@ARTICLE{TreeBASE2Ref26615,
author = {Noor D White and Charles Mitter and Michael J. Braun},
title = {Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae)},
year = {2016},
keywords = {Potoos, Nyctibiidae, ultraconserved elements, UCEs},
doi = {},
url = {http://},
pmid = {},
journal = {Journal of Avian Biology},
volume = {},
number = {},
pages = {},
abstract = {In this study, we apply a genome?scale set of molecular markers, ultraconserved elements, to fully resolve the phylogeny of a family of secretive, nocturnal birds, the potoos (Nyctibiidae). This dataset provides an opportunity to explore some challenges of phylogenetic analysis of genome?scale datasets, which we address in several ways. We generate data matrices ranging between 2,610?4,175 loci (1,477,319?3,848,295 aligned base pairs) that represent versions of the data differing in whether or not alignments were trimmed prior to concatenation, and whether 100% or 75% of all taxa were required to be present for inclusion of a given locus. These matrices are analyzed with both maximum likelihood and coalescent algorithms, to check for artifacts of concatenation. Then, we subsample our data matrix into randomly?selected replicates between 125?1,000 loci, and compare the statistical support of the resulting trees to look for evidence of systematic error. In analyses of complete matrices, we find strong statistical support for all ingroup nodes with no evidence for systematic error introduced by alignment trimming, missing data, or concatenation, and we find further support for that topology in our subsampling analyses and statistical topology tests. Finally, we compare our strongly supported topology to those of previous studies, and use the phylogeny to examine the evolutionary history of potoos.}
}
Citation for Study 20258
Citation title:
"Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae)".
Study name:
"Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae)".
This study is part of submission 20258
(Status: Published).
Citation
White N.D., Mitter C., & Braun M. 2016. Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae). Journal of Avian Biology, .
Authors
-
White N.D.
(submitter)
2026339064
-
Mitter C.
301 405 3912
-
Braun M.
Abstract
In this study, we apply a genome?scale set of molecular markers, ultraconserved elements, to fully resolve the phylogeny of a family of secretive, nocturnal birds, the potoos (Nyctibiidae). This dataset provides an opportunity to explore some challenges of phylogenetic analysis of genome?scale datasets, which we address in several ways. We generate data matrices ranging between 2,610?4,175 loci (1,477,319?3,848,295 aligned base pairs) that represent versions of the data differing in whether or not alignments were trimmed prior to concatenation, and whether 100% or 75% of all taxa were required to be present for inclusion of a given locus. These matrices are analyzed with both maximum likelihood and coalescent algorithms, to check for artifacts of concatenation. Then, we subsample our data matrix into randomly?selected replicates between 125?1,000 loci, and compare the statistical support of the resulting trees to look for evidence of systematic error. In analyses of complete matrices, we find strong statistical support for all ingroup nodes with no evidence for systematic error introduced by alignment trimming, missing data, or concatenation, and we find further support for that topology in our subsampling analyses and statistical topology tests. Finally, we compare our strongly supported topology to those of previous studies, and use the phylogeny to examine the evolutionary history of potoos.
Keywords
Potoos, Nyctibiidae, ultraconserved elements, UCEs
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S20258
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref26615,
author = {Noor D White and Charles Mitter and Michael J. Braun},
title = {Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae)},
year = {2016},
keywords = {Potoos, Nyctibiidae, ultraconserved elements, UCEs},
doi = {},
url = {http://},
pmid = {},
journal = {Journal of Avian Biology},
volume = {},
number = {},
pages = {},
abstract = {In this study, we apply a genome?scale set of molecular markers, ultraconserved elements, to fully resolve the phylogeny of a family of secretive, nocturnal birds, the potoos (Nyctibiidae). This dataset provides an opportunity to explore some challenges of phylogenetic analysis of genome?scale datasets, which we address in several ways. We generate data matrices ranging between 2,610?4,175 loci (1,477,319?3,848,295 aligned base pairs) that represent versions of the data differing in whether or not alignments were trimmed prior to concatenation, and whether 100% or 75% of all taxa were required to be present for inclusion of a given locus. These matrices are analyzed with both maximum likelihood and coalescent algorithms, to check for artifacts of concatenation. Then, we subsample our data matrix into randomly?selected replicates between 125?1,000 loci, and compare the statistical support of the resulting trees to look for evidence of systematic error. In analyses of complete matrices, we find strong statistical support for all ingroup nodes with no evidence for systematic error introduced by alignment trimming, missing data, or concatenation, and we find further support for that topology in our subsampling analyses and statistical topology tests. Finally, we compare our strongly supported topology to those of previous studies, and use the phylogeny to examine the evolutionary history of potoos.}
}
- Show RIS reference
TY - JOUR
ID - 26615
AU - White,Noor D
AU - Mitter,Charles
AU - Braun,Michael J.
T1 - Ultraconserved Elements Resolve the Phylogeny of Potoos (Aves: Nyctibiidae)
PY - 2016
KW - Potoos
KW - Nyctibiidae
KW - ultraconserved elements
KW - UCEs
UR - http://dx.doi.org/
N2 - In this study, we apply a genome?scale set of molecular markers, ultraconserved elements, to fully resolve the phylogeny of a family of secretive, nocturnal birds, the potoos (Nyctibiidae). This dataset provides an opportunity to explore some challenges of phylogenetic analysis of genome?scale datasets, which we address in several ways. We generate data matrices ranging between 2,610?4,175 loci (1,477,319?3,848,295 aligned base pairs) that represent versions of the data differing in whether or not alignments were trimmed prior to concatenation, and whether 100% or 75% of all taxa were required to be present for inclusion of a given locus. These matrices are analyzed with both maximum likelihood and coalescent algorithms, to check for artifacts of concatenation. Then, we subsample our data matrix into randomly?selected replicates between 125?1,000 loci, and compare the statistical support of the resulting trees to look for evidence of systematic error. In analyses of complete matrices, we find strong statistical support for all ingroup nodes with no evidence for systematic error introduced by alignment trimming, missing data, or concatenation, and we find further support for that topology in our subsampling analyses and statistical topology tests. Finally, we compare our strongly supported topology to those of previous studies, and use the phylogeny to examine the evolutionary history of potoos.
L3 -
JF - Journal of Avian Biology
VL -
IS -
ER -
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