Phylogeography and population structure of the Japanese wild boar Sus scrofa leucomystax: mitochondrial DNA variation

Phylogeographic characteristics and population structure of Japanese wild boar (Sus scrofa leucomystax) were investigated using mitochondrial DNA (mtDNA) sequence data. Sixteen Japanese wild boar haplotypes detected from partial sequences of the mtDNA control region (574-bp) from 180 Japanese wild boar specimens from 10 local populations on Honshu, Shikoku, and Kyushu islands and 41 haplotypes from other S. scrofa were analyzed using the neighbor-joining method. The Japanese wild boars were more closely related to Northeast Asian wild boars from Mongolia than to the other Asian continental S. scrofa. The Japanese and Northeast Asian wild boars were not significantly distinguished by corrected average pairwise difference analysis. The ancestors of Japanese wild boars are suggested to have been part of the continental S. scrofa population that spread from Southeast to Northeast Asia during the Middle to Late Pleistocene. The Japanese wild boar mtDNA haplotype cladogram shows 95% parsimoniously plausible branch connections supporting three sympatric clades. Nested clade analysis indicates that these three clades are the result of distinct historical events or gene flow. The present population of Japanese wild boars may have been formed by a few independent migrations of distinct clades from the continent with subsequent mixing on the Japanese Islands.     

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.     

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.     

Pleistocene and Holocene rhinocerotids (Mammalia,Perissodactyla) from the Indochinese Peninsula

Rhinocerotids were abundant and diverse in southern Asia during the Pleistocene and the Holocene epochs, as shown by palaeontological and archaeological discoveries published throughout the last century, whereas the only living rhinoceros in the Indochinese Peninsula is Rhinoceros sondaicus (Cat Loc Reserve, Vietnam). The Pleistocene-Holocene Indochinese rhinocerotid record consists of the extinct species Dicerorhinus gwebinensis (Early Pleistocene, Myanmar) and representatives of the Recent Asian Species Rhinoceros unicornis (Middle-Late Pleistocene), R. sondaicus (Middle Pleistocene-Recent), and Dicerorhinus sumatrensis (Middle Pleistocene-Holocene). This fossil record is synthesized, mapped for Early/Middle/Late Pleistocene and Holocene/Recent times, and then compared with coeval rhinocerotid assemblages from the adjacent areas (South China), subregions (Indian, Sundaic, Philippine, and Wallacean), and region (Palearctic), from a biochronological and biogeographical perspective.     

人熊冲突缓解措施研究进展——以三江源国家公园为例

人与熊科动物之间的冲突已成为亚洲、欧洲和美洲地区的一个普遍问题,科学有效的人熊冲突管控措施有助于人熊共存机制的建立。目前,全球范围内肇事熊科动物涉及7种,分别为棕熊、亚洲黑熊、美洲黑熊、北极熊、马来熊、懒熊和眼镜熊。肇事类型主要包括伤人、捕食牲畜、入侵房屋、损害庄稼、袭击蜂箱以及翻食垃圾。引发人熊冲突的原因与人类活动范围扩大、熊科动物种群数量上升、熊科动物生境质量下降、熊科动物自然食源周期性短缺、人类食物来源易获得性以及公众对肇事熊的容忍度下降有关。国际上已有的人熊冲突缓解措施包括物理措施、生物措施、化学措施以及政策导向性措施,然而,多数措施的制定仅停留在措施本身的技术层面上,缺乏对地方实际情况和冲突驱动因素的分析。西藏棕熊属于棕熊的一种稀有亚种,生活在靠近人类的中亚高海拔地区。在中国三江源国家公园地区,人类与西藏棕熊的冲突引起了人们的关注,为协助制订有效的保育目标、解决区内人熊冲突问题,提出以下缓解建议:(1)缓解措施的制定需因地而异,综合考虑地方实际情况,如地理环境、法律法规、民俗文化以及宗教信仰等;(2)冲突类型多样,防熊措施需持续更新与完善;(3)加强人类社会发展与熊科动物生存之间的关系研究,探索人们生产生活方式的改变与熊科动物行为变化之间的关系;(4)加强棕熊生态学方面的研究,从棕熊生境质量、种群动态、自然食源以及生态系统完整性等方面去深入挖掘人熊冲突的驱动因素,进而从根本上制定缓解措施,促进三江源国家公园地区人熊共存。     

A Phylogeny of the Bears (Ursidae) Inferred from Complete Sequences of Three Mitochondrial Genes

Complete sequences of DNA are described for the cytochrome b, tRNA^Thrand tRNA^Progenes of mitochondria of four extant species of ursids and compared to sequences of four other species of ursids previously studied by us. Phylogenetic analyses indicate that the giant panda and the spectacled bear are the basal taxa of the ursid radiation. The ursines, a group which includes the sun bear, sloth bear, American black bear, Asiatic black bear, brown bear, and polar bear, experienced a rapid radiation during the mid Pliocene to early Pleistocene. The Asiatic black bear and American black bear are sister taxa. The brown bear and polar bear are the most recently derived of the ursines, with the polar bear originating from within a clade of brown bears during the Pleistocene. This paraphyletic association suggests that the rate of morphological evolution may be accelerated relative to that of molecular evolution when a new ecological niche is occupied. Calibration of the corrected average number of nucleotide differences per site with the fossil record indicates that transitions at third positions of codons in the ursid cytochrome b gene occur at a rate of approximately 6% per million years, which is considerably slower than comparable values reported for other species of mammal.     

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.     

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.     

河南舞阳县贾湖遗址中的龟鳖类

本文记述了贾湖遗址中的龟鳖类甲壳。主要为现生黄缘闭壳龟（Ｃｕｏｒａ ｆｌａｖｏｍａｒｇｉｎａｔａ）,背、腹甲完整者有５０多件。其它龟类和鳖类只有部分甲壳或碎片为代表。文中除属种鉴定外,还对甲壳上的个体变异和有关人类活动等问题作了探讨。     

Dental anthropological indications of agriculture among the Jomon people of central Japan. X. Peopling of the Pacific

The high rate of crown caries (8.6%; 119/1,377 teeth) and other oral pathologies in 101 central Japan Middle to Late Jomon Period (ca. 1000 B.C.) crania indicate a level of carbohydrate consumption consistent with an agriculture hypothesis. Because Jomon dental crown and root morphology shows strong resemblances with past and present Southeast Asians, but not with ancient Chinese or modern Japanese, Jomon agriculture could be of great antiquity in the isolated Japanese islands. These dental data and other assembled facts suggest that ancestral Jomonese might have carried to Japan a cariogenic cultigen such as taro before the end of the Pleistocene from tropical Sundaland by way of the now-submerged east Asian continental shelf.     

Functional dietary response of Asian black bears to changes in sika deer density

Omnivores are generally opportunistic foragers and have a flexible dietary response to resource abundance and availability. Their populations may consist of individuals that differ from each other in terms of their trophic positions, which implies that the dietary response to resource fluctuations differs within a population. We investigated how changes in the abundance of sika deer (Cervus nippon) affected dietary variation and body condition in the Asian black bear (Ursus thibetanus). We used fecal analysis, nitrogen stable isotopes (δ¹⁵N), and body measurements to determine whether the variation in dietary meat content of Asian black bears is positively related to variations in the density of the sika deer population, whether male bears have a higher trophic position compared to females, and whether dietary meat content is positively related with body mass or body condition of bears. We found a positive correlation between the occurrence of deer remains in bear feces and deer density, suggesting that bears change their diet in response to temporal changes in deer density. Male bears had higher δ¹⁵N values than females, and neither values varied when deer density decreased. Males selectively consumed deer after a reduction in deer density, whereas females consistently consumed more plant-based diet. The δ¹⁵N values were positively related with body mass of adult (>4 yr) bears but had no relationship with body condition of bears of either sex or any age class. Deer seem to be an important food source for large adult males, which have an advantage in mating. Thus, increasing herbivore abundance and availability altered the foraging strategy of Asian black bears, but the importance of herbivore on bear diet differs within a population.     

Genetic status of Asiatic black bear (Ursus thibetanus) reintroduced into South Korea based on mitochondrial DNA and microsatellite loci analysis

The Asiatic black bear is one of the most endangered mammals in South Korea owing to population declines resulting from human exploitation and habitat fragmentation. To restore the black bear population in South Korea, 27 bear cubs from North Korea and Russian Far East (Primorsky Krai) were imported and released into Jirisan National Park, a reservoir of the largest wild population in South Korea, in 2004. To monitor the success of this reintroduction, the genetic diversity and population structure of the reintroduced black bears were measured using both mitochondrial and nuclear DNA markers. Mitochondrial D-loop region DNA sequences (615 bp) of 43 Japanese black bears from previous study and 14 Southeast Asian black bears in this study were employed to obtain phylogenetic inference of the reintroduced black bears. The mitochondrial phylogeny indicated Asiatic black bear populations from Russian Far East and North Korea form a single evolutionary unit distinct from populations from Japan and Southeast Asia. Mean expected heterozygosity (H(E)) across 16 microsatellite loci was 0.648 for Russian and 0.676 for North Korean populations. There was a moderate but significant level of microsatellite differentiation (F(ST) = 0.063) between black bears from the 2 source areas. In addition, genetic evidences revealed that 2 populations are represented as diverging groups, with lingering genetic admixture among individuals of 2 source populations. Relatedness analysis based on genetic markers indicated several discrepancies with the pedigree records. Implication of the phylogenetic and genetic evidences on long-term management of Asiatic black bears in South Korea is discussed.     

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.     

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.     

Hominin teeth from the early Late Pleistocene site of Xujiayao,Northern China

It is generally accepted that from the late Middle to the early Late Pleistocene (～340–90 ka BP), Neanderthals were occupying Europe and Western Asia, whereas anatomically modern humans were present in the African continent. In contrast, the paucity of hominin fossil evidence from East Asia from this period impedes a complete evolutionary picture of the genus Homo, as well as assessment of the possible contribution of or interaction with Asian hominins in the evolution of Homo sapiens and Homo neanderthalensis. Here we present a comparative study of a hominin dental sample recovered from the Xujiayao site, in Northern China, attributed to the early Late Pleistocene (MIS 5 to 4). Our dental study reveals a mosaic of primitive and derived dental features for the Xujiayao hominins that can be summarized as follows: i) they are different from archaic and recent modern humans, ii) they present some features that are common but not exclusive to the Neanderthal lineage, and iii) they retain some primitive conformations classically found in East Asian Early and Middle Pleistocene hominins despite their young geological age. Thus, our study evinces the existence in China of a population of unclear taxonomic status with regard to other contemporary populations such as H. sapiens and H. neanderthalensis. The morphological and metric studies of the Xujiayao teeth expand the variability known for early Late Pleistocene hominin fossils and suggest the possibility that a primitive hominin lineage may have survived late into the Late Pleistocene in China. Am J Phys Anthropol 156:224–240, 2015. © 2014 Wiley Periodicals, Inc.     

Distinguishing Asiatic Black Bears and Sun Bears by Claw Marks on Climbed Trees

Abstract: Asiatic black bears (Ursus thibetanus) and sun bears (Helarctos malayanus) are sympatric in mainland Southeast Asia and face similar threats of habitat loss and commercial poaching. They are rarely seen but leave distinct signs, especially claw marks on climbed trees. These markings, which are potentially valuable indicators of presence, population status, and behavior of black bears and sun bears, have limited usefulness if the 2 species cannot be differentiated. We measured 121 claw mark imprints on climbed trees from 43 known (mainly captive) individual black bears and sun bears of both sexes in Thailand and Cambodia. The span across the markings made by 3, 4, or 5 claws from the hind foot was significantly greater for black bears than sun bears. We developed discriminant function models with these variables and arranged them in a 3-step process that distinguished claw marks as either sun bear, black bear, or indeterminate. This procedure correctly classified 95% of claw marks from the experimental animals. Tested on wild bears (at sites where only one species occurred), the procedure correctly classified 91% of claw marks of black bears in China (n = 94) and 100% of claw marks of sun bears in Indonesia (n = 32). The main limitation of the method was in distinguishing young, small black bears (cubs and yearlings) from sun bears. Nevertheless, application of these findings will be valuable in bear research and monitoring programs throughout Southeast Asia, where sign surveys have, until now, been hampered by the inability to differentiate these 2 ecologically and behaviorally similar species. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):814–821; 2008)