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Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/aja.1000360106openalex-snapshot
On the nature of mitochondria. IX. Demonstration of the bacterial nature of mitochondria
inferredcites →https://doi.org/10.1002/bies.201100062openalex-snapshot
Orthology prediction methods: A quality assessment using curated protein families
inferredcites →https://doi.org/10.1002/prot.24575openalex-snapshot
Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins
inferredcites →https://doi.org/10.1007/978-1-4939-9074-0_5openalex-snapshot
Inferring Orthology and Paralogy
inferredcites →https://doi.org/10.1007/978-1-61779-582-4_9openalex-snapshot
Inferring Orthology and Paralogy
inferredcites →https://doi.org/10.1007/978-1-61779-585-5_3openalex-snapshot
Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life
inferredcites →https://doi.org/10.1007/s002390010184openalex-snapshot
The Closest BLAST Hit Is Often Not the Nearest Neighbor
inferredcites →https://doi.org/10.1007/s00285-009-0319-yopenalex-snapshot
Analyzing and reconstructing reticulation networks under timing constraints
inferredcites →https://doi.org/10.1016/0022-5193(67)90079-3openalex-snapshot
On the origin of mitosing cells
inferredcites →https://doi.org/10.1016/j.jtbi.2013.01.009openalex-snapshot
Identifying a species tree subject to random lateral gene transfer
inferredcites →https://doi.org/10.1038/nature06510openalex-snapshot
Palaeotemperature trend for Precambrian life inferred from resurrected proteins
inferredcites →https://doi.org/10.1038/nature09649openalex-snapshot
Rapid evolutionary innovation during an Archaean genetic expansion
inferredcites →https://doi.org/10.1038/nrmicro1991openalex-snapshot
Hydrothermal vents and the origin of life
inferredcites →https://doi.org/10.1073/pnas.0603780103openalex-snapshot
Collective evolution and the genetic code
inferredcites →https://doi.org/10.1073/pnas.0606318104openalex-snapshot
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
inferredcites →https://doi.org/10.1073/pnas.1117774109openalex-snapshot
Origin of first cells at terrestrial, anoxic geothermal fields
inferredcites →https://doi.org/10.1073/pnas.1308215110openalex-snapshot
Experimental evidence for the thermophilicity of ancestral life
inferredcites →https://doi.org/10.1073/pnas.70.12.3725openalex-snapshot
Sequence Homologies Among Bacterial and Mitochondrial Superoxide Dismutases
inferredcites →https://doi.org/10.1086/667878openalex-snapshot
The Future of Systematics: Tree Thinking without the Tree
inferredcites →https://doi.org/10.1089/cmb.2010.0045openalex-snapshot
A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance
inferredcites →https://doi.org/10.1089/cmb.2010.0185openalex-snapshot
Comparison of Phylogenetic Trees and Search for a Central Trend in the “Forest of Life”
inferredcites →https://doi.org/10.1093/bib/bbr030openalex-snapshot
Computational methods for Gene Orthology inference
inferredcites →https://doi.org/10.1093/bioinformatics/btl313openalex-snapshot
Efficient parsimony-based methods for phylogenetic network reconstruction
inferredcites →https://doi.org/10.1093/bioinformatics/btl452openalex-snapshot
Maximum likelihood of phylogenetic networks
inferredcites →https://doi.org/10.1093/bioinformatics/bts386openalex-snapshot
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
inferredcites →https://doi.org/10.1093/bioinformatics/btu492openalex-snapshot
Big data and other challenges in the quest for orthologs
inferredcites →https://doi.org/10.1093/molbev/msp123openalex-snapshot
Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model
inferredcites →https://doi.org/10.1093/molbev/msp240openalex-snapshot
Inference and Characterization of Horizontally Transferred Gene Families Using Stochastic Mapping
inferredcites →https://doi.org/10.1093/molbev/msq297openalex-snapshot
Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths
inferredcites →https://doi.org/10.1093/molbev/msu305openalex-snapshot
Toward More Accurate Ancestral Protein Genotype–Phenotype Reconstructions with the Use of Species Tree-Aware Gene Trees
inferredcites →https://doi.org/10.1093/nar/gks1217openalex-snapshot
LUCApedia: a database for the study of ancient life
inferredcites →https://doi.org/10.1093/nar/gks485openalex-snapshot
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
inferredcites →https://doi.org/10.1093/nar/gks568openalex-snapshot
Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components
inferredcites →https://doi.org/10.1093/nar/gkt610openalex-snapshot
Minimal genome encoding proteins with constrained amino acid repertoire
inferredcites →https://doi.org/10.1093/sysbio/syp103openalex-snapshot
Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity
inferredcites →https://doi.org/10.1093/sysbio/syt003openalex-snapshot
Lateral Gene Transfer from the Dead
inferredcites →https://doi.org/10.1098/rstb.2008.0177openalex-snapshot
A likelihood framework to analyse phyletic patterns
inferredcites →https://doi.org/10.1099/00207713-52-1-7openalex-snapshot
The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.
inferredcites →https://doi.org/10.1101/sqb.2009.74.002openalex-snapshot
Eradicating Typological Thinking in Prokaryotic Systematics and Evolution
inferredcites →https://doi.org/10.1109/tcbb.2007.1019openalex-snapshot
Computing the Hybridization Number of Two Phylogenetic Trees Is Fixed-Parameter Tractable
inferredcites →https://doi.org/10.1111/j.1601-5223.1968.tb02169.xopenalex-snapshot
EVOLUTION FROM FISH TO MAMMALS BY GENE DUPLICATION
inferredcites →https://doi.org/10.1126/science.278.5338.631openalex-snapshot
A Genomic Perspective on Protein Families
inferredcites →https://doi.org/10.1128/mmbr.68.3.518-537.2004openalex-snapshot
Determination of the Core of a Minimal Bacterial Gene Set
inferredcites →https://doi.org/10.1146/annurev.micro.55.1.709openalex-snapshot
Horizontal Gene Transfer in Prokaryotes: Quantification and Classification
inferredcites →https://doi.org/10.1186/1471-2105-11-324openalex-snapshot
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
inferredcites →https://doi.org/10.1186/1471-2105-14-s15-s4openalex-snapshot
Lateral gene transfer, rearrangement, reconciliation
inferredcites →https://doi.org/10.1186/1471-2105-14-s2-s4openalex-snapshot
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs
inferredcites →https://doi.org/10.1186/1471-2148-13-274openalex-snapshot
Inferring explicit weighted consensus networks to represent alternative evolutionary histories
inferredcites →https://doi.org/10.1186/1471-2148-3-2openalex-snapshot
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
inferredcites →https://doi.org/10.1186/1745-6150-4-34openalex-snapshot
Prokaryotic evolution and the tree of life are two different things
inferredcites →https://doi.org/10.1186/1745-6150-8-32openalex-snapshot
Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life
inferredcites →https://doi.org/10.1371/journal.pbio.0030130openalex-snapshot
Evolutionary Origins of Genomic Repertoires in Bacteria
inferredcites →https://doi.org/10.1371/journal.pcbi.1000262openalex-snapshot
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
inferredcites →https://doi.org/10.1371/journal.pone.0022099openalex-snapshot
Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer
inferredcites →https://doi.org/10.2741/3031openalex-snapshot
Gene content of LUCA, the last universal common ancestor
inferredcites →https://doi.org/10.7208/chicago/9780226511993.001.0001openalex-snapshot
Error and the Growth of Experimental Knowledge
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.7287/peerj.preprints.1293v1openalex-snapshot
Accessing and applying molecular history
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