Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

Abstract

Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus.

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

“…thynnus branch is supported by 3 analyses only when lowering the BV to 80% (Table 1). As reported by other studies (Cruaud et al, 2014;Hipp et al, 2014;Hou et al, 2015;Jones et al, 2013;Leaché et al, 2015;Rubin et al, 2012;Wagner et al, 2013), the use of IUPAC encoded sites and allowing higher missing data percentages not only produces larger matrices, but also results in better resolved trees (Table 1). Yet, although high bootstrap alone is not evidence of tree accuracy (Rodríguez-Ezpeleta et al, 2007), the congruence obtained among our different analyses is considered a good indicator of true evolutionary signal in the data (Hillis, 1995;Rubin et al, 2012).…”

“…Cruaud et al, 2014;Herrera and Shank, 2015;Leaché et al, 2015). Yet some studies have shown that gathering a suitable set of phylogenetically informative markers from RAD-seq data relies on the ability to discover enough orthologous loci among the species under study, which largely depends on divergence times between lineages and filtering and assembly parameters applied for orthology inference (Jones et al, 2013;Leaché et al, 2015;Rubin et al, 2012;Wagner et al, 2013). It is therefore recommended to explore the results applying different parameter combinations (Ree and Hipp, 2015;Rubin et al, 2012 Cells and Animal Tissue".…”

Troublesome Trimes: Potential cryptic speciation of the Trimeresurus (Popeia) popeiorum complex (Serpentes: Crotalidae) around the Isthmus of Kra (Myanmar and Thailand)

“…Instead, we prefer to wait for a study that addresses these issues by incorporating nuclear DNA (preferably RadSeq or UCE; e.g. Leaché et al 2015), additional morphological characters, and new material from potential sampling gaps. Until then, we refer to the populations representing the southern clade as Trimeresurus (Popeia) sp.…”

In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

“…Next, the pipeline conducts multiple sequence alignments for all candidate loci using ClustalW (Larkin et al 2007), and paired AE/UCE flanking sequences are concatenated to form each individual locus. Loci found on the same chromosomes should be sufficiently separated from each other in order for their gene trees to be effectively independent of each other (Hudson and Coyne 2002;Jennings and Edwards 2005;Wakeley 2009;McCormack et al 2012;Reilly et al 2012;O'Neill et al 2013;Leaché et al 2015). Thus, the user must input a second distance threshold (in base pairs) separating sampled loci.…”