The United Nations Convention on Biological Diversity (CBD) Kunming-Montreal Global Biodiversity Framework (GBF) outlines a pathway toward ‘living in harmony with nature’, with significant progress targeted by 2030 (CBD 2022). A key innovation of the GBF is that it explicitly commits to conserving the genetic diversity of all species (not only economically valuable or domesticated taxa). To monitor genetic diversity, the GBF proposes three complementary genetic indicators: (1) genetic structure of populations (to maintain genetically distinct populations), (2) estimators of effective population size (Nₑ) to ensure populations are large enough to retain genetic diversity and long-term viability, and (3) an increase in the number of species subject to DNA-based monitoring of genetic diversity.

With >4000 species, snakes are amongst the most speciose vertebrate groups and occupy nearly all ecological niches, giving them a broad footprint in ecosystem functioning. Despite this, snakes remain amongst the least studied vertebrates from a conservation-management and conservation-genetics perspective. Hong Kong (HKG) supports a diverse reptile fauna, including 45 species of terrestrial snakes. However, for essentially all of these species, nothing is known about their genetic structure, genetic diversity, effective population size (Nₑ), or by extension their viability and adaptive potential. At least 10 Hong Kong terrestrial snake species are listed by IUCN as Vulnerable (VU) or higher, including one Critically Endangered species. Local pressures such as poaching for the pet trade and traditional medicine, limited direct legislative protection for most species, and persistent landscape restructuring over the last two centuries create substantial risks for HKG ophidiofauna.

We propose a high-resolution conservation genomic study of 11 Hong Kong snake species to quantify genetic structure, effective population size, and genomic health, consistent with GBF genetic indicators. Using whole- genome resequencing (25 individuals per species at ~20× coverage), we will:

Infer demographic trajectories over thousands of years and look for recent deviations consistent with intensified anthropogenic pressure in the past ~200 years;

Estimate contemporary Nₑ and recent Nₑ trajectories using state-of-the-art genome-wide approaches, interpreting values against commonly applied benchmarks for genetic viability;

Assess inbreeding situation using genome-wide runs of homozygosity, including ROH length spectra as indicators of recent fragmentation and inbreeding;

Estimate mutation load via functional variant annotation and deleteriousness prediction, partitioning burden into heterozygous and homozygous components as complementary indicators of risk.

Identify genetically distinct management units and connectivity patterns within HKG to support conservation prioritisation.

The 11 focal species span a broad phylogenetic range of extant snakes and include relict lineages (e.g., python and blind snakes). Loss of such populations would represent a disproportionate loss of local phylogenetic diversity. Nine focal species have IUCN Red List status of Vulnerable (VU) or higher; one is Data Deficient; and one (Tonkin pit viper) is included because it is a high-altitude habitat specialist that occurs in Hong Kong only on a few high peaks on Lantau and the New Territories. Although its global status is Least Concern (LC), Hong Kong populations are geographically isolated from the main distribution in mainland China and Vietnam and warrant focused assessment. Our field observations suggest this species requires cooler conditions primarily found at these peaks. Under climate warming, upward tracking of suitable thermal niche may be constrained by Hong Kong’s relatively low peak elevations and habitat fragmentation, increasing potential vulnerability.

Focal species (IUCN; Chinese Red List):

Chinese cobra (Naja atra) - VU; VU

King cobra (Ophiophagus hannah) - VU; EN

Many-banded krait (Bungarus multicinctus) - VU; EN

Tonkin pit viper (Ovophis tonkinensis) - LC; LC

Many-spotted cat snake (Boiga multomaculata) - NT; LC

Hong Kong blind snake (Indotyphlops lazelli) - CR; CR

Mountain keelback (Hebius atemporalis) - DD; NT

Burmese python (Python bivittatus) - VU; CR

Beauty rat snake (Elaphe taeniura) - VU; EN

Indochinese rat snake (Ptyas korros) - NT; VU

Anderson’s stream snake (Ophisthotropis anderssonii) - NT; NT

(DD = Data Deficient; LC = Least Concern; NT = Near Threatened; VU = Vulnerable; CR = Critically Endangered)