Bayesian phylogenetic tree of Macrostomum lignano NRs.
The Bayesian tree was constructed with the deduced amino sequences of the DNA binding domain (DBD) with a mix amino acid replacement model + invgamma rates. The PPs values are shown above each branch, branches under the PPs 0.5 are shown as polytomies. The same data set is also tested by ML method u...
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ftsmithonian:oai:figshare.com:article/15166037 2023-05-15T15:58:43+02:00 Bayesian phylogenetic tree of Macrostomum lignano NRs. Wenjie Wu (81279) Philip T. LoVerde (7548587) 2021-08-13T17:31:53Z https://doi.org/10.1371/journal.pone.0250750.s001 unknown https://figshare.com/articles/figure/Bayesian_phylogenetic_tree_of_i_Macrostomum_lignano_i_NRs_/15166037 doi:10.1371/journal.pone.0250750.s001 CC BY 4.0 CC-BY Biochemistry Medicine Cell Biology Genetics Evolutionary Biology Ecology Infectious Diseases Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified free-living intertidal zone flatworm novel zinc finger motif Platyhelminth NRs flatworm genome data NR subfamily 3 CHC 2 motif Platyhelminth HR 96b DBD DNA binding domain C 4-type zinc finger motifs NR gene duplication Image Figure 2021 ftsmithonian https://doi.org/10.1371/journal.pone.0250750.s001 2021-12-20T04:22:30Z The Bayesian tree was constructed with the deduced amino sequences of the DNA binding domain (DBD) with a mix amino acid replacement model + invgamma rates. The PPs values are shown above each branch, branches under the PPs 0.5 are shown as polytomies. The same data set is also tested by ML method using PHYML (v2.4.4) under LG+G+I substitution model (Equilibrium frequencies: Model, Proportion of invariable sites: Estimated (0.158), Number of substitution rate categories: 4, Gamma shape parameter: Estimated (0.956). Support values for the tree are obtained by bootstrapping a 1,000 replicates and bootstrap values above 500 and are indicated below each branch (or after MrBAYES BPPs separated by Slash). Star indicates the node obtained by Bayesian inference which is different from that obtained by ML method. Bg: Biomphalaria glabrata , Cg: Crassostrea gigas , d: Drosophila melanogaster , h: Homo sapiens , Lg: Lottia gigantean , Ml: Macrostomum lignano , Px: Protopolystoma xenopodis , Sm: Schistosoma mansoni . Red highlighted NRs show M . lignano NRs. (TIF) Still Image Crassostrea gigas Unknown |
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op_collection_id |
ftsmithonian |
language |
unknown |
topic |
Biochemistry Medicine Cell Biology Genetics Evolutionary Biology Ecology Infectious Diseases Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified free-living intertidal zone flatworm novel zinc finger motif Platyhelminth NRs flatworm genome data NR subfamily 3 CHC 2 motif Platyhelminth HR 96b DBD DNA binding domain C 4-type zinc finger motifs NR gene duplication |
spellingShingle |
Biochemistry Medicine Cell Biology Genetics Evolutionary Biology Ecology Infectious Diseases Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified free-living intertidal zone flatworm novel zinc finger motif Platyhelminth NRs flatworm genome data NR subfamily 3 CHC 2 motif Platyhelminth HR 96b DBD DNA binding domain C 4-type zinc finger motifs NR gene duplication Wenjie Wu (81279) Philip T. LoVerde (7548587) Bayesian phylogenetic tree of Macrostomum lignano NRs. |
topic_facet |
Biochemistry Medicine Cell Biology Genetics Evolutionary Biology Ecology Infectious Diseases Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified free-living intertidal zone flatworm novel zinc finger motif Platyhelminth NRs flatworm genome data NR subfamily 3 CHC 2 motif Platyhelminth HR 96b DBD DNA binding domain C 4-type zinc finger motifs NR gene duplication |
description |
The Bayesian tree was constructed with the deduced amino sequences of the DNA binding domain (DBD) with a mix amino acid replacement model + invgamma rates. The PPs values are shown above each branch, branches under the PPs 0.5 are shown as polytomies. The same data set is also tested by ML method using PHYML (v2.4.4) under LG+G+I substitution model (Equilibrium frequencies: Model, Proportion of invariable sites: Estimated (0.158), Number of substitution rate categories: 4, Gamma shape parameter: Estimated (0.956). Support values for the tree are obtained by bootstrapping a 1,000 replicates and bootstrap values above 500 and are indicated below each branch (or after MrBAYES BPPs separated by Slash). Star indicates the node obtained by Bayesian inference which is different from that obtained by ML method. Bg: Biomphalaria glabrata , Cg: Crassostrea gigas , d: Drosophila melanogaster , h: Homo sapiens , Lg: Lottia gigantean , Ml: Macrostomum lignano , Px: Protopolystoma xenopodis , Sm: Schistosoma mansoni . Red highlighted NRs show M . lignano NRs. (TIF) |
format |
Still Image |
author |
Wenjie Wu (81279) Philip T. LoVerde (7548587) |
author_facet |
Wenjie Wu (81279) Philip T. LoVerde (7548587) |
author_sort |
Wenjie Wu (81279) |
title |
Bayesian phylogenetic tree of Macrostomum lignano NRs. |
title_short |
Bayesian phylogenetic tree of Macrostomum lignano NRs. |
title_full |
Bayesian phylogenetic tree of Macrostomum lignano NRs. |
title_fullStr |
Bayesian phylogenetic tree of Macrostomum lignano NRs. |
title_full_unstemmed |
Bayesian phylogenetic tree of Macrostomum lignano NRs. |
title_sort |
bayesian phylogenetic tree of macrostomum lignano nrs. |
publishDate |
2021 |
url |
https://doi.org/10.1371/journal.pone.0250750.s001 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
https://figshare.com/articles/figure/Bayesian_phylogenetic_tree_of_i_Macrostomum_lignano_i_NRs_/15166037 doi:10.1371/journal.pone.0250750.s001 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0250750.s001 |
_version_ |
1766394493832003584 |