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Conserved Non-exonic Elements: A Novel Class of Marker for Phylogenomics

Scott V. Edwards, Alison Cloutier, Allan J. Baker
doi: https://doi.org/10.1101/093070
Scott V. Edwards
1Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
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  • For correspondence: sedwards@fas.harvard.edu
Alison Cloutier
1Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
2Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada M5S 2C6
3Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada M5S3B2
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Allan J. Baker
2Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada M5S 2C6
3Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada M5S3B2
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Abstract

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 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.

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Posted December 11, 2016.
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Conserved Non-exonic Elements: A Novel Class of Marker for Phylogenomics
Scott V. Edwards, Alison Cloutier, Allan J. Baker
bioRxiv 093070; doi: https://doi.org/10.1101/093070
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Conserved Non-exonic Elements: A Novel Class of Marker for Phylogenomics
Scott V. Edwards, Alison Cloutier, Allan J. Baker
bioRxiv 093070; doi: https://doi.org/10.1101/093070

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