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Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae)
Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood ana...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Pensoft Publishers
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10209274/ https://www.ncbi.nlm.nih.gov/pubmed/37250917 http://dx.doi.org/10.3897/zookeys.1149.85627 |
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author | Estupiñán, Ruth Amanda Torres de Farias, Sávio Gonçalves, Evonnildo Costa Camargo, Mauricio Cruz Schneider, Maria Paula |
author_facet | Estupiñán, Ruth Amanda Torres de Farias, Sávio Gonçalves, Evonnildo Costa Camargo, Mauricio Cruz Schneider, Maria Paula |
author_sort | Estupiñán, Ruth Amanda |
collection | PubMed |
description | Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories. |
format | Online Article Text |
id | pubmed-10209274 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Pensoft Publishers |
record_format | MEDLINE/PubMed |
spelling | pubmed-102092742023-05-26 Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae) Estupiñán, Ruth Amanda Torres de Farias, Sávio Gonçalves, Evonnildo Costa Camargo, Mauricio Cruz Schneider, Maria Paula Zookeys Research Article Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories. Pensoft Publishers 2023-02-22 /pmc/articles/PMC10209274/ /pubmed/37250917 http://dx.doi.org/10.3897/zookeys.1149.85627 Text en Ruth Amanda Estupiñán, Sávio Torres de Farias, Evonnildo Costa Gonçalves, Mauricio Camargo, Maria Paula Cruz Schneider https://creativecommons.org/licenses/by/4.0/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. |
spellingShingle | Research Article Estupiñán, Ruth Amanda Torres de Farias, Sávio Gonçalves, Evonnildo Costa Camargo, Mauricio Cruz Schneider, Maria Paula Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae) |
title | Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae) |
title_full | Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae) |
title_fullStr | Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae) |
title_full_unstemmed | Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae) |
title_short | Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae) |
title_sort | performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: an example using gladiator frogs, boana gray, 1825 (anura, hylidae, cophomantinae) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10209274/ https://www.ncbi.nlm.nih.gov/pubmed/37250917 http://dx.doi.org/10.3897/zookeys.1149.85627 |
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