Genetic Differentiation of Reintroduced Père David’s Deer (Elaphurus davidianus) Based on Population Genomics Analysis

The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David’s deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David’s deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David’s deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David’s deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David’s deer, and low levels of genome-wide genetic diversity were observed in Père David’s deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David’s deer, especially between the captive population in Beijing Père David’s deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David’s deer started to decline ~25.8ka, and the similar levels of three populations’ LD reflected the genetic impacts of long-term population bottlenecks in the Père David’s deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.

Variation In The PRNP Gene Of Pere David’s Deer (Elaphurus Davidianus) May Impact Genetic Vulnerability To Chronic Wasting Disease

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy caused by prions that has spread across cervid species in North America since the 1960s and recently spread to cervids in Eurasia. The Association of Zoos and Aquariums (AZA) considers CWD to be of major concern for cervids in AZA-accredited facilities because of the indirect transmission risk of the disease and the impact of CWD regulatory protocols on captive breeding programs. Vulnerability to CWD is affected by variation in the PRNP gene that encodes the prion protein. We therefore sequenced PRNP in Pere David’s deer (Elaphurus davidianus), a species that was extinct in the wild for more than a century, and descends from ca. 11 founders. In 27 individuals, we detected two PRNP haplotypes, designated Elad1 (51 of 54 chromosomes) and Elad2 (3 of 54 chromosomes). The two haplotypes are separated by four single nucleotide polymorphisms (SNPs), three of which are non-synonymous. Both Elad1 and Elad2 have polymorphisms that in other cervid taxa are associated with reduced vulnerability to CWD. The two haplotypes are more similar in sequence to PRNP in other cervids than to each other. This suggests that PRNP in cervids may have been under long-term balancing selection, as has been shown for PRNP in non-cervid taxa, and which could account for the presence of multiple haplotypes among founders. There may be a fitness benefit in maintaining both PRNP haplotypes in the species because variation in the prion amino acid sequence can limit transmission of CWD.

Widespread Prevalence of Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli from Père David's Deer in China

ABSTRACTPère David’s deer (Elaphurus davidianus or milu) is an endangered species, and the prevalence of antimicrobial resistance (AMR) such as mcr-1-positive strains among them has been unknown. In this study, we aimed to investigate the genomic characterizations of mcr-1-positive strains and provide insight into the dissemination of AMR in nature reserve settings. Sixty-seven mcr-1-positive Escherichia coli isolates from 97 fecal samples were identified by PCR and found resistant to colistin. The prevalence of β-lactam resistance was very high, and there were 64 mcr-1-positive isolates containing β-lactamase genes. Transconjugants of 66 mcr-1-positive isolates were acquired through conjugation experiments. PCR-based replicon typing (PBRT) showed that 44 strains harbored IncI2 mcr-1-bearing plasmids, eight strains harbored IncX4 mcr-1-carrying plasmids, and 14 strains harbored IncHI2 mcr-1-positive plasmids. Notably, mcr-1 was located in the chromosome of LD27-1. Clonal dissemination and horizontal dissemination of mcr-1 by plasmids coexist. We first report the prevalence of plasmid-mediated mcr-1 in E. coli from Père David’s deer in China. mcr-1-bearing IncI2 plasmid was the most frequent plasmid type, and the first IncI2 plasmid harboring both blaCTX-M-132 and mcr-1 is characterized here. Our results support the implication of Père David’s deer as a potential reservoir for MCR-1-producing E. coli.IMPORTANCE The mcr-1 gene is widely reported around the world and has been identified on various plasmids with different replicon types. Resistance to the last-line antibiotic colistin mediated by mcr-1 still represents a threat to global public health. Père David’s deer is a highly endangered species originating in China, and many deer are currently being raised in captivity for gradual reintroduction to the wild. If this species carries AMR bacteria, it will pose a potential threat to the environment. Therefore, research on the dissemination of mcr-1-positive E. coli from Père David’s deer is of great significance. This is the first study to investigate the microbiological and genomic surveillance of MCR-1-producing bacteria colonized among Père David’s deer in China, and we uncovered a high prevalence of MCR-1-producing E. coli. The importance of constant surveillance for AMR bacteria in nature reserve settings is emphasized.

First report on the prevalence of Fasciola hepatica in the endangered Père David’s deer (Elaphurus davidianus) in China

Background Fasciola hepatica is an important zoonotic parasite that causes fasciolosis in a broad range of animals. No information is available about the prevalence of F. hepatica in Père David’s deer (Elaphurus davidianus), an endangered species in the world. Therefore, the purpose of the study was to evaluate the prevalence of fasciolosis in Père David’s deer in the Dafeng Elk National Natural Reserve, Jiangsu province, China. Results In this study, 142 fecal samples from Père David’s deer were analyzed for F. hepatica by microscopy and nest-PCR. Only one sample was positive for F. hepatica according to microscopy examination, while 18 of 142 (12.68, 95%CI: 2.841–22.45%) samples were positive for F. hepatica according to nest-PCR results. Conclusions This is the first report of prevalence of F. hepatica in Père David’s deer. The prevalence data indicated that F. hepatica was also present in this endangered animal, which may cause a potential threat to this precious species.