Hua Wu

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.

THE PARASITES OF GIANT PANDAS: INDIVIDUAL-BASED MEASUREMENT IN WILD ANIMALS

There is a growing recognition of parasites as a significant factor in the successful conservation of endangered species. Determining parasite infection and load in free-ranging populations traditionally is done via necropsy or coproscopy. For studies of wild animals, fecal sample collection can result in bias because the individual identity of animals is unknown and multiple samples may be collected from the same individual, yet treated as unrelated samples. We studied parasite load in wild giant pandas (Ailuropoda melanoleuca) across six mountain ranges in China. Genetic identification was used to determine the exact number of individuals sampled. The parasite fauna consisted of five species, dominated by Baylisascaris shroederi. The pattern of statistical difference between mountains was artificially inflated when animal identity was not included in the model. Our results suggest that caution should be exercised in inferring patterns from comparative parasitologic studies when samples cannot be attributed to specific individuals. Using noninvasive genetic sampling to avoid such bias should form a standard tool in the management of endangered species and their parasites.

Factors Predicting Den Use by Maternal Giant Pandas

Abstract We studied the denning ecology of giant pandas (Ailuropoda melanoleuca) in the Foping Nature Reserve, China. We identified 17 used and 21 unused cavities of appropriate size to accommodate denning and measured several variables potentially affecting the suitability of these cavities for panda denning. Principal component analysis, combined with traditional univariate tests, indicated that maternal females preferred deeper cavities with a high interior-to-entrance ratio for height and width, suggesting a preference for narrow entrances and roomy chambers. Microhabitat features, including slope and distance to water, were also useful in predicting den use by maternal females. We believe that the availability of suitable dens may limit population size, especially in areas where tree dens have been eliminated by logging of old growth forests. Conservation managers in giant panda reserves can use our data to determine the number of suitable panda dens that are in an area, estimate whether there are enough for the adult female population to use as birthing dens, and—if needed—construct suitable artificial dens to increase the rate of reproduction.

Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA

Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence‐based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai‐Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above‐mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite‐based Bayesian clustering clearly identified three groups (Qionglai‐Liangshan, Xiaoxiangling and Gaoligong‐Tibet). A significant isolation‐by‐distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large‐scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai‐Tibetan Plateau, subspecies classification and conservation of red pandas are discussed.

Thirty-three microsatellite loci for noninvasive genetic studies of the giant panda (Ailuropoda melanoleuca)

Limited microsatellite markers useable in noninvasive genetic methods have hampered the studies of dispersal patterns and mating systems of giant pandas. Therefore, we describe in this paper the characterization of 15 novel microsatellite loci from genomic DNA-enriched libraries and 18 redesigned microsatellite loci from published papers on the giant panda. The number of alleles per locus in 60 individuals ranged from 2 to 13, the average observed heterozygosity per locus from 0.168 to 0.800, and the average expected heterozygosity per locus from 0.152 to 0.882. All loci followed Hardy-Weinberg expectations. Four pairs of significant linkage association were found among all these loci. Moreover, the 33 microsatellite loci showed high amplification successes rate in noninvasive samples, which indicated that these loci will be of use in studying dispersal patterns and mating systems of giant pandas using noninvasive genetic methods.

Major histocompatibility complex alleles associated with parasite susceptibility in wild giant pandas

Major histocompatibility complex (MHC) polymorphism is thought to be driven by antagonistic coevolution between pathogens and hosts, mediated through either overdominance or frequency-dependent selection. However, investigations under natural conditions are still rare for endangered mammals which often exhibit depleted variation, and the mechanism of selection underlying the maintenance of characteristics remains a considerable debate. In this study, 87 wild giant pandas were used to investigate MHC variation associated with parasite load. With the knowledge of the MHC profile provided by the genomic data of the giant panda, seven DRB1, seven DQA1 and eight DQA2 alleles were identified at each single locus. Positive selection evidenced by a significantly higher number of non-synonymous substitutions per non-synonymous codon site relative to synonymous substitutions per synonymous codon site could only be detected at the DRB1 locus, which leads to the speculation that DRB1 may have a more important role in dealing with parasite infection for pandas. Coprological analyses revealed that 55.17% of individuals exhibited infection with 1–2 helminthes and 95.3% of infected pandas carried Baylisascaris shroederi. Using a generalized linear model, we found that Aime-DRB1*10 was significantly associated with parasite infection, but no resistant alleles could be detected. MHC heterozygosity of the pandas was found to be uncorrelated with the infection status or the infection intensity. These results suggested that the possible selection mechanisms in extant wild pandas may be frequency dependent rather than being determined by overdominance selection. Our findings could guide the candidate selection for the ongoing reintroduction or translocation of pandas.

Isolation and characterization of fourteen microsatellite loci for striped field mouse (Apodemus agrarius)

We describe the isolation and characterization of 14 microsatellite loci in the striped field mouse from genomic DNA-enriched libraries in this paper. The 14 new loci were tested in 24 individuals from four populations in Southwest China. These loci were highly polymorphic with numbers of alleles per locus ranging from 6 to 14 and expected heterozygosities from 0.789 to 0.925. All loci followed Hardy–Weinberg expectations except SFM4, SFM11 and SFM13 loci. No significant linkage association was found among all loci. The 14 novel polymorphic microsatellite loci will be useful in studying phylogeography and population genetics of the striped field mouse.

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.

Isolation and characterization of 12 novel microsatellite loci for the red panda (Ailurus fulgens)

The information on dispersal patterns and mating systems of red pandas is quite important for the understanding of the genetic diversity and divergence of this species. And microsatellite marker is an ideal tool to analyze dispersal patterns and mating systems. Thus, we describe in this paper the isolation and characterization of 12 microsatellite loci in the red panda from genomic DNA-enriched libraries. These loci were highly polymorphic with numbers of alleles per locus in 24 individuals ranging from 2 to 14, observed heterozygosity from 0.143 to 0.864 and expected heterozygosity from 0.297 to 0.872. All loci except for RP6 locus followed Hardy–Weinberg expectations. No significant linkage association was found among all these loci. The 12 novel polymorphic microsatellite loci will be of use in studying dispersal patterns and mating systems of red pandas.

Isolation and characterization of 11 microsatellite loci for the Sichuan snub-nosed monkey, Rhinopithecus roxellana

We report on the isolation and characterization of 11 microsatellite loci in the Sichuan snub-nosed monkey (Rhinopithecus roxellana) from AC-enriched genomic libraries. 20 microsatellite loci were screened from the libraries, of which 11 were polymorphic. The number of observed alleles among 32 samples of snub-nosed monkey ranged from three to nine. The observed and expected heterozygosity were 0.071–0.815 and 0.201–0.819, respectively. The high variability revealed in this study should be useful tools for further study on social structure and population genetics of snub-nosed monkey in the future.