Inferring Phylogenies from RAD Sequence Data

By B. E. Rubin, Richard H. Ree, C. Moreau. PLoS ONE, 2012

315 citations recorded by the source corpus.

Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD) to sequence restriction-site associated DNA (RAD) – the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts) and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct “known” phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for “total evidence” phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively). RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in which sufficient numbers of orthologous restriction sites are retained across species.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6ea9f3c5375b18f9903434064c2205f51be3201a

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Citations in the corpus

Species Delimitation using Genome-Wide SNP Data (2013, result): “…ﬁnd the typical trade-oﬀ between missing data and high sample representation as is found in other studies utilizing RADseq data Wagner et al. (2013); Rubin et al. (2012); Cariou et al. (2013), namely, the data matrix with the lowest tolerance for missing data has the fewest number of SNPs shared…”
Special features of RAD Sequencing data: implications for genotyping (2012, unknown): “…is suitable for ﬁne-scale linkage mapping (Amores et al. 2011; Chutimanitsakun et al. 2011; Baxter et al. 2011), phylogenetics and phylogeography (Rubin et al. 2012; Nadeau et al. 2012, Emerson et al. 2010), genome scaffolding (Catchen et al. 2011; He-liconius Genome Consortium 2012) and…”
Stacks: an analysis tool set for population genomics (2013, methodology): “Because the use of GBS data for phylogenetic studies is very recent (Rubin et al. 2012), researchers should bear in mind several caveats.”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, background): “2013), which places the clade within the time frame of where simulation studies suggest that RAD loci should provide accurate phylogenetic relationships (Rubin et al. 2012; Cariou et al. 2013).”
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses (2013, background): “…genome alignments have been shown to retain accurate phylogenetic information over evolutionary divergences as deep as 60 million years (Rubin et al. , 2012; Cariou et al. , 2013), however, to date all empirical RADseq studies conducted above the species-level were done at much…”
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies (2014, unknown): “[11-24]).”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, methodology): “Such data can be obtained through the sequencing of expressed sequence tags (Philippe and Telford 2006), restriction site associated DNA (Rubin et al. 2012), and probebased target enrichment of nuclear ultraconserved elements 4 The New Systematics of Scleractinia: Integrating Molecular and Morpholog”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “This problem results largely from evolution of restriction sites across taxa, particularly across deeper phylogenetic scales, which leads to inconsistent locus recovery during size selection and, consequently, missing data (Figure 2; Rubin et al. 2012).”
The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics (2017, background): “Several computer simulation studies have evaluated whether SNPs can provide accurate and robust phylogenetic results for groups as old as 60 million years (Rubin et al. 2012, Cariou et al. 2013).”