Sex-biased natal dispersal in Hokkaido brown bears revealed through mitochondrial DNA analysis

Understanding natal dispersal patterns is fundamental in the ecology and conservation biology of large wild carnivores. In this study, we used two approaches to determine genetic variation and dispersal patterns of brown bears in the Shiretoko Peninsula, eastern Hokkaido, Japan. The first approach was a large-scale genetic analysis. We analyzed haplotypes from the mitochondrial DNA (mtDNA) control region of 760 individual samples collected throughout the peninsula during 1998–2016. We detected seven haplotypes, including two that were confirmed for the first time. In females, the distribution of haplotypes was geographically structured, whereas haplotypes in males were distributed widely throughout the peninsula. Only some males in the lower peninsula had haplotypes that were not detected within the peninsula. The second approach was a local-scale genetic analysis, including intensive focal sampling in the Rusha area, a special wildlife protection area on the peninsula. Proportions of mtDNA haplotypes in adult bears were investigated and compared between the sexes. Although more than half of the females had the same haplotype, males had more diverse haplotypes, suggesting that they came to the Rusha area from other regions. Thus, our study revealed that mtDNA haplotype distribution has been maintained by female philopatry, and that bears exhibit male-biased dispersal. Furthermore, the lower peninsula appears to act as a contact zone between the peninsula and mainland Hokkaido, which is important for maintaining genetic diversity.     

Microsatellite analysis of population structure in Canadian polar bears

Attempts to study the genetic population structure of large mammals are often hampered by the low levels of genetic variation observed in these species. Polar bears have particularly low levels of genetic variation with the result that their genetic population structure has been intractable. We describe the use of eight hypervariable microsatellite loci to study the genetic relationships between four Canadian polar bear populations: the northern Beaufort Sea, southern Beaufort Sea, western Hudson Bay, and Davis Strait - Labrador Sea. These markers detected considerable genetic variation, with average heterozygosity near 60% within each population. Interpopulation differences in allele frequency distribution were significant between all pairs of populations, including two adjacent populations in the Beaufort Sea. Measures of genetic distance reflect the geographic distribution of populations, but also suggest patterns of gene flow which are not obvious from geography and may reflect movement patterns of these animals. Distribution of variation is sufficiently different between the Beaufort Sea populations and the two more eastern ones that the region of origin for a given sample can be predicted based on its expected genotype frequency using an assignment test. These data indicate that gene flow between local populations is restricted despite the long-distance seasonal movements undertaken by polar bears.     

Increased brown bear predation on sika deer fawns following a deer population irruption in eastern Hokkaido, Japan

By the 1970s, brown bears (Ursus arctos) in Hokkaido, northern Japan, were opportunistic omnivores that mainly depended on plant materials. Because the sika deer (Cervus nippon) population irrupted in eastern Hokkaido in the 1990s, we expected that brown bears might prey on sika deer fawns. First, we developed a simple and cost-effective method of monitoring possible bear predation on deer fawns by analyzing the widths of deer hairs remained in bear scats. Based on hair thickness standards, we distinguished the brown bear consumption of deer fawns from adults by analyzing bear scats (n?=?108) collected during the deer birthing season (late May?Clate July) in 1999?C2008. To evaluate the importance of fawns to bears, we compared the occurrence of fawn and adult deer hairs in bear scats among three periods (I, 1999?C2000; II, 2003?C2005; III, 2006?C2008) in eastern Hokkaido. The occurrence of fawn hairs in bear scats increased from 12.5 to 27.3?% in volume and from 6.3 to 33.6?% in frequency from period I to period III, whereas adult hairs in scats decreased from 42.8 to 26.1?% in volume and from 34.4 to 22.7?% in frequency during the same time. These data suggest that bears increasingly preyed on deer fawns after the deer population irruption and decreasingly used adult carcasses because of the enforcement of deer carcass treatment by the Hokkaido government.     

Selection of rub trees by brown bears (Ursus arctos) in Hokkaido, Japan

Tree rubbing by brown bears (Ursus arctos) is a well-known behavior throughout the animal’s distribution. There is still insufficient information on the characteristics and function of the behavior. We investigated seasonal frequency of tree rubbing by brown bears, characteristics and reasons for selection of rub trees, and characteristics of bear signs on and around rub trees in a mixed coniferous–broad-leaved deciduous forest in Hokkaido, Japan. Between 1998 and 2009, we found 172 rub trees and confirmed 995 tree rubbings. We found that the rub trees were used repeatedly by bears within a year and for multiple years (more than 10 years). Tree rubbing by brown bears was observed from April to November, with a peak between May and June that corresponds to the mating season of brown bears. Abies sachalinensis was selected and broad-leaved trees were avoided for tree rubbing based on estimated availability in natural forest. The preference for Abies sachalinensis might be because the strong odor of resin attracts bears for rubbing their head and neck in resinous substances and for increasing the detectability of their markings by receptor bears. Selected trees for rubbing were located right beside the trail on relatively level ground among trees along roads or trails. Trees had a relatively large diameter at breast height. These characteristics would also serve to increase the access and detectability of their markings. Series of pad-shaped depressions was the most frequently observed (70 %) indication of bear rubbing, followed by debarking (51 %) and clawing (30 %). In terms of visual and olfactory signal amplification, physical damage by bears to the trees might have a function to enhance the smell as a result of increase in outflow of the resin. We conclude that tree rubbing behavior is associated with the mating season of brown bears and that the main purpose of this behavior is scent marking to communicate intraspecifically during the mating season.     

黑龙江省完达山东部林区马鹿种群遗传多样性的微卫星分析

黑龙江省完达山东部林区是东北马鹿(Cervus elaphus xanthopygus)种群密度较高的分布区之一,本文对2年冬季采集的167份马鹿粪便进行了7个微卫星座位的个体识别,评价了马鹿种群遗传多样性,并分析近期马鹿数量的急剧下降对种群遗传结构的影响。结果表明:167份粪便DNA分属66只个体;种群平均等位基因数9.00±2.77;平均有效等位基因数3.97±0.99;平均多态信息含量0.69±0.09;平均期望杂合度0.74±0.08;平均观察杂合度0.69±0.08。整个种群显著偏离Hardy-Weinberg平衡,但种群固定系数Fis为0.060,没有显著偏离零。可见,完达山东部林区马鹿种群遗传多样性较高,数量的急剧下降近期还没有表现在种群遗传结构上。     

Estimation of breeding population size using DNA‐based pedigree reconstruction in brown bears

Robust estimates of demographic parameters are critical for effective wildlife conservation and management but are difficult to obtain for elusive species. We estimated the breeding and adult population sizes, as well as the minimum population size, in a high‐density brown bear population on the Shiretoko Peninsula, in Hokkaido, Japan, using DNA‐based pedigree reconstruction. A total of 1288 individuals, collected in and around the Shiretoko Peninsula between 1998 and 2020, were genotyped at 21 microsatellite loci. Among them, 499 individuals were identified by intensive genetic sampling conducted in two consecutive years (2019 and 2020) mainly by noninvasive methods (e.g., hair and fecal DNA). Among them, both parents were assigned for 330 bears, and either maternity or paternity was assigned to 47 and 76 individuals, respectively. The subsequent pedigree reconstruction indicated a range of breeding and adult (≥4 years old) population sizes: 128–173 for female breeders and 66–91 male breeders, and 155–200 for female adults and 84–109 male adults. The minimum population size was estimated to be 449 (252 females and 197 males) in 2019. Long‐term continuous genetic sampling prior to a short‐term intensive survey would enable parentage to be identified in a population with a high probability, thus enabling reliable estimates of breeding population size for elusive species.     

Age estimation based on blood DNA methylation levels in brown bears

Age is an essential trait for understanding the ecology and management of wildlife. A conventional method of estimating age in wild animals is counting annuli formed in the cementum of teeth. This method has been used in bears despite some disadvantages, such as high invasiveness and the requirement for experienced observers. In this study, we established a novel age estimation method based on DNA methylation levels using blood collected from 49 brown bears of known ages living in both captivity and the wild. We performed bisulfite pyrosequencing and obtained methylation levels at 39 cytosine-phosphate-guanine (CpG) sites adjacent to 12 genes. The methylation levels of CpGs adjacent to four genes showed a significant correlation with age. The best model was based on DNA methylation levels at just four CpG sites adjacent to a single gene, SLC12A5, and it had high accuracy with a mean absolute error of 1.3 years and median absolute error of 1.0 year after leave-one-out cross-validation. This model represents the first epigenetic method of age estimation in brown bears, which provides benefits over tooth-based methods, including high accuracy, less invasiveness, and a simple procedure. Our model has the potential for application to other bear species, which will greatly improve ecological research, conservation, and management.     

Unfolding of population structure in Baltic sheep breeds using microsatellite analysis

Studies of domestic animals are performed on breeds, but a breed does not necessarily equate to a genetically defined population. The division of sheep from three native and four modern Baltic sheep breeds was studied using 21 microsatellite loci and applying a Bayesian clustering method. A traditional breed-wise approach was compared to that relying on the pattern of molecular diversity. In this study, a breed was found to be inconsistent with a distinct genetic population for three reasons: (i) a lack of differentiation between modern Baltic breeds, since the majority of the studied sheep formed a single population; (ii) the presence of individuals of foreign ancestry within the breed; and (iii) an undefined local Saaremaa sheep was referred to as a breed, but was shown to consist of separate populations. In the breed-wise approach, only the clearly distinct Ruhnu sheep demonstrated low within-breed variation, although the newly identified Saaremaa populations also have low variability. Providing adequate management recommendations for the Saaremaa sheep is not possible without further studies, but the potential harmful effects of inbreeding in the Ruhnu sheep could be reduced through the use of two genetically related Saaremaa populations. In other breeds, excessive crossing appears to be a larger concern than inbreeding. Assigning individuals into populations based on the pattern of genetic diversity offers potentially unbiased means of elucidating the genetic population structure of species. Combining these genetic populations with phenotypic and aetiological data will enable formulation of the most informed recommendations for gene resource management.     

Seasonal and diel movement patterns of brown bears in a population in southeastern Europe

Most animals concentrate their movement into certain hours of the day depending on drivers such as photoperiod, ambient temperature, inter‐ or intraspecific competition, and predation risk. The main activity periods of many mammal species, especially in human‐dominated landscapes, are commonly set at dusk, dawn, and during nighttime hours. Large carnivores, such as brown bears, often display great flexibility in diel movement patterns throughout their range, and even within populations, striking between individual differences in movement have been demonstrated. Here, we evaluated how seasonality and reproductive class affected diel movement patterns of brown bears of the Dinaric‐Pindos and Carpathian bear populations in Serbia. We analyzed the movement distances and general probability of movement of 13 brown bears (8 males and 5 females) equipped with GPS collars and monitored over 1–3 years. Our analyses revealed that movement distances and probability of bear movement differed between seasons (mating versus hyperphagia) and reproductive classes. Adult males, solitary females, and subadult males showed a crepuscular movement pattern. Compared with other reproductive classes, females with offspring were moving significantly less during crepuscular hours and during the night, particularly during the mating season, suggesting temporal niche partitioning among different reproductive classes. Adult males, solitary females, and in particular subadult males traveled greater hourly distances during the mating season in May‐June than the hyperphagia in July–October. Subadult males significantly decreased their movement from the mating season to hyperphagia, whereas females with offspring exhibited an opposite pattern with almost doubling their movement from the mating to hyperphagia season. Our results provide insights into how seasonality and reproductive class drive intrapopulation differences in movement distances and probability of movement in a recovering, to date little studied, brown bear population in southeastern Europe.     

Assumed and inferred spatial structure of populations: the Scandinavian brown bears revisited

We reanalysed the spatial structure of the Scandinavian brown bear (Ursus arctos) population based on multilocus genotypes. We used data from a former study that had presumed a priori a specific population subdivision based on four subpopulations. Using two independent methods (neighbour-joining trees and Bayesian assignment tests), we analysed the data without any prior presumption about the spatial structure. A subdivision of the population into three subpopulations emerged from our study. The genetic pattern of these subpopulations matched the three geographical clusters of individuals present in the population. We recommend considering the Scandinavian brown bear population as consisting of three (instead of four) subpopulations. Our results underline the importance of determining genetic structure from the data, without presupposing a structure, even when there seems to be good reason to do so.     

Range-wide population genetic structure of the European bitterling (Rhodeus amarus) based on microsatellite and mitochondrial DNA analysis

An understanding of recent evolutionary processes is essential for the successful conservation and management of contemporary populations, especially where they concern the introduction or invasion of species outside their natural range. However, the potentially negative implications of intraspecific introductions and invasions have attracted less attention, although they also represent a potential threat to biodiversity, and are commonly facilitated through human activities. The European bitterling (Rhodeus amarus) is a small cyprinid fish that decreased greatly in its distribution during the 1970s and 1980s and was subsequently included on many European conservation lists. This decline appears to have reversed, and the extent of its distribution now exceeds its former range. We used a combination of 12 microsatellite markers and cytochrome b sequences on a large data set (693 individuals) across the current range of the European bitterling to investigate possible scenarios for its colonization of Europe. We show that the inferred history of colonization of Europe was largely congruent between mitochondrial and nuclear markers. The most divergent mtDNA lineages occur in the Aegean region but probably are not reproductively isolated as the Aegean populations also displayed mtDNA haplotypes from other lineages and nuclear data indicated their close relationship to Danubian populations. Much of Europe is currently populated by descendants of two main lineages that came to natural secondary contact in western Europe. An approximate Bayesian computation analysis indicates different dates for admixture events among western and central European populations ranging from the last deglaciation (natural) to the last few centuries (human-assisted translocations).     

Phylogeography of mitochondrial DNA variation in brown bears and polar bears

We analyzed 286 nucleotides of the middle portion of the mitochondrial cytochrome b gene of 61 brown bears from three locations in Alaska and 55 polar bears from Arctic Canada and Arctic Siberia to test our earlier observations of paraphyly between polar bears and brown bears as well as to test the extreme uniqueness of mitochondrial DNA types of brown bears on Admiralty, Baranof, and Chichagof (ABC) islands of southeastern Alaska. We also investigated the phylogeography of brown bears of Alaska's Kenai Peninsula in relation to other Alaskan brown bears because the former are being threatened by increased human development. We predicted that: (1) mtDNA paraphyly between brown bears and polar bears would be upheld, (2) the mtDNA uniqueness of brown bears of the ABC islands would be upheld, and (3) brown bears of the Kenai Peninsula would belong to either clade II or clade III of brown bears of our earlier studies of mtDNA. All of our predictions were upheld through the analysis of these additional samples.     

Temporal changes of genetic population structure and diversity in the endangered Blakiston's fish owl (Bubo blakistoni) on Hokkaido Island, Japan, revealed by microsatellite analysis

The Blakiston's fish owl (Bubo blakistoni) population on Hokkaido Island, Japan, decreased to less than one hundred individuals over the last century due to habitat disruption by human activity. Although the ongoing conservation management has slightly restored the population, it remains endangered. In order to assess the genetic variation and population structure of the Blakiston's fish owl in Hokkaido, we genotyped eight microsatellite loci on 120 individuals sampled over the past three decades. The genotype data set showed low levels of genetic variation and gene flow among the geographically isolated five subpopulations. Comparative analysis of past and current populations indicated that some alleles shared by past individuals had been lost, and that genetic variation had declined over the last three decades. The result suggests that the genetic decline may have resulted from inbreeding and/or genetic drift due to bottlenecks in the Hokkaido population. The present study provides invaluable genetic information for the conservation and management of the endangered Blakiston's fish owl in Hokkaido.     

Estimating the spatial distribution of wintering little brown bat populations in the eastern United States

Depicting the spatial distribution of wildlife species is an important first step in developing management and conservation programs for particular species. Accurate representation of a species distribution is important for predicting the effects of climate change, land‐use change, management activities, disease, and other landscape‐level processes on wildlife populations. We developed models to estimate the spatial distribution of little brown bat (Myotis lucifugus) wintering populations in the United States east of the 100th meridian, based on known hibernacula locations. From this data, we developed several scenarios of wintering population counts per county that incorporated uncertainty in the spatial distribution of the hibernacula as well as uncertainty in the size of the current little brown bat population. We assessed the variability in our results resulting from effects of uncertainty. Despite considerable uncertainty in the known locations of overwintering little brown bats in the eastern United States, we believe that models accurately depicting the effects of the uncertainty are useful for making management decisions as these models are a coherent organization of the best available information.     

Evidence of non-hibernation in Cantabrian brown bears

Evidence of non-hibernation in brown bears Ursus arctos Linnaeus, 1758 on the Iberian Peninsula has existed since the Middle Ages. We systematically monitored brown bears in the Cantabrian Mountains (Northern Spain) by recording tracks and sightings from 1998 to 2007 to document hibernation behaviour. Our results indicate that females with yearlings and solitary yearlings were more active in winter than bears over two years old. Intensive snow tracking and direct observations of five family groups indicated that they travelled, fed and defecated in winter, which are activities not compatible with the physiological state of hibernation. Also, based on tracking data, the maximum period between two consecutive locations of active family groups in winter was less than that needed by bears to emerge from a state of hibernation (6 days). We conclude that the family groups which we monitored in winter did not hibernate.     

Benefit of migration in a female sika deer population in eastern Hokkaido,Japan

The major factors affecting migration in large herbivores have been shown to be access to food resources and the risk of predation. Three migratory types of deer (resident, north migrant and east migrant) occur within a wintering female sika deer (Cervus nippon) population in eastern Hokkaido, Japan. We tested the hypothesis that north and east migrants feed on a higher quality diet than residents during summer, based on analyses of fecal nitrogen content. Fresh fecal pellets were collected in 18 summer ranges in the wintering area, northern area and eastern area between 1–5 August 2000. Fecal nitrogen content for all sampling sites was positively correlated with elevation, but was not correlated with distance from the wintering area. North migrants that inhabited higher (above 300m elevation) summer ranges fed on a higher quality diet than residents. In contrast, the dietary quality of east migrants that migrated over a long distance and inhabited lower (below 300m elevation) summer ranges was similar to that of residents. We conclude that east migrants may have gained significant benefit from the use of agricultural pastures with low population density conditions and without hunting; however, the recent population control program has reduced this benefit by avoiding the use of pasturelands.     

The relative importance of direct and indirect effects of hunting mortality on the population dynamics of brown bears

There is increasing evidence of indirect effects of hunting on populations. In species with sexually selected infanticide (SSI), hunting may decrease juvenile survival by increasing male turnover. We aimed to evaluate the relative importance of direct and indirect effects of hunting via SSI on the population dynamics of the Scandinavian brown bear (Ursus arctos). We performed prospective and retrospective demographic perturbation analyses for periods with low and high hunting pressures. All demographic rates, except yearling survival, were lower under high hunting pressure, which led to a decline in population growth under high hunting pressure (λ = 0.975; 95% CI = 0.914–1.011). Hunting had negative indirect effects on the population through an increase in SSI, which lowered cub survival and possibly also fecundity rates. Our study suggests that SSI could explain 13.6% of the variation in population growth. Hunting also affected the relative importance of survival and fecundity of adult females for population growth, with fecundity being more important under low hunting pressure and survival more important under high hunting pressure. Our study sheds light on the importance of direct and indirect effects of hunting on population dynamics, and supports the contention that hunting can have indirect negative effects on populations through SSI.     

Recombination and local population structure of the root endophytic fungus Glutinomyces brunneus based on microsatellite analyses

Dispersal limitation can affect the distribution pattern of organisms. Little is known, however, about the dispersal ecology of root endophytic fungi such as Glutinomyces brunneus (Hyaloscyphaceae, Helotiales), whose dispersal structure has not been observed. To examine gene flow on a local (<8 km) scale, we collected G. brunneus isolates from three sites encompassing four Quercus serrata- and Castanopsis cuspidata-dominated subsites. No significant linkage disequilibrium was detected among seven of eight newly developed microsatellite loci, which indicates that recombination has taken place in this species. Significant population structure was observed on a site-wide scale, which suggests limited dispersal across sites and/or frequent within-site gene flow. At the same time, the occurrence of identical multilocus genotypes at different sites suggests the occurrence of dispersal events, possibly infrequent. Our results provide novel information on the local dispersal ability of root endophytic fungi.     

Genetic population structure of Norwegian brown trout

Biochemical genetic variation in populations of anadromous and resident brown trout, Salmo trutta L., was studied. Altogether 50 Norwegian populations were screened for 32 enzyme loci. Genetic polymorphism was found at the following 11 loci: AAT-4 * (E.C. 2.6.1.1), CK-1 * (E.C. 2.7.3.2), G3PDH-2 * (E.C. 1.1.1.8), IDHP-2 * (E.C. 1.1.1.42), LDH-5 * (E.C. 1.1.1.27), MDH-2 * (E.C. 1.1.1.37), MDH-3/4 * (E.C. 1.1.1.37), MEP-2 * (E.C. 1.1.1.40), GPI-2 * (E.C. 5.3.1.9). GPI-5 * (E.C. 5.3.1.9) and PGM-1 * (E.C. 5.4.2.2), giving an overall polymorphism of 34%, ranging from 3.7 to 29.6% among individual populations. The average calculated heterozygosity ranged from 1.4 to 10.2% among populations. Genetic heterogeneity was observed among anadromous populations, and significant differences in allelic frequencies were found between anadromous populations in neighbouring watercourses, among resident populations and between anadromous and resident populations inhabiting the same watercourses. Significant heterogeneity was also found among 12 populations from Lake Mjøsa, with a major division between the western and eastern populations of the lake. Differences in allelic frequencies were found between wild stocks and their hatchery derivatives, and between different hatchery derivatives originating from the same wild population. In some cases release of hatchery populations into wild stocks may have influenced the genetic characteristics of wild stocks. The data support the hypothesis of eastern as well as western postglacial colonization lines for Norwegian brown trout.