David Mindell, Ph.D. - Publications

Affiliations: 
California Academy of Sciences, San Francisco, CA, United States 
Area:
avian phylogenetics

87 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Cho YS, Jun JH, Kim JA, Kim HM, Chung O, Kang SG, Park JY, Kim HJ, Kim S, Kim HJ, Jang JH, Na KJ, Kim J, Park SG, Lee HY, ... ... Mindell DP, et al. Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles. Genome Biology. 20: 181. PMID 31464627 DOI: 10.1186/S13059-019-1793-1  0.4
2017 Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. Genome Biology and Evolution. 9: 2522-2545. PMID 28992302 DOI: 10.1093/Gbe/Evx158  0.4
2016 Johnson JA, Brown JW, Fuchs J, Mindell DP. Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae). Molecular Phylogenetics and Evolution. PMID 27601346 DOI: 10.1016/J.Ympev.2016.08.025  1
2015 Cracraft J, Houde P, Ho SY, Mindell DP, Fjeldså J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MT, Zhang G, Braun EL, Jarvis ED. Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science (New York, N.Y.). 349: 1460. PMID 26404820 DOI: 10.1126/Science.Aab1578  1
2015 Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP. Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample. Genome Announcements. 3. PMID 26404604 DOI: 10.1128/Genomea.01081-15  0.4
2015 Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, ... ... Mindell DP, et al. Phylogenomic analyses data of the avian phylogenomics project. Gigascience. 4: 4. PMID 25741440 DOI: 10.1186/S13742-014-0038-1  1
2015 Fuchs J, Johnson JA, Mindell DP. Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene. Molecular Phylogenetics and Evolution. 82: 166-82. PMID 25256056 DOI: 10.1016/j.ympev.2014.08.010  1
2014 Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, ... ... Mindell DP, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science (New York, N.Y.). 346: 1320-31. PMID 25504713 DOI: 10.1126/Science.1253451  0.6
2014 Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, ... ... Mindell DP, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, N.Y.). 346: 1311-20. PMID 25504712 DOI: 10.1126/Science.1251385  0.6
2014 Fuchs J, Simmons RE, Mindell DP, Bowie RCK, Oatley G. Lack of mtDNA genetic diversity in the Black Harrier Circus maurus, a Southern African endemic Ibis. 156: 227-230. DOI: 10.1111/Ibi.12103  1
2014 Fuchs J, Simmons RE, Mindell DP, Bowie RCK, Oatley G. Lack of mtDNA genetic diversity in the Black Harrier Circus maurus, a Southern African endemic Ibis. 156: 227-230. DOI: 10.1111/ibi.12103  0.4
2013 Losos JB, Arnold SJ, Bejerano G, Brodie ED, Hibbett D, Hoekstra HE, Mindell DP, Monteiro A, Moritz C, Orr HA, Petrov DA, Renner SS, Ricklefs RE, Soltis PS, Turner TL. Evolutionary biology for the 21st century. Plos Biology. 11: e1001466. PMID 23319892 DOI: 10.1371/Journal.Pbio.1001466  1
2013 Mindell DP. The tree of life: metaphor, model, and heuristic device. Systematic Biology. 62: 479-89. PMID 23291311 DOI: 10.1093/sysbio/sys115  1
2012 Barnosky AD, Hadly EA, Bascompte J, Berlow EL, Brown JH, Fortelius M, Getz WM, Harte J, Hastings A, Marquet PA, Martinez ND, Mooers A, Roopnarine P, Vermeij G, Williams JW, ... ... Mindell DP, et al. Approaching a state shift in Earth's biosphere. Nature. 486: 52-8. PMID 22678279 DOI: 10.1038/Nature11018  1
2012 Fuchs J, Johnson JA, Mindell DP. Molecular systematics of the caracaras and allies (Falconidae: Polyborinae) inferred from mitochondrial and nuclear sequence data Ibis. 154: 520-532. DOI: 10.1111/j.1474-919X.2012.01222.x  0.4
2012 Fuchs J, Johnson JA, Mindell DP. Molecular systematics of the caracaras and allies (Falconidae: Polyborinae) inferred from mitochondrial and nuclear sequence data Ibis. 154: 520-532. DOI: 10.1111/j.1474-919X.2012.01222.x  1
2011 Mindell DP, Fisher BL, Roopnarine P, Eisen J, Mace GM, Page RD, Pyle RL. Aggregating, tagging and integrating biodiversity research. Plos One. 6: e19491. PMID 21829594 DOI: 10.1371/Journal.Pone.0019491  1
2011 Fuchs J, Chen S, Johnson JA, Mindell DP. Pliocene diversification within the South American Forest falcons (Falconidae: Micrastur). Molecular Phylogenetics and Evolution. 60: 398-407. PMID 21621621 DOI: 10.1016/j.ympev.2011.05.008  1
2010 Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP. The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America. Plos One. 5: e14042. PMID 21124969 DOI: 10.1371/Journal.Pone.0014042  1
2010 Hull JM, Mindell DP, Talbot SL, Kay EH, Hoekstra HE, Ernest HB. Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani. Bmc Evolutionary Biology. 10: 224. PMID 20650000 DOI: 10.1186/1471-2148-10-224  1
2009 Lerner HR, Johnson JA, Lindsay AR, Kiff LF, Mindell DP. It's not too late for the harpy eagle (Harpia harpyja): high levels of genetic diversity and differentiation can fuel conservation programs. Plos One. 4: e7336. PMID 19802391 DOI: 10.1371/Journal.Pone.0007336  1
2009 Mindell DP. Evolution in the everyday world. Scientific American. 300: 82-9. PMID 19186754  1
2009 Johnson JA, Tingay RE, Culver M, Hailer F, Clarke ML, Mindell DP. Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle. Molecular Ecology. 18: 54-63. PMID 19140964 DOI: 10.1111/j.1365-294X.2008.04012.x  1
2008 Brown JW, Rest JS, García-Moreno J, Sorenson MD, Mindell DP. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. Bmc Biology. 6: 6. PMID 18226223 DOI: 10.1186/1741-7007-6-6  1
2008 Lerner HRL, Klaver MC, Mindell DP. Molecular phylogenetics of the Buteonine birds of prey (Accipitridae) Auk. 125: 304-315. DOI: 10.1525/auk.2008.06161  1
2008 Lerner HRL, Klaver MC, Mindell DP. Molecular phylogenetics of the Buteonine birds of prey (Accipitridae) Auk. 125: 304-315. DOI: 10.1525/auk.2008.06161  1
2008 Johnson JA, Gilbert M, Virani MZ, Asim M, Mindell DP. Temporal genetic analysis of the critically endangered oriental white-backed vulture in Pakistan Biological Conservation. 141: 2403-2409. DOI: 10.1016/j.biocon.2008.07.001  0.4
2008 Johnson JA, Gilbert M, Virani MZ, Asim M, Mindell DP. Temporal genetic analysis of the critically endangered oriental white-backed vulture in Pakistan Biological Conservation. 141: 2403-2409. DOI: 10.1016/j.biocon.2008.07.001  1
2007 Johnson JA, Burnham KK, Burnham WA, Mindell DP. Genetic structure among continental and island populations of gyrfalcons. Molecular Ecology. 16: 3145-60. PMID 17651193 DOI: 10.1111/j.1365-294X.2007.03373.x  1
2007 Brown JW, Payne RB, Mindell DP. Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: a comment on Ericson et al. Biology Letters. 3: 257-9; discussion 26. PMID 17389215 DOI: 10.1098/Rsbl.2006.0611  1
2007 Johnson JA, Thorstrom R, Mindell DP. Systematics and conservation of the hook-billed kite including the island taxa from Cuba and Grenada Animal Conservation. 10: 349-359. DOI: 10.1111/j.1469-1795.2007.00118.x  0.4
2007 Johnson JA, Thorstrom R, Mindell DP. Systematics and conservation of the hook-billed kite including the island taxa from Cuba and Grenada Animal Conservation. 10: 349-359. DOI: 10.1111/j.1469-1795.2007.00118.x  1
2006 Watanabe M, Nikaido M, Tsuda TT, Kobayashi T, Mindell D, Cao Y, Okada N, Hasegawa M. New candidate species most closely related to penguins. Gene. 378: 65-73. PMID 16806742 DOI: 10.1016/J.Gene.2006.05.003  1
2006 Watanabe M, Nikaido M, Tsuda TT, Inoko H, Mindell DP, Murata K, Okada N. The rise and fall of the CR1 subfamily in the lineage leading to penguins. Gene. 365: 57-66. PMID 16368202 DOI: 10.1016/j.gene.2005.09.042  1
2006 Johnson JA, Lerner HRL, Rasmussen PC, Mindell DP. Systematics within Gyps vultures: A clade at risk Bmc Evolutionary Biology. 6. DOI: 10.1186/1471-2148-6-65  1
2006 Johnson JA, Lerner HRL, Rasmussen PC, Mindell DP. Systematics within Gyps vultures: A clade at risk Bmc Evolutionary Biology. 6. DOI: 10.1186/1471-2148-6-65  1
2005 Johnson JA, Watson RT, Mindell DP. Prioritizing species conservation: does the Cape Verde kite exist? Proceedings. Biological Sciences / the Royal Society. 272: 1365-71. PMID 16006325 DOI: 10.1098/rspb.2005.3098  1
2005 Lerner HR, Mindell DP. Phylogeny of eagles, Old World vultures, and other Accipitridae based on nuclear and mitochondrial DNA. Molecular Phylogenetics and Evolution. 37: 327-46. PMID 15925523 DOI: 10.1016/j.ympev.2005.04.010  1
2005 Hietpas J, McMullan LK, Hanson HL, Rice CM, Mindell DP. Keeping Track of Viruses Microbial Forensics. 55-97. DOI: 10.1016/B978-012088483-4/50007-X  1
2003 Mindell DP, Villarreal LP. Don't forget about viruses. Science (New York, N.Y.). 302: 1677. PMID 14657474 DOI: 10.1126/science.302.5651.1677b  1
2003 Rest JS, Mindell DP. SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 3: 219-25. PMID 14522185 DOI: 10.1016/J.Meegid.2003.08.001  1
2003 Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, Hay JM, Mindell DP. Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Molecular Phylogenetics and Evolution. 29: 289-97. PMID 13678684 DOI: 10.1016/S1055-7903(03)00108-8  1
2003 Lee SI, Parr CS, Hwang Y, Mindell DP, Choe JC. Phylogeny of magpies (genus Pica) inferred from mtDNA data. Molecular Phylogenetics and Evolution. 29: 250-7. PMID 13678680 DOI: 10.1016/S1055-7903(03)00096-4  1
2003 García-Moreno J, Sorenson MD, Mindell DP. Congruent avian phylogenies inferred from mitochondrial and nuclear DNA sequences. Journal of Molecular Evolution. 57: 27-37. PMID 12962303 DOI: 10.1007/S00239-002-2443-9  1
2003 Rest JS, Mindell DP. Retroids in archaea: phylogeny and lateral origins. Molecular Biology and Evolution. 20: 1134-42. PMID 12777534 DOI: 10.1093/Molbev/Msg135  1
2003 Sorenson MD, Oneal E, Garcia-Moreno J, Mindell DP. More taxa, more characters: the hoatzin problem is still unresolved. Molecular Biology and Evolution. 20: 1484-98. PMID 12777516 DOI: 10.1093/Molbev/Msg157  1
2002 Metzker ML, Mindell DP, Liu XM, Ptak RG, Gibbs RA, Hillis DM. Molecular evidence of HIV-1 transmission in a criminal case. Proceedings of the National Academy of Sciences of the United States of America. 99: 14292-7. PMID 12388776 DOI: 10.1073/Pnas.222522599  1
2002 Dimmic MW, Rest JS, Mindell DP, Goldstein RA. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of Molecular Evolution. 55: 65-73. PMID 12165843 DOI: 10.1007/S00239-001-2304-Y  1
2002 Dimcheff DE, Drovetski SV, Mindell DP. Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes. Molecular Phylogenetics and Evolution. 24: 203-15. PMID 12144757 DOI: 10.1016/S1055-7903(02)00230-0  1
2002 Yuri T, Mindell DP. Molecular phylogenetic analysis of Fringillidae, "New World nine-primaried oscines" (Aves: Passeriformes). Molecular Phylogenetics and Evolution. 23: 229-43. PMID 12069553 DOI: 10.1016/S1055-7903(02)00012-X  1
2001 Meshnick SR, Hossler PA, Enger KS, Kazanjian P, Rest JS, Mindell D, Li B, Lee CH, Nimri LF, Carter JL, Beard CB, Huang L. Distribution of DHPS mutations among ITS subtypes of P. carinii f. sp. hominis. The Journal of Eukaryotic Microbiology. 126S-128S. PMID 11906022 DOI: 10.1111/J.1550-7408.2001.Tb00481.X  1
2001 Herlocher ML, Elias S, Truscon R, Harrison S, Mindell D, Simon C, Monto AS. Ferrets as a transmission model for influenza: sequence changes in HA1 of type A (H3N2) virus. The Journal of Infectious Diseases. 184: 542-6. PMID 11494159 DOI: 10.1086/322801  1
2001 Dimcheff DE, Krishnan M, Mindell DP. Evolution and characterization of tetraonine endogenous retrovirus: a new virus related to avian sarcoma and leukosis viruses. Journal of Virology. 75: 2002-9. PMID 11160701 DOI: 10.1128/Jvi.75.4.2002-2009.2001  1
2001 Mindell DP, Meyer A. Homology evolving Trends in Ecology and Evolution. 16: 434-440. DOI: 10.1016/S0169-5347(01)02206-6  1
2000 Cao Y, Sorenson MD, Kumazawa Y, Mindell DP, Hasegawa M. Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes. Gene. 259: 139-48. PMID 11163971 DOI: 10.1016/S0378-1119(00)00425-X  1
2000 García-Moreno J, Mindell DP. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD. Molecular Biology and Evolution. 17: 1826-32. PMID 11110898  1
2000 Dimmic MW, Mindell DP, Goldstein RA. Modeling evolution at the protein level using an adjustable amino acid fitness model. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 18-29. PMID 10902153  1
2000 Mory RN, Mindell D, Bloom DA. The leech and the physician: biology, etymology, and medical practice with Hirudinea medicinalis. World Journal of Surgery. 24: 878-83. PMID 10833259 DOI: 10.1007/S002680010141  1
2000 Dimcheff DE, Drovetski SV, Krishnan M, Mindell DP. Cospeciation and horizontal transmission of avian sarcoma and leukosis virus gag genes in galliform birds. Journal of Virology. 74: 3984-95. PMID 10756010 DOI: 10.1128/Jvi.74.9.3984-3995.2000  1
1999 Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Systematic Biology. 48: 138-52. PMID 12078637 DOI: 10.1080/106351599260490  1
1999 Waddell PJ, Cao Y, Hasegawa M, Mindell DP. Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework. Systematic Biology. 48: 119-37. PMID 12078636  1
1999 Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution. 12: 105-14. PMID 10381314 DOI: 10.1006/Mpev.1998.0602  1
1999 Koshi JM, Mindell DP, Goldstein RA. Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes. Molecular Biology and Evolution. 16: 173-9. PMID 10028285 DOI: 10.1093/Oxfordjournals.Molbev.A026100  1
1998 Mindell DP, Sorenson MD, Dimcheff DE. An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Molecular Biology and Evolution. 15: 1568-71. PMID 12572620 DOI: 10.1093/Oxfordjournals.Molbev.A025884  1
1998 Mindell DP, Sorenson MD, Dimcheff DE. Multiple independent origins of mitochondrial gene order in birds. Proceedings of the National Academy of Sciences of the United States of America. 95: 10693-7. PMID 9724766 DOI: 10.1073/Pnas.95.18.10693  1
1997 Koshi JM, Mindell DP, Goldstein RA. Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models. Genome Informatics. Workshop On Genome Informatics. 8: 80-89. PMID 11072308 DOI: 10.11234/Gi1990.8.80  1
1997 Mindell DP. "Misleading" molecules? Science (New York, N.Y.). 276: 1629. PMID 9206819 DOI: 10.1126/science.276.5319.1629  1
1997 Lane BR, Ast JC, Hossler PA, Mindell DP, Bartlett MS, Smith JW, Meshnick SR. Dihydropteroate synthase polymorphisms in Pneumocystis carinii. The Journal of Infectious Diseases. 175: 482-5. PMID 9203679 DOI: 10.1093/Infdis/175.2.482  1
1997 Miranda HC, Kennedy RS, Mindell DP. Phylogenetic placement of Mimizuku gurneyi (Aves: Strigidae) inferred from mitochondrial DNA Auk. 114: 315-323.  1
1996 Quinn TW, Mindell DP. Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara. Molecular Phylogenetics and Evolution. 5: 344-51. PMID 8728392 DOI: 10.1006/mpev.1996.0029  1
1996 Mindell DP. Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees. Proceedings of the National Academy of Sciences of the United States of America. 93: 3284-8. PMID 8622929 DOI: 10.1073/pnas.93.8.3284  1
1995 Govindaswami M, Feldhake DJ, Kinkle BK, Mindell DP, Loper JC. Phylogenetic comparison of two polycyclic aromatic hydrocarbon-degrading mycobacteria. Applied and Environmental Microbiology. 61: 3221-6. PMID 7574631  1
1995 Farris JS, Källersjö M, Albert VA, Allard M, Anderberg A, Bowditch B, Bult C, Carpenter JM, Crowe TM, De Laet J, Fitzhugh K, Frost D, Goloboff P, Humphries CJ, Jondelius U, ... ... Mindell D, et al. Explanation Cladistics. 11: 211-218. DOI: 10.1016/0748-3007(95)90012-8  1
1995 Mindell DP, Shultz JW, Ewald PW. The AIDS pandemic is new, but is HIV new? Systematic Biology. 44: 77-92.  1
1994 Seutin G, Lang BF, Mindell DP, Morais R. Evolution of the WANCY region in amniote mitochondrial DNA. Molecular Biology and Evolution. 11: 329-40. PMID 8015429  1
1994 Knight A, Mindell DP. On the phylogenetic relationship of Colubrinae, Elapidae, and Viperidae and the evolution of front-fanged venom systems in snakes Copeia. 1-9.  1
1993 Knight A, Styer D, Pelikan S, Campbell JA, Densmore LD, Mindell DP. Choosing among hypotheses of rattlesnake phylogeny: A best-fit rate test for DNA sequence data Systematic Biology. 42: 356-367. DOI: 10.1093/Sysbio/42.3.356  1
1993 Mindell DP. Merger of taxa and the definition of monophyly (reply to Jan Zrzavý and Zdeněk Skála) Biosystems. 31: 130-133. DOI: 10.1016/0303-2647(93)90041-A  1
1993 Knight A, Mindell DP. Substitution bias, weighting of DNA sequence evolution, and the phylogenetic position of FEA's viper Systematic Biology. 42: 18-31.  1
1992 Mindell DP. Phylogenetic consequences of symbioses: Eukarya and Eubacteria are not monophyletic taxa. Bio Systems. 27: 53-62. PMID 1391691 DOI: 10.1016/0303-2647(92)90046-2  1
1991 Ellis DH, Ellis CH, Mindell DP. Raptor responses to low-level jet aircraft and sonic booms. Environmental Pollution (Barking, Essex : 1987). 74: 53-83. PMID 15092075 DOI: 10.1016/0269-7491(91)90026-S  1
1991 Mindell DP, Dick CW, Baker RJ. Phylogenetic relationships among megabats, microbats, and primates. Proceedings of the National Academy of Sciences of the United States of America. 88: 10322-6. PMID 1658803 DOI: 10.1073/Pnas.88.22.10322  1
1991 Mindell DP. Similarity and congruence as criteria for molecular homology [4] Molecular Biology and Evolution. 8: 897-900.  1
1990 Mindell DP, Honeycutt RL. Ribosomal RNA in vertebrates: Evolution and phylogenetic applications Annual Review of Ecology and Systematics. 21: 541-566.  1
1989 Cracraft J, Mindell DP. The early history of modern birds: A comparison of molecular and morphological evidence The Hierarchy of Life. Molecules and Morphology in Phylogenetic Analysis: Proceedings From Nobel Symposium 70. Ics824. 389-403.  1
1988 Mindell DP, White CM. Fluctuations of observed breeding Rough-legged Hawks and Gyrfalcons: regularity reconsidered Oecologia. 77: 14-18. DOI: 10.1007/BF00380918  1
1987 Mindell DP, Albuquerque JLB, White CM. Breeding population fluctuations in some raptors Oecologia. 72: 382-388. DOI: 10.1007/BF00377568  1
Show low-probability matches.