If you use the phyluce code in any form, please cite the following manuscript:

[BCF2015]Faircloth BC. 2016. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32:786-788. doi:10.1093/bioinformatics/btv646.

If you are processing UCE data that you have collected by targeted enrichment using our probes/protocols, please cite the following manuscripts, which describes the first use of the general approach:

[BCF2012]BC Faircloth, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61: 717–726. doi:10.1093/sysbio/SYS004.

Then, if you are working in groups other than tetrapods, please cite the appropriate manuscript for the organisms you are working on.


Here are some additional references that have used UCE data for phylogenomic inference at both “deep” and “shallow” timescales. Most of these manuscripts used an older version of the code:

[JEM2012]McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Res 26:746-754. doi:10.1101/gr.125864.111.
[NGC2012]Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC. 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol Lett 8:783-786. doi:10.1098/rsbl.2012.0331.
[BCF2013]Faircloth BC, Sorenson L, Santini F, Alfaro ME. 2013. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements. PlosONE 8:e65923. doi:10.1371/journal.pone.0065923.
[JEM2013]McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. 2013. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PlosOne 8:e54848. doi:10.1371/journal.pone.0054848.
[BTS2013]BT Smith, MG Harvey, BC Faircloth, TC Glenn, RT Brumfield. 2013. Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales. Syst Biol 63:83-95. doi:10.1093/sysbio/syt061.
[MGH2014]Sequence capture versus restriction site associated dna sequencing for phylogeography. MG Harvey, BT Smith, TC Glenn, BC Faircloth, RT Brumfield. arXiv:1312.6439.

Other UCE References

[GB2004]Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, et al. (2004) Ultraconserved elements in the human genome. Science 304: 1321–1325. doi:10.1126/science.1098119.
[AS2004]Sandelin A, Bailey P, Bruce S, Engström PG, Klos JM, et al. (2004) Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5: 99. doi:10.1186/1471-2164-5-99.
[ED2005]Dermitzakis ET, Reymond A, Antonarakis SE (2005) Opinion: Conserved non-genic sequences — an unexpected feature of mammalian genomes. Nat Rev Genet 6:151–157. doi:10.1038/nrg1527.
[AS2005]Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034–1050. doi:10.1101/gr.3715005.
[AW2005]Woolfe A, Goodson M, Goode D, Snell P, McEwen G, et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3:116–130. doi:10.1371/journal.pbio.0030007.
[LP2006]Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499–502. doi:10.1038/nature05295.
[NA2007]Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, et al. (2007) Deletion of Ultraconserved Elements Yields Viable Mice. PLoS Biol 5: e234. doi:10.1371/journal.pbio.0050234.
[WM2007]Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, et al. (2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res 17: 1797–1808. doi:10.1101/gr.6761107.
[AG2009]Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology 27: 182–189. doi:10.1038/nbt.1523.
[BB2010]Blumenstiel B, Cibulskis K, Fisher S, DeFelice M, Barry A, et al. (2010) Targeted exon sequencing by in-solution hybrid selection. Curr Protoc Hum Genet Chapter 18: Unit18.4. doi:10.1002/0471142905.hg1804s66.