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Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

https://doi.org/10.3390/genes10070509
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What this work says

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

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Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad
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Signals of positive selection in mitochondrial protein‐coding genes of woolly mammoth: Adaptation to extreme environments?
inferredcites →https://doi.org/10.1016/j.cell.2019.03.049openalex-snapshot
Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series
inferredcites →https://doi.org/10.1016/j.cub.2019.04.021openalex-snapshot
Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations
inferredcites →https://doi.org/10.1016/j.fsigen.2019.02.013openalex-snapshot
Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines
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DNA species identification of archaeological salmon bone from the Pacific Northwest Coast of North America
inferredcites →https://doi.org/10.1016/j.tree.2015.06.008openalex-snapshot
Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene
inferredcites →https://doi.org/10.1038/312282a0openalex-snapshot
DNA sequences from the quagga, an extinct member of the horse family
inferredcites →https://doi.org/10.1038/hdy.2014.81openalex-snapshot
Genome data from a sixteenth century pig illuminate modern breed relationships
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/nature12788openalex-snapshot
A mitochondrial genome sequence of a hominin from Sima de los Huesos
inferredcites →https://doi.org/10.1038/nature14507openalex-snapshot
Population genomics of Bronze Age Eurasia
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature17993openalex-snapshot
The genetic history of Ice Age Europe
inferredcites →https://doi.org/10.1038/nature25738openalex-snapshot
The Beaker phenomenon and the genomic transformation of northwest Europe
inferredcites →https://doi.org/10.1038/nature25778openalex-snapshot
The genomic history of southeastern Europe
inferredcites →https://doi.org/10.1038/ncomms15694openalex-snapshot
Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
inferredcites →https://doi.org/10.1038/nprot.2007.247openalex-snapshot
Ancient DNA extraction from bones and teeth
inferredcites →https://doi.org/10.1038/s41586-018-0094-2openalex-snapshot
137 ancient human genomes from across the Eurasian steppes
inferredcites →https://doi.org/10.1038/s41586-018-0097-zopenalex-snapshot
Ancient hepatitis B viruses from the Bronze Age to the Medieval period
inferredcites →https://doi.org/10.1073/pnas.0704665104openalex-snapshot
Patterns of damage in genomic DNA sequences from a Neandertal
inferredcites →https://doi.org/10.1073/pnas.0708855104openalex-snapshot
Parallel genomic evolution and metabolic interdependence in an ancient symbiosis
inferredcites →https://doi.org/10.1073/pnas.1318934111openalex-snapshot
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
inferredcites →https://doi.org/10.1073/pnas.1720554115openalex-snapshot
A comprehensive genomic history of extinct and living elephants
inferredcites →https://doi.org/10.1080/23802359.2018.1456371openalex-snapshot
Species identification and mitochondrial genomes of ancient fish bones from the Riverine Kachemak tradition of the Kenai Peninsula, Alaska
inferredcites →https://doi.org/10.1093/bfgp/elv027openalex-snapshot
The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?
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/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btt193openalex-snapshot
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
inferredcites →https://doi.org/10.1093/gigascience/gix049openalex-snapshot
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
inferredcites →https://doi.org/10.1093/nar/29.23.4793openalex-snapshot
DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
inferredcites →https://doi.org/10.1093/nar/gkx033openalex-snapshot
Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase
inferredcites →https://doi.org/10.1098/rspb.2002.2218openalex-snapshot
Biological identifications through DNA barcodes
inferredcites →https://doi.org/10.1098/rstb.2013.0371openalex-snapshot
Ancient DNA: the first three decades
inferredcites →https://doi.org/10.1101/gr.076091.108openalex-snapshot
Identification of ancient remains through genomic sequencing
inferredcites →https://doi.org/10.1101/gr.122747.111openalex-snapshot
True single-molecule DNA sequencing of a pleistocene horse bone
inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot
A Draft Sequence of the Neandertal Genome
inferredcites →https://doi.org/10.1126/science.1224344openalex-snapshot
A High-Coverage Genome Sequence from an Archaic Denisovan Individual
inferredcites →https://doi.org/10.1126/science.aas9411openalex-snapshot
Ancient goat genomes reveal mosaic domestication in the Fertile Crescent
inferredcites →https://doi.org/10.1146/annurev-animal-022516-022747openalex-snapshot
Taming the Past: Ancient DNA and the Study of Animal Domestication
inferredcites →https://doi.org/10.1177/0959683616641741openalex-snapshot
Ancient DNA identification of domestic animals used for leather objects in Central Asia during the Bronze Age
inferredcites →https://doi.org/10.1186/2041-2223-2-2openalex-snapshot
An overview to the investigative approach to species testing in wildlife forensic science
inferredcites →https://doi.org/10.1186/s12862-014-0246-4openalex-snapshot
Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys
inferredcites →https://doi.org/10.1186/s13059-015-0790-2openalex-snapshot
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle
inferredcites →https://doi.org/10.1186/s13104-016-1900-2openalex-snapshot
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
inferredcites →https://doi.org/10.13188/2330-0396.1000025openalex-snapshot
A Comparison of Mitochondrial DNA Amplification Strategies for Species Identification
inferredcites →https://doi.org/10.1371/journal.pbio.1001127openalex-snapshot
How Many Species Are There on Earth and in the Ocean?
inferredcites →https://doi.org/10.1371/journal.pone.0015136openalex-snapshot
Molecular Species Identification with Rich Floristic Sampling: DNA Barcoding the Pteridophyte Flora of Japan
inferredcites →https://doi.org/10.1371/journal.pone.0034131openalex-snapshot
Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA
inferredcites →https://doi.org/10.2139/ssrn.3316802openalex-snapshot
Palaeogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations
inferredcites →https://doi.org/10.2193/2007-272openalex-snapshot
Using DNA Barcodes to Identify Bird Species Involved in Birdstrikes
inferredcites →https://doi.org/10.3390/genes8060169openalex-snapshot
Identifying Bird Remains Using Ancient DNA Barcoding

What points at this work

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

inferred← citeshttps://doi.org/10.12688/openreseurope.14936.1zenodo-depositor-declared
MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes
inferred← citeshttps://doi.org/10.12688/openreseurope.14936.2zenodo-depositor-declared
MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes
inferred← citeshttps://doi.org/10.12688/openreseurope.14936.3zenodo-depositor-declared
MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes
inferred← citeshttps://doi.org/10.1002/ece3.7056openalex-snapshot
An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole‐genome sequencing data
inferred← citeshttps://doi.org/10.1016/j.fsiae.2021.100030openalex-snapshot
Current methods, future directions and considerations of DNA-based taxonomic identification in wildlife forensics
inferred← citeshttps://doi.org/10.1016/j.isci.2023.108191openalex-snapshot
Antibody-based sex determination of human skeletal remains
inferred← citeshttps://doi.org/10.1186/s40494-022-00798-zopenalex-snapshot
Animal species identification utilising DNAs extracted from traditionally manufactured gelatin (Wanikawa)
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1820786/v1openalex-snapshot
Animal Species Identification Utilising DNAs Extracted from Traditionally Manufactured Gelatin
inferred← citeshttps://doi.org/10.3390/microorganisms13102325openalex-snapshot
Red Foxes (Vulpes vulpes) and European Badgers (Meles meles) as Overlooked Wildlife Hosts of Canine Parvovirus in Slovakia: First Evidence by Molecular Characterization and Virus Isolation
inferred← citeshttps://doi.org/10.5821/dissertation-2117-356730openalex-snapshot
Genomics tools in the cloud: the new frontier in omics data analysis
inferred← citeshttps://doi.org/10.6084/m9.figshare.21542240openalex-snapshot
Additional file 1 of Animal species identification utilising DNAs extracted from traditionally manufactured gelatin (Wanikawa)
inferred← citeshttps://doi.org/10.6084/m9.figshare.21542243openalex-snapshot
Additional file 2 of Animal species identification utilising DNAs extracted from traditionally manufactured gelatin (Wanikawa)
inferred← citeshttps://doi.org/10.6084/m9.figshare.21542246openalex-snapshot
Additional file 3 of Animal species identification utilising DNAs extracted from traditionally manufactured gelatin (Wanikawa)
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