A Retrospective Analysis on the Population Viability of the Yangtze River Dolphin or Baiji (Lipotes vexillifer)

A study was conducted to investigate the growth parameters, mortality and recruitment pattern of Mastacembelus armatus collected in the Taojiang River fish landing site, Xinfeng County. M. armatus were collected from March, 2018 to February, 2019. Growth parameters, asymptotic length (L¥) = 58.8cm and growth coefficient (k) = 0.13 year-1. Growth performance index(Ø2 ) =2.65, total mortality (Z) = 0.75 year-1, natural mortality (M) = 0.32 year-1, fishing mortality (F) = 0.43 year-1 and exploitation rate (E) = 0.57year-1.The estimated exploitation rate (E) has slightly exceeded the optimum value of E indicating this species was over exploited mainly due to fishing in the study area. The exploitation ratios were computed as Emax= 0.59, E10= 0.45, E50= 0.31. The length at first capture at 50%, (Lc) was 19.51 cm. The Steady biomass also increased with length class until 36.0-36.9 cm and the total steady state biomass was found to be 19.12 tons.

Poyang Lake in China is the most critical habitat and final refuge for the Yangtze finless porpoise (Neophocaena asiaeorientalis), YFP. In 2022, its population reached approximately 492 individuals, an increase of 35 from the 457 individuals recorded in 2017, showing a steady upward trend. The infrequent movement of YFPs between Poyang Lake and the Yangtze River represents a considerable threat to the long-term viability of this population. Additionally, serious water shortages in the lake during the dry season have led the government to consider the establishment of a hydraulic project. Therefore, a reliable risk assessment and quantitative analysis of conservation scenarios are urgently needed for this population. Population viability analysis of the YFP population in Poyang Lake was conducted using the VORTEX software. The baseline model predicted a probability of extinction of 0.241 over the next 100 years, with no probability of extinction in the first 30 years; the genetic diversity would be on a continuous downward trend and decline by 91.5%. The comprehensive protection model predicted a probability of extinction of 0.0028 and that the genetic diversity would be maintained at about 0.996 in 100 years. Breeding rate, sex ratio at birth, mortality rate, and gene flow were the factors that were sensitive to maintaining population viability. The results showed that the population of YFPs in Poyang Lake was at a high risk of extinction due to the decline in genetic diversity and the higher mortality and lower birth rate caused by habitat degradation. A total ban on productive fishing and the rescue and interchange of YFPs are conducive to enhancing the viability of the YFP population in Poyang Lake.

Background: Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis), is the first class protected animal in China. In order to analyze the adaptive evolution of fecundity traits in YFP, the rapidly evolving gene families of YFP were obtained. At the same time, the major genes controlling ovulation, GDF9, BMP15, FSHβ and FSHR were also analyzed. Methods: Orthofinder software was employed to search homologous genes based on protein sequence. CAFÉ software was used to obtain the expansion and contraction gene families of YFP. Then, GO terms and pathway enrichment analyses were performed using TBtools software and Swissprot database. PAML package was used to calculate Ka/Ks (i.e., ω). Evolution rate changes in the positive selected genes were examined using the GU99 process in Diverge (v3.0) program. Result: In YFP, 501 rapid expansion gene families GO enrichment results showed that the reproductive activities related pathways were mainly three significant enrichment process, participation of germline stem cells maintain androgen receptors signaling pathways regulating and male reproductive tract stem cell population to maintain. The most significant GO terms of 220 rapidly contraction gene families associated with reproductive activities mainly consisted of biological processes which were involved in positive regulation of estrogen secretion, mating and estrogen metabolic process. GDF9 and BMP15 genes exhibited purifying selection. However, significant signs of positive selection were detected in FSHR and FSHβ genes, but only FSHβ showed specific changes in the YFP lineage.

To explore the genetic diversity and evolutionary differentiation of Mastacembelus armatus from the headwaters of the Dongjiang and Ganjiang Rivers, we performed whole-genome resequencing on three populations, including Xunyushui (XW) and Jiuqu River (DN) from the Dongjiang River source as well as Taojiang River (XF) from the Ganjiang River source. We analyzed population structure, genetic differentiation, nucleotide diversity (π), pairwise FST, linkage disequilibrium, kinship, and neutrality tests (Tajima’s D, Fu and Li’s D). A total of 209.05 Gbp of clean data were obtained, with high quality and reliable alignment. Average nucleotide diversity (π) was higher in XW (0.00490 ± 0.00248) and DN (0.00478 ± 0.00312) and lower in XF (0.00463 ± 0.00158). Pairwise FST values revealed moderate differentiation between XW and DN (FST = 0.12) and strong divergence between XF and the other two populations (FST = 0.19 and 0.17). Neutrality tests showed no significant deviation from neutrality. XW and DN exhibited positive values, indicating stable demography, while XF showed negative values, suggesting a tendency of population expansion. Phylogenetic, admixture, and PCA analyses supported that all three populations belonged to one evolutionary clade with two ancestral components. XF showed the slowest linkage disequilibrium decay and distant kinship, indicating a small effective population size. Significant genetic divergence was primarily driven by geographic isolation and limited gene flow. This study reveals the genetic diversity and differentiation pattern of M. armatus and provides a genomic basis for its conservation and management.

To explore the genetic diversity and adaptive evolutionary mechanism of Mastacembelus armatus in the Dongjiang and Ganjiang River Sources, whole-genome resequencing was performed on three populations of M. armatus from Xunwushui (XW) and Jiuqu River (DN) in the Dongjiang River Source, and Taojiang (XF) in the Ganjiang River Source. Population genetics methods were integrated to analyze their genetic structure, differentiation characteristics and selection signals. The results showed that a total of 209.05 Gbp of Clean Data was obtained from the three populations, with the Q30 base percentage reaching 94.42% and the average mapping rate to the reference genome being 97.85%, indicating high reliability of the sequencing data. A mean of 7,459,686 single nucleotide polymorphisms (SNPs) were detected, with a transition/transversion ratio of 1.52 and a heterozygous SNP ratio of 2.22%. The total number of genome-wide insertions and deletions (InDels) was 1,902,722±23,247. Gene Ontology (GO) functional annotation revealed a consistent variation pattern of core genes among the three populations. Phylogenetic tree, Admixture and principal component analysis (PCA) confirmed that the three populations belonged to a single evolutionary clade and shared a genetic origin from two ancestral populations (the lowest cross-validation error at K=2), while significant genetic differentiation was observed among populations: XW and DN populations had similar genetic backgrounds and closer genetic relationships, both biased towards the blue ancestral component, whereas XF population was inclined to the red ancestral component, with the DN population showing the highest degree of genetic admixture. Individuals within the XF population had more distant genetic relationships and the longest linkage disequilibrium (LD) decay distance, which was speculated to be associated with its small population size and low recombination rate; in contrast, the XW population had the shortest LD decay distance, corresponding to the characteristics of large population size and high recombination rate. Analysis of population genetic diversity indicated that XW and DN populations were classified as the high-diversity group (with more than 440,000 polymorphic markers, expected heterozygosity >0.31 and polymorphism information content (PIC) ≈0.25), while the XF population was the low-diversity group (with 342,646 polymorphic markers, expected heterozygosity of 0.2608 and PIC of 0.2073). Only the minor allele frequency (MAF) of the XF population (0.2829) was slightly higher than that of the other two populations. This study systematically elucidated the characteristics of genetic differentiation and diversity differences of M. armatus in the Dongjiang and Ganjiang River Sources, providing a genome-level scientific basis for the conservation of genetic resources, development of molecular markers and analysis of environmental adaptive mechanisms of this species.