The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis
SIMPLE SUMMARY: Phylogenomics is an effective method to resolve phylogenetic problems. Herein, the phylogenetic relationships among 12 Sciaenidae species were reconstructed using genome-wide data. Two major phylogenetic groups were distinguished in our study, namely, the Western Atlantic species gro...
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ftpubmed:oai:pubmedcentral.nih.gov:9741161 2023-05-15T18:15:25+02:00 The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis Han, Xiaolu Jin, Shihuai Han, Zhiqiang Gao, Tianxiang 2022-12-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9741161/ http://www.ncbi.nlm.nih.gov/pubmed/36496907 https://doi.org/10.3390/ani12233386 en eng MDPI http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9741161/ http://www.ncbi.nlm.nih.gov/pubmed/36496907 http://dx.doi.org/10.3390/ani12233386 © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). CC-BY Animals (Basel) Article Text 2022 ftpubmed https://doi.org/10.3390/ani12233386 2022-12-18T01:57:57Z SIMPLE SUMMARY: Phylogenomics is an effective method to resolve phylogenetic problems. Herein, the phylogenetic relationships among 12 Sciaenidae species were reconstructed using genome-wide data. Two major phylogenetic groups were distinguished in our study, namely, the Western Atlantic species group, which contained four species, and the Eastern Atlantic, Indian Ocean, and West Pacific species group, which contained eight species. The Western Atlantic species were indicted as the more ancient group in the studied species. Meanwhile, the Eastern Atlantic, Indian Ocean, and West Pacific species were the younger group. However, a close phylogenetic relationship between the Collichthys and Larmichthys genera was not supported. ABSTRACT: 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: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) 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 Collichthys and ... Text Sciaenops ocellatus PubMed Central (PMC) Indian Pacific Animals 12 23 3386 |
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Article Han, Xiaolu Jin, Shihuai Han, Zhiqiang Gao, Tianxiang The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis |
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description |
SIMPLE SUMMARY: Phylogenomics is an effective method to resolve phylogenetic problems. Herein, the phylogenetic relationships among 12 Sciaenidae species were reconstructed using genome-wide data. Two major phylogenetic groups were distinguished in our study, namely, the Western Atlantic species group, which contained four species, and the Eastern Atlantic, Indian Ocean, and West Pacific species group, which contained eight species. The Western Atlantic species were indicted as the more ancient group in the studied species. Meanwhile, the Eastern Atlantic, Indian Ocean, and West Pacific species were the younger group. However, a close phylogenetic relationship between the Collichthys and Larmichthys genera was not supported. ABSTRACT: 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: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) 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 Collichthys and ... |
format |
Text |
author |
Han, Xiaolu Jin, Shihuai Han, Zhiqiang Gao, Tianxiang |
author_facet |
Han, Xiaolu Jin, Shihuai Han, Zhiqiang Gao, Tianxiang |
author_sort |
Han, Xiaolu |
title |
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_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_sort |
phylogenetic relationships of the family sciaenidae based on genome-wide data analysis |
publisher |
MDPI |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9741161/ http://www.ncbi.nlm.nih.gov/pubmed/36496907 https://doi.org/10.3390/ani12233386 |
geographic |
Indian Pacific |
geographic_facet |
Indian Pacific |
genre |
Sciaenops ocellatus |
genre_facet |
Sciaenops ocellatus |
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Animals (Basel) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9741161/ http://www.ncbi.nlm.nih.gov/pubmed/36496907 http://dx.doi.org/10.3390/ani12233386 |
op_rights |
© 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3390/ani12233386 |
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Animals |
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12 |
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23 |
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3386 |
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1766188507655569408 |