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...
Main Authors: | , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
Data Archiving and Networked Services (DANS)
2017
|
Subjects: | |
Online Access: | https://doi.org/10.5061/dryad.25f7g |
id |
fttriple:oai:gotriple.eu:50|dedup_wf_001::ba5ae13ccfc435a96c45b83a76c83d47 |
---|---|
record_format |
openpolar |
spelling |
fttriple:oai:gotriple.eu:50|dedup_wf_001::ba5ae13ccfc435a96c45b83a76c83d47 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. 2017-01-01 https://doi.org/10.5061/dryad.25f7g undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.25f7g https://dx.doi.org/10.5061/dryad.25f7g lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:102146 10.5061/dryad.25f7g oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:102146 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 Life sciences medicine and health care Multispecies coalescent incomplete lineage sorting 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 envir lang Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2017 fttriple https://doi.org/10.5061/dryad.25f7g 2023-01-22T17:15:38Z 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 Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care Multispecies coalescent incomplete lineage sorting 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 envir lang |
spellingShingle |
Life sciences medicine and health care Multispecies coalescent incomplete lineage sorting 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 envir lang Edwards, Scott V. Cloutier, Alison Baker, Allan J. Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics |
topic_facet |
Life sciences medicine and health care Multispecies coalescent incomplete lineage sorting 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 envir lang |
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 |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2017 |
url |
https://doi.org/10.5061/dryad.25f7g |
genre |
Falco peregrinus Pygoscelis adeliae |
genre_facet |
Falco peregrinus Pygoscelis adeliae |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:102146 10.5061/dryad.25f7g oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:102146 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 |
op_relation |
http://dx.doi.org/10.5061/dryad.25f7g https://dx.doi.org/10.5061/dryad.25f7g |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.25f7g |
_version_ |
1765995289729040384 |