ArticleMolecular biology and evolution2020
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 64 citations in OpenAlex.
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- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi's paleo-archipelago.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Iguanas rafted more than 8,000 km from North America to Fiji.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies.Royal Society open science · 2024Article
- Integrative methods reveal multiple drivers of diversification in rice paddy snakes.Scientific reports · 2024Article
- UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics.Molecular biology and evolution · 2023Article
- Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation of Anolis Lizards.Systematic biology · 2023Article
- Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae).Genome biology and evolution · 2023Article
- Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes.BMC genomics · 2023Article
- Characterization of Two Transposable Elements and an Ultra-Conserved Element Isolated in the Genome ofLife (Basel, Switzerland) · 2023Article
- Hooking the scientific community on thorny-headed worms: interesting and exciting facts, knowledge gaps and perspectives for research directions on Acanthocephala.Parasite (Paris, France) · 2023Article
- A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.Molecular ecology · 2022Article
- Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.Systematic biology · 2022Article
- Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model.Systematic biology · 2022Article
- Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree.Genome biology and evolution · 2021Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 data sets 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 (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.