Population genomic analysis provides strong evidence of the past success and future strategies of South China tiger breeding

Abstract The South China tigers (Panthera tigris amoyensis) are extinct in the wild, but viable populations remain in breeding centers and zoos after 60 years of effective conservation efforts. At present, however, the existing genetic variation of these tigers remains unknown. In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. We identified two significantly differentiated genomic ancestries in the extant populations, which also harbored some rare genetic variants introgressed from other subspecies, suggesting limited but essential genetic diversity to sustain the South China tigers. The unique pattern of dual ancestry and the genomic resources generated in our study pay the way for a genomics-informed conservation, following the real-time monitoring and controlled exchange of all reproductive South China tigers.

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Sorting Out the Genetic Background of the Last Surviving South China Tigers

Journal of Heredity ◽

10.1093/jhered/esz034 ◽

2019 ◽

Vol 110 (6) ◽

pp. 641-650 ◽

Cited By ~ 1

Author(s):

Wenping Zhang ◽

Xiao Xu ◽

Bisong Yue ◽

Rong Hou ◽

Junjin Xie ◽

...

Keyword(s):

South China ◽

Phylogenetic Analyses ◽

Diagnostic System ◽

Panthera Tigris ◽

Genetic Introgression ◽

The South ◽

In Captivity ◽

In The Wild ◽

Tiger Population ◽

Genetic Assessment

Abstract The South China tiger (Panthera tigris amoyensis) is endemic to China and also the most critically endangered subspecies of living tigers. It is considered extinct in the wild and only about 150 individuals survive in captivity to date, whose genetic heritage, however, is ambiguous and controversial. Here, we conducted an explicit genetic assessment of 92 studbook-registered South China tigers from 14 captive facilities using a subspecies-diagnostic system in the context of comparison with other voucher specimens to evaluate the genetic ancestry and level of distinctiveness of the last surviving P. t. amoyensis. Three mtDNA haplotypes were identified from South China tigers sampled in this study, including a unique P. t. amoyensis AMO1 haplotype not found in other subspecies, a COR1 haplotype that is widespread in Indochinese tigers (P. t. corbetti), and an ALT haplotype that is characteristic of Amur tigers (P. t. altaica). Bayesian STRUCTURE analysis and parentage verification confirmed the verified subspecies ancestry (VSA) as the South China tiger in 74 individuals. Genetic introgression from other tigers was detected in 18 tigers, and subsequent exclusion of these and their offspring from the breeding program is recommended. Both STRUCTURE clustering and microsatellite-based phylogenetic analyses demonstrated a close genetic association of the VSA South China tigers to Indochinese tigers, an issue that could only be elucidated by analysis of historical South China tiger specimens with wild origin. Our results also indicated a moderate level of genetic diversity in the captive South China tiger population, suggesting a potential for genetic restoration.

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Paleoproductivity records for the past 30 ka in the southern Nansha area, the South China Sea

Chinese Science Bulletin ◽

10.1007/bf02886085 ◽

2000 ◽

Vol 45 (13) ◽

pp. 1227-1230 ◽

Cited By ~ 11

Author(s):

Dianyong Fang ◽

Zhimin Jian ◽

Pinxian Wang

Keyword(s):

South China Sea ◽

South China ◽

The South China Sea ◽

The South ◽

China Sea ◽

The Past

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Temporal Trends and Pattern Changes of Short- and Medium-Chain Chlorinated Paraffins in Marine Mammals from the South China Sea over the Past Decade

Environmental Science & Technology ◽

10.1021/acs.est.5b02473 ◽

2015 ◽

Vol 49 (19) ◽

pp. 11348-11355 ◽

Cited By ~ 70

Author(s):

Lixi Zeng ◽

James C. W. Lam ◽

Yawei Wang ◽

Guibin Jiang ◽

Paul K. S. Lam

Keyword(s):

South China Sea ◽

South China ◽

Marine Mammals ◽

Temporal Trends ◽

The South China Sea ◽

The South ◽

Medium Chain ◽

China Sea ◽

The Past ◽

Chlorinated Paraffins

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The decline and impending extinction of the South China tiger

Oryx ◽

10.1046/j.1365-3008.1997.d01-123.x ◽

1997 ◽

Vol 31 (4) ◽

pp. 243-252 ◽

Cited By ~ 3

Author(s):

Ronald Tilson ◽

Kathy Traylor-Holzer ◽

Qiu Ming Jiang

Keyword(s):

Field Study ◽

South China ◽

Reproductive Output ◽

Wild Population ◽

Local People ◽

Conservation Priorities ◽

Panthera Tigris ◽

Captive Population ◽

Wild Populations ◽

The South

The South China tiger Panthera tigris amoyensis is the rarest of the five living tiger subspecies, the most critically threatened and the closest to extinction. No wild South China tigers have been seen by officials for 25 years and one was last brought into captivity 27 years ago. The 19 reserves listed by the Chinese Ministry of Forestry within the presumed range of the tiger are spatially fragmented and most are too small to support viable tiger populations. Over the last 40 years wild populations have declined from thousands to a scattered few. Despite its plight and occasional anecdotal reports of sightings by local people, no intensive field study has been conducted on this tiger subspecies and its habitat. The captive population of about 50 tigers, derived from six wild-caught founders, is genetically impoverished with low reproductive output. Given the size and fragmentation of potential tiger habitat, saving what remains of the captive population may be the only option left to prevent extinction of this tiger subspecies, and even this option is becoming increasingly less probable. This precarious dilemma demands that conservation priorities be re-evaluated and action taken immediately to decide if recovery of the wild population will be possible.

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Is canine distemper virus (CDV) a lurking threat to large carnivores? A case study from Ranthambhore landscape in Rajasthan, India

Journal of Threatened Taxa ◽

10.11609/jott.4569.11.9.14220-14223 ◽

2019 ◽

Vol 11 (9) ◽

pp. 14220-14223

Author(s):

Nadisha Sidhu ◽

Jimmy Borah ◽

Sunny Shah ◽

Nidhi Rajput ◽

Kajal Kumar Jadav

Keyword(s):

Canine Distemper Virus ◽

Management Strategies ◽

Canine Distemper ◽

Preliminary Assessment ◽

The Past ◽

Close Proximity ◽

In The Wild ◽

Effective Conservation ◽

Insight Into

Canine distemper virus (CDV) was reported in wild tigers from Russia and recently from India. Very few studies, however, have been carried out to gain an insight into the prevalence of the disease in India, particularly in the wild. CDV is the etiological agent of one of the most infectious diseases of domestic dogs. With the aim of exploring the threat CDV poses for tigers, a preliminary assessment was carried out to determine its prevalence from villages near Ranthambhore National Park in Rajasthan, India. Free-roaming dog populations within a 4-km-radius of the park’s periphery were tested for antibodies against CDV. The seroprevalence of CDV antibodies in the sampled dogs was 86% (95% CI 78–91 %), indicating the probability of the dogs acting as a reservoir and having been exposed to CDV in the past. The seroprevalence of CAV antibodies was 44.23% (95% CI 35–54 %) and CPV antibodies was 95.19% (95% CI 91–99 %). This could threaten the tiger populations in the park, considering the close proximity of dogs to tigers. It is, therefore, crucial to assess disease threats at the domestic-wildlife interface and to establish management strategies for more effective conservation practices in the landscape.

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Historical change on distribution and quantity of the South-China Tiger (Panthera tigris amoyensis)

Journal of Forestry Research ◽

10.1007/bf02865006 ◽

1998 ◽

Vol 9 (2) ◽

pp. 136-138 ◽

Cited By ~ 1

Author(s):

Jin Kun ◽

Zheng Dong ◽

Hong Meiling ◽

Wang Lijun

Keyword(s):

South China ◽

Historical Change ◽

Panthera Tigris ◽

The South

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Weakening of the Kuroshio Intrusion into the South China Sea over the Past Two Decades

Journal of Climate ◽

10.1175/jcli-d-12-00315.1 ◽

2013 ◽

Vol 26 (20) ◽

pp. 8097-8110 ◽

Cited By ~ 39

Author(s):

Feng Nan ◽

Huijie Xue ◽

Fei Chai ◽

Dongxiao Wang ◽

Fei Yu ◽

...

Keyword(s):

South China Sea ◽

South China ◽

Luzon Strait ◽

The South China Sea ◽

Negative Trend ◽

Kuroshio Intrusion ◽

The South ◽

China Sea ◽

The Past ◽

The Kuroshio

Abstract Inferred from the satellite and in situ hydrographic data from the 1990s and 2000s, the Kuroshio intrusion into the South China Sea (SCS) had a weakening trend over the past two decades. Associated with the weakened Kuroshio intrusion, the Kuroshio loop and eddy activity southwest of Taiwan became weaker, whereas the water above the salinity minimum became less saline in the northern SCS. The sea surface height southwest of Taiwan increased at a slower rate compared to other regions of the SCS because of the weakened Kuroshio intrusion. Simulations using the Regional Ocean Modeling System (ROMS) Pacific model show that the strength of the Kuroshio intrusion into the SCS decreased from 1993 to 2010 with a negative trend, −0.24 sverdrups (Sv) yr−1 (1 Sv ≡ 106 m3 s−1), in the total Luzon Strait transport (LST). Although wind-induced Ekman transport through the Luzon Strait became weaker, the magnitude at 0.001 Sv yr−1 was too small to compensate for the negative trend of the LST. On the other hand, the piling up of the water induced by monsoon winds was an important mechanism for changing the pressure gradient across the Luzon Strait and eventually affecting the LST. The sea level gradient between the western Pacific and the SCS had a negative trend, −0.10 cm yr−1, corresponding to a negative trend in the geostrophic transport at −0.20 Sv yr−1. The Kuroshio transport east of Luzon Island also had a negative trend, which might also be linked to the weakening Kuroshio intrusion.

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