Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Abstract

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation datasets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (greater than 1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC dataset to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of ten snakes and seven lizards. The RELEC dataset (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

“…Both methods are reduced‐representation approaches that rely on the utilization of a phylogenetically informative subset of the study organisms' genomes. Other target enrichment methods have been proposed, with varied locus selection criteria, including Hyb‐Seq (Weitemier et al ., ), Compositae COS loci (Mandel et al ., ) and RELEC (Karin, ), but AHE and UCEs have thus far been the most commonly used methods in phylogenomic studies of animals.…”

Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

“…A more common approach for phylogenomic studies is targeted sequence capture, generating so-called reduced-representation datasets, with typically longer sequences for distantly related species than with RADseq data. Examples include exome sequencing, ultraconserved elements (UCEs, Faircloth et al ., 2012), anchored hybrid enrichment (AHE, Lemmon et al ., 2012), conserved nonexonic elements (CNEEs, Edwards et al ., 2017), or rapidly evolving long exon capture (RELEC, Karin et al ., 2020).…”

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

“…One solution is to use a diverse assortment of markers sampled from across the genome with different properties (Dool et al 2016;Chen et al 2017). The inclusion of a diversity of marker types allows downstream filtering of markers by desirable properties, such as length or informativeness, which can improve phylogenetic estimates (Mirarab et al 2014;Springer & Gatesy 2016;Chakrabarty et al 2017;Streicher et al 2018; Karin et al 2019). When considering these factors, using a HybSeq approach that targets a variety of marker types may represent an optimal solution; however, substantial genomic resources are required for the initial probe design for the target markers.…”