Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we an...
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ftzenodo:oai:zenodo.org:4989798 2023-05-15T16:10:02+02:00 Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics Edwards, Scott V. Cloutier, Alison Baker, Allan J. 2017-06-07 https://zenodo.org/record/4989798 https://doi.org/10.5061/dryad.25f7g unknown doi:10.1093/sysbio/syx058 https://zenodo.org/communities/dryad https://zenodo.org/record/4989798 https://doi.org/10.5061/dryad.25f7g oai:zenodo.org:4989798 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Dromaius novaehollandiae Struthio camelus Gavia stellata Tinamus guttatus Pygoscelis adeliae biased-gene conversion Falco peregrinus Picoides pubescens intron Alligator mississippiensis Taeniopygia guttata Anas platyrhynchos Nothoprocta perdicaria Phoenicopterus ruber Manacus vitellinus Podiceps cristatus conserved element Meleagris gallopavo Gallus gallus Haliaeetus leucocephalus info:eu-repo/semantics/other dataset 2017 ftzenodo https://doi.org/10.5061/dryad.25f7g10.1093/sysbio/syx058 2023-03-10T17:43:35Z Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600 - ∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically-derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine+falcon clade, was resolved differently and with moderate (> 70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis. Supplementary_Files_Edwards_CNEEs_2017Supplementary Files S1, S3, S4, S5, and S6.Supplementary File S2Alignment summary measures for all ... Dataset Falco peregrinus Pygoscelis adeliae Zenodo |
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Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
Dromaius novaehollandiae Struthio camelus Gavia stellata Tinamus guttatus Pygoscelis adeliae biased-gene conversion Falco peregrinus Picoides pubescens intron Alligator mississippiensis Taeniopygia guttata Anas platyrhynchos Nothoprocta perdicaria Phoenicopterus ruber Manacus vitellinus Podiceps cristatus conserved element Meleagris gallopavo Gallus gallus Haliaeetus leucocephalus |
spellingShingle |
Dromaius novaehollandiae Struthio camelus Gavia stellata Tinamus guttatus Pygoscelis adeliae biased-gene conversion Falco peregrinus Picoides pubescens intron Alligator mississippiensis Taeniopygia guttata Anas platyrhynchos Nothoprocta perdicaria Phoenicopterus ruber Manacus vitellinus Podiceps cristatus conserved element Meleagris gallopavo Gallus gallus Haliaeetus leucocephalus Edwards, Scott V. Cloutier, Alison Baker, Allan J. Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics |
topic_facet |
Dromaius novaehollandiae Struthio camelus Gavia stellata Tinamus guttatus Pygoscelis adeliae biased-gene conversion Falco peregrinus Picoides pubescens intron Alligator mississippiensis Taeniopygia guttata Anas platyrhynchos Nothoprocta perdicaria Phoenicopterus ruber Manacus vitellinus Podiceps cristatus conserved element Meleagris gallopavo Gallus gallus Haliaeetus leucocephalus |
description |
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600 - ∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically-derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine+falcon clade, was resolved differently and with moderate (> 70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis. Supplementary_Files_Edwards_CNEEs_2017Supplementary Files S1, S3, S4, S5, and S6.Supplementary File S2Alignment summary measures for all ... |
format |
Dataset |
author |
Edwards, Scott V. Cloutier, Alison Baker, Allan J. |
author_facet |
Edwards, Scott V. Cloutier, Alison Baker, Allan J. |
author_sort |
Edwards, Scott V. |
title |
Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics |
title_short |
Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics |
title_full |
Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics |
title_fullStr |
Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics |
title_full_unstemmed |
Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics |
title_sort |
data from: conserved non-exonic elements: a novel class of marker for phylogenomics |
publishDate |
2017 |
url |
https://zenodo.org/record/4989798 https://doi.org/10.5061/dryad.25f7g |
genre |
Falco peregrinus Pygoscelis adeliae |
genre_facet |
Falco peregrinus Pygoscelis adeliae |
op_relation |
doi:10.1093/sysbio/syx058 https://zenodo.org/communities/dryad https://zenodo.org/record/4989798 https://doi.org/10.5061/dryad.25f7g oai:zenodo.org:4989798 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.25f7g10.1093/sysbio/syx058 |
_version_ |
1765995288031395840 |