Population Patterns and Dynamics of <scp><i>Ilisha elongata</i></scp> (Clupeiformes: Pristigasteridae) Revealed by Target Enrichment Data

The elongate ilisha (<i>Ilisha elongata</i>) is an important commercial species found along the Northwestern Pacific Coast. A sharp decline in the annual catch of <i>I. elongata</i> over recent decades implies a concerning situation regarding its fishery stocks. Nonetheless, inadequate knowledge of the genetic diversity, population structure, and historical demography of this species has hindered the establishment of sustainable fishery policies and appropriate conservation measures. In this study, the genetic structure and population demography of <i>I. elongata</i> stocks along the Northwestern Pacific Coast were examined using target-gene enrichment data from 144 <i>I. elongata</i> individuals collected from 18 locations. The analysis revealed an average heterozygosity value of 0.2321 across variable sites in all <i>I. elongata</i> populations. Furthermore, inter-population differentiation is relatively low, with most geographical populations displaying minimal genetic distinctions or none from one another. Population clustering analysis identified four lineages of <i>I. elongata</i> stocks. Through historical demography simulations, it was proposed that the Yalu River Estuary population diverged initially around 32,802 generations before present, while the remaining lineage split into two about 9120 generations ago. One lineage represents the southern population, while the other further separated into the northern population and the Japanese population approximately 4200 generations ago. Furthermore, secondary contact between the southern and northern population was evidenced by either population clustering or demography simulation results. These results underscore that the current phylogeographic patterns of <i>I. elongata</i> may result from directional selection due to low temperature and geographic barriers during and post glacial periods.