Population Patterns and Dynamics of Ilisha elongata (Clupeiformes: Pristigasteridae) Revealed by Target Enrichment Data

TL;DR

This study uses genetic data to understand the population structure and history of Ilisha elongata, a fish species in decline, to inform conservation efforts.

Contribution

The study provides new insights into the genetic diversity and historical demography of Ilisha elongata using target enrichment data.

Findings

Ilisha elongata populations show low genetic differentiation across most geographical regions.

Four distinct lineages were identified, with divergence events dated to around 32,802 and 9120 generations ago.

Secondary contact between southern and northern populations suggests complex historical interactions.

Abstract

The elongate ilisha (
Ilisha elongata
) is an important commercial species found along the Northwestern Pacific Coast. A sharp decline in the annual catch of
I. elongata
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. elongata
stocks along the Northwestern Pacific Coast were examined using target‐gene enrichment data from 144
I. elongata
individuals collected from 18 locations. The analysis revealed an average heterozygosity value of 0.2321 across variable sites in all
I. elongata
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. elongata
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. elongata
may result from directional selection due to low temperature and geographic barriers during and post glacial periods.

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