Genetic structure in species with shallow evolutionary lineages: a case study of the rare flatfish Verasper variegatus

Abstract

We examined the genetic population divergence of the spotted halibut Verasper variegatus. A previous report suggested two conservation units for this species along the Japanese Pacific coast. Extending the coverage of the genomes (29 microsatellites and three mitochondrial DNA segments) revealed hitherto-undetected genetic population boundaries. We screened population samples from the major habitats along the Japanese coast and the Yellow Sea coast (East Asian Continent). Significant genetic differentiation was found in every comparison between the habitats. In most cases, the nuclear and mitochondrial population divergences were incongruent, most likely caused by differences between the two genomes in the effects of genetic drift after recent population isolation and bottleneck events. We discuss the ecological and evolutionary mechanisms of the genetic structure as well as the units of conservation. The present study illustrates the merits of wider coverage of genomes in genetic population analysis especially for species with a shallow population history.

Population structure of the ocellate spot skate (Okamejei kenojei) inferred from variations in mitochondrial DNA (mtDNA) sequences and from morphological characters of regional populations

“…1). Similarly, genetic divergence between the Yellow Sea and Japanese coast of the East China Sea has been noted in several marine fishes, including the white croaker (Pennahia argentata), spotted halibut (Verasper variegatus), and gizzard shad (Konosirus punctatus) (see Han et al, 2008;Sekino et al, 2011;Gwak et al, 2015). As noted in the above examples with C, haematocheilus and K. punctatus, 3 regional populations (EC, YS, and SJ) of O. kenojei also diverged on account of Tsushima Strait and the Tsushima Current, which act as geographical barriers.…”

Habitat utilization, feeding, and growth of wild spotted halibut Verasper variegatus in a shallow brackish lagoon: Matsukawa-ura, northeastern Japan

“…This study demonstrates that spotted halibut, a rare pleuronectid flatfish, is more dependent on limited shallower nurseries than two common species: stone flounder and marbled flounder. This result is also supported by the fact that the remaining small local populations of spotted halibut in Japan are distributed mainly around areas with estuarine tidal flats or brackish inlets [9]. These results suggest that stock enhancement of spotted halibut should be promoted based on the long-term concepts of conservation and reconstruction of coastal environments aimed at improving recruitment of wild fish, with particular care taken to ensure the genetic diversity of local populations [5,9].…”

“…These results showed that the total amount of eggs and larvae of spotted halibut, which had the lowest size-fecundity relation [22,25], were quite low compared with those of two common species. Furthermore, the main spawning area of spotted halibut off Fukushima Prefecture is far offshore (approximately 40 km offshore with 120 m depth) [4], and larvae have longer pelagic duration than those of stone flounder and marbled flounder [26], suggesting that a lower proportion of larvae can reach and settle into the shallower nurseries [8,9]. Although the ontogenetic migration processes of spotted halibut larvae have not been elucidated at all, similar transport and habitat selection mechanisms of stone flounder off Miyagi Prefecture might be applicable to spotted halibut; eggs and larvae are transported passively by the western wind-driven Ekman onshore transport.…”

“…Recent degradation and/or loss of these key habitats have been presumed to contribute to reduced recruitment of wild fish and isolation of small local populations [8]. Genetic population structure analyses along the Japanese and Chinese coasts revealed significant genetic differentiation between samples from every habitat examined, suggesting that stock enhancement activities should be promoted and managed based on each local population unit [9]. In 2008, a total of 177,000 hatcheryreared juveniles were released in northeastern (Iwate, Miyagi, and Fukushima), central (Aichi), and western (Nagasaki Prefecture) parts of Japan [10].…”

“…Most age-1 juveniles migrate to deeper waters during the subsequent May-June. In contrast, ecological characteristics of wild juveniles in northeastern Japan including Iwate, Miyagi, and Fukushima Prefectures [9] have not been elucidated. The collection records of small juveniles \10 cm TL have been reported only from Matsukawa-ura Lagoon in Fukushima Prefecture [3], and a small number of larger juveniles (103-182 mm TL) from Mangoku-ura Inlet in Miyagi Prefecture [13].…”