RAD-seq revealed the endangered mechanism of Hydrocera triflora (Balsaminaceae)

Abstract

The genetic diversity of species is a key factor in their adaptability and survival capability. Habitat fragmentation is recognized as one of the key factors causing biodiversity loss, and it has significant impacts on the genetic diversity of plant populations. Hydrocera triflora is an endangered species. Its genetic diversity is unclear and endangered mechanism has not been reported. In this study, 34 samples of H. triflora from seven populations were used to obtain single-nucleotide polymorphisms (SNP) by Restriction-site Associated DNA sequencing (RAD-seq). We discussed the endangered mechanisms of H. triflora by analyzing population genetic diversity and structure. Additionally, we combined these results with historical population dynamics analysis and predictions of potential species distribution in different climate scenarios. The results were as follows: (1) H. triflora had low genetic diversity (Ho=0.156 9, He=0.165 4, π=0.186 5) and high genetic differentiation coefficient; AMOVA analysis showed that genetic variation mainly occurred within populations. (2) The Mantel test indicated that there was a significant positive correlation between environmental distance and genetic distance, as well as geographical distance, with respective P-values of 0.041 2 and 0.008 2. (3) The effective population size of H. triflora had been continuously declining since the mid-Holocene. (4) The total potential distribution area of H. triflora change slightly in the future compared to that in the modern climate. However, in scenarios of high CO2 emissions, the high suitable area decreased significantly and changed into low suitable area, especially in the Malay Islands where the suitable habitat was almost to extinction. The results indicate that habitat fragmentation caused a sustained decrease in the genetic diversity and effective population size of H. triflora. Therefore, the low self-renewal capacity, as well as detrimental environmental conditions such as human disturbance and urbanization, are the primary factors contributing to its endangered state. It is recommended to strengthen the in-situ protection of H. triflora, employing techniques such as artificial pollination to enhance gene flow among populations and thereby increase genetic diversity, and at the same time, we should focus on protecting wetlands from destruction.

Keywords

• habitat fragmentation
• restriction-site associated dna sequencing (rad-seq)
• genetic diversity
• genetic structure
• species distribution models
• demographic history