ArticleBMC evolutionary biology2015
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards.
Article in BMC evolutionary biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity.International journal of molecular sciences · 2019Pooled it
- A Workflow for Phytoplasma Discovery and Characterization in Potential Insect Vectors: From Non-destructive DNA Extraction and Vouchering to Next-Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- pipesnake: generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci.Bioinformatics (Oxford, England) · 2024Article
- Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae).Genome biology and evolution · 2023Article
- Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles.Animals : an open access journal from MDPI · 2023Review
- Comparing the potential for maternal-fetal signalling in oviparous and viviparous lizards.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Different Genes are Recruited During Convergent Evolution of Pregnancy and the Placenta.Molecular biology and evolution · 2022Article
- Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements.Molecular biology and evolution · 2020Article
- Phylogenomic Analysis of a Putative Missing Link Sparks Reinterpretation of Leech Evolution.Genome biology and evolution · 2019Article
- Plant phylogenomics based on genome-partitioning strategies: Progress and prospects.Plant diversity · 2018Review
- Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics.Toxins · 2018Article
- Anchored phylogenomics illuminates the skipper butterfly tree of life.BMC evolutionary biology · 2018Article
- Phylogenomics of a rapid radiation: the Australian rainbow skinks.BMC evolutionary biology · 2018Article
- Diversification in wild populations of the model organismEcology and evolution · 2016Article
- Reptile Pregnancy Is Underpinned by Complex Changes in Uterine Gene Expression: A Comparative Analysis of the Uterine Transcriptome in Viviparous and Oviparous Lizards.Genome biology and evolution · 2016Article
- Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.BMC evolutionary biology · 2016Article
- A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference.Genome biology and evolution · 2016Article
- Reticulation, divergence, and the phylogeography-phylogenetics continuum.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.Applications in plant sciences · 2016Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.
resultsPhylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.
conclusionsAnchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.