What are UCEs?
As their name implies, ultraconserved elements (UCEs) are highly conserved regions of organismal genomes shared among evolutionary distant taxa - for instance, birds share many UCEs with humans. UCEs were first described in a wonderful manuscript by Gil Bejerano et al. (2004) from David Haussler’s group and subsequently identified in several classes of organisms outside the group of original taxa (Siepel et al. 2005) used to identify these genomic elements. The 27-way vertebrate genome alignment (Miller et al. 2007) identified additional regions of high conservation.
Why are UCEs useful?
We have discovered (see Citations) that we can collect data from UCEs and the DNA adjacent to UCE locations (flanking DNA), and that these data are useful for reconstructing the evolutionary history and population-level relationships of many organisms. Because UCEs are conserved across disparate taxa, UCEs are also
What do UCEs do?
That's an extremely good question, and one to which we do not entirely know the answer (Dermitzakis et al. 2005). UCEs have been associated with gene regulation (Pennachio et al. 2006) and development (Sandelin et al. 2004, Woolfe et al. 2004) and we generally assume that UCEs must be important by the very nature of their near-universal conservation across extremely divergent taxa. However, gene knockouts of UCE loci in mice resulted in viable, fertile offspring (Ahituv et al. 2007), suggesting that their role in the biology of the genome may be cryptic.
How do I identify UCEs?
You can identify UCEs in organismal genome sequences by aligning several genomes to each other, scanning the resulting genome alignments for areas of very high (95-100%) sequence conservation, and filtering on user-defined criteria, such as length (e.g., Bejerano et al. 2004). There are a number of different ways to do this, and we have detailed one approach to identifying UCEs for use as genetic markers and designing baits to target them Faircloth 2017. There is also a tutorial that shows how to use this approach available as part of the PHYLUCE documentation.
How do I collect UCE data?
From a set of UCEs shared among a taxonomic group, we design sequence capture (AKA solution hybrid selection sensu Gnirke et al. 2009) baits that are similar in sequence to the UCE loci we are targeting. These bait sets differ in number and composition, depending on the types of questions we are asking and the taxa with which we are working. Once we design a bait set, we follow sequence capture protocols to enrich DNA libraries for the target UCEs, usually in multiplex. Following enrichment, we sequence the DNA enriched for UCEs using massively parallel sequencing, usually on Illumina platforms.
How do I analyze UCE data?
The most complex part of using UCEs to understand evolutionary relationships, population structure, and population relationships is analyzing the DNA sequence data. We have created several software packages and we're working on tutorials to help get you started. Many of the steps, at this point, require that you are comfortable working with computer software on the command line. We encourage everyone interested to get the software and contribute to the effort of documenting, improving, and extending our computer code.
FAQ Frequently asked questions.
We compiled a list of questions you may have that go beyond the details provided above. If you do not find your answer in the FAQ, please get in contact with us via twitter (@ultraconserved).
Citations Peer-reviewed manuscripts describing our work.
The manuscripts listed below are the primary citations establishing UCEs as useful phylogenomic markers, markers from which we can collect empirical data, markers we can use to infer shallow-level relationships, and markers that can do all of these things across a variety of vertebrate and invertebrate lineages.
Faircloth BC, Branstetter MG, White ND, Brady SG. 2014. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol Ecol Res (Early Access). doi:10.1111/1755-0998.12328.
Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT. 2014. 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.
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 (UCEs). PLoS ONE 8: e65923. doi:10.1371/journal.pone.0065923.
Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. 2012. Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. Syst Biol 61:717-726. pmid: 22232343 doi:10.1093/sysbio/sys004.
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 22: 746–754. pmid: 22207614 doi: 10.1101/gr.125864.111.
News and Updates Sometimes, we change things.
- Method Arbor Biosciences and RAPiD Genomics offer UCE capture as a service (April 13, 2014)
- Method Arbor Biosciences now offers UCE capture kits (September 20, 2013)
- Method UCEs for population-level studies available online (September 10, 2013)
- Method qPCR enrichment verification protocol added (June 18, 2013)
- Manuscript Fish manuscript available online (June 18, 2013)
- Method Protocols updated (March 28, 2013)
- Method Protocols updated (January 31, 2013)
- Manuscript Neoaves manuscript available online (January 29, 2013)
- Manuscript Turtle manuscript available online (May 16, 2012)
- Method UCEs as genetic markers manuscript available online (January 9, 2012)
- Method UCEs resolve placental mammal phylogeny manuscript available online (December 12, 2011)
Enrichment As A Service
Below are several commercial laboratories offering UCE enrichment as a service. Generally speaking, these commercial vendors will accept DNA extracts for enrichment, conduct the library preparation and enrichment steps, sequence the enriched libraries, and return the sequence data to you. We do not derive any referall revenue from these companies, but we list each here to help interested labs get started.
Tetrapod probe sets.
Below are several probe designs that we have used to study relationships among amniotes/tetrapods (e.g. Crawford
You can now buy each of these probe sets direct from Arbor Biosciences in the form of a capture kit. Arbor Biosciences has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.
2,560 baits for 2,386 UCEs
(Tetrapods-UCE-2.5Kv1)
Described as part of Faircloth et al. 2012. First use as part of Faircloth et al. 2012.
5,472 baits for 5,060 UCEs
(Tetrapods-UCE-5Kv1)
Described in Faircloth et al. 2012 and first use as part of Keping et al. 2014.
Fish probe sets.
Below are two bait set designs that we have used (1) to understand relationships among the early diverging teleosts (Faircloth
You can now buy both probe sets directly from Arbor Biosciences in the form of a capture kit. Arbor Biosciences has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.
Actinopterygians
2,001 baits for 500 UCEs
(Actinopterygians 0.5Kv1)
Described as part of Faircloth et al. 2013. First use as part of Faircloth et al. 2013.
Acanthomorphs
2,628 baits for 1,314 UCEs
(Acanthomorphs 1Kv1)
Described as part of Alfaro et al. 2013. First used as part of McGee et al. 2016.
Invertebrate probe sets.
Below are a number of bait designs targeting UCEs in different invertebrate groups. The baits designs described below derive from Faircloth 2017.
You can buy many of these probe set direct from Arbor Biosciences in the form of a capture kit. Arbor Biosciences has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.
Arachnida
14,799 baits for 1,120 UCEs
(Arachnida 1.1Kv1)
Described as part of Faircloth 2017. First use as part of Starret et al. 2017.
Coleoptera
13,674 baits for 1,172 UCEs
(Coleoptera 1.1Kv1)
Described as part of Faircloth 2017. First use as part of Baca et al. 2017.
Diptera
31,328 baits for 2,711 UCEs
(Diptera 2.7Kv1)
Described as part of Faircloth 2017. First use has not been published, yet.
Hemiptera
40,207 baits for 2,731 UCEs
(Hemiptera 2.7Kv1)
Described as part of Faircloth 2017. First use has not been published, yet.
Hymenoptera (ver. 1)
2,749 baits for 1,510 UCEs
(Hymenoptera 1.5Kv1)
Described as part of Faircloth et al. 2015. First used as part of Faircloth et al. 2015.
Hymenoptera (ver. 2)
31,829 baits for 2,590 UCEs
(Hymenoptera 2.5Kv2)
Described as part of Branstetter et al. 2017. First use as part of Branstetter et al. 2017.
Anthozoa
16,306 baits for 720 UCEs and 1,071 exons
(Anthozoa 1.7Kv1)
Described as part of Quattrini et al. 2017. First use as part of Quattrini et al. 2017.
Software Computer code for data analysis.
Below are several software packages we have developed to help analyze data collected from UCE loci. All computer code is available under a flexible open-source license (BSD). We welcome all code contributions, from helping to improve the code, fix bugs, improve usability, and improve documentation, which is rather sparse, at the moment. Please contact us through twitter (@ultraconserved) if you are interested in helping and/or post an issue on github for the respective package.
Note: All software packages are likely to contain bugs - use at your own risk.
phyluce
Our main code repository for analyzing data collection from UCE loci. Contains command-line applications for assembling contigs from sequence data, finding which contigs align to UCEs, aligning UCE contigs, and preparing data for downstream analysis in mrbayes, raxml, and cloudforest.
Report an issue with phyluce.
illumiprocessor Helper code
A program for automated cleaning of fastq files from sequencing. Removes adapter contamination using scythe and trims reads for quality using sickle. Concatenates reads into an "interleaved" fastq.gz file for use with velvet.
Report an issue with illumiprocessor
Protocols Our sequence capture protocols.
References Manuscripts about UCEs, sequence capture, and data analysis.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.