Project description:Eld's deer (Rucervus eldii) is a rare and globally endangered tropical Southeast Asian deer species. There is no research on pathogens in Eld's deer in Hainan, China. This study aimed to understand the virus diversity and novel viruses in Eld's deer, and provided important epidemiological baseline information for conservation of this endangered species. 33 nasal swabs, 33 anal swabs, and 9 wound (bitten by ticks) swabs were collected from 33 wild Eld's deer in a nature reserve in Hainan, which constituted into 5 pools. Based on next-generation sequencing (NGS) and macrogenomic analysis, there were differences in the 5 pools of viral reads, while the overall viral reads were closely related to mammals. The novel papillomavirus (PsPV-HMU-1) and Circular Rep-encoding (replication-associated protein encoding) single-stranded DNA (CRESS DNA) virus (PsaCV-HMU-1) were identified in Eld's deer, with amino acid homology of the less than 77.20% of the L1 and less than 45.43% of the rep, respectively. PsPV-HMU-1 and PsaCV-HMU-1 are relatively independent on their phylogenetic trees, and with the overall prevalence of 24.24% (8/33) and 3.03% (1/33) in Eld's deer, respectively. Our results expanded the viral genomic information and host range, and implied that it is necessary for continued epidemiological surveillance in order to understand pathogenicity and the potential for cross-species transmission of viruses in wild Eld's deer.
Project description:Eld's deer (Rucervus eldii) with three recognised subspecies (R. e. eldii, R. e. thamin, and R. e. siamensis) represents one of the most threatened cervids found in Southeast Asia. The species has experienced considerable range contractions and local extinctions owing to habitat loss and fragmentation, hunting, and illegal trade across its distribution range over the last century. Understanding the patterns of genetic variation is crucial for planning effective conservation strategies. This study investigated the phylogeography, divergence events and systematics of Eld's deer subspecies using the largest mtDNA dataset compiled to date. We also analysed the genetic structure and demographic history of R. e. eldii using 19 microsatellite markers. Our results showed that R. e. siamensis exhibits two divergent mtDNA lineages (mainland and Hainan Island), which diverged around 0.2 Mya (95% HPD 0.1-0.2), possibly driven by the fluctuating sea levels of the Early Holocene period. The divergence between R. e. eldii and R. e. siamensis occurred around 0.4 Mya (95% HPD 0.3-0.5), potentially associated with the adaptations to warm and humid climate with open grassland vegetation that predominated the region. Furthermore, R. e. eldii exhibits low levels of genetic diversity and small contemporary effective population size (median = 7, 4.7-10.8 at 95% CI) with widespread historical genetic bottlenecks which accentuates its vulnerability to inbreeding and extinction. Based on the observed significant evolutionary and systematic distance between Eld's deer and other species of the genus Rucervus, we propose to classify Eld's deer (Cervus eldii) in the genus Cervus, which is in congruent with previous phylogenetic studies. This study provides important conservation implications required to direct the ongoing population recovery programs and planning future conservation strategies.
