Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

By B. Faircloth, J. McCormack, Nicholas G. Crawford, Michael G. Harvey, R. T. Brumfield, Travis C. Glenn. Systematic Biology, 2012

1,140 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a4e2a379616fedf9a70a99c7b226ac120cf35244

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Citations in the corpus

Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera (2017, methodology): “The main difference between the updated workflow and the standardUCEworkflow (sensu Faircloth et al. 2012) is that instead of performing synteny-based, genome-genome alignment to identify UCEs, short reads from multiple genomes are permissively mapped to a single base genome.”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, methodology): “Lemmon et al. (2012) and Faircloth et al. (2012) published alternative solutions to this problem.”
Next‐generation sequencing technologies for environmental DNA research (2012, background): “These tools are currently in use in studies of human and other model organisms, but they show significant potential for applications in environmental DNA research (Adey et al. 2010; Barzon et al. 2011; Jones et al. 2011; Faircloth et al. 2012).”
MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics (2019, background): “The field has witnessed the rapid parallel development of exon capture from transcriptome-de - rived baits (Bi et al., 2012), anchored hybrid enrichment techniques (Lemmon, Emme, & Lemmon, 2012), and the capture of ultraconserved DNA elements (UCEs; Faircloth et al., 2012).”
Phylogenetic classification of bony fishes (2017, background): “, target enrichment [93, 94]), has ushered in a promising future to tackle difficult phylogenetic questions by analyzing hundreds or thousands of gene fragments [95].”
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes (2013, methodology): “Next-generation sequencing strategie s and phylogenomic methods should help resolve difficult nodes [16,20,36,198-200], as should application of species-tree methods [201,202].”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, neutral): “…244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318”
Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, background): “Third, because variability increases moving toward the flanks, UCEs and flanking DNA might harbor phylogenetic signal useful for phylogenetic reconstruction at multiple evolutionary timescales (Faircloth et al., 2012).”
Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “…2008; Elshire et al. 2011; Peterson et al. 2012), transcriptomic (Dunn et al. 2008; Smith et al. 2011; Misof et al. 2014) and targeted enrichment (Bi et al. 2012; Faircloth et al. 2012; Pe~nalba et al. 2014; Ali et al. 2015; Hoffberg et al. 2016; Hugall et al. 2016; Suchan et al. 2016) approaches.”
Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’ (2017, background): “Ultraconserved elements allow for effective alignment of the more variable (and phylogenetically informative) UCE-flanking regions across divergent taxa (Faircloth et al., 2012), with comparable or potentially decreased frequencies of homoplasy versus other types of marker (Meiklejohn et al., 2016).”
Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches (2015, background): “…to PCRgenerated or cDNA-derived baits (Penalba et al., 2014), noncoding nuclear gene regions flanking Ultra Conserved Elements (UCEs) in the genomes of many phyla allow sequence capture using the same baits across species separated by up to hundreds of millions of years (Faircloth et al., 2012).”
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life (2016, methodology): “…genome similarity methods (Sims et al., 2008), or approaches that target different types of data (e.g. genome skimming, targeted enrichment, ultraconserved elements: Faircloth et al., 2012; Lemmon & Lemmon, 2013; McCormack et al., 2013; Weitemier et al., 2014), could also improve resolution.”
Species Delimitation: A Decade After the Renaissance (2013, neutral): “NGS technol‐ ogies have been recently applied to development of thousands of gene regions spanning multiple divergence times [78], or loci targeted for “shallow-scale” phylogenetic/phylogeo‐ graphic studies [79], and microsatellites [80] or SNPs [81] for extremely shallow phylogeo‐ The Species Probl”
Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels (2012, methodology): “), normalized library concentration across samples, and enriched individual or pooled libraries for ultraconserved elements using 2560 probes [50,52].”
Phylogeography unplugged: comparative surveys in the genomic era (2014, background): “A major promise of genomic approaches is developing access to an abundance of nuclear markers (Etter et al. 2011, Faircloth et al. 2012, Lemmon and Lemmon 2012, Rocha et al. 2013), perhaps with the eventual goal of a core set of nuclear markers applicable across a wide range of species.”
Species Delimitation using Genome-Wide SNP Data (2013, background): “Genomic data are having a dramatic impact on our ability to resolve the tree of life (Faircloth et al. 2012), but delimiting species at the tips of the tree has yet to see comparable gains.”