RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean

Abstract

Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise FST: 0.00036–0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies.

Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus

“…Mutations in genes associated with the immune response may provide evidence of resistance specificity to temperature stress in different geographic populations (Additional file 1 ). For example, the immune response was shown to be related to local adaptation to different water temperatures in Tylosurus crocodilus crocodilus [ 23 ], Trachidermus fasciatus [ 13 ], and Larimichthys polyactis [ 24 ].…”

Evaluation of Spawning- and Natal-Site Fidelity of Larimichthys polyactis in the Southern Yellow Sea Using Otolith Microchemistry

“…According to previous studies on fish morphology and spawning migration routes, three populations are distinguished: the East China Sea, the southern Yellow Sea, and the Bohai/northern Yellow Sea populations (Lin, 1987;Liu, 1990). With the introduction of various methods of population division analysis, such as evaluation of otolith morphology and microchemistry (Zhang et al, 2014;Wang et al, 2016), morphometric characteristics (Zhang et al, 2015), and population genomics (Zhang B. D. et al, 2019), an increasing number of cryptic populations have been reported. In addition to an unrecognized L. polyactis cryptic population, its spawning grounds also should also be considered in the design of management strategies.…”

Changes in overwintering ground of small yellow croaker (Larimichthys polyactis) based on MaxEnt and GARP models: A case study of the southern Yellow Sea stock

“…Transboundary overwintering migratory habits limit the investigation and assessment of the overwintering grounds of SYS (Liu et al ., 2020), resulting in a lack of understanding of suitable habitat distribution for the overwintering stock. Overwintering migration of L. polyactis is an essential component of its population dynamics and is closely related to elements of the marine environment, such as sea bottom temperature (SBT), sea bottom salinity (SBS), chlorophyll‐a concentration (Chla) and water depth (Depth) (Liu et al ., 2020; Tang et al ., 2018; Zhang et al ., 2019). Recruitment and surplus require a suitable marine environment for overwintering, which is the determining factor for the rise and fall of L. polyactis resources.…”