Fuwen Wei

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.

Molecular censusing doubles giant panda population estimate in a key nature reserve

The giant panda (Ailuropoda melanoleuca), a flagship species for conservation, once inhabited most of China and its neighboring countries in Southeast Asia. Nowadays, giant pandas are confined to fragmented mountain habitats in Western China because of ecological and anthropogenic pressure 1 and 2. In order to establish effective conservation strategies, it is critical to know the number and distribution of giant pandas in the wild. However, accurately censusing panda populations remains problematic, because individuals are elusive, wary and very difficult to observe in their complex habitat. Previously, a number of indirect censusing methods have been used 1, 2 and 3 D. Lindburg and K. Baragona, Giant Pandas: Biology and Conservation, University of California Press, London (2004).3. These methods were essentially based on transect lines and proved poor at identifying individuals, resulting in a questionable precision of estimates. Considering the keen interest of the conservation community and the millions of dollars already spent on three major national surveys, it is important to find an accurate method for censusing giant pandas. Recently, microsatellite analysis using fecal DNA has proven effective in estimating population size of elusive animals 4 and 5. Large numbers of fecal samples can be easily obtained from giant panda habitat without disturbance due to its diet and high deposition rates [2]. Here, we conducted for the first time an exhaustive non-invasive genetic survey of giant pandas in a key reserve and found that the molecular census was double that previously estimated.

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.

HABITAT USE AND SEPARATION BETWEEN THE GIANT PANDA AND THE RED PANDA

Abstract Habitat use and separation between 2 sympatric species, the giant panda (Ailuropoda melanoleuca) and the red panda (Ailurus fulgens), were studied in Yele Natural Reserve, Mianning County of Sichuan Province, China, to elucidate the coexistence of these specialized carnivores. Nineteen variables describing proximate habitat structure were measured at each fecal-group site. We tested if habitat structure differed between pandas and examined habitat separation between the species. Habitats used by each species differed significantly. The 2 pandas exhibited different patterns in microhabitat use, although their habitats overlapped in the study area. The giant panda occurred at sites on gentle slopes with lower density of fallen logs, shrubs, and bamboo culms. Sites also were close to trees and far from fallen logs, shrubs, and tree stumps. The red panda occurred at sites on steeper slopes with higher density of fallen logs, shrubs, and bamboo culms. Sites also were close to fallen logs, shrubs, and tree stumps. We conclude that microhabitat separation contributes to coexistence of giant and red pandas in areas of sympatry.

A Widely Applicable Protocol for DNA Isolation from Fecal Samples

Feces are increasingly used as sources of DNA for genetic and ecological research. This paper describes a new method for isolation of DNA from animal feces. This method combines multiple purification steps, including pretreatment with ethanol and TE, an inhibitor-absorber made of starch, the CTAB method, the phenol–chloroform extraction method, and the guanidinium thiocyanate-silica method. The new method is efficient according to PCR results of 585 fecal samples from 23 species and costs much less than the commercial kits. The protocol can be tailored to the specific purpose of examining different diets of animals and can be performed with routine laboratory reagents.

Obligate herbivory in an ancestrally carnivorous lineage: the giant panda and bamboo from the perspective of nutritional geometry

Summary Herbivores face various nutritional challenges in their life cycles, challenges that may become increasingly acute under ongoing environmental changes. Here, focusing on calcium, phosphorus and nitrogen, we used nutritional geometry to analyse individual-based data on foraging and extraction efficiencies, and combined these with data on reproduction and migratory behaviour to understand how a large herbivorous carnivore can complete its life cycle on a narrow and seemingly low quality bamboo diet. Behavioural results showed that pandas during the year switched between four main food categories involving the leaves and shoots of two bamboo species available. Nutritional analysis suggests that these diet shifts are related to the concentrations and balances of calcium, phosphorus and nitrogen. Notably, successive shifts in range use and food type corresponded with a transition to higher concentrations and/or a more balanced intake of these multiple key constituents. Our study suggests that pandas obligatorily synchronize their seasonal migration and reproduction with the disjunct nutritional phenologies of two bamboo species. This finding has potentially important implications for habitat conservation for this species and, more generally, draws attention to the need for understanding the nutritional basis of food selection in devising management plans for endangered species.

Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level.

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.

The effect of landscape features on population genetic structure in Yunnan snub-nosed monkeys (Rhinopithecus bieti) implies an anthropogenic genetic discontinuity.

The Tibetan Plateau is one of the top 10 biodiversity hotspots in the world and acts as a modern harbour for many rare species because of its relatively pristine state. In this article, we report a landscape genetic study on the Yunnan snub‐nosed monkey (Rhinopithecus bieti), a primate endemic to the Tibetan Plateau. DNA was extracted from blood, tissue and fecal samples of 135 wild individuals representing 11 out of 15 extant monkey groups. Ten microsatellite loci were used to characterize patterns of genetic diversity. The most striking feature of the population structure is the presence of five subpopulations with distinct genetic backgrounds and unique spatial regions. The population structure of R. bieti appears to be shaped by anthropogenic landscape features as gene flow between subpopulations is strongly impeded by arable land, highways and human habitation. A partial Mantel test showed that 36.23% (r = 0.51, P = 0.01) of the genetic distance was explained by habitat gaps after controlling for the effect of geographical distance. Only 4.92% of the genetic distance was explained by geographical distance in the partial Mantel test, and no significant correlation was found. Estimation of population structure history indicates that environmental change during the last glacial maximum and human impacts since the Holocene, or a combination of both, have shaped the observed population structure of R. bieti. Increasing human activity on the Plateau, especially that resulting in habitat fragmentation, is becoming an important factor in shaping the genetic structure and evolutionary potential of species inhabiting this key ecosystem.

Sleeping Cave Selection, Activity Pattern and Time Budget of White-Headed Langurs

We describe the activity patterns and time budgets of white-headed langurs that were confined to about 4 km2 of Longlin habitat in Fusui County, Guangxi Province, China. Between February and December 1996, we observed 6 langur groups monthly via group focal sampling and continuously recording the behavior of a focal group. Our results indicate that the langur groups selected stone caves on cliffs as sleeping sites. The daily activity pattern outside caves had 8 stages: (1) leaving the cave in the early morning; (2) moving and resting; (3) morning feeding; (4) moving a long distance; (5) resting at noon; (6) afternoon feeding; (7) moving back to the cave, and (8) entering the cave. Over the year, langurs spent a daily average of about 11.5 h outside caves and about 12.5 h inside caves. Moving accounted for 7% (spring), 7% (summer-autumn) and 13% (winter) of the time budget, and langurs spent 9% (summer-autumn) and 14% (spring) to 20% (winter) of their time feeding. Resting accounted for 79% of the time budget in spring, 84% in summer-autumn, and 57% in winter. Sunbathing only occurred in winter and accounted for about 10% of the time budget. One-way ANOVA and multiple range tests demonstrated that time budgets differed significantly among seasons. Langurs spent significantly more time feeding and moving in winter than in spring and summer-autumn, but significantly less time resting in winter than in spring and summer-autumn.