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There is also a tutorial that shows how to use this approach available as part of the PHYLUCE documentation. 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.

2007), suggesting that their role in the biology of the genome may be cryptic.

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. 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.Frequently asked questions » 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. 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.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.Removes adapter contamination using scythe and trims reads for quality using sickle.

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