Kadoorie Farm and Botanic Garden

Background Early in the coronavirus disease 2019 (COVID-19) pandemic, Sunda pangolins (Manis javanica) involved in the illegal wildlife trade in mainland China were identified as hosts of severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). Although it is unconfirmed whether pangolins or other traded wildlife served as intermediate hosts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the trafficking of pangolins presents a clear risk for transmission of viruses with zoonotic and epizootic potential regardless. We have investigated the origins of pangolin carcasses seized in Hong Kong and have evaluated their potential exposure to SARSr-CoVs, other coronaviruses, and paramyxoviruses, aiming to address a gap in our knowledge with regard to the role of wildlife trade in the maintenance and emergence of pathogens with zoonotic and epizootic potential. Results Using a combination of virological and wildlife forensics tools, we investigated 89 Sunda pangolin carcasses seized by Hong Kong authorities during anti-smuggling operations in the territory conducted in 2013 (n = 1) and 2018 (n = 88). Swabs, organ tissues, blood, and other body fluids were collected during post-mortem examination. Two enzyme-linked immunosorbent assays (ELISAs), which employ a double-antigen sandwich format, were used to detect antibodies reactive against SARSr-CoVs. One individual was found to be seropositive with support from both methods, while five individuals exhibited a putatively seropositive result from one ELISA method. Polymerase chain reaction (PCR) screening for coronavirus and paramyxovirus ribonucleic acid (RNA) did not yield any positives. Based on genomic data, the seropositive individual was determined to have likely originated from Java, while the putatively seropositive individuals were determined to have originated from populations in Borneo, Java, and Singapore/Sumatra. Conclusions While the role of pangolins in the evolution and ecology of SARS-CoV-2 is uncertain, our results suggest susceptibility and potential exposure of pangolins to SARSr-CoVs, occurring naturally or associated with the illegal trafficking of these animals. Complex dynamics between natural populations, traded individuals, and pathogen susceptibility complicate conclusions about the role of pangolins, as well as other host species, in the ecology of SARSr-CoVs and potentially zoonotic viruses with risk of future emergence.

Floral mimics deceive their pollinators by developing visual and olfactory resemblance to various models. We report a flower that exhibits phenotypes like aerial litter and deceives an aerial litter specialist beetle to achieve pollination. We assessed the floral phenology and the effective pollinators of an Australian understorey treelet, Meiogyne heteropetala (Annonaceae). The similarities of morphology, colour and odour between the flowers and co‐occurring aerial litter were investigated. The terpene synthase involved in floral scent emission was identified by expression patterns and product profile. The behavioural responses of the pollinator to various odours were assessed using bioassays. The erotylid beetle Loberus sharpi is the most likely effective pollinator because it was the only pollen‐laden visitor during the pistillate phase. Loberus sharpi was exclusively found in aerial litter and M. heteropetala flowers. The flowers offer an honest shelter reward. The beetle also oviposits there, but most larvae eventually perished as the petals dropped onto the forest floor. The morphology and spectral reflectance of the flowers overlap with aerial litter. The floral scent was dominated by monoterpenes, especially 1,8‐cineole. The cineole synthase MhCINS was the only highly expressed floral terpene synthase and possessed a highly similar product profile to the floral scent composition. The volatile composition of M. heteropetala flowers is distinct from other congeners and highly similar to aerial litter, indicating advergence to aerial litter. Visual and odour resemblance, coupled with low larval survivorship, provides evidence that the beetles were deceived into pollinating the flowers. Behavioural experiments showed that the pollinator was attracted to both aerial litter and M. heteropetala flowers. The beetles were also attracted to 1,8‐cineole and synthetic mixes of floral odour and MhCINS products. The beetles were unable to distinguish floral scent from MhCINS products nor from 1,8‐cineole, suggesting MhCINS alone sufficed to attract the pollinator olfactorily. The beetles, however, preferred aerial litter over flowers. The beetles likely categorised the flower as a general, but not the most preferred, brood substrate. Synthesis. This study reports the first case of floral mimicry of aerial litter and characterises the biochemical process responsible for olfactory mimicry.

Many shark species have been overexploited for international markets, including fins for shark fin soup in Southeast Asia. Previous studies highlighted the value of large, threatened shark species, regulated under CITES Appendix II. However, sampling biases may have overlooked small shark species. Here, we address this by identifying species from ~4000 small shark fins in Hong Kong. These fins included species not recorded in previous surveys, raising the market’s species diversity to 106. Nearly 75% of the small fins came from small shark species and 58.1% of small species were threatened with extinction. We identified an important CITES listing gap: Trade in 19 small, threatened species, especially from the family Triakidae, is unregulated. In addition, a quarter of small fins come from large sharks, indicating that substantial exploitation of juveniles is occurring and may be affecting fisheries sustainability. Enhanced surveillance of small shark fin trade is essential to ensure effective conservation under emerging trade regulations.

With 90 recognized species, kukri snakes in the genus Oligodon Fitzinger constitute the second largest snake radiation in the world. Oligodon species are collectively distributed across the Asian continent and possess several ecological and morphological attributes that are unique amongst other snakes. Despite their high levels of species richness, evolutionary relationships within Oligodon are poorly understood due to a limited number of samples and genetic markers available in earlier phylogenies. In this study, we assembled the largest molecular dataset of Oligodon to date, which we use to assess the systematics and biogeography of the entire genus. Based on a combination of maximum likelihood and Bayesian phylogenies using fragments of three mitochondrial genes (12 s, 16 s, CytB) and three nuclear genes (Rag1, C-mos, BDNF), we identify eight deeply divergent clades within Oligodon, of which only two correspond with species groupings that were recognized by previous morphological classifications. Four species delimitation methods employed on the mitochondrial portion of the dataset resulted in dramatically divergent estimations of molecular operational taxonomic units (mOTUs). When combined, all four methods support the existence of unrecognized species-level lineages, but also indicate that several other Oligodon species are poorly differentiated genetically and require additional integrative taxonomic research to properly resolve. Based on divergence dating, we demonstrate that Oligodon began to diversify during the early Neogene and hypothesize that the most recent common ancestor of the genus originated in mainland Southeast Asia. We conclude by recognizing eight phylogenetically defined species groups and identify sampling gaps that require further investigation once new data becomes available. This study contributes to a greater understanding of snake evolution on the Asian continent and acts as a baseline for future studies of this speciose genus.

Eld's deer Rucervus eldii (McClelland, 1842) is an ungulate that lives in tropical lowland forests in several countries of Indochina and Hainan Island of China. Its remaining population is small and scattered, and the species is listed as an Endangered species on the IUCN Red List. The debate over the taxonomic status of the Hainan population has persisted for over a century—as an island‐endemic subspecies R. e. hainanus, or an insular population of the subspecies R. e. siamensis, would have significant conservation implications. And, given the Hainan population had experienced both population bottleneck and multiple translocations in the past, conservation genomics would be a powerful tool to evaluate the genetic impacts of these events. In this study, we used conservation genomics assessment to study population differentiation and genetic diversity of R. e. siamensis in Cambodia and three Eld's deer subpopulations on Hainan Island. Based on the unique genetic profile and demographic analysis, this study corroborated previous studies using genetic markers that the Hainan Eld's deer warrants the taxonomic status of a distinct subspecies. The Hainan population exhibits a reduction in genetic diversity and an increase in the level of inbreeding when compared to the population of Cambodia. The signs of purifying selection were found against homozygous loss‐of‐function mutations to decrease the deleterious burden in the Hainan population. However, there was an accumulation of more deleterious missense mutations. Furthermore, significant differences in genetic diversity and level of inbreeding found among the three Hainan subpopulations indicated population isolation and suboptimal translocation strategies, which calls for urgent, coordinated, and science‐based genetic management to ensure the long‐term viability of the endemic subspecies hainanus. This study provides guidance for the conservation and management of Eld's deer.

Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7–36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).

Platalea minor, or black-faced spoonbill (Threskiornithidae), is a wading bird confined to coastal areas in East Asia. Due to habitat destruction, it was classified as globally endangered by the International Union for Conservation of Nature. However, the lack of genomic resources for this species hinders the understanding of its biology and diversity, and the development of conservation measures. Here, we report the first chromosomal-level genome assembly of P. minor using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (1.24 Gb) contains 95.33% of the sequences anchored to 31 pseudomolecules. The genome assembly has high sequence continuity with scaffold length N50 = 53 Mb. We predicted 18,780 protein-coding genes and measured high BUSCO score completeness (97.3%). Finally, we revealed 6,155,417 bi-allelic single nucleotide polymorphisms, accounting for ∼5% of the genome. This resource offers new opportunities for studying the black-faced spoonbill and developing conservation measures for this species.

The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO.

Southeast Asia is a biodiversity hotspot characterized by a complex paleogeography, and its Polypodiopsida flora is particularly diverse. While hybridization is recognized as common in ferns, investigations into the relationship between hybridization events and fern diversity are notably lacking. Lecanopteris s.s., an ant-associated fern, has been subject to debate regarding species delimitations primarily due to limited DNA markers and species sampling. Our study integrates 22 newly generated plastomes, 22 transcriptomes, and flow cytometry of all native species along with two cultivated hybrids. Our objective is to elucidate the reticulate evolutionary history within Lecanopteris through the integration of phylo-biogeography reconstruction, gene flow inference, and genome size estimation. Key findings of our study include: (1) An enlarged plastome size in Lecanopteris, attributed to extreme expansion of the Inverted Repeat (IR) regions; (2) The traditional 'pumila' and 'crustacea' groups are paraphyletic; (3) Significant cytonuclear discordance attributed to gene flow; (4) Natural hybridization and introgression in the 'pumila' and 'darnaedii' groups; (5) L. luzonensis is the maternal parent of L. 'Yellow Tip', with L. pumila suggested as a possible paternal parent; (6) L. 'Tatsuta' is a hybrid between L. luzonensis and L. crustacea; (7) Lecanopteris first diverged during the Neogene and then during the middle Miocene climatic optimum in Indochina and Sundaic regions. In conclusion, the biogeographic history and speciation of Lecanopteris have been profoundly shaped by past climate changes and geodynamics of Southeast Asia. Dispersals, hybridization and introgression between species act as pivotal factors in the evolutionary trajectory of Lecanopteris.

Begonia hongkongensis F.W.Xing is described and illustrated. Begonia section Platycentrum series Aequilateralibus , to which it belongs, is likely to be an artificial group defined by its symmetrical leaf base, a feature that is atypical for the genus as a whole, but which may have evolved as an adaptation to flash floods since it is associated with rheophytic and streamside species of tropical areas with very high annual rainfall. Variation within the species and relationships with morphologically similar species are discussed.

A peculiar population of Ravenna nivea (Nire, 1920) was discovered from the Yinggeling Mountain Mass of central Hainan. Its wing pattern and COI barcode data show considerable distinction from other geographic populations of R. nivea, including that of Bawangling, approximately only 40 km away and also located in Hainan. The p-distance value of the COI barcode between the Yinggeling and Bawangling populations was 1.1%, considerably higher than the value (0.6%) between Bawangling population and populations in eastern China, where the subspecific name howarthi Saigusa, 1993 applies. The population is regarded as a distinct subspecies ngiunmoiae Lo & Hsu, subsp. nov. The distinctness and high degree of COI haplotype diversity of R. nivea found in Hainan and Taiwan suggest continental islands may serve as glacial refugees for the butterfly and other organisms during previous glaciations, and the presence of the relict populations of montane butterflies like R. nivea may provide useful clues towards a better understanding of the geological history of mountain formation within islands.

The degree of specificity between fully myco-heterotrophic (MH) orchids and mycorrhizal fungi is regarded as high, but some species undergo a mycobiont shift as they transition from juvenile to adult plant. We investigated morphological and physiological aspects of the interaction between the fully MH Cyrtosia septentrionalis and its four known mycobionts to elucidate developmental consequences of variable, life-stage-dependent specificity. Of five randomly sampled germinated seeds co-cultured with each mycobiont, Physisporinus sp. ‘TK-10’ colonized all, Armillaria gallica and Desarmillaria tabescens colonized one, and A. mellea subsp. nipponica colonized none. Whereas 16.2% of aseptically germinated seeds exhibited onward growth when co-cultured with TK-10, just 1.5-2.6% did so with the other species. Even so, A. gallica colonized and formed internal rhizomorphs within rhizomes established with TK-10, suggesting that this mycobiont can replace and potentially can oust the latter. We infer that the orchid can associate with Armillaria and Desarmillaria mycobionts throughout its life, but that TK-10 enhances early growth. However, because TK-10 has a higher wood-rotting capacity than A. gallica, rapid resource exhaustion may cause nutrient supply shortages. We hypothesize that secondary colonization by Armillaria or Desarmillaria species triggers TK-10 displacement and that this mycobiont shift sustains orchid growth for longer.

Warming can have profound impacts on ecological communities. However, explorations of how differences in biogeography and productivity might reshape the effect of warming have been limited to theoretical or proxy-based approaches: for instance, studies of latitudinal temperature gradients are often conflated with other drivers (e.g., species richness). Here, we overcome these limitations by using local geothermal temperature gradients across multiple high-latitude stream ecosystems. Each suite of streams (6-11 warmed by 1-15°C above ambient) is set within one of five regions (37 streams total); because the heating comes from the bedrock and is not confounded by changes in chemistry, we can isolate the effect of temperature. We found a negative overall relationship between diatom and invertebrate species richness and temperature, but the strength of the relationship varied regionally, declining more strongly in regions with low terrestrial productivity. Total invertebrate biomass increased with temperature in all regions. The latter pattern combined with the former suggests that the increased biomass of tolerant species might compensate for the loss of sensitive species. Our results show that the impact of warming can be dependent on regional conditions, demonstrating that local variation should be included in future climate projections rather than simply assuming universal relationships.

This case series investigates a cluster of deaths in a captive colony of Leschenault's rousettes (Rousettus leschenaultii). Six of seven bats that died between March and September 2021 were diagnosed postmortem with both iron overload (IO) and neoplasia, neither of which have previously been reported in this species. Iron status was assessed via hepatic histopathological grading, hepatic iron concentration, and, in two cases, serum iron concentration. On histopathological grading, all cases had hemochromatosis except one, which had hemosiderosis. Hepatic iron concentrations did not correlate with histopathological grading. Neoplasms in these six bats included hepatocellular carcinoma (HCC; 4), bronchioloalveolar adenocarcinoma (1), pancreatic adenocarcinoma (1), and sarcoma of the spleen and stomach (1). One bat had two neoplasms (HCC and sarcoma of the spleen and stomach). One additional case of HCC in 2018 was identified on retrospective case review. Etiology was investigated to the extent possible in a clinical setting. Nutritional analysis and drinking water testing found oral iron intake within acceptable bounds; however, dietary vitamin C was potentially excessive and may have contributed to IO. Panhepadnavirus PCR testing of liver tissue was negative for all bats. A species-associated susceptibility to IO, as seen in Egyptian fruit bats (Rousettus aegyptiacus), is possible. The high incidence of HCC is suspected to be related to IO; other differentials include viral infection. Causes or contributing factors were not definitively identified for the other neoplasms seen but could include age, inherited risk (given a high level of inbreeding), or an oncogenic virus. Pending further research in this species, it is recommended that keepers of Leschenault's rousettes offer conservative amounts of vitamin C and iron (as for Egyptian fruit bats), submit for postmortem examination any euthanized or found dead, and share records of similar cases.

Six Passiflora species from SW China were studied: Passiflora menghaiensis X.D.Ma, L.C.Yan & J.Y.Shen, P. xishuangbannaensis Krosnick, P. siamica Craib, P. altebilobata Hemsl., P. henryi Hemsl. and P. papilio Li. Chromosomes squashes could be obtained by using the conventional tableting method and the karyotypes were analyzed. The results showed that all six species of passion flower were diploid and the chromosome number was 2n=12. The karyotype formula of P. menghaiensis was 2n=2x=12=8m+2sm+2sm(sat), P. xishuangbannaensis was 2n=2x=12=8m+4sm, P. siamica was 2n=2x=12=10m+2sm, P. altebilobata was 2n=2x=12=10m+2sm, P. henryi was 2n=2x=12=8m+4sm, P. papilio was 2n=2x=12=12m. The karyotypes of all six species are reported for the first time. This study provides comprehensive cytological data for the conservation and genetic study of Passiflora in Asia. The evolutionary relationships between the six species were discussed at the cytological level and compared with published classifications based on morphological and molecular data.

The white-bellied pangolin ( Phataginus tricuspis ) is the world’s most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales from Asia between 2012 and 2018, we found that poaching pressures shifted over time from West to Central Africa. Recently, Cameroon’s southern border has emerged as a site of intense poaching. Using data from seizures representing nearly 1 million African pangolins, we identified Nigeria as one important hub for trafficking, where scales are amassed and transshipped to markets in Asia. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.