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). 21). The evaluation was done in two separate analyses: (a) with a simulated data set and (b) on a data set of 500 random GFs (Supplementary Methods). Supervision, Sci. Incorporating information about local densities of sympatric Asiatic black bears, which might suppress local sun bear populations in mainland Southeast Asia in areas of high food availability [26,56], could improve estimates by accounting for species competition. Google Scholar. 94, 447462 (2016). McKenna, A. et al. CAS This assumption requires that the probability of detecting bears, when present, is similar across the range of tree cover values (if detection is lower in areas of dense forest, estimators of regression coefficients would be biased low). Orlando, L. et al. The space-for-time assumption is common in published assessments of biodiversity and ecosystem functioning, but is not always reliable; to test whether our assumption of space-for-time holds, and that our model projections are reasonable, a future study should ideally test the response of sun bear populations to tree cover with before-after control data (i.e. 19). 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. PDF Projecting range-wide sun bear population trends using tree cover and The authors declare no competing financial interests. Google Scholar. Aside from the restrictive expense of these techniques for researchers working on low budgets in the tropics, these methods have been difficult to employ with sun bears. Monitoring population trends of threatened species requires standardized techniques that can be applied over broad areas and repeated through time. X-axis:time, y-axis:effective population size (N e). The genomic era allows a detailed analyses of how gene flow from hybridization affects genomes, and has revealed much more complex evolutionary histories than previously anticipated for many species, including our own18,19,20. The use of habitat change to directly infer population change is currently one of the best available options for monitoring many threatened species for which long-term data are not available [30]. CAS A.J. PubMed Central To calculate tree cover at camera traps around the time they were active (between 2000 and 2015), we downloaded the three satellite-based tree cover rasters that were available at the time of writing from open source Global Forest Watch (www.globalforestwatch.org, accessed 14th Feb 2017). "As we've learned more, we've realized that in some of these areas, previous estimates were too low and we now believe there are more bears there than we previously thought," Amstrup said. Projecting range-wide sun bear population trends using tree - PLOS Mol. You are using a browser version with limited support for CSS. CAS Conservation Ecology Program, King Mongkuts University of Technology Thonburi, Bangkok, Thailand, Roles Sun bears Helarctos malayanus are a forest dependent tropical bear found throughout most of Southeast Asia. "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. wrote the paper with the help of all authors. As with most species distribution models, we assume regression parameters capture spatial variability in the relative density of individuals (e.g., [41]). J. Evol. Paintings by Jon Baldur Hlidberg (www.fauna.is). We found that the relative risk ratio of finding bears in 80% tree cover versus 20% tree cover was 1.46. The amount of heterozygous sites differs among species and individuals, and is highest in the Asiatic black bear genome and, as expected2 lowest in the polar bears and spectacled bears (Supplementary Fig. Three were estimated to have "likely decreased.". Kutschera, V. E. et al. The graph shows a rise from 1965 to 1981 coinciding with an international ban on polar bear hunting, which started in 1973 with exceptions for some indigenous communities. hunting, resource availability, competition), is unaccounted for in our models. Davison, J. et al. Using this space for time substitution, by assuming that the drivers of the spatial gradient between sun bears and % tree cover also drive temporal changes [35], we provide a standardized proximate measure of sun bear population change through time based on deforestation data, at least until better data become available. Our estimates are regional, and we did not combine them to create an over-all global measure of decline because sun bear densities may vary greatly between insular and mainland populations [20,56] and a simple combination would be biased and/or conceal a steeper decline in a significant part of sun bear range. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The D-statistics analyses find evidence of gene flow between most sister bear species (Fig. Increasing evidence for post-speciation gene flow among primates, canines, and equids19,20 suggests that interspecific gene flow is a common biological phenomenon. Trends Genet. As an alternative to expert opinion, changes in forest cover and rates of deforestation can be used to calculate changes in areas of occupancy and to infer population decline, by assuming that the rate of population change is equal to the rate of forest loss [8,9,29]. The topological agreement of the mtDNA tree to previous studies and placement of the new individuals corroborates that the studied individuals are representative for their species. Results of these studies cannot be readily extrapolated to other regions because they use model predictors that cannot be derived for areas outside those sampled, nor are they easily compared between sites because of differences in field methods. 8). Sun bears have been known to cause damage to crops such as oil . Raffles Bull. (A) In the coalescent species tree all branches receive 100% bootstrap support. We collected the largest catalogue of sun bear detection data to date, and made an objective estimate of global population change. The figures are based on estimates from 17 zones dating back as far as 1969. All rights reserved. Population declines associated with changes in habitat extent and quality could be driven by several cumulative and inter-related mechanisms that reduce reproductive rates and access to resources, and increase mortality [4244]. 10). Mol. We used the relationship between catch rates and tree cover across space to infer temporal trends in sun bear abundance in response to tree cover loss at country and global-scales. A. PhyloNet32 has been developed to detect hybridization events in genomic data while accounting for ILS. Numerous studies have shown how climate change and shrinking sea ice pose a threat to polar bears and their habitat. John Fieberg, Roles Mol. The ancestor of extant sun bears might have settled in the Malay Archipelago during the marine isotope stage (MIS)6. Green, R. E. et al. 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. Pease, J. Additional analysis using CoalHMM33 supports the findings of gene flow from D-, DFOIL, and PhyloNet analyses (Supplementary Fig. 8596 (1994). Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Yu, Y., Dong, J., Liu, K. J. Is the Subject Area "Trees" applicable to this article? These authors also contributed equally to this work. BMC Bioinformatics 15, 356 (2014). For the two high coverage (>30X) genomes, SNVs calling parameters (-min-coverage) were set as one-half of the average read depth after marking duplicates. Models assumed log catch rate of sun bears at camera traps was a linear function of % tree cover averaged over a 6-km2 circular area around camera traps. D.N was funded by The National Science and Technology Development Agency (NSTDA P-11-00390), International Association for Bear Research and Management (Research & Conservation grant). They breed throughout the year. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. and measure just 47 - 59 in. Evol. 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. 14). PubMed Heterozygous sites, and repeat elements were all marked N and removed using custom Perl scripts. Ursus 19, 8586 (2008). volume7, Articlenumber:46487 (2017) & Eggert, L. S. Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture. and JavaScript. The term 'viviparity' and its adjective form 'viviparous' Arboreal locomotion is the locomotion of animals in trees. long. The IUCN Red List and other sources dont provide the number of the Sun bear total population size. 20, 12971303 (2010). Conservation | Sun Bears - Oakland Zoo Cahill, J. In the mtDNA tree, the brown bears are paraphyletic, because the brown bear mt genome introgressed into the polar bear population8. Country-level declines were predicted to be the most severe in Malaysia and Indonesia, which form the bulk of the insular region. Liu, S. et al. Likewise, introgressive gene flow between south-east Asiatic bear species and polar bears requires an explanation, because they have been evolving in geographically and climatically distinct areas, from the time when polar bears diverged from brown bears and began parapatric speciation in the Arctic. Detecting gene flow for these deep divergences is difficult and therefore most of the reticulations and inconsistent trees have so far been attributed to ILS46. First the selected GFs were used to create individual ML-trees using RAxML version 8.2.458. "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. 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. Cubs are born blind and hairless. Maximum likelihood networks in a coalescent framework, thus incorporating ILS and gene flow, were inferred using PhyloNet32,64 allowing 0, 1 and 2 reticulations in 50 runs and returning the five best networks. "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. No, Is the Subject Area "Bears" applicable to this article? here. Syst. BMC Bioinformatics 9, 322 (2008). Polar Bear Population Status in the Southern Beaufort Sea & Doan-Crider, D. L. Phylogeographic Patterns within a Metapopulation of Black Bears (Ursus americanus) in the American Southwest. However, some 600 mammalian hybrids are known4 and the importance of hybridization has started to gain attention in evolutionary biology5. Article Bioinformatics 30, 13123 (2014). 28, 22392252 (2011). In addition, we analyzed the data using DFOIL-statistics26, to detect signatures of introgression. 14, 851865 (2001). 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. 109, E2382E2390 (2012). Our approach could be repeated for other cryptic forest dependent species for which optimal habitat may be reflected in selection for tree cover, such as clouded leopard Neofelis spp. It is therefore possible that some gene flow events occurred through an intermediate species. Genet. Tree cover (%) reflects differences in habitat assemblages, and is highest in tropical evergreen forests, lower in secondary degraded forest, and lowest in lowland dry dipterocarp forest (S3 Fig). Here's the most recent (8/21/2021) version of the North American Sun Bear population. This plotting of estimated numbers over time however reflects improved estimates rather than growth in numbers.". 5) are older than previous estimates based on nuclear gene data2, but consistent with that from mtDNA data15 (Supplementary Table 7). PubMed Central 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. Download scientific diagram | Location and scale of sun bear population declines between 2000-2014, based on the modelled relationship between sun bear catch rate at camera traps and % tree cover. Mol. Sun bears lead the most arboreal (tree-living) lifestyle among all bears. Garca-Rangel, S. Andean bear Tremarctos ornatus natural history and conservation. Zool. However, several nodes of the mtDNA tree differ notably from the coalescent species tree (Fig. The well-resolved coalescent species tree appears to be without conflict from genomic data. Blood samples were kindly provided by Carsten Ludwig (Allwetter Zoo Mnster), Tim Schikora (Zoo Schwerin), Christian Wenker (Basel Zoo) and Eva Martinez Nevado (Zoo Madrid). . 42, 85119 (2012). Korneliussen, T. S., Albrechtsen, A. These adorable bears are excellent climbers; they sunbathe or sleep in trees 2 to 7 meters (7 to 23 feet) above the ground. 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. 16). Additionally, the brown bear mitochondrial (mt) genome was captured by polar bears during ancient hybridization8 and polar bear alleles are distributed across brown bear populations all over the world by male-biased migration and gene flow7,9,10. Deep metazoan phylogeny: when different genes tell different stories. These bears also control the insect populations that they prey on. The poaching and trade of Malayan Sun Bears in - ResearchGate Estimated distribution of the Sun Bear - ResearchGate Article While PSMC plots from low coverage genomes may vary and not be ultimately accurate, the plots inferred for the brown, polar and American black bear are very similar to previous published on higher coverage genome (Supplementary Fig. The sequence and de novo assembly of the giant panda genome. Proc. Basic facts about Sun Bear: lifespan, distribution and habitat map, lifestyle and social behavior, mating habits, diet and nutrition, population size and status. In Europe and North America, most knowledge of population demographics of bears comes from genetic and telemetry studies (e.g. Methods 9, 333337 (2012). Two whirls occur on the shoulders, from whence the hair radiates in all directions. Useful landscape variables include habitat fragmentation metrics, which in combination with sun bear movement parameters, could be used to investigate the role of range connectivity and movement potential in determining the ability of populations to respond to losses in tree cover. Abella, J. et al. Thus, it is unlikely that American black bears came into contact with the Asiatic sun and sloth bears40. Some anima Solitary animals are those that live singly and meet only for courtship and mating. Conceptualization, Pooling the data led to narrower confidence intervals and a slightly higher estimate of 1 (the small change in the estimate is attributable to the pooling of data and reduction of the insular data to detection/non-detection data so that a common binary regression model (Eq 2) could be applied in the global model). 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. 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. 85, 140147 (2004). Heterozygous sites, gaps, repetitive sequences, and transposable element sequences were removed from GF alignments (Supplementary Fig. But experts told AFP the data used in the graph shared online are incomplete. We recorded the number of independent sun bear detections per camera trap (independent count data) at sites where camera data included timestamps for each picture, or, if time intervals between images were not known, the detection/non-detection of sun bears within a trapping period. We applied the ML approach implemented in PhyloNet32 to detect hybridization among bear species. Cast forward over 30-years, from the year 2000, by assuming a constant rate of change in tree cover, we projected population declines in the insular region that surpassed 50%, meeting the IUCN criteria for endangered if sun bears were listed on the population level. Data curation, Jarvis, E. D. et al. Using a complete sun bea Google Scholar. The mainland data were collected in Thailand, Lao Peoples Democratic Republic (here after Lao PDR) and Cambodia, and these data were assumed to be representative of all other countries in that region (Fig 1). As a result of the interaction between ice, sun, and heat, the polar regions are widely expected to warm 2-3x as much as the world average, as the map below from the Intergovernmental Panel on Climate Change (IPCC) suggests (five degrees centigrade (C) is equivalent to nine degrees Fahrenheit (F)). The most arboreal (tree-living) of all bears, the Sun bear is an excellent climber and often sunbathes or sleeps in trees 2 to 7 meters (7 to 23 feet) above the ground. Until now, polling field biologists (i.e., expert opinion) has been the only method used to generate estimates of regional and global population trends for sun bears [20]. 15) shows reticulations between ABC island brown bear and polar bears, and also between the Asiatic black bear and the ancestral branch to American black, brown and polar bears. Finally, there is a gene flow signal between the American and Asiatic black bears. 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. In the latter case, we reduced the insular data to presence-absence records and fit the binary regression model given by Eq 2 to the combined (insular and mainland) data. Historic (within 500 years) sun bear range extends southwards, from southeast Bangladesh, northeast India and southern China, throughout most of mainland southeast Asia, and all of Malaysia and Indonesia [23]. A. et al. The occurrences of gene flow and to a lesser extent ILS, of which a fraction in the phylogenetic signal cannot be excluded, suggest that the expectation of a fully resolved bifurcating tree for most species might be defied by the complex reality of genome evolution. Evol. Nakhleh, L. Computational approaches to species phylogeny inference and gene tree reconciliation. They lack hair or down, are not able to obtain food Zoochory animals are those that can disperse plant seeds in several ways. The 1965 figures come from a paragraph in a scientific meeting report and are based on three estimates. McLellan, B. Sun bear catch rates at camera traps were positively correlated with % tree cover. & Orr, H. A. Speciation. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in There's very little data behind them.". Trends Ecol. Seemingly conflicting phylogenetic signals in evolutionary analyses can be explained by incomplete lineage sorting (ILS) or gene flow among species. Asiatic black bears live in eastern Asia, including Afghanistan, Bangladesh, Bhutan, Cambodia, China, India, Islamic Republic of Iran, Japan, Democratic People's Republic of Korea, Lao People's Democratic Republic, Malaysia, Mongolia, Myanmar, Nepal, Pakistan, Russian Federation, Taiwan and Vietnam. Edwards, S. V. et al. Regardless if spectacled bear or giant panda is used as outgroup, the involved species and relative signal strengths of gene flow in the tested topologies remain the same (Supplementary Table 6). There has been no sustained statistically significant decline in any subpopulation. No, Is the Subject Area "Malaysia" applicable to this article? Click through the PLOS taxonomy to find articles in your field. Permutations of species for the DFOIL analysis including other polar, sloth and brown bear individuals show that the results are taxon independent (Table 1). PLOS ONE promises fair, rigorous peer review, Another conflict between mitogenomics, morphology and autosomal sequence data is the position of the morphologically distinct sloth bears (Ursus ursinus). We analyzed data globally, with mainland and insular data combined, and regionally, with mainland and insular data analyzed separately (Table 1). Evidence from the fossil record, morphology and mitochondrial phylogeny suggested a closer relationship between the Asiatic and the American black bears13,14,15. Sun bears stand on their hind feet for a broader view of their surroundings or smell far-off objects; they try to intimidate their enemies by displaying the chest patch if threatened. Resources, Tree cover within non-natural vegetation (e.g. To compare our estimates with the IUCNs Red List classification for sun bears, we cast our estimates over a 30-year period, assuming a constant rate of tree cover change over that period. But it is good only in a temporary sense if societies don't halt global warming.". 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. Especially, the evolution of the American (Ursus americanus) and Asiatic black bear is difficult to resolve, despite being geographically separated (Fig. Model-based projections of sun bear population change across southeast In order to create a data set with reduced assembly and mapping artefacts, genome data was masked for TEs and simple repeats19 using the RepeatMasker54 output file of the polar bear reference genome available from http://gigadb.org/23. Genome Res. We log-transformed detection rates and increased by 1 to avoid infinite values. Sun bears also feed in, and travel through non-natural vegetation, using agricultural areas close to the forest edge [1619]. Furthermore, the geographical range of brown bears overlaps with all other ursine bear species (Fig. Researchers have had difficulty in collecting viable hair samples from sun bears due to their short pelt [26] and in collecting scats, which persist for a very short time in the rainforest, and are rarely encountered [61,62]. They also break termite mounds and quickly lick and suck the contents, holding pieces of the broken mound with their front paws. A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. Polar Bears In The Wild. Precise numbers for four of the subregions are listed as "unknown.". Next all bear genomes were masked with bedtools version 2.17.055 and custom Perl scripts. 6), a migration of the Asiatic black bear into North America has not been shown. ADW: Helarctos malayanus: INFORMATION Sun bears and other threatened species require long-term, systematic and standardized monitoring of population trends across space and time. 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. empty forest syndrome; [46]). Figure has been created using ArcGIS 10 (http://desktop.arcgis.com/en/arcmap/) with base map from GADM v 2.0.