Shanning Zhang

Evidence of cellulose metabolism by the giant panda gut microbiome

The giant panda genome codes for all necessary enzymes associated with a carnivorous digestive system but lacks genes for enzymes needed to digest cellulose, the principal component of their bamboo diet. It has been posited that this iconic species must therefore possess microbial symbionts capable of metabolizing cellulose, but these symbionts have remained undetected. Here we examined 5,522 prokaryotic ribosomal RNA gene sequences in wild and captive giant panda fecal samples. We found lower species richness of the panda microbiome than of mammalian microbiomes for herbivores and nonherbivorous carnivores. We detected 13 operational taxonomic units closely related to Clostridium groups I and XIVa, both of which contain taxa known to digest cellulose. Seven of these 13 operational taxonomic units were unique to pandas compared with other mammals. Metagenomic analysis using ∼37-Mbp contig sequences from gut microbes recovered putative genes coding two cellulose-digesting enzymes and one hemicellulose-digesting enzyme, cellulase, β-glucosidase, and xylan 1,4-β-xylosidase, in Clostridium group I. Comparing glycoside hydrolase profiles of pandas with those of herbivores and omnivores, we found a moderate abundance of oligosaccharide-degrading enzymes for pandas (36%), close to that for humans (37%), and the lowest abundance of cellulases and endohemicellulases (2%), which may reflect low digestibility of cellulose and hemicellulose in the pandas unique bamboo diet. The presence of putative cellulose-digesting microbes, in combination with adaptations related to feeding, physiology, and morphology, show that giant pandas have evolved a number of traits to overcome the anatomical and physiological challenge of digesting a diet high in fibrous matter.

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

The panda lineage dates back to the late Miocene and ultimately leads to only one extant species, the giant panda (Ailuropoda melanoleuca). Although global climate change and anthropogenic disturbances are recognized to shape animal population demography their contribution to panda population dynamics remains largely unknown. We sequenced the whole genomes of 34 pandas at an average 4.7-fold coverage and used this data set together with the previously deep-sequenced panda genome to reconstruct a continuous demographic history of pandas from their origin to the present. We identify two population expansions, two bottlenecks and two divergences. Evidence indicated that, whereas global changes in climate were the primary drivers of population fluctuation for millions of years, human activities likely underlie recent population divergence and serious decline. We identified three distinct panda populations that show genetic adaptation to their environments. However, in all three populations, anthropogenic activities have negatively affected pandas for 3,000 years.

Old-growth forest is what giant pandas really need

Giant pandas (Ailuropoda melanoleuca) are an iconic conservation species, but despite significant research effort, do we understand what they really need? Estimating and mapping suitable habitat play a critical role in conservation planning and policy. But if assumptions about ecological needs are wrong, maps with misidentified suitable habitat will misguide conservation action. Here, we use an information-theoretic approach to analyse the largest, landscape-level dataset on panda habitat use to date, and challenge the prevailing wisdom about panda habitat needs. We show that pandas are associated with old-growth forest more than with any ecological variable other than bamboo. Other factors traditionally used in panda habitat models, such as topographic slope, are less important. We suggest that our findings are disparate from previous research in part because our research was conducted over a larger ecological scale than previous research conducted over more circumscribed areas within individual reserves. Thus, extrapolating from habitat studies on small scales to conservation planning on large scales may entail some risk. As the Chinese government is considering the renewal of its logging ban, it should take heed of the pandas dependency on old growth.

Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China

Understanding population history and genetic structure are key drivers of ecological research. Here, we studied two highly fragmented and isolated populations (Xiaoxiangling and Daxiangling) of giant pandas (Ailuropoda melanoleuca) at the extreme southwestern edge of their distribution. This area also contains the Dadu River, national road 108 and various human infrastructure and development, providing an ideal region in which we can identify the effects of different barriers on animal movements. We used partial mitochondrial control region (mtDNA) and nine microsatellite loci (nuclear DNA) data derived from 192 faecal and one blood sample collected from the wild. We found 136 genotypes corresponding to 53 unique multilocus genotypes and eight unique control region haplotypes (653 bp). Significant genetic boundaries correlated spatially with the Dadu River (K = 2). We estimate that a major divergence took place between these populations 26 000 years bp, at around the similar time the rock surface of valley bottom formed in Dadu River. The national road has resulted in further recent population differentiation (Pairwise FS on mtDNA and nuclear DNA) so that in effect, four smaller sub‐populations now exist. Promisingly, we identified two possible first‐generation migrants and their migration paths, and recommended the immediate construction of a number of corridors. Fortunately, the Chinese government has accepted our advice and is now planning corridor construction.

Conservation Implications of Drastic Reductions in the Smallest and Most Isolated Populations of Giant Pandas

In conservation biology, understanding the causes of endangerment is a key step to devising effective conservation strategies. We used molecular evidence (coalescent simulations of population changes from microsatellite data) and historical information (habitat and human population changes) to investigate how the most-isolated populations of giant pandas (Ailuropoda melanoleuca) in the Xiaoxiangling Mountains became highly endangered. These populations experienced a strong, recent demographic reduction (60-fold), starting approximately 250 years BP. Explosion of the human population and use of non-native crop species at the peak of the Qing Empire resulted in land-use changes, deforestation, and habitat fragmentation, which are likely to have led to the drastic reduction of the most-isolated populations of giant pandas. We predict that demographic, genetic, and environmental factors will lead to extinction of giant pandas in the Xiaoxiangling Mountains in the future if the population remains isolated. Therefore, a targeted conservation action--translocation--has been proposed and is being implemented by the Chinese government.

Twelve novel polymorphic microsatellite loci developed from the Asiatic black bear (Ursus thibetanus)

Since the number and range of Asiatic black bear (Ursus thibetanus) are declining due to habitat loss and illegal trade, it is essential to take effective actions to reinforce the conservation of the remaining bear populations. In order to aid such conservation efforts, we developed 12 novel polymorphic microsatellite loci of Asiatic black bear from genomic DNA-enriched libraries in this paper. The number of alleles per locus in 24 individuals ranged from 3 to 10, the average observed heterozygosity per locus from 0.214 to 0.950, and the average expected heterozygosity per locus from 0.243 to 0.891. Eight loci followed Hardy–Weinberg expectations after Bonferroni correction for multiple comparisons. No significant linkage association was found among all these loci. The 12 polymorphic microsatellite loci will be helpful to the conservation of the Asiatic black bear.