Article

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA.
Systematic Biology (Impact Factor: 14.39). 05/2012; 61(5):727-44. DOI: 10.1093/sysbio/sys049
Source: PubMed

ABSTRACT

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci × 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.

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    • "However, the ability to capture loci across relatively deep phylogenetic scales has remained challenging because of the inverse relationship between capture efficiency and the evolutionary distance from the individual(s) used to design the probes (Bi et al., 2012;Lemmon, Emme & Lemmon, 2012;Peñalba et al., 2014;Weitemier et al., 2014). For very deep divergences in animals, to understand amniote evolution or deep divergences in vertebrate evolution for example, ultra-conserved elements (Faircloth et al., 2012) and anchored hybrid enrichment (Lemmon, Emme & Lemmon, 2012) have been used to target conserved loci that are flanked by less conserved regions. However, these regions were developed using animal genomes and are unsuitable for use in plants (Reneker et al., 2012). "
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    • "Target capture of conserved genomic regions (Faircloth et al. 2012; Lemmon et al. 2012) combined with massively parallel sequencing produce data matrices containing thousands of unlinked loci distributed across the genome suitable for phylogenetic inference. These markers can be generated efficiently, cost-effectively, and are useful across deeper evolutionary scales than restriction enzyme based reduced-representation libraries (Rubin et al. 2012). "
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    • "Recent advances in DNA sequencing technologies provide great opportunities for using genome-scale data to reconstruct phylogenetic history (Rokas and Abbot 2009; Hittinger et al. 2010; Faircloth et al. 2012; Lemmon et al. 2012). However, recent phylogenomic studies in diverse taxonomic groups, including plants (Zhong et al. 2013; Wickett et al. 2014), fungi (Hess and Goldman 2011; Salichos and Rokas 2013), and animals (Song et al. 2012; Jarvis et al. 2014), have shown that a large number of individual gene trees are topologically incongruent with each other. "
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