Genetic diversity and population structure of cutlassfish (Lepturacanthus savala) along the coast of mainland China, as inferred by mitochondrial and microsatellite DNA markers

Gu, Sijia; Yi, Mu-Rong; He, Xiongbo; Lin, Po-Tsun; Liu, Wei‐Han; Luo, Zhisen; Lin, Hung‐Du; Yan, Yunrong

doi:10.1016/j.rsma.2021.101702

Cited by 17 publications

(27 citation statements)

References 66 publications

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“…Overfishing and habitat loss can lead to reduced spatial occupancy (Helen et al, 2021) and genetic diversity in marine fish (Miguel et al, 2020). In the present study, the analyses of mtDNA fragments of large yellow croaker populations revealed high haplotype diversity (Hd COI+Cytb = 0.983) and moderate nucleotide diversity (π COI+Cytb = 0.0042) in wild populations, which was consistent with a previous study in L. crocea (Hd COI+Cytb = 0.990, π COI+Cytb = 0.005) and findings in a variety of other marine species along the coast of mainland China, such as L. polyactis (Hd COI = 0.936, π COI = 0.0043) (Zhang et al, 2017), Lepturacanthus savala (Hd COI = 0.977, π COI = 0.0037) (Gu et al, 2021) and N. albiflora (Hd COI = 0.697, π COI = 0.002) (Xu et al, 2012). However, our study reveals that large yellow croaker has always maintained relatively high genetic diversity relative to other marine fish in this region.…”

Section: Discussionsupporting

confidence: 93%

“…The temporo-spatial genetic architecture of marine fish is typically characterized by genetic homogeneity due to their high dispersal potential and an absence of obvious physical barriers to gene flow among separate ocean basins (Ding et al, 2018;Gu et al, 2021). Such a scenario may have been discovered in many marine fish along the coast of mainland China [e.g., L. polyactis (Kim et al, 2010;Li et al, 2013) and Nibea albiflora (Xu et al, 2012)].…”

Section: Discussionmentioning

confidence: 99%

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Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Yuan

Lin

et al. 2021

Front. Mar. Sci.

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The large yellow croaker, Larimichthys crocea, was once the most abundant and economically important marine fish in China. Thus far, it has also been the most successful mariculture fish species in China. However, its wild stock severely declined in the 1970s because of overexploitation, and therefore hatchery release has been carried out for stock enhancement since 2000. As a migratory fish, large yellow croaker was divided into three geographical stocks according to ambiguous morphological and biological characteristics in early documents. To investigate the identity of wild large yellow croaker populations and assess the influence of hatchery supplementation on wild populations, a total of 2,785 cultured individuals and 591 wild individuals were collected from 91 hatcheries and six wild populations along the coast of mainland China and analyzed using two mitochondrial genes [cytochrome oxidase I (COI) and cytochrome b (Cyt b)] and one nuclear gene (RyR3). The higher haplotype diversity and moderate nucleotide diversity of wild large yellow croaker indicated that overexploitation, which caused a sharp decrease in biomass, did not lead to a loss of genetic diversity. According to phylogenetic construction and network analysis, the absence of a significant population structure pattern revealed a single panmictic population of wild large yellow croaker with exception of a population collected from the Sansha Bay, which showed high genetic relatedness to the cultured population, suggesting significant genetic effects resulting from stock enhancement. Overall, our study suggests no genetic differentiation in the entire wild population of large yellow croaker, which means that we have great flexibility in mixing and matching farmed and wild populations. However, since the result showed that domestication, the relaxation of purifying selection, increased genetic loads, and maladapted farmed fish will be at a selective disadvantage when cultured juveniles are released in the wild, the effectiveness of stock enhancement and the negative impact of hatchery-wild fish hybridization on the wild population must be carefully evaluated in future.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Yuan

Lin

et al. 2021

Front. Mar. Sci.

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“…3 ); thus, we did not observe influences of the last glacial period with fluctuation of sea level or primary productivity on size as suggested by He et al (2014) . Pre-LGM expansion is also observed in another con-familial cutlassfish species Lepturacanthus savala along the coast of China ( Gu et al, 2021 ) and a bentho-pelagic fishery species, silver pomfret Pampus argenteus from the Indo-Pacific region ( Ni et al, 2014 ; Zhao et al, 2011 ). Causes of the pre-LGM population expansion for these fishes could be an interesting subject for future studies.…”

Section: Discussionmentioning

confidence: 93%

“…For another warm-affiliated species T. brevis , population genetic data based on allozyme markers are limited from a few adjacent locations in the coasts of China of the South China Sea ( Wang et al, 1994 ). A recent study applied both mitochondrial COI gene and 13 microsatellite loci as the markers to infer the intra-specific genetic variation of L. savala and found no clear pattern in relation to geographic areas along the coast of China ( Gu et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Variation in global distribution, population structures, and demographic history for fourTrichiuruscutlassfishes

Lin

Tsai

Wang

2021

PeerJ

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Background Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific. Methods We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22–39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations. Results In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these differences, a single well-mixing fish stock, thus one management unit, was identified in each of the four species, presumably due to expansion of their population sizes predated the Last Glacial Maximum and a lack of distribution barrier. The most dominant T. japonicus, which have at least one magnitude higher effective population size than the others, show a unique abrupt size expansion event at 75 to 50-kilo years ago when the low sea level occurred during the ice age. Main conclusions The demographic history revealed by our genetic analyses advances understanding of the current distribution and population structure for these congeneric species. Moreover, the uncovered population structure provides insight into the assessment and management of these species. Such information complements contemporary knowledge about these species and enables us to forecast their ability to resist future environmental and anthropogenic disturbances.

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“…Total genomic DNA was extracted from muscle tissue using a Genomic DNA Purification Kit (Gentra Systems, Valencia, CA). The COI gene was amplified by polymerase chain reaction (PCR) using the primers Fish-F2 (5´-ACCTCTGTGTGTGGGGC-TAC-3´) and Fish-R2 (5´-GTGATGCATTGGCTTGAAA-3´) (Gu et al 2021). Each 50-µl PCR mixture contained 5 ng of template DNA, 5 µl of 10× reaction buffer, 4 µl of dNTP mix (10 mM), 5 pmol of each primer and 2 U of Taq polymerase (TaKaRa, Taq polymerase).…”

Section: Sampling and Species Identificationmentioning

confidence: 99%

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

Yi¹,

Hsu²,

Gu³

et al. 2022

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Four Trichiurus species, T. japonicus, T. lepturus, T. nanhaiensis, and T. brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T. gangeticus. The mitogenomes contained 16.568–16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T. lepturus nor T. nanhaiensis but they are T. gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

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Genetic diversity and population structure of cutlassfish (Lepturacanthus savala) along the coast of mainland China, as inferred by mitochondrial and microsatellite DNA markers

Cited by 17 publications

References 66 publications

Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Variation in global distribution, population structures, and demographic history for fourTrichiuruscutlassfishes

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

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Genetic diversity and population structure of cutlassfish (Lepturacanthus savala) along the coast of mainland China, as inferred by mitochondrial and microsatellite DNA markers

Cited by 17 publications

References 66 publications

Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Resource Status and Effect of Long-Term Stock Enhancement of Large Yellow Croaker in China

Variation in global distribution, population structures, and demographic history for fourTrichiuruscutlassfishes

﻿Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

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Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex