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.

An extinct and deeply divergent tiger lineage from northeastern China recognized through palaeogenomics

“…Two Amur tigers (SRR65 & SRR70) were excluded in mitochondrial analyses, as their de novo assembly mitogenomes, even after manual inspection, continuously show a closer relationship to other subspecies, e.g. the Indochinese tiger and Bengal tiger, possibly owing to their mixed ancestry as reflected in a previous study [12]. Using 38 modern tiger mitogenomes, the MCC (figure 2 b ) and NJ (electronic supplementary material, figure S3a) trees are identical in topology and are consistent with those from earlier results [9].…”

“…An underlying mechanism could be the extinction or dramatic decrease of other ancient lineages, which could have enabled an increase in modern tiger census population size via emptying habitats. Furthermore, a loss or decrease in these divergent lineages may have also reduced the introduction of divergent alleles into the modern lineage through gene flow at a biparental level, which could explain the continuous effective population size decline since 100 ka, reflected by previous nuclear PSMC results [9,10,12]. Although the above explanations may appear somewhat contradictory, the mitochondrial genome is a single exclusively maternally inherited marker whereas the nuclear genome contains thousands of independent pieces of biparental ancestry so different results are expected to an extent.…”

“…According to previous PSMC (pairwise sequentially Markovian coalescent) analyses, all modern tigers exhibit similar evolutionary patterns of demographic histories, implying only one lineage that was ancestral to all modern tiger populations that survived the late Pleistocene bottleneck event [9,10,12]. The ancestral modern tiger lineage had a relatively small but stable effective population size between 1 Ma and 110 ka, suggesting radiation did not occur until the Late Pleistocene.…”

The year of the tiger and the year of tiger genomes!

“…The genome assemblies presented by Zhang et al ( 2022 ) are some of the best tiger assemblies available so far and comparable even to the domestic cat reference genomes. Three out of six extant tiger subspecies account for a total of six chromosome‐level assemblies (two South China tigers [Wang et al, 2021 ; Zhang et al, 2022 ], two Amur tigers [Zhang et al, 2022 , dnazoo.org ], two Bengal tigers [Shukla et al, 2022 ]). Malayan tigers also have a decent genome assembly (Armstrong et al, 2021 ).…”

“…Additionally, Zhang et al ( 2022 ) observe that the populations of Amur and South‐china tiger subspecies had been declining until 5000 years ago, after which the South China tiger population declined sharply. It is possible that in recent timescales (10,000–800 years ago), tiger populations could have become fragmentated and multiple South China tiger subpopulations could have existed (Wang et al, 2021 ) just like there were multiple Bengal tiger populations in this time period (Armstrong et al, 2021 ). Signals of structured populations may be indistinguishable from that of changes in population size (Mazet et al, 2015 ).…”