Onorato, D. P., Hellgren, E. C., van Den Bussche, R. A. The two sun bears have radically different, non-overlapping population histories (Supplementary Fig. Mapping Illumina reads against the polar bear genome23 yielded an average coverage of 11X. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Li, H. et al. ADS Yu, Y., Dong, J., Liu, K. J. Supervision, John Fieberg, Roles https://doi.org/10.1371/journal.pone.0185336.s001, https://doi.org/10.1371/journal.pone.0185336.s002, https://doi.org/10.1371/journal.pone.0185336.s003, https://doi.org/10.1371/journal.pone.0185336.s004, https://doi.org/10.1371/journal.pone.0185336.s005, https://doi.org/10.1371/journal.pone.0185336.s006. Engl. Read all of AFP's climate-related fact checks here. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. PubMed Central However, several nodes of the mtDNA tree differ notably from the coalescent species tree (Fig. Regional models were fit to data from either the insular and mainland countries, allowing the response of sun bears to tree cover to vary by region. We used the combined model to project population trends over time following tree cover loss. The genic view of the process of speciation. . Because the estimates (and CIs) were similar between regions, we combined data from the two regions and refit the binary regression model (Eq 2), giving . 1), they have reportedly migrated several times across continents and islands41, and numerous brown bear hybrids with other bears in either direction are known4. Ursine bears are the largest living terrestrial carnivores and have evolved during the last five million years, attaining a wide geographical distribution range (Fig. PubMed These wild polar bears are divided into 19 subspecies, 13 of which can be found in North America. Ecol. Yes Speciation with gene flow in equids despite extensive chromosomal plasticity. 4, Table 1). The best fitting substitution model was selected on 10Mb of genomic data using jModelTest 2.1.159 available in RAxML version 8.2.458 and applied to all ML analyses. Projecting range-wide sun bear population trends using tree - PLOS Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. "If you plot estimated global population over time, it may look like a rising curve. Climate skeptics often point to the growth of certain bear populations to downplay the role of humans in driving global warming, as AFP has previously reported. They consume figs in large amounts and like to eat them whole. CAS View in full-text Context 2 . If, in fact gene flow across is frequent, and can last for several hundred-thousand years after divergence, evolutionary histories of genomes will be inherently complex and phylogenetic incongruence will depict this complexity. habitat change for forest dependent species). Genome scale studies in brown and polar bears find that 8.8% of individual brown bear genomes have a polar bear origin7. Permutations of species for the DFOIL analysis including other polar, sloth and brown bear individuals show that the results are taxon independent (Table 1). Google Scholar. Science 336, 344347 (2012). Bioinforma. Tree cover (0100%) at camera traps, taken from rasters of tree cover closest in time to when cameras were active, were averaged over a 6-km2 area around camera traps to represent tree cover at the scale of a core sun bear range. and measure just 47 - 59 in. The complex phylogeny requires exceptional computational time so we analyzed only networks with up to two reticulations. Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. The two major threats to Sun bears are habitat loss and commercial hunting. (Johns Hopkins Press, 1991). The program ANGSD62 was used for admixture analysis (D-statistics) among the ursine bears using the spectacled bear-Chappari as outgroup. Nature 463, 311317 (2010). We further assume the population distribution is in equilibrium (i.e., that the number of bears is relatively constant within the surveyed habitat at the time it was surveyed [trapping periods were limited to < 3 months]) and that future changes in forest tree cover will result in similar relative and absolute densities of bears for any given level of forested tree cover. The brown bear has been shown to distribute polar bear alleles across its range7 and may therefore be a plausible vector species for genetic exchange between Asiatic bears and the polar, or American black bear. Furthermore, the geographical range of brown bears overlaps with all other ursine bear species (Fig. Methods 9, 772 (2012). Polar bears rely on sea ice to forage for the seals that they eat. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow. As such, tree cover may encompass several predictors or underlying processes that influence bears, much like greenness, a satellite derived measure of vegetation reflectance that has strong predictive power in modelling grizzly bear population dynamics [45]. PubMed Sun bear cubs are usually kept on buttress roots at the base of trees until they learn how to walk and climb properly. Writing review & editing. Red List assessments are often based on a combination of anecdotal data and expert opinion [13]. The underfur is particularly thick and black in adults, while the guard hairs are lighter. Seattle. Our study demonstrates the potential of using camera trap data to monitor threatened species even when most were collected on studies for which bears were not a primary focus. As the bootstrap replicates do not overlap, the different curves support a hypothesis of separate population dynamics (Supplementary Fig. Evol. (2005). Sun bears are noted for their intelligence; a captive bear observed sugar being stored in a cupboard then locked by a key, and later used its own claw to open the lock. Evol. Methods 9, 333337 (2012). Acad. types of bear bile products were. Resources, Population and landscape genetic analysis of the Malayan sun bear Our studies, ongoing since 1985, are focused on population dynamics, health and energetics . 4). Multiple genomic studies on polar, brown bears and the giant panda10,21,22,23 lead to a wealth of available genomic data in these species. ADS Bioinformatics 30, 13123 (2014). Little is known about the mating system of Sun bears. All rights reserved. The declines predicted by our models are unlikely to be instantaneous, and bears presumably did redistribute themselves in the landscape in the short-term, with an unknown time-lag between when deforestation occurred and the resulting population declines. The smallest species of bear in the world! Engl. Copyright AFP 2017-2023. During the same period, sun bear populations in insular southeast Asia (Malaysia, Indonesia and Brunei) were projected to have declined at a much higher rate (22%). In particular, relative use of different habitats, and thus measures of habitat suitability or selection, will vary with both habitat availability and population density [5355]. This study was supported by Hesses funding program LOEWE (Landes-Offensive zur Entwicklung Wissenschaftlich-konomischer Exzellenz) and the Leibniz Society. Reliable density estimates of regional sun bear populations would allow an area/density weighted measure to generate more accurate decline estimates. Rates of forest loss in sun bear range suggest that by 2030, the decline in the global population size of sun bears in the wild would be enough to raise their threat status from 'Vulnerable' to . J. Natl. 212, 98108 (2010). Sian Henley, an academic specializing in the polar ocean at Edinburgh University, agreed. The ice has been disappearing, with the far north warming up to four times faster than the rest of the world, according to an August 2022 study published in Nature. For these data, we recorded detection/non-detection within a known trapping period. Bioinformatics 30, (2014). We found evidence for two genetically distinct populations in the West and East of Cambodia. DNA extraction from blood samples was done in a pre-PCR environment on different occasions to avoid confusion by standard phenol/chloroform protocols and yielded between 1 to 6g DNA for each of the six bear individuals (Supplementary Table 1). I identified seven potential sun bear subpopulations; two that are fully isolated with no potential . Yes According to the PSMC analyses the Asiatic black bear maintained a stable and a relatively high long-term Ne since 500ka (Fig. However, they have been seen in farmlands, plantations, and orchards. Paired end libraries (500bp) were made by Beijing Genome Institute (BGI) using Illumina TrueSeq and sequencing was done on Illumina HiSeq2000 resulting in 100bp reads. Blue arrows show values >1%, and dashed lavender for <0.1% (Table 1). https://doi.org/10.1371/journal.pone.0185336.g004. The latter is based in part on knowledge of sea ice and habitats, Amstrup said. PubMed A block jackknife procedure (with 10Mb blocks) with parameters: -minQ 30 and -minMapQ30, was used to assess the significance of the deviation from zero. A. et al. Higher tree cover may be associated with more food resources, further distance to forest edges, and lower accessibility by humans (e.g. Un-modelled effects from hunting and habitat fragmentation pressures may cause higher declines than we have estimated. https://doi.org/10.1371/journal.pone.0185336, Editor: Tim A. Mousseau, University of South Carolina, UNITED STATES, Received: April 10, 2017; Accepted: September 11, 2017; Published: September 29, 2017. Evol. The brown bear is a likely extant candidate, because it has been and is geographically wide-spread41. It is estimated the sun bear population has declined by at least 30% in the last 30 years, and sun bears were classified as 'vulnerable' in 2007, meaning they are at high risk of extinction in the wild (IUCN 2007). Article Sun bears are among the three primary bear species specifically targeted for the bear bile ( a digestive fluid produced by the liver and stored in the gallbladder, which is used by some in traditional Chinese medicine) trade in Southeast Asia, and are kept in bear farms in Laos, Vietnam, and Myanmar. "So in half the area that polar bears reside in, we know nothing.". Future researchers might test, refine, and improve our analysis with the addition of a more informative suite of predictor variables, either at a small geographical scale, or across sun bear range as those data become available. Polar bear numbers are derived from a combination of estimates for well-studied areas and "educated guesses" for less well-known areas. Phylogenetic networks show that evolutionary histories of numerous GFs, i.e. To visually explore the data prior to model fitting, we pooled data from camera traps into % tree cover categories (<20%, 2130, 3140, 91100), and calculated the detection rate within each category by dividing the total number of cameras that detected a sun bear at least once during a trapping period by the total number of traps nights cameras were active. The reads of the other bears were mapped to the consensus sequence of the spectacled bear as described in method section. Using a complete sun bea Green, R. E. et al. The mutation rate is close to a pedigree-based mutation rate of 1.1108 changes/site/generation in humans66 that is considered to be typical for mammals. The analyses of the ursine phylogeny suggest that gene flow and not incomplete lineage sorting are major cause for the reticulations in the evolutionary tree. We are grateful to Luay Nakhleh (Rice University) for expert help with Phylo-Net analyses, Yichen Zheng for valuable comments on the manuscript and to Jon Baldur Hlidberg (www.fauna.is), and Aidin Niamir for artwork. The two sun bears have radically different, non-overlapping population histories (Supplementary Fig. Today, between 22,000 and 31,000 polar bears are living in the wild. "The apparent increase in polar bear numbers is more likely to reflect the increase in our understanding and the reliability of the data, rather than an actual increase in numbers," she said. PLoS Genet 8, e1003125 (2012). Quat. long. Conceptualization, Bears Their Biol. Sun bear | Size, Location, & Facts | Britannica Finally, there is a gene flow signal between the American and Asiatic black bears. Mus. Sun bears are found in the tropical rainforest of Southeast Asia ranging from northeastern India, Bangladesh, Myanmar, Thailand, Peninsular Malaysia, Laos, Cambodia, and Vietnam to southern Yunnan Province in China, and on the islands of Sumatra and Borneo in Indonesia. https://doi.org/10.1371/journal.pone.0185336.g002, We analyzed data separately by region to allow for potential differences in the response of bears to tree cover in the mainland and insular regions. Other efforts, using structured village workshops [27] and mark-recapture estimates by individually identifying sun bear chest markings with camera traps [63], are best suited to small spatial scales and while successful in generating robust site-level estimates of population parameters, results cannot be extrapolated to other sites, and the logistics and associated costs (time, money) of these methods make it unlikely they could be conducted over a large enough area to monitor regional or global bear populations. 11). Current Population Trend: Decreasing The reclusive sun bear, smallest member of the bear family, lives an insular life in the dense lowland forests of Southeast Asia. Weights range greatly from the sun bear, which can be as low as 35 kg (77 lb), to the polar bear, which can be as high as 726 kg (1,600 lb). A study of nuclear introns with multiple individuals for each ursine species was unable to reconstruct a well-supported species tree and suggested that incomplete lineage sorting (ILS) and/or gene flow caused the complexities in the ursine tree2. Using this criteria of one hour removed all instances of multiple consecutive photos from of a bear hanging around a camera trap, and in the resulting database no detections occurred < 3 hours apart (most occurred > 1 day apart). Writing review & editing, Affiliation In contrast to the largely random process of ILS, gene flow produces a bias in the phylogenetic signal, because it is a directed process. = 0.47 (95% CI = 0.210.78; Fig 3). Especially, the evolution of the American (Ursus americanus) and Asiatic black bear is difficult to resolve, despite being geographically separated (Fig. Get the most important science stories of the day, free in your inbox. In the absence of long-term data sets that measure sun bears response to changes in % tree cover through time, a key assumption in our approach is that it was reasonable to substitute spatial relationships for temporal ones [32,35]. Projected country-level sun bear population declines between 2000-2014 Ursus 19, 8586 (2008). This plotting of estimated numbers over time however reflects improved estimates rather than growth in numbers.". We develop a simple, replicable univariate model, relating sun bear presence to tree cover (i.e. Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Google Scholar. Bears are a prominent case where conflicting gene trees and an ambiguous fossil record1 make the interpretation of their evolutionary history difficult2. BMC Bioinformatics 9, 322 (2008). These percentages do not indicate the amount of introgressed DNA, which can be a fraction of the GF sequence. Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Data driven models have the benefit over expert opinion in that they can be repeated, and, as these models have explicit assumptions, they can also be debated, modified, and improved. The global model pooled all data, assuming bears responded similarly to tree cover throughout the range, and modelled detection/non-detection per camera trap within a trapping period using the binary regression model (Eq 2). These authors also contributed equally to this work. To generate estimates comparable with the IUCN classification of sun bears, we projected sun bear population decline between 20002030, following the IUCNs guidelines of assuming the annual rate of % tree cover change remained constant through time [30]. The animal gets its name from the characteristic orange-to-cream-colored chest patch. CAS Mol. But it is good only in a temporary sense if societies don't halt global warming.". Sun Bear | National Geographic Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. No, Is the Subject Area "Dendrology" applicable to this article? designed the research and obtained funding. Sun bear catch rates at camera traps were positively correlated with % tree cover. The insular region was projected to experience a higher relative level of decline than the mainland region (Fig 5). You are using a browser version with limited support for CSS. Proc. These have presumably a higher assembly quality than smaller fragments and still represent>96% of the genome (Supplementary Fig. and both species range between 60 - 176 lbs. 4, Supplementary Tables 4 and 5 and Supplementary Fig. which does not depend on any unknown parameters. The graph's footnote indicates the curve rests on eight sets of data, including six from the PBSG's latest status report in 2021. Some gene flow cannot have occurred directly between species, because the species exist in different habitats, but may be remnants of ancestral gene flow or gene flow through a vector species. Internet Explorer). Sun bears Helarctos malaya-nus are a forest dependent tropical bear found throughout most of Southeast Asia. The sun bear ( Helarctos malayanus) is a species in the family Ursidae (the only species in the genus Helarctos) occurring in the tropical forests of Southeast Asia. Funding acquisition, Kutschera, V. E. et al. Here we present a genome analysis of the bear family with representatives of all living species. Nat. collected the data; V.K. 5) are older than previous estimates based on nuclear gene data2, but consistent with that from mtDNA data15 (Supplementary Table 7). IUCN/SSC Polar Bear Specialist Group July 2021 Status Report 3 | P a g e historically allowed polar bears to gain enough weight in spring to survive a long summer fast. You can't trust these at all," Vongraven said. Although it is illegal to kill sun bears, laws protecting them are rarely enforced. However, former PBSG chairman Dag Vongraven of the Norwegian Polar Institute told AFP the 1965 and 1981 estimates are not valid due to limitations in tracking polar bears at the time. Conceptualization, Mitochondrial DNA Profiling Reveals Two Lineages of Sun Bears - PubMed "Data from the 50's and 60's are at best highly unreliable guesstimates that cannot be compared to the modern polar bear population monitoring methods we use today," said Thea Bechshoft, a staff scientist at Polar Bears International. Furthermore, sun bear populations respond to more than just tree cover, and site-level variation in bear population status, and the associated pressures (e.g. Yet, our knowledge of the extent of post speciation gene flow is limited, because few genomes of closely related species have been sequenced. For the mainland, for which independent catch rate data were not available, we fit binary regression models to the detection/non-detection data (Zi = 1 if detected at site i and 0 otherwise), using a complimentary log-log link: Species range maps IUCN2015 (http://www.iucnredlist.org). Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. They are shy and reclusive animals and usually do not attack humans unless provoked to do so, or if they are injured or with their cubs; their timid nature led these bears to be tamed often and kept as pets in the past. We analyzed data globally, with mainland and insular data combined, and regionally, with mainland and insular data analyzed separately (Table 1). e0185336. Graph on polar bear population uses unreliable data | Fact Check Google Scholar. Projecting range-wide sun bear population trends using tree cover and The consense program in Phylip version 3.6960 built from 18,621 ML-trees, a majority rule consensus tree. Mol. The Etruscan bear was geographically overlapping with other bear species and was, like the Asiatic black bear, widely distributed30. Science Polar Bear Population Dynamics Active By Alaska Science Center December 15, 2017 Overview Science Publications Partners Information on the status and trends of polar bear populations are needed to inform management of polar bears under US laws and international agreements. Thus, it is unlikely that American black bears came into contact with the Asiatic sun and sloth bears40. Bioinforma. A check-list with bibliography. 8596 (1994). Any other use, in particular any reproduction, communication to the public or distribution of the content of this website, in whole or in part, for any other purpose and/or by any other means, without a specific licence agreement signed with AFP, is strictly prohibited. Biol. Of all the bear species, sun bears are the smallest. Oxf. Two are extrapolations of bear counts in Alaska in 1959 and Canada in 1964; the other is a 1961 global range estimate from a Soviet scientist. Sun bears and other threatened species require long-term, systematic and standardized monitoring of population trends across space and time. A. et al. 25, 17541760 (2009). The brown bear from the Admiralty, Baranof, and Chichagof (ABC) islands groups in different arrangements with other brown and polar bears, consistent with gene flow between the two species7,8,23. Writing review & editing, Affiliation Conceptualization, No, Is the Subject Area "Forests" applicable to this article? Sun bears were detected in all levels of tree cover above 20% and detections were higher in areas of high % tree cover (Fig 2). Proc. All rights reserved. A Bayesian tree from 37 complete mt genomes (colored circles) and stars indicate the new mt genomes. Sun bears Helarctos malayanus inhabit the tropical forests of Southeast Asia, use a broad spectrum of forest types, and select habitat based on food availability and security, favoring interior forest but also using secondary, logged and regenerating burnt forests [1116]. We investigated all living Ursinae and Tremarctinae bear species based on six newly sequenced bear genomes and published ones. The extinct cave bear (Ursus spelaeus) is the sister group to polar and brown bears. Continue Reading after the facts. Article . Additional variables might include human disturbance variables such as human density, road density, levels and types of land use [57], forest types and their relative abundance of sun bear foods, agricultural lands and their relationship to forest cover and sun bear foods, spatial variation in hunting, predation and competitive pressure. Management and conservation of species and sub-populations threatened with extinction requires accurate and reproducible estimates of population trend. No, PLOS is a nonprofit 501(c)(3) corporation, #C2354500, based in San Francisco, California, US, Corrections, Expressions of Concern, and Retractions, https://doi.org/10.1371/journal.pone.0185336. Inst. Evidence from the fossil record, morphology and mitochondrial phylogeny suggested a closer relationship between the Asiatic and the American black bears13,14,15. Puckett, E. E., Etter, P. D., Johnson, E. A. Biol. Sun Bear - Facts, Diet, Habitat & Pictures on Animalia.bio (1) Previous estimates of global population trends have relied on expert opinion and cannot be systematically replicated. Science 346, 13201331 (2014). Wagner, J. Pliocene to early Middle Pleistocene ursine bears in Europe: a taxonomic overview. What are the main threats? gested that sun bear population declines associated with tree cover loss between 2000- 2014 in mainland southeast Asia were ~9%, with declines highest in Cambodia and lowest in Myanmar. The PBSG's most recent estimate for the global polar bear population is 26,000 -- an average from a range of 22,000 to 31,000. "A global estimate, therefore, is a combination of some really good numbers and others about which we are much less confident," he told AFP in an email. "Intense Arctic warming, caused by emissions of greenhouse gases by human activity has already caused, and is continuing to cause, dramatic reductions in sea ice coverage," said Sian Henley of Edinburgh University. 1). Evol. Heterozygous sites, gaps, repetitive sequences, and transposable element sequences were removed from GF alignments (Supplementary Fig. Sun bear information, pictures, video and interesting facts for kids and adults. Biol. For forest dependent species, such as sun bears, changes in tree cover over time, derived from satellite imagery, provides a standardized, model-based, objective and reproducible method to monitor changes in global populations through time, and a data driven alternative to using expert opinion to estimate population trends. 111, 1644816453 (2014). In bears, natural mating between grizzlies (brown bears Ursus arctos), and polar bears (Ursus maritimus) results in hybrid offspring, the grolars6. And the 19 distinct subpopulations of polar bears, which enable accurate counting, were not yet delineated by 1981. Phylogenetic topology testing on real and simulated sequence data shows that GFs with this information content significantly reject alternative topologies (Supplementary Figs 6 and 7). The D-statistics is limited to four-taxon topologies and therefore gene flow signals are difficult to interpret when they occur between distant species, as it cannot determine if it is a direct, indirect, or ancestral signal. Project administration, AFP and its logo are registered trademarks. Animals that do not make seasonal movements and stay in their native home ranges all year round are called not migrants or residents. SplitsTree version 461 created a consensus network from the 18,621 GF ML-trees with various threshold settings (5%, 7%, 10% and 30%), to explore the phylogenetic conflict among the bear species. & Zhang, Y. P. Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. The test assumes that the ancestral population of the in-group taxa was randomly mating and recently diverged29. This should not compromise the test as long as there was a panmictic population ancestral to the progenitor populations of the eventual daughter species at some point in time, which is a reasonable assumption. Many desirable variables, including landscape, anthropogenic and biological measures were not available for inclusion. There's very little data behind them.". A Draft Sequence of the Neandertal Genome. 20, 12971303 (2010). Nakhleh, L. Computational approaches to species phylogeny inference and gene tree reconciliation. PLoS ONE 7, e48985 (2012). But "carrying capacity" -- the number of bears that a given environment can sustain -- has held those numbers in check. In order to complete the taxon sampling of the ursine bears, reads from six previously published genomes (Supplementary Table 1) selected and on the basis of geographic distribution, availability and sequence depth and SNVs were called as described above. In addition, we analyzed the data using DFOIL-statistics26, to detect signatures of introgression. McKenna, A. et al. The D-statistic measures the excess of shared polymorphisms of two closely related lineages with respect to a third lineage18 and can thus discriminate between gene flow and ILS. It is noteworthy, that the second reticulation has a high inheritance probability (41.8%), which agrees with the strongest gene flow signal identified by DFOIL analyses (Fig. Notably, in the insular region, the upper confidence limits of our predictions meet the Red List criteria for endangered, based on a declining population trend of > 50% over a 30-year period. Harrison, R. G. & Larson, E. L. Hybridization, Introgression, and the Nature of Species Boundaries. The insular data, catch rate per camera trap, were modelled using log-linear regression (Eq 1) and the mainland data, detection/non-detection per camera trap within a trapping period, were modelled using a binary regression model with complementary log-log link (Eq 2). It shows that a migration model fits most pair wise comparisons significantly better than ILS, and is robust under a broad range of parameters (Supplementary Figs 17 and 18). We used the spatial relationship between % tree cover and sun bear density to estimate temporal population declines associated with habitat loss between 2000 and 2014 within global sun bear range.
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