Tao Pan

Demographic recovery is often used as evidence of conservation success, yet population growth does not necessarily restore maternally inherited genetic diversity. The Critically Endangered Chinese alligator ( Alligator sinensis ) has increased numerically under captive breeding, but contemporary maternal‐lineage representation remains poorly resolved. Here, we assembled control‐region‐excluded mitochondrial genomes from 356 individuals across six groups (F1, F2, F3, F4, wild and ZJ). Mitochondrial nucleotide diversity was extremely low ( π = 5.41 × 10 ⁻⁵ ). Although 16 haplotypes were detected, 88.2% of sampled individuals carried only two dominant haplotypes, revealing pronounced matrilineal lineage compression. These findings show that demographic recovery can coexist with restricted contemporary representation of maternal lineages, underscoring that census growth alone does not constitute matrilineal recovery. Monitoring maternal lineages alongside nuclear genomic variation and census size can therefore provide a more complete assessment of conservation recovery.

Inbreeding depression is a major threat to the long‐term viability of small populations. Although captive breeding and genetic rescue are the main alternative in conservation, their genomic impacts are largely unknown, and the unintended effects of these approaches may intensify the depression by introducing new deleterious mutations. Based on whole‐genome sequencing data from 247 critically endangered Chinese alligators, we constructed a high‐resolution genetic variation map and identified three distinct genetic populations, clarifying their demographic history and further supporting the independent origin of the American population. Comparisons between captive and semi‐wild populations revealed that captive management outperforms semi‐wild management in reducing inbreeding and increasing genetic diversity, while simultaneously elevating the accumulation of deleterious mutations, which may result from relaxed purifying selection. Although the inbreeding coefficient in this species is notably higher than in other endangered species, purging has likely played a significant role in reducing the amount of recessive deleterious mutations. Forward‐in‐time simulations indicated that mixing populations can mitigate the risk of demographic decline, yet current populations still remain vulnerable to future environmental changes. These findings provide valuable genomic evidence to guide balanced and effective conservation strategies for the Chinese alligator.

Background: Cadmium (Cd ²⁺ ) and lead (Pb ²⁺ ) are two common heavy metal pollutants in rivers and lakes that have multiple toxic effects on organisms. However, their toxic mechanisms are not fully understood. The loach ( Misgurnus anguillicaudatus ), belonging to the genus Misgurnus (Cypriniformes, Cobitidae), is an important benthic fish species whose physiological activities are highly susceptible to heavy metal pollutants. Such exposure can adversely affect its growth, development, and reproduction, leading to disease occurrence and significant economic losses in the M. anguillicaudatus farming industry. Methods: After M. anguillicaudatus was exposed to Cd ²⁺ (3.625 mg L ⁻¹ , 7.25 mg L ⁻¹ , and 14.5 mg L ⁻¹ ) and Pb ²⁺ (47.5 mg L ⁻¹ , 95 mg L ⁻¹ , and 190 mg L ⁻¹ ) for 96 h, frozen sections of their visceral organs (heart, hepatopancreas, gills, kidneys, stomach, and intestine) were prepared. The activities of six metabolic and immune-related enzymes in these organs were assessed using enzyme histochemical staining and optical density quantitative analysis technology. Results: The distribution of the six metabolic and immune-related enzymes exhibited significant tissue specificity. Acid phosphatase (ACP) was mainly distributed in the stomach, intestine, and gills; alkaline phosphatase (ALP) exhibited high activity in the stomach and intestine; and adenosine triphosphatase (ATPase) displayed greater activity in the heart, hepatopancreas, and stomach. In addition, non-specific esterase (NSE) was abundant in the hepatopancreas, stomach, gills, and kidney; peroxidase (POX) activity was prominent in the kidney, gills, and heart; and succinate dehydrogenase (SDH) activity was enriched in the heart and hepatopancreas. Exposure to Cd ^2 + markedly inhibited ACP activity in all six organs, significantly inhibiting ALP activity in the hepatopancreas, gills, and stomach, ATPase activity in all six organs, NSE activity in the hepatopancreas and stomach, POX activity in the heart, gills, and kidney, and SDH activity in the heart, hepatopancreas, and stomach. Similarly, Pb ^2 + exposure significantly inhibited ACP and ATPase activities in all organs except the kidney and stomach, the ALP and NSE activities of the hepatopancreas, gills, and stomach, the POX activities of the heart, gills, and kidney, and the SDH activities of the heart, hepatopancreas, and stomach. Conclusions: Compared with Pb ²⁺ , Cd ²⁺ exerted a broader toxic effect across the six organs. Both heavy metal ions disrupted the blood circulation of M. anguillicaudatus by inhibiting enzymatic activity, impairing detoxification and respiration, and reducing the digestion and absorption of nutrients.

The number and survival rate of juveniles play a key role in the recovery of Chinese alligators ( Alligator sinensis ). The differences between artificial and semi‐wild environments can directly affect the growth and development of juvenile alligators. This study analyzed the physical conditions (lengths and weights) and cloacal microbial communities of juvenile alligators in both artificial breeding (DJ, ZX) and semi‐wild (GJM) environments to reveal the significant effects of environmental pressure on their physiological state and microbiome. The results revealed that the body length (23.15 ± 1.06 cm) and weight (22.8 ± 3.08 g) of juvenile alligators in the GJM were significantly lower than those in the artificial environment (body length = 29.5 cm, weight = 68.6 g; p < 0.01). Moreover, the microbial α diversity (ACE, Shannon) of the GJM was significantly reduced, and the community structure was significantly separated (NMDS analysis), suggesting that the pressure of the semi‐wild environment inhibited growth. In terms of microbial composition, the relative abundance of Actinobacteria in the GJM group was significantly, increased, whereas that of Bacteroidetes was decreased, and Microbacteria and Cyanobacteria were unique; at the genus level, environmentally specific marker genera were identified (such as Limnohabitans and Pseudomonas in GJM and Fluviicola and Deinococcus in the artificial environments). LEfSe analysis further elucidated the differential marker microbiota (such as Actinobacteria/Cyanobacteria in GJM). In summary, stress (such as food shortages) in semi‐wild environments affects the growth and development of juvenile alligators by changing their microbial communities (such as enriched actinomycetes), This finding provides a microbial ecological basis for optimizing the conservation strategy of the Chinese alligator.

In line with the new coronavirus occurrence, bats are an important carrier of viruses, which are extremely important to public safety. Hipposideros armiger is a large bat species with a wingspan of approximately 50–60 cm. A comparatively large body and wingspread lead to a greater dispersal ability, which in turn leads to a wider habitat. In this study, we employed the CYTB gene sequence (1117 bp) derived from H. armiger within five caves of southern Anhui province to undertake the landscape genetics research across the mountainous region. Our study revealed the relatively low genetic variation observed in all five populations. Two clades were distinguished within the phylogenetic tree of 7 haplotypes, and significant population differentiation (F _ST) was detected among all populations by AMOVA. In terms of the geographical distance, the group from the Caihuadong cave (CHD) exhibits a relatively close distance to the group from the Longkoudong cave (LKD) but shows the largest genetic distance. Additionally, both show a relatively independent clustering pattern based on haplotypes, particularly CHD (H1, H2). The bats from the Yanzidong cave (YZD) shares a common haplotype (H3) with all other populations and lowest genetic diversity, suggesting the formation of this population might have been influenced by the founder effect. The mantel test between geographical and genetic distances indicates a relatively weak correlation among H. armiger populations at a small scale, further suggesting their robust dispersal capabilities, which also is supported by the AMOVA results. In population demography, only CHD shows a significant population expansion, which corresponds to its geographic environment being suitable for the survival of H. armiger, consistent with network analysis. This study provides an initial analysis of the landscape genetic structure of H. armiger, offering a foundational reference for larger scale population genetics in this species.

The Boulenger’s slug snake (Pareas boulengeri Angel, 1920) has previously been documented as relatively widely distributed across the eastern, southern, and southwestern regions of China. In the present study, integrated morphological comparisons and molecular phylogenetic analyses were undertaken to reevaluate the taxonomic status of P. boulengeri and to describe two new species: Pareas dabieshanensissp. nov. and Pareas orientalissp. nov. Phylogenetic reconstruction based on CYTB gene sequences indicated that populations previously identified as P. boulengeri comprise three distinct lineages: true P. boulengeri, P. dabieshanensissp. nov., and P. orientalissp. nov. The two new species exhibit significant genetic divergence from their congeners, with uncorrected pairwise distances of 4.1–4.5%, consistent with interspecific divergence within the genus. Morphologically, P. dabieshanensissp. nov. is distinguished by the presence of two subocular scales, the absence of preocular scales, and higher ventral (184–187) and subcaudal (68–74) counts. P. orientalissp. nov. is characterized by a single preocular scale and fused subocular and postocular scales. The revised distributions restrict P. boulengeri to southwestern China, while the new species are confined to the Dabie Mountains (Anhui, Hubei, Henan) and eastern China (southern Anhui, Jiangsu, Jiangxi, Zhejiang), respectively. The non-overlapping ranges of P. dabieshanensissp. nov. and P. orientalissp. nov., bisected by the Yangtze River, suggest that this major hydrological system acted as a biogeographic barrier driving speciation. This study expands the genus Pareas to 33 recognized species (27 in China) and underscores the prevalence of cryptic diversity within morphologically conserved lineages.

Increasing the quality of offspring to optimize population reproductive efficiency represents a viable approach for increasing population size. The population of Chinese alligators has a growing age structure, but the high mortality rate of juveniles is a serious problem that needs to be solved. We investigated the relationship between the weight of juvenile Chinese alligators and the microbiota to improve the survival rate and provide better protection for Chinese alligators. The results revealed significant differences in body weight among the selected individuals. Among the 35 most abundant microbial genera in the different weight groups, four genera (Stenoxybacter, Gracilibacteria, Absconditabacteriales_(SR1) and Saccharimonadales) were significantly positively correlated with weight. These genera can help the host shape the anaerobic environment of the intestine, degrade organic acids and proteins, and promote the production of growth-promoting factors. This study provided valuable insights into the relationship between the microbiota and weight, along with theoretical guidance for improving the survival rate of juvenile Chinese alligators.

The internal and external environments affect the Chinese alligator (Alligator sinensis) eggs during the incubation period. This study aimed to explore the composition, diversity, and function of microorganisms on the surface of Chinese alligator eggs with different phenotypes during artificial incubation, providing a theoretical basis for improving the hatching success rate of Chinese alligator eggs. The development of high-throughput sequencing technology has enabled microbial DNA sequencing. In this study, the microbial community on the surface of Chinese alligator eggs (42 samples) was analyzed via 16S rRNA sequencing. The microbial profiles significantly varied among Chinese alligator eggs with a clean, shiny, crack-free surface (G group) and those with a dirty, dull, cracked surface (B group). The composition and abundance of microorganisms markedly varied between the B and G groups. The predominant bacterial taxa on the surface of Chinese alligator eggs were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidota, with Proteobacteria exhibiting the highest abundance. The abundance of Actinobacteria and Firmicutes in the G group was greater than that of the B group. Moreover, the abundance of Proteobacteria and Bacteroidota in the B group was greater than that of the G group. These findings indicate that the structure and diversity of microbial communities significantly varied on the surface of Chinese alligator eggs with different phenotypes during the incubation period and that different developmental stages of the eggs are dependent on microbes. The findings of this study provide a novel perspective on microbial dynamics during the incubation of Chinese alligator eggs and provide a scientific basis for the optimization of artificial incubation environments in the future.

Despite 40 years of conservation of the critically endangered Chinese alligator ( Alligator sinensis ), the genomic underpinnings of its status remained uncharted. Genome sequencing data of 244 individuals uncovered relatively low overall genomic diversity/heterozygosity and long runs of homozygosity, with captive populations exhibiting higher heterozygosity and smaller inbreeding coefficients compared to wild individuals. The decreased level of inbreeding in the captive population demonstrates the contribution of the large captive breeding population. The estimated recent effective population size was around a few dozen. To combat challenges of inbreeding depression and reduced adaptability, we used genome-wide SNP-based kinship analysis on captive populations to enable a genome-informed breeding program that minimizes inbreeding. Long-term field monitoring revealed that the Chinese government greatly advanced the conservation of A. sinensis through conservation measures and reintroduction programs. Our research enriches the understanding of the Chinese alligator’s genetic landscape, offering invaluable genomic resources for breeding and conservation strategies.