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![Geographic distribution of the giant panda. The samples in this study are indicated by the red dot. The historical geographic distribution is indicated by light green shading. Different extant populations are shown by different colors, as indicated by the key at the top left of the figure [7,9].](profile/Guilian-Sheng/publication/324279940/figure/fig1/AS:613019910410240@1523166744599/Geographic-distribution-of-the-giant-panda-The-samples-in-this-study-are-indicated-by.png)
Geographic distribution of the giant panda. The samples in this study are indicated by the red dot. The historical geographic distribution is indicated by light green shading. Different extant populations are shown by different colors, as indicated by the key at the top left of the figure [7,9].
Source publication
The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controve...
Contexts in source publication
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... samples of Holocene sub-fossil giant pandas (Specimens Nos.: 05001, 97001) were collected from a natural sinkhole, 41-60 m deep from the surface, at Jiangdong Hill, Tengchong County in Yunnan Province, south-western China (Figure 1). The samples were associated with Elephas maximus, Bos gaurus, Dicerorhinus sumatraensis, Equus yunnanesis, Cervus unicolor, and several other species [34][35][36][37]. They were accelerator mass spectrometry (AMS)-radiocarbon dated at the Quaternary Geology and Archaeological Chronology Laboratory at Peking University at 5025 ± 35 (No. 05001) and 8470 ± 45 (No. 97001) years B.P. respectively [37]. These dates are the latest record of the giant panda before it disappeared from Yunnan Province. ...
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... DNA extractions and polymerase chain reactions (PCRs) were set up in an ancient DNA facility at China University of Geosciences (Wuhan), in a building physically separated from post-PCR facilities. Ancient DNA was extracted from approximately 250 mg bone powder following a silica method optimized for ancient DNA extraction [38]. Extraction and PCR blanks were performed to monitor for potential contamination. Overlapping primer pairs were newly designed based on the mitochondrial genome of an extant giant panda (GenBank accession number of EF212882.1) [39] using Primer 5.0 ( Figure S1 and Table S1). Amplifications were performed using a two-step multiplex approach [40]. The annealing temperatures were set at 50 • C in both steps. PCR products were purified using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) and cloned into the pMD18-T vector (Takara, Tokyo, Japan) following the supplier's instructions. Plasmids were transformed into competent E. coli DH5α. White transformants obtained from LB plates were screened by PCR with the M13 primer pair. For each fragment, a minimum of eight clones, four from each of two independent primary amplifications, were sequenced at Nanjing Genscript Ltd. Company on an ABI 3700 sequencer. When consistent differences were found between the two independent amplifications due to sequence errors, most likely resulting from template damage, a third amplification was performed to determine which sequence was reproducible ...
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... Materials: The following are available online at http://www.mdpi.com/2073-4425/9/4/198/s1, Figure S1: Schematic view of the complete or partial mitochondrial genes for the Holocene giant panda specimens using overlapping PCR fragments. Figure S2: Variable nucleotide positions in the 4054 bp data set of 12s, 16s, cytb, and ND1 fragments from 54 giant panda individuals. Figure S3: Genetic diversity distribution of the four subsampled species when random subsampling and pairwise identity computation have been performed 10, 100, and 1000 times, respectively. Table S1: PCR primers for giant panda mitochondrial genes. Table S2: Sequence information used in this study. Table S3: Haplotypes identification of 54 giant panda individuals used for phylogenetic analyses in Figure 3. Table S4: Optimal data partitions and substitution models selected by partitionfinder for the BEAST analyses. Table S5: Optimal data partitions selected by partitionfinder for maximum likelihood phylogenetic analysis. Table S6: Variable sites in the aligned 655 bp D-loop data ...
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... amplified 67 overlapping fragments (size range was 53-159 bp excluding primers) from the two Holocene samples. The fragments were used to build the complete cytb (1140 bp) and 12s rRNA (966 bp) genes, partial 16s rRNA (1126 bp for 05001, 1103 bp for 97001), and partial ND1 (905 bp for 05001, 923 bp for 97001) genes, and D-loop sequences (1052 bp for both specimens) ( Figure S1 and Table S2). Identical sequences were obtained when experiments were independently replicated at the State Key Laboratory for Biogeology and Environmental Geology at China University of Geosciences (Wuhan) and the Australian Centre for Ancient DNA at the University of Adelaide, ...
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... samples of Holocene sub-fossil giant pandas (Specimens Nos.: 05001, 97001) were collected from a natural sinkhole, 41-60 m deep from the surface, at Jiangdong Hill, Tengchong County in Yunnan Province, south-western China (Figure 1). The samples were associated with Elephas maximus, Bos gaurus, Dicerorhinus sumatraensis, Equus yunnanesis, Cervus unicolor, and several other species [34][35][36][37]. They were accelerator mass spectrometry (AMS)-radiocarbon dated at the Quaternary Geology and Archaeological Chronology Laboratory at Peking University at 5025 ± 35 (No. 05001) and 8470 ± 45 (No. 97001) years B.P. respectively [37]. These dates are the latest record of the giant panda before it disappeared from Yunnan Province. ...
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... DNA extractions and polymerase chain reactions (PCRs) were set up in an ancient DNA facility at China University of Geosciences (Wuhan), in a building physically separated from post-PCR facilities. Ancient DNA was extracted from approximately 250 mg bone powder following a silica method optimized for ancient DNA extraction [38]. Extraction and PCR blanks were performed to monitor for potential contamination. Overlapping primer pairs were newly designed based on the mitochondrial genome of an extant giant panda (GenBank accession number of EF212882.1) [39] using Primer 5.0 ( Figure S1 and Table S1). Amplifications were performed using a two-step multiplex approach [40]. The annealing temperatures were set at 50 • C in both steps. PCR products were purified using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) and cloned into the pMD18-T vector (Takara, Tokyo, Japan) following the supplier's instructions. Plasmids were transformed into competent E. coli DH5α. White transformants obtained from LB plates were screened by PCR with the M13 primer pair. For each fragment, a minimum of eight clones, four from each of two independent primary amplifications, were sequenced at Nanjing Genscript Ltd. Company on an ABI 3700 sequencer. When consistent differences were found between the two independent amplifications due to sequence errors, most likely resulting from template damage, a third amplification was performed to determine which sequence was reproducible ...
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... amplified 67 overlapping fragments (size range was 53-159 bp excluding primers) from the two Holocene samples. The fragments were used to build the complete cytb (1140 bp) and 12s rRNA (966 bp) genes, partial 16s rRNA (1126 bp for 05001, 1103 bp for 97001), and partial ND1 (905 bp for 05001, 923 bp for 97001) genes, and D-loop sequences (1052 bp for both specimens) ( Figure S1 and Table S2). Identical sequences were obtained when experiments were independently replicated at the State Key Laboratory for Biogeology and Environmental Geology at China University of Geosciences (Wuhan) and the Australian Centre for Ancient DNA at the University of Adelaide, ...
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... Materials: The following are available online at http://www.mdpi.com/2073-4425/9/4/198/s1, Figure S1: Schematic view of the complete or partial mitochondrial genes for the Holocene giant panda specimens using overlapping PCR fragments. Figure S2: Variable nucleotide positions in the 4054 bp data set of 12s, 16s, cytb, and ND1 fragments from 54 giant panda individuals. Figure S3: Genetic diversity distribution of the four subsampled species when random subsampling and pairwise identity computation have been performed 10, 100, and 1000 times, respectively. Table S1: PCR primers for giant panda mitochondrial genes. Table S2: Sequence information used in this study. Table S3: Haplotypes identification of 54 giant panda individuals used for phylogenetic analyses in Figure 3. Table S4: Optimal data partitions and substitution models selected by partitionfinder for the BEAST analyses. Table S5: Optimal data partitions selected by partitionfinder for maximum likelihood phylogenetic analysis. Table S6: Variable sites in the aligned 655 bp D-loop data ...
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Citations
... Such restriction to bamboo-dominated habitats has shaped the distribution and evolutionary trajectory of the giant panda [59,60] It is important to highlight that we used modern occurrence (i.e., not fossil) records to generate the ellipsoidal models. Thus, the fact that the present distribution of some species like the giant panda represents only a fraction of what it occupied in the past [59,61,62], suggests that some of the estimated historical niches could be broader. ...
Assessing niche evolution remains an open question and an actively developing area of study. The family Ursidae consists of eight extant species for which, despite being the most studied family of carnivores, little is known about the influence of climate on their evolutionary history and diversification. We evaluated their evolutionary patterns based on a combined phylogeography and niche modeling approach. We used complete mitogenomes, estimated divergence times, generated ecological niche models and applied a phyloclimatic model to determine the species evolutionary and diversification patterns associated with their respective environmental niches. We inferred the family evolutionary path along the environmental conditions of maximum temperature and minimum precipitation, from around 20 million years ago to the present. Our findings show that the phyloclimatic niches of the bear species occupy most of the environmental space available on the planet, except for the most extreme warm conditions, in accordance with the wide geographic distribution of Ursidae. Moreover, some species exhibit broader environmental niches than others, and in some cases, they explore precipitation axes more extensively than temperature axes or vice versa, suggesting that not all species are equally adaptable to these variables. We were able to elucidate potential patterns of niche conservatism and evolution, as well as niche overlapping, suggesting interspecific competitive exclusion between some of the bear species. We present valuable insights into the ecological and evolutionary processes driving the diversification and distribution of the Ursidae. Our approach also provides essential information for guiding effective conservation strategies, particularly in terms of distribution limits in the face of climate change.
... Whether the shape of the teeth has changed together with its size, however, has never been investigated. During the Late Quaternary, the giant panda was distributed all over southern China, and these populations have complicated evolutionary position regarding the modern two subspecies (Min-Shan Ko et al. 2018;Sheng et al. 2018Sheng et al. , 2019Barlow et al. 2019). ...
... A general trend of reduced genetic diversity in current compared with ancient populations is well documented among species that have undergone postglacial or historical population declines where ancient or historical diversity is directly compared with current diversity [32][33][34][35][36][37][38] . ...
Genetic diversity is lost in small and isolated populations, affecting many globally declining species. Interspecific admixture events can increase genetic variation in the recipient species’ gene pool, but empirical examples of species-wide restoration of genetic diversity by admixture are lacking. Here we present multi-fold coverage genomic data from three ancient Iberian lynx (Lynx pardinus) approximately 2,000–4,000 years old and show a continuous or recurrent process of interspecies admixture with the Eurasian lynx (Lynx lynx) that increased modern Iberian lynx genetic diversity above that occurring millennia ago despite its recent demographic decline. Our results add to the accumulating evidence for natural admixture and introgression among closely related species and show that this can result in an increase of species-wide genetic diversity in highly genetically eroded species. The strict avoidance of interspecific sources in current genetic restoration measures needs to be carefully reconsidered, particularly in cases where no conspecific source population exists.
... Museum sample genetic analysis was found to be useful in establishing a phylogenetic relationship between extinct quagga and extant mountain zebra (Higuchi et al. 1984). Based on the mitochondrial DNA analysis of Holocene sub-fossil giant panda and modern panda, Sheng et al. (2018) concluded that extant panda populations do not suffer any immediate threat from the perspective of genetic evolutionary potential. Ancient DNA analysis was also found useful to elucidate the evolutionary history of Yakutian brown bears and Japanese otters (Park et al. 2019;Rey-Iglesia et al. 2019). ...
The genetic investigation of the archeological or museum samples, including endangered species, provides vital information necessary to plan, implement, and revisit conservation strategies. In South Korea, the Asian black bear went almost extinct in wild by 2002, without leaving any authentic specimens representing the native population. Recently researchers found a set of animal bones in a natural cave in Mt. Taebaek (South Korea), suspected to be of a bear. In the present study, we undertook a molecular investigation and radiocarbon dating to establish the species’ identity, phylogenetic position, and approximate age of the recovered specimen. The genetic investigation (CytB, COI, D-loop, SRY, and ZFX-ZFY) identified the sample as a male Asian black bear with close phylogenetic affinity with Northeast Asian bears. Radiocarbon dating estimated the bones to be aged 1800–1942 calAD. These findings indicate that the bone specimens found in the natural cave in Mt. Taebaek were from an individual that naturally inhabited South Korea long before the importing of farm bears (the 1980s) and initiation of wild population restoration (2004). The present study provides the first genetic information record of the native South Korean black bear. Our findings reaffirm the appropriateness of the ongoing bear restoration program in South Korea, with the reintroduction of individuals from North Korea and Russia.
... 20 . The largest species, Ailuropoda baconi, was thought to be restricted to middle and late Pleistocene, with the modern species, A. melanoleuca, as Holocene 20 , although Sheng et al. 34 recognized the initial divergence of the living lineage in the late Pleistocene. The false thumb from late Pleistocene Shuanghe Cave was adopted from Wang et al. 10 The strength of the giant panda grip is dependent on the flexor muscles of the fingers, with the radial sesamoid acting as a passive stop against flexion of the fingers. ...
Of the many peculiarities that enable the giant panda (Ailuropoda melanoleuca), a member of the order Carnivora, to adapt to life as a dedicated bamboo feeder, its extra “thumb” is arguably the most celebrated yet enigmatic. In addition to the normal five digits in the hands of most mammals, the giant panda has a greatly enlarged wrist bone, the radial sesamoid, that acts as a sixth digit, an opposable “thumb” for manipulating bamboo. We report the earliest enlarged radial sesamoid, already a functional opposable “thumb,” in the ancestral panda Ailurarctos from the late Miocene site of Shuitangba in Yunnan Province, China. However, since the late Miocene, the “thumb” has not enlarged further because it must be balanced with the constraints of weight bearing while walking in a plantigrade posture. This morphological adaptation in panda evolution thus reflects a dual function of the radial sesamoid for both bamboo manipulation and weight distribution. The latter constraint could be the main reason why the panda’s false thumb never evolved into a full digit. This crude “thumb” suggests that the origin of the panda’s dedicated bamboo diet goes back to as early as 6–7 Ma.
... Besides, we also analyzed the 655 bp mitochondrial CR sequence and 1140 bp Cyt b gene to compare with previous studies [17,18,20,31]. We obtained 113 CR sequences, including 48 captive samples and 65 wild samples in our study, and collected public data from 665 samples [32]. For Cyt b gene, we obtained 116 sequences from 48 captive samples, 68 wild samples and published data from 449 samples. ...
... Although single marker could also provide valuable information, as in our analysis of CR sequences and Cyt b genes, different genetic markers may yield different results in terms of Hd and nucleotide diversity. A study providing association analysis of a few genes (12 s, 16 s, Cyt b, and ND1 fragments, total length of 4054 bp) reached to a high Hd (Hd = 0.9572 ± 0.0171) but relatively low nucleotide diversity (π = 0.0054 ± 0.0003) [32]. For the two ancient samples 97001 and 05001, we didn't find haplotypes identical to them. ...
Background
Research on genetic diversity based on mitochondrial DNA of giant pandas mainly focused on a single marker or a few genes.
Objective
To provide a more comprehensive assessment of the genetic diversity on giant pandas based on 13 mitochondrial protein coding genes.
Methods
We assembled 13 protein coding genes in the mitochondrial genome of the giant panda based on the whole genome sequencing data, including ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, ND6 and Cyt b.
Results
We successfully obtained long sequence of 11,416 base pairs with all 13 genes for 110 giant panda individual, accounting for 67.93% in length of the mitochondrial reference genome. Haplotype diversity was 0.9518 ± 0.009 and nucleotide diversity (π) was 0.00157 ± 0.00014. We detected three new haplotypes, including GPC10 and GPC21 for the CR sequence and GPB12 for the Cyt b gene.
Conclusion
These multi-gene sequences provided more genetic variable information to compare captive and wild giant panda population.
... Furthermore, we evidence a historical directional niche change along which the panda currently has reached the lower limits of temperature and precipitation conditions existing on the geography where its food is available (Fig. 5). Previous work has shown populations reductions and genetic diversity loss in the giant panda as a result of habitat contraction during the Holocene (Hu et al. 2010;Sheng et al. 2018). In accord, our findings show that the current conditions associated with the panda's known distribution do not encompass the entire conditions it was able to inhabit during the LGM, which were warmer and wetter. ...
The giant panda (Ailuropoda melanoleuca) is the most basal living species in the phylogeny of the family Ursidae, with a specialized diet composed of a variety of bamboo species. The evolutionary history and past distribution patterns of the giant panda remain poorly understood. Our aim was to integratively apply distinct methods to evaluate the evolutionary history and distributional patterns of the giant panda; these included phylogeography, ecological niche modeling (ENM), and fossil data. To this end, we characterized the panda’s past and present ecological niches and the environmental conditions that define them. To estimate the panda’s phylogeographic patterns and the environmental conditions (precipitation and temperature) available across its historical geographic range, we evaluated its past distribution during the Last Glacial Maximum (LGM). Considering that modeling biotic interactions (e.g., foraging, predation) is still an enormous challenge, we propose a novel modeling strategy based on the panda’s specialized diet, using an ensemble of three bamboo genera with distribution across the panda’s historical geographic range. Finally, we tested the accuracy of our approach by evaluating its ability to predict the LGM fossils. Our results support that the panda’s diversification across its distribution happened ca. 2.7 million years (Mya), coinciding with the likely period when the panda changed from a carnivorous to a vegetarian diet (from the Pleistocene to the Pliocene), acquiring its exclusively bamboo-feeding habits until the mid-Holocene. Our findings provide evidence of a historical directional niche change along which the panda has currently reached the lower limits of temperature and precipitation conditions existing on the geography where its food is available. Our proposed ENM based on the panda’s food habits accurately predicted 85.7% of the LGM fossils, in stark contrast with the traditional approach of modeling the distribution of species by using exclusively its own occurrences. These results provide insights on how to include Eltonian components to undertake more robust ENM when only abiotic variables are available. We emphasize the importance of integrating fossil information, whenever available, into the niche modeling process to include the historical component when estimating species ecological niches.
... Thus, the diversity within species might not be reflected to its full extent. However, a loss of genetic diversity over time has been documented for other species [90][91][92], including wolves in North America [93] and Europe [94], leopards [2], giant pandas [95] and South American mammals [96]. ...
The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.
... As such ecologists and palaeontologists can work together. For example, Sheng et al. (2018) and Min-Shan Ko et al. (2018) demonstrate with aDNA sequences from the remains of a Late Pleistocene to Middle Holocene chronological subspecies of giant panda (Ailuropoda melanoleuca baconi), found in sink holes in southern China, that while the modern panda (Ailuropoda melanoleuca melanoleuca) populations in Central China are vulnerable, from an evolutionary point of view, their genetic diversity is still substantial since the Middle Holocene. This is beneficial for modern panda conservation programmes and may even result in a continuing increase of wild panda populations. ...
Since the 1980's, micro-analysis techniques applied to worldwide extinctions of Quaternary megafauna have resulted in revolutionary insights. However, in the Asia-Pacific, the infrastructure facilitating micro-analyses is still relatively limited. In this review, the potential of micro-analytical research applied to iconic megafauna will be discussed and evaluated. To address the imbalance between hominin versus faunal focused research we highlight the lack of knowledge of some taxa, the extent of unexplored regions and specific underutilised techniques that are relevant to megafaunal sites. Increased exchange of techniques, facilities and ideas is recommended to bridge the gap with Euro-American regions. This could provide a toolbox for conservation of modern megafauna across the Asia-Pacific to ensure these do not succumb to the same fate as mammoths, megalanias and other megabeasts.
... Following a series of inquiries in the communities of Sichuan Province, David acquired a pelt from a local hunter and taxonomically positioned the species in the genus Ursus, naming it Ursus melanoleucus, the black and white bear. Scientists later determined the species did not belong in the genus Ursus, but rather in a genus all to itself (Kumar et al. 2017;Sheng et al. 2018). This is one way in which the giant panda (Ailuropoda melanoleuca) has, and continues to, defied convention. ...
... The current species range, for instance, is subdivided among 33 different populations, which will likely have genetic consequences for the species as a whole given their isolation by distance (Kang & Li 2016) (Fig. 3). There is good reason to believe giant pandas have been comparatively rare for some time (Sheng et al. 2018). Early in their expedition in 1929, one of the hunting parties led by the Roosevelt brothers included 13 experienced Chinese hunters and their dogs. ...
In November 1928, Theodore Jr. and Kermit Roosevelt led an expedition to China with the expressed purpose of being the first Westerners to kill the giant panda (Ailuropoda melanoleuca). The expedition lasted 8 months and resulted in the brothers shooting a giant panda in the mountains of Sichuan Province. Given the concurrent attention in the popular press describing this celebrated expedition, the giant panda was poised to be trophy hunted much like other large mammals around the world. Today, however, the killing of giant pandas, even for the generation of conservation revenue, is unthinkable for reasons related to the species itself and the context, in time and space, in which the species was popularized in the West. We found that the giant panda's status as a conservation symbol, exceptional charisma and gentle disposition, rarity, value as a nonconsumptive ecotourism attraction, and endemism are integral to the explanation of why the species is not trophy hunted. We compared these intrinsic and extrinsic characteristics with 20 of the most common trophy‐hunted mammals to determine whether the principles applying to giant pandas are generalizable to other species. Although certain characteristics of the 20 trophy‐hunted mammals aligned with the giant panda, many did not. Charisma, economic value, and endemism, in particular, were comparatively unique to the giant panda. Our analysis suggests that, at present, exceptional characteristics may be necessary for certain mammals to be excepted from trophy hunting. However, because discourse relating to the role of trophy hunting in supporting conservation outcomes is dynamic in both science and society, we suspect these valuations will also change in future.
