Panda Species Research Articles

Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution.

Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo-eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo-eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo-eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.

Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation

BackgroundIt is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species.ResultsThe clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn’t exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region.ConclusionsOur results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.

Diet drives convergent evolution of gut microbiomes in bamboo-eating species.

Gut microbiota plays a critical role in host physiology and health. The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche. Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota. However, the relative contribution of each factor in shaping the structure of gut microbiota remains unclear. The giant (Ailuropoda melanoleuca) and red (Ailurus styani) pandas belong to different families of order Carnivora. They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution. Here, we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing. We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives. This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea. Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis. These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.

The uneven weight distribution between predators and prey: Comparing gut fill between terrestrial herbivores and carnivores

The general observation that secondary consumers ingest highly digestible food and have simple short guts and small abdominal cavities intuitively results in the assumption that mammalian carnivores carry less digesta in their gut compared to herbivores. Due to logistic constraints, this assumption has not been tested quantitatively so far. In this contribution, we estimated the dry matter gut contents (DMC) for 25 species of the order Carnivora (including two strictly herbivorous ones, the giant and the red panda) using the physical ‘Occupancy Principle’, based on a literature data collection on dry matter intake (DMI), apparent dry matter digestibility (aD DM) and retention time (RT), and compared the results to an existing collection for herbivores. Scaling exponents with body mass (BM) for both carnivores and herbivores were in the same range with DMI ~ BM0.75; aD DM ~ BM0; RT ~ BM0.11 and DMC ~ BM0.88. The trophic level (carnivore vs herbivore) significantly affected all digestive physiology parameters except for RT. Numerically, the carnivore DMI level reached 77%, the RT 32% and DMC only 29% of the corresponding herbivore values, whereas the herbivore aD DM only reached 82% of that of carnivores. Thus, we quantitatively show that carnivores carry less inert mass or gut content compared to herbivores, which putatively benefits them in predator-prey interactions and might have contributed to the evolution towards unguligradism in herbivores. As expected, the two panda species appeared as outliers in the dataset with low aD DM and RT for a herbivore but extremely high DMI values, resulting in DMC in the lower part of the herbivore range. Whereas the difference in DMI and DMC scaling in herbivores might allow larger herbivores to compensate for lower diet quality by ingesting more, this difference may allow larger carnivores not to go for less digestible prey parts, but mainly to increase meal intervals, i.e. not having to hunt on a daily basis.

The effect of diffusion on giant pandas that live in complex patchy environments

The habitat loss and fragmentation is almost the greatest threat to the survival of the wild giant panda. In this paper, we construct a mathematical model to consider the effect of diffusion on giant pandas that live in complex patchy environments. Our discussion includes the studying of a diffusive n-dimensional single species model, sufficient conditions are derived for the permanence and extinction of the giant panda species. Especially, we also discuss the situations of diffusion of giant pandas between two patches, and numerical simulations are presented to illustrate the results. Furthermore, we consider the existence, uniqueness, and global stability of the positive periodic solution of the n-dimensional single species model. The implications of these results are significant for giant panda conservation.

Three-dimensional computer simulations of feeding behaviour in red and giant pandas relate skull biomechanics with dietary niche partitioning

The red (Ailurus fulgens) and giant (Ailuropoda melanoleuca) pandas are mammalian carnivores convergently adapted to a bamboo feeding diet. However, whereas Ailurus forages almost entirely on younger leaves, fruits and tender trunks, Ailuropoda relies more on trunks and stems. Such difference in foraging mode is considered a strategy for resource partitioning where they are sympatric. Here, we use finite-element analysis to test for mechanical differences and similarities in skull performance between Ailurus and Ailuropoda related to diet. Feeding simulations suggest that the two panda species have similar ranges of mechanical efficiency and strain energy profiles across the dentition, reflecting their durophagous diet. However, the stress distributions and peaks in the skulls of Ailurus and Ailuropoda are remarkably different for biting at all tooth locations. Although the skull of Ailuropoda is capable of resisting higher stresses than the skull of Ailurus, the latter is able to distribute stresses more evenly throughout the skull. These differences in skull biomechanics reflect their distinct bamboo feeding preferences. Ailurus uses repetitive chewing in an extended mastication to feed on soft leaves, and Ailuropoda exhibits shorter and more discrete periods of chomp-and-swallow feeding to break down hard bamboo trunks.

Mandible of the giant panda (Ailuropoda melanoleuca) compared with other Chinese carnivores: functional adaptation

The aim of this study was to understand the mandible of the giant panda in morphometric terms to explore differences between the giant panda and other carnivores distributed in China, in terms of functional adaptation. Twelve mandibular variables were studied using bivariate (allometry) and multivariate (principal components analysis, PCA, and discriminant functional analysis, DFA) tools. When deviations were produced from allometric baselines consisting of all the species studied, the giant panda displayed a much more developed mandibular structure than the bear, leopard, and tiger. This may be related to its specific dietary preference for bamboo, which has very strong fibers. Results also indicate that the mandibular structure among carnivores mainly reflects the differences in their dietary preferences and functional adaptation. Three groups were found referring to dispersal profiles expressed by the first two axes of PCA and DFA: (1) the two panda species – the herbivorous carnivores; (2) the black bear – the omnivorous carnivore; and (3) the tiger and leopard – the hypercarnivores. Nevertheless, a significant separation between the two panda species was also found with the profiles displayed by the first and third axes of DFA. In addition to no close evolutionary relationship and phylogenetic development, a noticeable separation between the two panda species found in DFA analysis may be associated with their variation in consuming different parts of the bamboo plant: the giant panda feeds on stems and the red panda feeds on leaves. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 449–456.

Phylogeny of the caniform carnivora: evidence from multiple genes

The monophyletic group Caniformia in the order Carnivora currently comprises seven families whose relationships remain contentious. The phylogenetic positions of the two panda species within the Caniformia have also been evolutionary puzzles over the past decades, especially for Ailurus fulgens (the red panda). Here, new nuclear sequences from two introns of the beta-fibrinogen gene (beta-fibrinogen introns 4 and 7) and a complete mitochondrial (mt) gene (ND2) from 17 caniform representatives were explored for their utilities in resolving higher-level relationships in the Caniformia. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Combined analyses of four nuclear and one mt genes (4417 bp) recover a branching order in which almost all nodes were strongly supported. The present analyses provide evidence in favor of Ailurus fulgens as the closest taxon to the procyonid-mustelid (i.e., Musteloidea sensu stricto) clade, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae (including Ailuropoda melanoleuca), and Canidae, the most basal lineage in the Caniformia. The potential utilities of different genes in the context of caniform phylogeny were also evaluated, with special attention to the previously unexplored beta-fibrinogen intron 4 and 7 genes.

Microhabitat separation during winter among sympatric giant pandas, red pandas, and tufted deer: the effects of diet, body size, and energy metabolism

The giant panda (Ailuropoda melanoleuca (David, 1869)), red panda (Ailurus fulgens F.G. Cuvier, 1825), and tufted deer (Elaphodus cephalophus Milne-Edwards, 1872) are endemic to the Himalayan Hengduan Mountains; the red panda extends into India, Burma, Bhutan, and Nepal, and the tufted deer extends marginally into Burma, while the giant panda is endemic to China. In Sichuan Province, uniquely, all three species occur sympatrically. We investigated microhabitat characteristics at 150 fecal-group sites from November 2002 to March 2003 to improve understanding of microhabitat separation among the three species at the Fengtongzhai Nature Reserve, Baoxing County, Sichuan Province, People's Republic of China. Density and height of bamboo were greater in the giant and red pandas' micro habitats than in those of the tufted deer. The red panda preferred microhabitats with greater tree-stump density, smaller trees, and shorter fallen log dispersion distance than the other two species. Tufted deer often occurred at sites with greater shrub density and herb cover and more open land with poorer concealment conditions than sites where the two panda species occurred. Both pandas' microhabitats were mostly concentrated on the upper hillside, unlike those of the tufted deer. The giant panda preferred microhabitats with a gentler slope and lower density of fallen logs. Selection of specific microhabitats by each species is an ecological adaptation dependent on behavior linked to its diet, body size, energy metabolism, and other factors. Microhabitat separation among these species reflects the integrated effects of their differences in diet, body size, and energy metabolism, which could facilitate their successful coexistence.

Patterns of Genetic Diversity in Remaining Giant Panda Populations

Abstract: The giant panda (Ailuropoda melanoleuca) is among the more familiar symbols of species conservation. The protection of giant panda populations has been aided recently by the establishment of more and better‐managed reserves in existing panda habitat located in six mountain ranges in western China. These remaining populations are becoming increasingly isolated from one another, however, leading to the concern that historic patterns of gene flow will be disrupted and that reduced population sizes will lead to diminished genetic variability. We analyzed four categories of molecular genetic markers (mtDNA restriction‐fragment‐length polymorphisms [RFLP], mtDNA control region sequences, nuclear multilocus DNA fingerprints, and microsatellite size variation) in giant pandas from three mountain populations (Qionglai, Minshan, and Qinling) to assess current levels of genetic diversity and to detect evidence of historic population subdivisions. The three populations had moderate levels of genetic diversity compared with similarly studied carnivores for all four gene measures, with a slight but consistent reduction in variability apparent in the smaller Qinling population. That population also showed significant differentiation consistent with its isolation since historic times. From a strictly genetic perspective, the giant panda species and the three populations look promising insofar as they have retained a large amount of genetic diversity in each population, although evidence of recent population reduction—likely from habitat loss—is apparent. Ecological management to increase habitat, population expansion, and gene flow would seem an effective strategy to stabilize the decline of this endangered species.

Comparative Behavior of Red and Giant Pandas in the Wolong Reserve, China

Feeding ecology of red pandas (Ailurus fulgens) was studied in the Wolong Reserve, China by evaluation of spoor and analysis of nutritional content of bamboo (Sinarundinaria fangiana). Radiotelemetry was used to monitor movement and activity patterns of a female red panda. Ecological overlap with the sympatric giant panda (Ailuropoda melanoleuca) was extensive in that both species feed primarily on bamboo, but differences in food selection and the abundance and constant nutritional level of bamboo facilitated coexistence. Red pandas subsisted almost exclusively on bamboo leaves whereas giant pandas also ate stems. Dietary overlap was only 40–43% although both species spent approximately 85% of the time in the same area eating the same species of bamboo. Home-range size of the red panda was 3.4 km2 during 9 months, that of a giant panda using the same area at the same time, 6.3 km2. Spatial overlap between the range of the red panda and five radio-collared giant pandas in the area averaged over 70%. Daily linear distances traveled (x̄ = 481 ± 312 m), percent of the home range used each month (26.6 ± 11.9), and size of core areas (26 ha) were similar for the red panda and one giant panda. Movements of both species were characterized by gradual shifts throughout the home range with certain bamboo areas being visited repeatedly. The red panda was primarily crepuscular and nocturnal, whereas giant pandas were intermittently active day and night. Probability of activity of the red panda (0.37) was significantly lower (P < 0.001) than that of giant pandas (0.57). The red panda exhibited constant monthly activity levels in contrast to giant pandas that showed significant seasonal variation. Different activity patterns, in spite of similarities in movements and food habits, indicated that the two panda species have different energetic strategies. The red panda has adjusted to a diet low in digestible energy by meticulous selection of individual leaves, extensive mastication, and complex reductions in metabolic rates. By comparison the giant panda is a relatively non-selective feeder that barely chews its food. The energetic and mechanical advantages associated with increased size suggest that the giant panda evolved from a small bamboo-eating animal resembling the red panda.