade were identified in northern continental Eurasia. Several haplotypes were found throughout the whole study area, while one haplogroup was restricted to Kamchatka. The haplotype network, estimated divergence times and various statistical tests indicated that bears in northern continental Eurasia recently underwent a sudden expansion, preceded by a severe bottleneck. This brown bear population was therefore most likely founded by a small number of bears that were restricted to a single refuge area during the last glacial maximum. This pattern has been described previously for other mammal species and as such may represent one general model for the phylogeography of Eurasian mammals. Bayesian divergence time estimates are presented for different brown and cave bear clades. Moreover, our results demonstrate the extent of substitution rate variation occurring throughout the phylogenetic tree, highlighting the need for appropriate calibration when estimating divergence times.     

Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)

In the 1930s, the Scandinavian brown bear was close to extinction due to vigorous extermination programmes in Norway and Sweden. Increased protection of the brown bear in Scandinavia has resulted in the recovery of four subpopulations, which currently contain close to 1000 individuals. Effective conservation and management of the Scandinavian brown bear requires knowledge of the current levels of genetic diversity and gene flow among the four subpopulations. Earlier studies of mitochondrial DNA (mtDNA) diversity revealed extremely low levels of genetic variation, and population structure that grouped the three northern subpopulations in one genetic clade and the southernmost subpopulation in a second highly divergent clade. In this study, we extended the analysis of genetic diversity and gene flow in the Scandinavian brown bear using data from 19 nuclear DNA microsatellite loci. Results from the nuclear loci were strikingly different than the mtDNA results. Genetic diversity levels in the four subpopulations were equivalent to diversity levels in nonbottlenecked populations from North America, and significantly higher than levels in other bottlenecked and isolated brown bear populations. Gene flow levels between subpopulations ranged from low to moderate and were correlated with geographical distance. The substantial difference in results obtained using mtDNA and nuclear DNA markers stresses the importance of collecting data from both types of genetic markers before interpreting data and making recommendations for the conservation and management of natural populations. Based on the results from the mtDNA and nuclear DNA data sets, we propose one evolutionarily significant unit and four management units for the brown bear in Scandinavia.     

Bear-hybrids: behaviour and phenotype

The behaviour of a female and a male bear hybrid (brown bear Ursus arctos x polar bear Ursus maritimus) was studied. Behavioural and morphological comparisons between the hybrids and the two parent-species were made.The observation period covered July to November 2007. Different objects were offered to the bears to evoke new patterns of behaviour. While manipulating the offered objects, both bears showed elements of behaviour also found in polar bears, though the male performed those to a larger extend. Not only in the way of manipulating objects but also in the male's type of stereotype parallels to polar bears can be drawn. Phenotypically both bears possess features of both species, brown bear and polar bear. Concerning it lighter colour of fur and the structure of hair the female hybrid resembles more a polar bear than the male. Summarising, the female appears phenotypically more like a polar bear, the male with respect to the behaviour.     

Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages

We estimated the phylogenetic relationships of brown bear maternal haplotypes from countries of northeastern Europe (Estonia, Finland and European Russia), using sequences of mitochondrial DNA (mtDNA) control region of 231 bears. Twenty-five mtDNA haplotypes were identified. The brown bear population in northeastern Europe can be divided into three haplogroups: one with bears from all three countries, one with bears from Finland and Russia, and the third composed almost exclusively of bears from European Russia. Four haplotypes from Finland and European Russia matched exactly with haplotypes from Slovakia, suggesting the significance of the current territory of Slovakia in ancient demographic processes of brown bears. Based on the results of this study and those from the recent literature, we hypothesize that the West Carpathian Mountains have served either as one of the northernmost refuge areas or as an important movement corridor for brown bears of the Eastern lineage towards northern Europe during or after the last ice age. Bayesian analyses were performed to investigate the temporal framework of brown bear lineages in Europe. The molecular clock was calibrated using Beringian brown bear sequences derived from radiocarbon-dated ancient samples, and the estimated mutation rate was 29.8% (13.3%-47.6%) per million years. The whole European population and Western and Eastern lineages formed about 175,000, 70,000 and 25,000 years before present, respectively. Our approach to estimating the time frame of brown bear evolution demonstrates the importance of using an appropriate mutation rate, and this has implications for other studies of Pleistocene populations.     

青海省人与藏棕熊冲突现状、特点与解决对策

人与野生动物冲突会造成重大经济损失,甚至造成人员伤亡,不利于野生动物的保护。藏棕熊主要分布于我国西部地区,与当地居民的冲突具有与大型食肉动物冲突的典型特点。2012-2015年我们对青海省人与藏棕熊冲突172起案件进行了统计分析,同时采用分层访谈法对86户牧民做了人与藏棕熊冲突调查,以期了解该省人与藏棕熊冲突现状,掌握冲突发生的特点和规律,探讨冲突发生的内在原因。研究结果显示：(1) 全省人与藏棕熊冲突案件集中发生在玉树州和海西州,其中玉树州治多县和曲麻莱县冲突最为严重;(2) 每年6-9月为冲突高发期,藏棕熊冬睡期的2月及11月也有发生;(3) 藏棕熊伤害类型主要表现为损毁房屋构件、取食房屋内储存的粮食以及造成人身伤亡;(4) 大部分受访者认为当地人与藏棕熊冲突事件严重,政府应以货币的形式对野生动物伤害给予适当补偿;(5) 目前牧民普遍采取的防熊措施效果并不理想。我们建议加强牧民游牧期间对房屋巡护、加固工作,建议撤户并村,妥善安置过冬食物与饲料,积极开展野生动物伤害补偿工作;同时建议进一步加强对藏棕熊的科学研究,为缓解人熊冲突现象提供科学理论依据。     

The presence of the brown bear Ursus arctos in Holocene Britain: a review of the evidence

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The dietary habits of the Brown bear (Ursus arctos) in western Greece

Knowledge of the dietary habits of an endangered species is essential to its management and conservation. The brown bear (Ursus arctos) exists in two isolated population in Greece, but only initial management actions have been taken to improve the habitat of this species. To improve our understanding of the ecology and habitat requirements of this species, we examined the dietary habits of the brown bear in the Panagia-Grevena region, of Macedonia, Greece. In total, 360 scats of brown bear were collected between 2002 and 2004 during spring, summer and autumn months. Scats were analyzed by their frequency of occurrence, volumetric and dry weights, and their importance values. Microhistological analysis was applied to estimate the proportion of wild and cultivated plants in the diet. The most important type of food in the spring was green vegetation, while, in the summer, fruits of Pyrus sp., Morus sp., Prunus sp. and Rubus sp. were important food items. In autumn, hard masts, mainly oak (Quercus sp.), were essential foods for the brown bear. The frequency of vertebrates in the diet was higher in the summer and autumn while that of invertebrates was higher in the spring. In summary, the brown bear is an omnivorous species that lives in Greece and adapts its diet according to food availability and human activities in its habitat. For this reason, human activities in the study area must take the needs and requirement of brown bears into consideration.