TreeBASE Search-Matrices for study 12156

@ARTICLE{TreeBASE2Ref20241, author = {Brant C Faircloth and John E McCormack and Nicholas Geoffrey Crawford and Michael G Harvey and Robb T. Brumfield and Travis C Glenn}, title = {Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales.}, year = {2011}, keywords = {ultra conserved elements, uce, genetic markers, sequence capture, target enrichment, phylogenomics, flanking sequence}, doi = {}, url = {http://}, pmid = {}, journal = {Systematic Biology}, volume = {}, number = {}, pages = {}, abstract = {Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota, because UCEs and phylogenetic relationships are well known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2,030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2,386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.} }

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Matrices for Study 12156

Citation title: "Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales.".

Study name: "Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales.".

This study is part of submission 12156 (Status: Published).

Matrices

ID	Matrix Title	Description	Data type	NTAX	NCHAR	Taxa
M10930	Nine bird species	Phylogeny of nine bird species representing the three basal lineages of birds based on a Bayesian analysis of concatenated data from 854 loci collected by target enrichment of UCE-anchored loci	Nucleic Acid	10	352120	View Taxa
M10931	Nine primate species	Phylogeny of nine primate species based on a Bayesian analysis of concatenated data from 2030 UCE-anchored loci	Nucleic Acid	10	876159	View Taxa