The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Parameters maximizing mapping specificity and sensitivity can be identified using aDNA read simulators such as 16 gargammel 180 , and depend on the evolutionary distance to the reference genome used, DNA fragment size and the amount of post-mortem damage 111,181-184 .”
From Ancient DNA analysis (2021) · cites this paper as [183]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“While some guidelines exist for the analysis of ancient genomic data, for example for mapping 162,181,183 or data authentication 56,57,329 , and automated tools embedding critical analytical procedures within open-source pipelines are available 187,188,241,242 , there is still no consensus on a”
From Ancient DNA analysis (2021) · cites this paper as [183]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F., & Orlando, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt193 · Cited by 1,669
Hofreiter, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4793 · Cited by 684
The Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419
Self-citationNuclear genomic sequences reveal that polar bears are an old and distinct bear lineage
Hailer, F., Kutschera, V. E., Hallström, B. M., Klassert, D., Fain, S. R., Leonard, J. A., Arnason, U., & Janke, A. (2012) · Science · doi:10.1126/science.1216424 · Cited by 308
Cahill, J. A., Green, R. E., Fulton, T. L., Stiller, M., Jay, F., Ovsyanikov, N., Salamzade, R., St. John, J., Stirling, I., Slatkin, M., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003345 · Cited by 221
Self-citation
Flagged first, then by citations
Research works printed but not linked: 50
- Becker, 2013, Hybridization may facilitate in situ survival of endemic species through periods of climate change, Nat Clim Change., 3, 1039, 10.1038/nclimate2027 · DOI
- Briggs, 2009, Targeted retrieval and analysis of five Neandertal mtDNA genomes, Science, 325, 318, 10.1126/science.1174462 · DOI
- Cahill, 2015, Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears, Mol Ecol, 24, 1205, 10.1111/mec.13038 · DOI
- Clark, 2012, Pattern and timing of retreat of the last British-Irish Ice Sheet, Quat Sci Rev, 44, 112, 10.1016/j.quascirev.2010.07.019 · DOI
- Cronin, 1991, Interspecific and intraspecific mitochondrial DNA variation in North American bears, Can. J. Zool., 69, 2985, 10.1139/z91-421 · DOI
- Dasmahapatra, 2012, Butterfly genome reveals promiscuous exchange of mimicry adaptations among species, Nature, 487, 94, 10.1038/nature11041 · DOI
- Delisle, 2002, Conserved primers for rapid sequencing of the complete mitochondrial genome from carnivores, applied to three species of bears, Mol. Biol. Evol., 19, 357, 10.1093/oxfordjournals.molbev.a004090 · DOI
- Doupé, 2007, Most northerly observation of a grizzly bear (Ursus arctos) in Canada: photographic and DNA evidence from Melville Island, Northwest Territories, Arctic, 60, 271
- Durand, 2011, Testing for ancient admixture between closely related populations, Mol Biol Evol, 28, 2239, 10.1093/molbev/msr048 · DOI · Paper page
- Edwards, 2014, Continuity of brown bear maternal lineages in northern England through the last-glacial period, Quat Sci Rev, 96, 131, 10.1016/j.quascirev.2013.10.015 · DOI
- Edwards, 2011, Ancient hybridization and an Irish origin for the modern polar bear matriline, Curr Biol, 21, 1251, 10.1016/j.cub.2011.05.058 · DOI
- Figueirido, 2009, Ecomorphological correlates of craniodental variation in bears and paleobiological implications for extinct taxa: an approach based on geometric morphometrics, J Zool, 277, 70, 10.1111/j.1469-7998.2008.00511.x · DOI
- Fulton, 2012, Setting up an ancient DNA laboratory, Methods Mol Biol, 840, 1, 10.1007/978-1-61779-516-9_1 · DOI
- Garroway, 2010, Climate change induced hybridization in flying squirrels, Glob Chang Biol, 16, 113, 10.1111/j.1365-2486.2009.01948.x · DOI
- Good, 2008, A complex genetic basis to X-linked hybrid male sterility between two species of house mice, Genetics, 179, 2213, 10.1534/genetics.107.085340 · DOI
- Graham, 1996, Spatial response of mammals to late quaternary environmental fluctuations, Science, 272, 1601, 10.1126/science.272.5268.1601 · DOI
- Green, 2010, A draft sequence of the Neandertal genome, Science, 328, 710, 10.1126/science.1188021 · DOI · Paper page
- Harington, 2008, The evolution of Arctic marine mammals, Ecol Appl, 18, S23, 10.1890/06-0624.1 · DOI
- Harington, 2014, Brown bear (Ursus arctos) (9880 ± 35bp) from late-glacial Champlain Sea deposits at Saint-Nicolas, Québec, Canada, and the dispersal history of brown bears, Can J Earth Sci, 51, 527, 10.1139/cjes-2013-0220 · DOI
- Heintzman, 2015, Genomic data from extinct North American camelops revise camel evolutionary history, Mol Biol Evol, 32, 2433, 10.1093/molbev/msv128 · DOI
- Hirata, 2013, Molecular phylogeography of the brown bear (Ursus arctos) in Northeastern Asia based on analyses of complete mitochondrial DNA sequences, Mol. Biol. Evol., 30, 1644, 10.1093/molbev/mst077 · DOI
- Hoffmann, 2011, Climate change and evolutionary adaptation, Nature, 470, 479, 10.1038/nature09670 · DOI
- Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 · DOI · Paper page
- Kelly, 2010, The Arctic melting pot, Nature, 468, 891., 10.1038/468891a · DOI
- Kumar, 2017, The evolutionary history of bears is characterized by gene flow across species, Sci Rep., 7, 46487., 10.1038/srep46487 · DOI
- Kunsch, 1989, The jackknife and the bootstrap for general stationary observations, Ann Stat, 17, 1217, 10.1214/aos/1176347265 · DOI
- Lamichhaney, 2015, Evolution of Darwin’s finches and their beaks revealed by genome sequencing, Nature, 518, 371, 10.1038/nature14181 · DOI
- Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat Methods., 9, 357, 10.1038/nmeth.1923 · DOI · Paper page
- Li, 2010, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, 26, 589, 10.1093/bioinformatics/btp698 · DOI · Paper page
- Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 · DOI · Paper page
- Liu, 2014, Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears, Cell, 157, 785, 10.1016/j.cell.2014.03.054 · DOI · Paper page
- Messer, 2013, SLiM: simulating evolution with selection and linkage, Genetics, 194, 1037, 10.1534/genetics.113.152181 · DOI
- Meyer, 2010, Illumina sequencing library preparation for highly multiplexed target capture and sequencing, Cold Spring Harb Protoc, 2010, prot5448, 10.1101/pdb.prot5448 · DOI
- Miller, 2012, Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change, Proc Natl Acad Sci. USA., 109, E2382, 10.1073/pnas.1210506109 · DOI · Paper page
- Muhlfeld, 2014, Invasive hybridization in a threatened species is accelerated by climate change, Nat Clim Change., 4, 620, 10.1038/nclimate2252 · DOI
- Ó Cofaigh, 2012, Late Pleistocene chronostratigraphy and ice sheet limits, southern Ireland, Quat Sci Rev, 44, 160, 10.1016/j.quascirev.2010.01.011 · DOI
- Parmesan, 2003, A globally coherent fingerprint of climate change impacts across natural systems, Nature, 421, 37, 10.1038/nature01286 · DOI · Paper page
- Peacock, 2015, Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming arctic, PLOS ONE., 10, e112021, 10.1371/journal.pone.0112021 · DOI
- Peters, 2015, Maximum extent and dynamic behaviour of the last British–Irish ice sheet west of Ireland, Quat Sci Rev, 128, 48, 10.1016/j.quascirev.2015.09.015 · DOI
- Poelstra, 2014, The genomic landscape underlying phenotypic integrity in the face of gene flow in crows, Science, 344, 1410, 10.1126/science.1253226 · DOI
- Pongracz, 2017, Recent hybridization between a polar bear and grizzly bears in the Canadian Arctic, Arctic, 70, 151, 10.14430/arctic4643 · DOI
- Preuß, 2009, Bear-hybrids: behaviour and phenotype, Der Zool Garten., 78, 204, 10.1016/j.zoolgart.2009.08.005 · DOI
- Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406
- Sánchez-Guillén, 2014, Hybridization rate and climate change: are endangered species at risk?, J Insect Conserv, 18, 295, 10.1007/s10841-014-9637-5 · DOI
- Sato, 2011, The white-colored brown bears of the Southern Kurils, Ursus, 22, 84, 10.2192/URSUS-D-10-00017.1 · DOI
- Seki, 2004, Reconstruction of paleoproductivity in the Sea of Okhotsk over the last 30 kyr, Paleoceanography, 19, PA1016, 10.1029/2002PA000808 · DOI
- Slater, Biomechanical consequences of rapid evolution in the polar bear lineage, PLoS One, 5, e13870, 10.1371/journal.pone.0013870 · DOI
- Stirling, 2011, Polar bears: the natural history of a threatened species.
- Stuart, 2004, Pleistocene to Holocene extinction dynamics in giant deer and woolly mammoth, Nature, 431, 684, 10.1038/nature02890 · DOI
- Woodman, 1997, The Irish quaternary fauna project, Quat Sci Rev, 16, 129, 10.1016/S0277-3791(96)00037-6 · DOI
Cited by
Sorted by citations
Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411
Ancient Cattle Genomics, Origins, and Rapid Turnover in the Fertile Crescent
Verdugo, M. P., Mullin, V. E., Scheu, A., Mattiangeli, V., Daly, K. G., Maisano Delser, P., Hare, A. J., Burger, J., Collins, M. J., Kehati, R., et al. (2019) · Science · doi:10.1126/science.aav1002 · Cited by 227
Self-citationSystematic benchmark of ancient DNA read mapping
Oliva, A., Tobler, R., Cooper, A., Llamas, B., & Souilmi, Y. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab076 · Cited by 63
Assessing DNA sequence alignment methods for characterizing ancient genomes and methylomes
Poullet, M., & Orlando, L. (2020) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2020.00105 · Cited by 61
Metadata
- Authors
- Cahill, J. A., Heintzman, P. D., Harris, K., Teasdale, M. D., Kapp, J., Soares, A. E. R., Stirling, I., Bradley, D., Edwards, C. J., Graim, K., Kisleika, A. A., Malev, A. V., Monaghan, N., Green, R. E., & Shapiro, B.
- Affiliations
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA
- Department of Genetics, Stanford University, Stanford, CA
- Smurfit Institute of Genetics, Dublin 2, Ireland
- Wildlife Research Division, Department of Environment, c/o Department of Biological Sciences, University of Alberta, Edmonton, AB
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, NJ
- Kurils Nature Reserve, Russia, Yuzhno-Kurilsk, Russia
- Kazan Zoobotanical Garden, Kazan, Russia
- National Museum of Ireland – Natural History, Dublin, Ireland
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-02-20
- Volume
- 35
- Issue
- 5
- Pages
- 1120-1129
- ISSN
- 0737-4038
- 1537-1719
- Cited by
- 83
- References
- 5
- Language
- en
- Funders
- NSF (ARC-1417036)
- Irish Research Council for Science Engineering and Technology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review