ArticleGenome research2004
Reconstructing large regions of an ancestral mammalian genome in silico.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 63 papers.
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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.
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Who cites it
63 citing papers in PubMed.
- GraphyloVar: predicting the impact of non-coding variants using a multi-species sequence model.Bioinformatics (Oxford, England) · 2026Article
- Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Evolution of chromosomes and nuclear architectures of amniotes.Nature communications · 2025Article
- Algorithms to reconstruct past indels: The deletion-only parsimony problem.PLoS computational biology · 2025Article
- Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding.Genome research · 2025Article
- Complete sequencing of ape genomes.Nature · 2025Article
- A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression.Molecular biology and evolution · 2025Article
- Complete sequencing of ape genomes.bioRxiv : the preprint server for biology · 2024Article
- Graphylo: A deep learning approach for predicting regulatory DNA and RNA sites from whole-genome multiple alignments.iScience · 2024Article
- Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.Nature ecology & evolution · 2023Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- Article
- Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.Genome biology and evolution · 2022Article
- Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Reaction Specificity of Mammalian ALOX15 Orthologs is Changed During Late Primate Evolution and These Alterations Might Offer Evolutionary Advantages for Hominidae.Frontiers in cell and developmental biology · 2022Article
- EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM.Bioinformatics (Oxford, England) · 2020Article
- Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse.PLoS computational biology · 2018Article
- Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.Nucleic acids research · 2017Article
- Ancestral Genome Reconstruction on Whole Genome Level.Current genomics · 2017Review
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can expect to get 98% of the bases correct in reconstructing megabase-scale euchromatic regions of an eutherian ancestral genome from the genomes of approximately 20 optimally chosen modern mammals. Using actual genomic sequences from 19 extant mammals, we reconstruct 1.1 Mb of ancient genome sequence around the CFTR locus. Detailed examination suggests the reconstruction is accurate and that it allows us to identify features in modern species, such as remnants of ancient transposon insertions, that were not identified by direct analysis. Tracing the predicted evolutionary history of the bases in the reconstructed region, estimates are made of the amount of DNA turnover due to insertion, deletion, and substitution in the different placental mammalian lineages since the common eutherian ancestor, showing considerable variation between lineages. In coming years, such reconstructions may help in identifying and understanding the genetic features common to eutherian mammals and may shed light on the evolution of human or primate-specific traits.
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Registered trials
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