The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis
Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sci...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/12/23/3386 |
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| author | Xiaolu Han Shihuai Jin Zhiqiang Han Tianxiang Gao |
| author_facet | Xiaolu Han Shihuai Jin Zhiqiang Han Tianxiang Gao |
| author_sort | Xiaolu Han |
| collection | DOAJ |
| description | Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic–Indo–West Pacific (EIP). The WA group included four species belonging to four genera: <i>Cynoscion nebulosus</i>, <i>Equetus punctatus</i>, <i>Sciaenops ocellatus</i>, and <i>Micropogonias undulatus</i>. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (<i>Argyrosomus regius</i>, <i>A. japonicus</i>, <i>Pennahia anea</i>, <i>Nibea albiflora</i>, <i>Miichthys miiuy</i>, <i>Collichthys lucidus</i>, <i>Larimichthys polyactis</i>, and <i>L. crocea</i>) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic–Indo–West Pacific (EIP) group was a younger group. Within the studied species, the genera <i>Collichthys</i> and <i>Larmichthys</i> were the youngest lineages, and we do not suggest that <i>Collichthys</i> and <i>Larmichthys</i> should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed. |
| first_indexed | 2024-03-09T17:55:31Z |
| format | Article |
| id | doaj.art-abb8452f78c54a129f38e7d3ca8fa8a2 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-09T17:55:31Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-abb8452f78c54a129f38e7d3ca8fa8a22023-11-24T10:26:16ZengMDPI AGAnimals2076-26152022-12-011223338610.3390/ani12233386The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data AnalysisXiaolu Han0Shihuai Jin1Zhiqiang Han2Tianxiang Gao3Fishery College, Zhejiang Ocean University, Zhoushan 316002, ChinaFishery College, Zhejiang Ocean University, Zhoushan 316002, ChinaFishery College, Zhejiang Ocean University, Zhoushan 316002, ChinaFishery College, Zhejiang Ocean University, Zhoushan 316002, ChinaUncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic–Indo–West Pacific (EIP). The WA group included four species belonging to four genera: <i>Cynoscion nebulosus</i>, <i>Equetus punctatus</i>, <i>Sciaenops ocellatus</i>, and <i>Micropogonias undulatus</i>. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (<i>Argyrosomus regius</i>, <i>A. japonicus</i>, <i>Pennahia anea</i>, <i>Nibea albiflora</i>, <i>Miichthys miiuy</i>, <i>Collichthys lucidus</i>, <i>Larimichthys polyactis</i>, and <i>L. crocea</i>) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic–Indo–West Pacific (EIP) group was a younger group. Within the studied species, the genera <i>Collichthys</i> and <i>Larmichthys</i> were the youngest lineages, and we do not suggest that <i>Collichthys</i> and <i>Larmichthys</i> should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed.https://www.mdpi.com/2076-2615/12/23/3386phylogenomicsorthologousSciaenidaegenome-widephylogeny |
| spellingShingle | Xiaolu Han Shihuai Jin Zhiqiang Han Tianxiang Gao The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis Animals phylogenomics orthologous Sciaenidae genome-wide phylogeny |
| title | The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis |
| title_full | The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis |
| title_fullStr | The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis |
| title_full_unstemmed | The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis |
| title_short | The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis |
| title_sort | phylogenetic relationships of the family sciaenidae based on genome wide data analysis |
| topic | phylogenomics orthologous Sciaenidae genome-wide phylogeny |
| url | https://www.mdpi.com/2076-2615/12/23/3386 |
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