The South China Sea is a crucial habitat and potential nursery for cetaceans. This study involved five ship-based visual surveys in three summers and two springs from 2020 to 2023, combined with environmental DNA (eDNA) metabarcoding, an emerging tool, to understand the relative abundance and spatial and temporal distribution of cetaceans in offshore and abyssal areas of the South China Sea. The combination of visual observations and eDNA metabarcoding enabled the detection of a total of 18 cetacean species, and 12 species were identified by both methods. Cetaceans showed temporal variation; 7 species in the springs, and 17 species in the summers. Expedition route design, meteorological conditions, and sea conditions between the two seasons can partly explain the seasonal differences. The Hyperoodontidae and Physeteridae species tend to occupy regions with high bathymetric drop gradients, particularly those situated on continental slopes and seamounts. The Delphinidae species are more widely distributed and relatively abundant. Of the cetaceans successfully amplified by eDNA metabarcoding, species with larger group sizes and closer distances tend to be more easily detected. Although the complex and turbulent hydrographic environment of the oceans reduces the duration of eDNA and increases the uncertainty in capturing eDNA signals, our findings indicate that eDNA techniques can provide additional information and hold promise as a potential complementary tool for cetacean monitoring.

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations and populations of known conservation concern, including a Scottish population, for which 37.8% of the autosomes comprised of ROH >1.5 Mb in length.