Molecular evidence reveals the distinctiveness of Indo-Pacific finless porpoises (Neophocaena phocaenoides) in the Pearl River Estuary and insights into genus Neophocaena’s origin

Much of the knowledge about the wide-ranging finless porpoise species (Neophocaena phocaenoides) remains limited, as well as its phylogenetic relationship with another taxa (N. asiaeorientalis) in genus Neophocaena. Using 11 microsatellite loci, we first investigated population differentiation of N. phocaenoides within the Pearl River Estuary (PRE). We then used mtDNA control region (CR) and cytochrome b (cyt b) sequences from the PRE population (75) as well as those from other geographic populations to reveal the divergence level and phylogeny of the PRE N. phocaenoides. Pairwise F ST analysis with mtDNA CR sequences determined that the PRE population was highly differentiated from other putative populations (with the closest population 400-km away in the Taiwan Strait) (F ST = 0.388–0.764, p < 0.01). The level of genetic divergence between the PRE and its conspecific population was as high as comparisons between the two subspecies under N. asiaeorientalis (F ST = 0.361, p < 0.01). Our results also revealed contrasting demographic histories between the PRE and the other geographic finless porpoise populations (the Taiwan Strait population, the southern and northern Yellow Sea population and the middle Yangtze River population), which suggested stability in the warmer waters of the Indo-Pacific and expansions in the colder waters of the North Pacific. Phylogenetic trees created using cyt b data indicated that some haplotypes exclusive to the PRE population were basal to the rest of the genus. Based on these results, we argue that the genus Neophocaena originated in tropical waters (because the PRE is the most southern location sampled, i.e., the closest location to tropical waters).