Genetic structure of marine and lake forms of Pacific herring <i>Clupea pallasii</i>

Orlova, S. Yu.; Rastorguev, Sergey; Bagno, Tatyana; Курносов, Д. С.; Nedoluzhko, Artem

doi:10.7717/peerj.12444

Cited by 6 publications

(8 citation statements)

References 49 publications

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“…Our previous studies allowed us to describe the genetic differentiation between the Pacific herring populations in the Russian part of its range using mitochondrial and nuclear genome markers [ 21 , 26 ]. Moreover, the comparative analysis of the genetic differentiation between the combined three lakes on one side and nine marine populations of Pacific herring on the other showed that lake form populations differ from the marine ones [ 26 ]. The origin of lake populations across the Russian Far East is still unclear.…”

Section: Discussionmentioning

confidence: 99%

“…However, they most likely arose independently due to the significant geographical distance between Sakhalin Island and the Kamchatka Peninsula habitats. Nevertheless, Pacific herring individuals who inhabit fresh-/brackish water in different regions are clustered together based on genetic data [ 26 ]. Perhaps, such differences are explained by their ongoing contact with marine individuals, which can spread “freshwater” alleles between lake populations across Russian Far East.…”

Section: Discussionmentioning

confidence: 99%

“…The sampling, DNA extraction, ddRAD library preparation and DNA sequencing were previously described [ 26 ]. Fifty-four individuals of two ecological forms of Pacific herring from the Northwest Pacific and the Kara Sea were involved in the present study.…”

Section: Methodsmentioning

confidence: 99%

“…Conversely, the lake ecological form prefers brackish lagoon-type lakes and small bays to spawn and spend the winter [ 25 ]. Recent genetic-based studies showed the level of genetic differentiation between populations from the Russian part of the North Pacific Ocean and the Kara Sea; moreover, lake populations from the Kamchatka Peninsula and Sakhalin Island separated from the marine populations of Pacific herring [ 21 , 26 ]. At the same time, it has been suggested that the lake ecological form has its genetic component associated with freshwater adaptation [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

“…Ethical permissions are not applicable to this article. The genomic datasets analyzed in this study were retrieved from previously published databases [ 26 ].…”

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confidence: 99%

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Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Nedoluzhko

Orlova

Курносов³

et al. 2022

Genes

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Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Ethical permissions are not applicable to this article. The genomic datasets analyzed in this study were retrieved from previously published databases [ 26 ].…”

mentioning

confidence: 99%

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Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Nedoluzhko

Orlova

Курносов³

et al. 2022

Genes

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Separated by Space and Time but United by Kinship: Phylogeographical and Phylogenetic History of Two Species of Eleginus (Gadidae) Based on the Polymorphism of Cyt b Mitochondrial DNA Gene

et al. 2023

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The Problems of DNA-Barcoding the Shads of Genus Alosa (Alosidae) of the Ponto-Caspian Basin

Orlova,

Emelyanova,

Nebesikhina

et al. 2024

J. Ichthyol.

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Abstract— Numerous studies show that species identification of representatives of the genus Alosa using various genetic markers is often difficult and the search for more specific biomarkers is required. For the first time we analyzed polymorphism of COI gene fragment of mitochondrial DNA of two representatives of this genus (A. tanaica and A. kessleri), supplemented with new data on A. immaculata, from the waters of the Ponto-Caspian basin in comparative aspect with other representatives of the herring (Clupeoidea) genera Alosa, Clupea, Clupeonella, Sprattus, and Sardinops. The main result was the conclusion that within the genus Alosa, it is not possible to identify species using the marker used. On the one hand, specimens collected from morphologically distinct individuals and identified as different species have the same haplotypes. On the other hand, samples belonging to different species differ from each other by an insignificant number of nucleotide substitutions and do not form independent clades on the phylogram and haplotype network. This indicates the absence of genetic differentiation between the studied samples of herrings of genus Alosa into separate species and species groups when using DNA barcoding based on the COI gene. The reasons for such a phenomenon may be the following: (1) incorrect identification of species in catches, since shads (Alosidae) have high morphological flexibility and in many species, the main external morphological characters often overlap; (2) recent time of speciation by the standards of biological evolution for shads of genus Alosa; (3) difference in proportion of interspecific hybrids, which can vary significantly between populations of the same species.

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Genetic structure of marine and lake forms of Pacific herring Clupea pallasii

Cited by 6 publications

References 49 publications

Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Separated by Space and Time but United by Kinship: Phylogeographical and Phylogenetic History of Two Species of Eleginus (Gadidae) Based on the Polymorphism of Cyt b Mitochondrial DNA Gene

The Problems of DNA-Barcoding the Shads of Genus Alosa (Alosidae) of the Ponto-Caspian Basin

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