Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey.

There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.

Virus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals.

Wildlife is reservoir of emerging viruses. Here we identified 27 families of mammalian viruses from 1981 wild animals and 194 zoo animals collected from south China between 2015 and 2022, isolated and characterized the pathogenicity of eight viruses. Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae. In addition to the reported SARSr-CoV-2 and HKU4-CoV-like viruses, picornavirus and respiroviruses also likely circulate between bats and pangolins. Pikas harbor a new clade of Embecovirus and a new genus of arenaviruses. Further, the potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified, complicating wildlife protection and the prevention and control of these diseases in domestic animals. This study provides a nuanced view of the frequency of host-jumping events, as well as assessments of zoonotic risk.

Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger.

The South China tiger (Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tiger due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first SCT genome and an improved Amur tiger (P. t. altaica, AT) genome named AmyTig1.0 and PanTig2.0. The two genomes are the most continuous and comprehensive among any tiger genomes yet reported at the chromosomal level. By using the two genomes and resequencing data of 15 SCT and 13 AT individuals, we investigated the genomic signature of inbreeding depression of the SCT. The results indicated that the effective population size of SCT experienced three phases of decline, ~5.0-1.0 thousand years ago, 100 years ago, and since captive breeding in 1963. We found 43 long runs of homozygosity fragments that were shared by all individuals in the SCT population and covered a total length of 20.63% in the SCT genome. We also detected a large proportion of identical-by-descent segments across the genome in the SCT population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites and loss-of-function mutations were found across genomes with extensive potential influences, despite a proportion of these loads having been purged by inbreeding depression. Our research provides an invaluable resource for the formulation of genetic management policies for the South China tiger such as developing genome-based breeding and genetic rescue strategy.

Molecular identification of Colpodella sp. of South China tiger Panthera tigris amoyensis (Hilzheimer) in the Meihua Mountains, Fujian, China.

A three-year-old male South China tiger died in the tiger enclosure of the China Tiger Park in the Meihua Mountains on December 2018 after being bitten by a tick. This tiger presented clinical symptoms like whole-body severe jaundice, hepatosplenomegaly, kidney, and lymph node hemorrhages. The Colpodella sp.-specific 18S rRNA gene was detected using nested PCR. Interestingly, the DNA isolated from the blood of the tiger was found to be 100% similar to that of the tick by NCBI BLAST analysis. However, the DNA fragments isolated from the tiger's blood were 90.1% similar to the Colpodella sp. strain human erythrocyte parasite (HEP, MH208621) and 90.4% similar to the Colpodella sp. strain Heilongjiang (HLJ, KT364261). To investigate the species of ticks and ticks-carried Colpodella parasites in this region, the species of ticks obtained from the grasses outside the tiger enclosure and the species of Colpodella carried by ticks were identified. The DNA from ticks as well as that from the tick-borne Colpodella sp. were amplified from each tick using PCR followed by amplicon sequencing. In total 402 adult ticks samples were collected, among which 22 were positive for Colpodella sp. (5.5%), and the species were further determined by morphology, DNA sequencing and phylogenetic analyses. Interestingly, one Colpodella sp. was found to have 94.2% sequence similarities to the Colpodella sp. strain HEP (MH208621). This strain was previously reported to infect a woman in Yunnan, China. In addition, three Colpodella sp. showed 87-91% sequence similarities to the Colpodella sp. strain HLJ (KT364261), which was previously reported to infect human in Heilongjiang, China. This study disclosed the possibility of zoonotic transmission of Colpodella sp. by ticks in China. Finally, it provides a basis for urgently determining and monitoring the repertoire of ticks-borne piroplasmid pathogens, with the ultimate aim of strategic control.

Colonization and Development of the Fecal Microflora of South China Tiger Cubs (Panthera tigris amoyensis) by Sequencing of the 16S rRNA Gene.

Postnatal colonization and development of the gut microbiota is linked to health and growth. A comprehensive understanding of the postnatal compositional changes and development of the microbial community is helpful to understand the gut health and improve the survival rate of South China tiger cubs (Panthera tigris amoyensis). Fecal samples from three tiger cubs were collected on the day of birth in 2018 (June 17-21 [G0], July 18 [G1], July 31 [G2], and August 7 [G3]). The 16S rRNA genes of the fecal microflora were sequenced. Results showed that 38 phyla, 58 classes, 134 orders, 272 families, and 636 genera of bacteria from 3,059 operational taxonomic units were identified from 12 fecal samples. The diversity and abundance of species of group G0 were significantly higher (p < 0.05 or 0.01) than those of groups G2 and G3. The predominant phylum was Proteobacteria in groups G0 and G1 (38.85% and 48%, respectively) and Firmicutes in groups G2 and G3 (71.42% and 75.29%, respectively). At the phylum level, the abundance of Deinococcus-Thermus was significantly decreased in groups G1, G2, and G3 as compared to group G0 (p < 0.05), while that of Firmicutes was significantly increased in groups G2 and G3 (p < 0.05). At the genus level, the abundance of Faecalibacterium, Ralstonia, and unidentified Rickettsiales was significantly decreased in groups G1, G2, and G3 as compared with group G0 (p < 0.05), while that of Pseudomonas was significantly decreased in groups G2 and G3 (p < 0.05). The composition and structure of fecal microbiota of South China tiger cubs changed after birth.

Detection and molecular characterisation of intestinal parasites in the South China tiger Panthera tigris amoyensis (Hilzheimer).

Parasitic infections of the South China tigers in the Meihua Mountains have not been explored previously. Faeces of 22 South China tigers from the China Tiger Park in the Meihua Mountains were examined. Eggs of ascaridoid nematodes and oocysts of coccidia were detected by Mini-FLOTAC assay. Morphological observation and molecular characterisation of the oocysts were carried out. The prevalence of Toxascaris leonina (von Linstow, 1902) was 18% (4/22), and the highest egg per gram (EPG) count in the faeces was 27,150. The prevalence of Cystoisospora sp. was 45% (1 0/22) and the highest oocysts per gram (OPG) in the faeces was 6,000. In addition, we found one ascaridoid nematode in the South China tiger's faeces and was molecularly and morphologically identified as T. leonina. The oocysts in the faeces were sporulated in vitro and identified as Cystoisospora sp. Amplification of full-length internal transcribed spacers (ITS) resulted in sequences 1,622 bp long. Using the sequences, Cystoisospora sp. of the South China tiger was closest to Isospora belli (Wenyon, 1923) and Cystoisospora suis (Biester, 1934).

Identification and molecular analysis of Ixodid ticks (Acari: Ixodidae) infesting wild boars (Sus scrofa) and tick-borne pathogens at the Meihua mountain of southwestern Fujian, China.

Wildlife is essential to the biodiversity of the Meihua mountain, southwestern Fujian province, China. However, there have been few surveys of the distribution of ixodid ticks (Acari: Ixodidae) and tick-borne pathogens affecting wild animals at these locations. In this study, 1197 adult ixodid ticks infesting wild boars were collected from 10 sampling sites during 2019. Ticks were identified to species based on morphology, and the identification was confirmed based on mitochondrial 16S, ITS1 and ITS2 rRNA sequences. Eight tick species belonging to 2 genera were identified, including H. longicornis (n = 373, 31.1%), H. flava (n = 265, 22.1%), D. auratus (n = 153, 12.8%), H. hystricis (n = 119, 9.9%), D. silvarum (n = 116, 9.7%), H. bispinosa (n = 114, 9.5%), D. atrosignatus (n = 33, 2.8%), and D. taiwanensis (n = 24, 2.0%). DNA sequences of Rickettsia spp. (spotted fever group) and Babesia spp. were detected in these ticks. Phylogenetic analyses revealed the possible existence of Candidatus Rickettsia laoensis and Rickettsia raoultii. This study illustrates the potential threat to wild animals and humans from tick-borne pathogens.