Short Communication |
Corresponding author: Zhiqiang Han ( d6339124@163.com ) Academic editor: Nina Bogutskaya
© 2020 Linlin Zhao, Tianzi Wang, Fangyuan Qu, Zhiqiang Han.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Zhao L, Wang T, Qu F, Han Z (2020) A non-exhaustive survey revealed possible genetic similarity in mitochondrial adaptive evolution of marine fish species in the northwestern Pacific. ZooKeys 974: 121-130. https://doi.org/10.3897/zookeys.974.55934
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Mitochondrial coding genes involved in the oxidative phosphorylation pathway play vitally important roles in energy production and thermal adaptation. Investigating the underlying molecular mechanism of mitochondrial adaptive evolution is crucial for understanding biodiversity and ecological radiation. In this study, we collated population genetic studies of marine fish species in the northwestern Pacific based on mitochondrial cytochrome b gene sequences, to investigate whether similar patterns could be detected in mitochondrial adaptive evolution. After filtering, nine studies containing eight marine fish species (Ammodytes personatus, Boleophthalmus pectinirostris, Larimichthys polyactis, Mugil cephalus, Pampus argenteus, Platycephalus sp.1, Sebastiscus marmoratus, and Trachidermus fasciatus) belonging to eight different families were retained. Multiple codon-based approaches were used to identify potential sites under selection in each species. By comparison, our results showed that the posterior part of the mitochondrial cytochrome b gene (particularly codon 372 and its neighboring sites) seemed to be involved in the adaptive evolution process, suggesting potential genetic similarity among distantly related species. We also summarized four types of adaptive patterns in the reviewed species, and suggest that the level of genetic differentiation and mitochondrial adaptive evolution might be correlated. Further studies are needed to confirm such relationship by detecting RNA-level evidence and investigating more species and samples.
Cytochrome b gene, genetic similarity, marine fish, Northwestern Pacific, population genetics
Understanding adaptive evolution of marine organisms is a focus topic in evolutionary biology, and can also provide essential information for fishery management and conservation (
Given the relatively fast mutation rate, mitochondrial cytochrome b (cytb) and the non-coding control region are the most two mitochondrial genes investigated in population genetics of marine fish species (
Considering that our major research field is population genetics of marine fish in the northwestern Pacific, we searched population genetics papers based on mitochondrial cytb gene sequences by using the search terms “population genetics”, “cytochrome b or cytb”, “marine fish species” and “northwestern Pacific” in Google Scholar and China National Knowledge Infrastructure (CNKI) literature databases. Our previous studies revealed few genetic variations in the front half of the cytb gene (
For each of the nine species, sequences were aligned using MAFFT method in Unipro UGENE v1.12.0 software (
Order | Family | Species | Latitudinal range | GenBank accession | NH2 | Reference |
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Perciformes | Sciaenidae | Larimichthys polyactis | 39.8–27.2N | FJ609001–FJ609137; JN601196–JN601289 | 231 |
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Gobiidae | Boleophthalmus pectinirostris | 34.8–20.8N | KF384522–KF384638, KF415515 | 118 |
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Ammodytidae | Ammodytes personatus | 45.5–35.9N | MK112908–MK113077 | 170 |
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Stromateidae | Pampus argenteus | 19.2–11.6N1 | JF790202–JF790259, KJ630414–KJ630460 | 105 |
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Scorpaeniformes | Sebastidae | Sebastiscus marmoratus | 37.9–21.5N | KX374371–KX374400, KX722503–KX722509 | 30 |
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Platycephalidae | Platycephalus sp.1 | 35.5–21.4N | MG913953–MG913986 | 34 |
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Cottidae | Trachidermus fasciatus | 39.8–30.4N | JX079997–JX080027, KC701150–KC701194 | 76 |
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Mugiliformes | Mugilidae | Mugil cephalus | 32.7–22.0N | EU083809–EU083903 | 95 |
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A total of 987 mitochondrial cytb complete gene sequences were downloaded from the GenBank database for intraspecific analyses (Table
Results of adaptive evolution analyses of reviewed marine species in this study.
Species | Model | Genetic background | Purifying site1 | Positively adaptive site2 | Fixed adaptive site3 |
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Larimichthys polyactis | 012032 | Weak genetic differentiation | 121 codons | Undetected | Undetected |
Sebastiscus marmoratus | 010010 | Weak genetic differentiation | Codon 287 | Codon 372 | Undetected |
Platycephalus sp.1 | 010000 | Weak genetic differentiation | 12 codons | Codon 314 | Undetected |
Trachidermus fasciatus | 010020 | Weak genetic differentiation | 26 codons | Codon 372 | Undetected |
Boleophthalmus pectinirostris | 010010 | Strong genetic differentiation | 50 codons | Undetected | Undetected |
Ammodytes personatus | 010020 | Strong genetic differentiation | 143 codons | Undetected | Codon 352, 371 |
Pampus argenteus | 010010 | Strong genetic differentiation | 100 codons | Codon 320, 374 | Codon 4, 14, 158, 214, 233, 240, 246, 320, 327, 356, 365, 366, 372, 376 |
Mugil cephalus | 010010 | Strong genetic differentiation | 42 codons | Undetected | Codon 3, 234, 239, 303, 320, 323, 369, 372 |
It is worth noting that codon 372 and its neighbors in cytb gene are likely favored in adaptation in the reviewed species. Codon 372 was identified as an adaptive site in four out of six species (codon 314 in P. sp.1 and codon 352, 371 in A. personatus) (Table
Adaptive evolution is ubiquitous. Due to environmental deviation, intraspecific differentiation would arise in distinct populations to adapt to the local environment. Adaptive evolution may also generate barriers to population connectivity and ultimately lead to further ecological differentiation (
Summary of the four types of adaptive patterns of the reviewed species in this study.
Genetic background | Adaptive pattern | Examples in this study | |
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Type I | weak and non-significant genetic differentiation | Undetected | Larimichthys polyactis |
Type II | weak but significant genetic differentiation | Detected | Sebastiscus marmoratus, Platycephalus sp.1, Trachidermus fasciatus |
Type III | synonymous substitution inducted strong genetic differentiation | Undetected | Boleophthalmus pectinirostris |
Type IV | non-synonymous substitution induced strong genetic differentiation | Detected | Ammodytes personatus, Pampus argenteus, Mugil cephalus |
This work was supported by the National Key Research and Development Program of China (2017YFA0604902) and National Natural Science Foundation of China (41706187).