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Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

https://doi.org/10.1101/407692
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting
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Site‐specific deamidation of glutamine: a new marker of bone collagen deterioration
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Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone
inferredcites →https://doi.org/10.1007/s11430-013-4702-6openalex-snapshot
Ancient DNA sequences from Coelodonta antiquitatis in China reveal its divergence and phylogeny
inferredcites →https://doi.org/10.1016/0006-291x(91)91564-sopenalex-snapshot
Identification of the leucine-rich amelogenin peptide (LRAP) as the translation product of an alternatively spliced transcript
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Golgi apparatus mammary gland casein kinase: monitoring by a specific peptide substrate and definition of specificity determinants
inferredcites →https://doi.org/10.1016/j.cub.2008.12.016openalex-snapshot
Evolution: Replacing Genes and Traits through Hybridization
inferredcites →https://doi.org/10.1016/j.quageo.2007.07.001openalex-snapshot
Closed-system behaviour of the intra-crystalline fraction of amino acids in mollusc shells
inferredcites →https://doi.org/10.1016/s1055-7903(03)00023-xopenalex-snapshot
Ancient DNA analysis reveals woolly rhino evolutionary relationships
inferredcites →https://doi.org/10.1017/qua.2017.53openalex-snapshot
Discovery of the skull ofStephanorhinus kirchbergensis(Jäger, 1839) above the Arctic Circle
inferredcites →https://doi.org/10.1021/acs.jproteome.6b00873openalex-snapshot
Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein
inferredcites →https://doi.org/10.1021/acs.jproteome.7b00670openalex-snapshot
Solid Digestion of Demineralized Bone as a Method To Access Potentially Insoluble Proteins and Post-Translational Modifications
inferredcites →https://doi.org/10.1021/pr200721uopenalex-snapshot
Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins
inferredcites →https://doi.org/10.1038/187411b0openalex-snapshot
Organic Matrix of Tooth Enamel
inferredcites →https://doi.org/10.1038/nature12323openalex-snapshot
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
inferredcites →https://doi.org/10.1038/nature14249openalex-snapshot
Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates
inferredcites →https://doi.org/10.1038/nature17405openalex-snapshot
Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
inferredcites →https://doi.org/10.1038/nbt.1511openalex-snapshot
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
inferredcites →https://doi.org/10.1038/nmeth.1322openalex-snapshot
Universal sample preparation method for proteome analysis
inferredcites →https://doi.org/10.1038/nmeth.2834openalex-snapshot
Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells
inferredcites →https://doi.org/10.1038/nmeth1109-786openalex-snapshot
Improved visualization of protein consensus sequences by iceLogo
inferredcites →https://doi.org/10.1038/nprot.2014.063openalex-snapshot
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
inferredcites →https://doi.org/10.1038/nprot.2016.136openalex-snapshot
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
inferredcites →https://doi.org/10.1038/s41559-018-0510-xopenalex-snapshot
A guide to ancient protein studies
inferredcites →https://doi.org/10.1039/c6ra05120kopenalex-snapshot
The identification of peptides by nanoLC-MS/MS from human surface tooth enamel following a simple acid etch extraction
inferredcites →https://doi.org/10.1073/pnas.1106638108openalex-snapshot
Earliest human occupations at Dmanisi (Georgian Caucasus) dated to 1.85–1.78 Ma
inferredcites →https://doi.org/10.1073/pnas.1605834113openalex-snapshot
Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne
inferredcites →https://doi.org/10.1074/mcp.m111.010587openalex-snapshot
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btq706openalex-snapshot
phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/bts199openalex-snapshot
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/bts578openalex-snapshot
Adding unaligned sequences into an existing alignment using MAFFT and LAST
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkp1163openalex-snapshot
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/nar/gkw1099openalex-snapshot
UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
inferredcites →https://doi.org/10.1098/rsbl.2006.0515openalex-snapshot
Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA
inferredcites →https://doi.org/10.1098/rspb.2017.0544openalex-snapshot
A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination
inferredcites →https://doi.org/10.1098/rstb.2012.0013openalex-snapshot
Why nature chose phosphate to modify proteins
inferredcites →https://doi.org/10.1101/cshperspect.a012567openalex-snapshot
Ancient DNA Damage
inferredcites →https://doi.org/10.1101/gr.114751.110openalex-snapshot
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
inferredcites →https://doi.org/10.1101/pdb.prot5448openalex-snapshot
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
inferredcites →https://doi.org/10.1111/eos.12214openalex-snapshot
Identification of proteins from human permanent erupted enamel
inferredcites →https://doi.org/10.1111/j.1096-3642.2009.00597.xopenalex-snapshot
A revision ofAceratherium blanfordiLydekker, 1884 (Mammalia: Rhinocerotidae) from the Early Miocene of Pakistan: postcranials as a key
inferredcites →https://doi.org/10.1111/j.1096-3642.2011.00752.xopenalex-snapshot
Molecular phylogeny and evolution of the Perissodactyla
inferredcites →https://doi.org/10.1111/zoj.12084openalex-snapshot
Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)
inferredcites →https://doi.org/10.1126/science.1133609openalex-snapshot
The Genome of the Sea Urchin Strongylocentrotus purpuratus
inferredcites →https://doi.org/10.1126/science.1206594openalex-snapshot
Out of Tibet: Pliocene Woolly Rhino Suggests High-Plateau Origin of Ice Age Megaherbivores
inferredcites →https://doi.org/10.1126/science.1217817openalex-snapshot
Secreted Kinase Phosphorylates Extracellular Proteins That Regulate Biomineralization
inferredcites →https://doi.org/10.1126/science.1238484openalex-snapshot
A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo
inferredcites →https://doi.org/10.1126/science.288.5468.1019openalex-snapshot
Earliest Pleistocene Hominid Cranial Remains from Dmanisi, Republic of Georgia: Taxonomy, Geological Setting, and Age
inferredcites →https://doi.org/10.1146/annurev-biochem-062917-012002openalex-snapshot
Ancient Biomolecules and Evolutionary Inference
inferredcites →https://doi.org/10.1186/1471-2148-9-95openalex-snapshot
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.2144/000112383openalex-snapshot
Comparison and Optimization of Ancient DNA Extraction
inferredcites →https://doi.org/10.5860/choice.37-3363openalex-snapshot
The Miocene land mammals of Europe
inferredcites →https://doi.org/10.7312/nei-92038openalex-snapshot
Molecular Evolutionary Genetics
inferredcites →https://doi.org/10.7554/elife.17092openalex-snapshot
Protein sequences bound to mineral surfaces persist into deep time
inferredcites →https://doi.org/10.7717/peerj.3033openalex-snapshot
Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.jas.2021.105354openalex-snapshot
AMELY deletion is not detected in systematically sampled reference populations: A Reply to Štamfelj
inferred← citeshttps://doi.org/10.1016/j.jas.2021.105383openalex-snapshot
Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids
inferred← citeshttps://doi.org/10.1016/j.jprot.2021.104187openalex-snapshot
Ancient enamel peptides recovered from the South American Pleistocene species Notiomastodon platensis and Myocastor cf. coypus
inferred← citeshttps://doi.org/10.1038/s41598-019-49562-7openalex-snapshot
Enamel peptides reveal the sex of the Late Antique ‘Lovers of Modena’
inferred← citeshttps://doi.org/10.1038/s41598-020-68550-wopenalex-snapshot
A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation
inferred← citeshttps://doi.org/10.1093/biosci/biz105openalex-snapshot
Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlz012openalex-snapshot
Palaeoproteomics of bird bones for taxonomic classification
inferred← citeshttps://doi.org/10.1098/rsos.191137openalex-snapshot
Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites
inferred← citeshttps://doi.org/10.1371/journal.pone.0239521openalex-snapshot
DNA from resin-embedded organisms: Past, present and future
inferred← citeshttps://doi.org/10.14264/17f4bd1openalex-snapshot
Coastal caprines: using ZooMS to trace the spread of domesticates in coastal eastern Africa
inferred← citeshttps://doi.org/10.26481/spe.20190613jjopenalex-snapshot
Ken uzelve
inferred← citeshttps://doi.org/10.48738/2021.iss1.72openalex-snapshot
Treacherous Evidence: Archival Documents and the Search for Peking Man
inferred← citeshttps://doi.org/10.7287/peerj.7647v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7647v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7647v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7647v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.7647v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.7647v0.2/reviews/3openalex-snapshot
Peer Review #3 of "Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers (v0.2)"
inferred← citeshttps://doi.org/10.7554/elife.46205openalex-snapshot
Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities
inferred← citeshttps://doi.org/10.7717/peerj.7647openalex-snapshot
Interspecific variation in the limb long bones among modern rhinoceroses—extent and drivers
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.