Crandall Lab

Publications

2009	2008	2007	2006	2005	2004	2003	2002	2001
2000	1999	1998	1997	1996	1995	1994	1993	1992

 

 

 

2009 Publications

Authors	Title	Reference	Data
Buhay, J.E., Crandall, K.A.	Taxonomic revision of cave crayfish in the genus Cambarus, subgenus Aviticambarus (Decapoda: Cambaridae) with descriptions of two new species, C. speleocoopi and C. laconensis, endemic to Alabama, U.S.A.	Journal of Crustacean Biology. 2009. 29:121-134
Bracken, H., Toon, A., Felder, D., Martin, J., Finley, M., Rasmussen, J., Palero, F., Crandall, K.A.	The Decapod Tree of Life: Compiling the Data and Moving toward a Consensus of Decapod Evolution	Arthropod Systematics & Phylogeny. 2009. 67(1):99-1116
Lewis-Rogers, N., Bendall, M.,  and Crandall, K.A.	Phylogenetic Relationships and Molecular Adaptation Dynamics of Human Rhinoviruses	Molecular Biology and Evolution 2009; doi: 10.1093/molbev/msp009
Xu, J., Perez-Losada, M., Jara, C., Crandall, K.A.	Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia	Molecular Ecology. 2009. 18(5):904-918.
Schultz, M., Smith, S., Horwitz, P., Richardson, A., Crandall, K.A., Austin, C.	Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson	Molecular Phylogenetics and Evolution. 2009. 50: 580–598

 

2008 Publications

Authors	Title	Reference	Data
Lewis-Rogers, N., D.A. McClellan, and  Crandall K.A..	The Evolution of Foot-and-Mouth Disease Virus:  Impacts of Recombination and Selection.	Infection, Genetics, and Evolution 8(6):786-798
Crandall, K.A., and J. Lagergren.	Algorithms in Bioinformatics	Springer-Verlag, Berlin, Germany. 2008
Toon, A., Finley, M., Staples, J., and Crandall, K.A.	Decapod Phylogenetics and Molecular Evolution.	Decapod Crustacean Phylogenetics. CRC. pp. 9-24
Weaver, K. F., M. Pérez-Losada, R. P. Guralnick, A. Nelson, S. Blatt, and K. A. Crandall.	Assessing the conservation status of the land snail Oreohelix peripherica wasatchensis (Family Oreohelicidae).	Conservation Genetics in press.
Carvajal-Rodríguez, A., D. Posada, M. Pérez-Losada, E. Keller, E. J. Abrams, K. A. Crandall, and R. P. Viscidi.	Disease progression and evolution of the HIV-1 env gene in 24 infected infants.	Infection, Genetics, and Evolution in press.
Schultz, M.B., Ierodiaconou, D. A., Smith, S.A., Horwitz, P., Ricardson, A.M.M.,Crandall, K.A., Austin, C.M.	Sea-level changes and palaeo-ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfish Engaeus sericatus Clark (Decapoda: Parastacidae)	Molecular Ecology. 2008. 17: 5291–5314.
Bond-Buckup, G., C. G. Jara, M. Pérez-Losada, L. Buckup, and K. A. Crandall	Global diversity of crabs (Aeglidae: Anomura: Decapoda) in freshwater.	Hydrobiologia 595:267-273.
Keele, B. F., L. Tazi, S. Gartner, Y. Liu, T. B. Burgon, J. D. Estes, T. C. Thacker, K. A. Crandall, J. C. McArthur, and G. F. Burton.	Characterization of the follicular dendritic cell reservoir of HIV-1	Journal of Virology. 2008. 82(11):5548-5561.
Woolley, S. M., D. Posada, and K. A. Crandall.	A comparison of phylogenetic network methods using computer simulation.	PLoS One. 2008. 3(4):1-12.
Song, H., J. E. Buhay, M. F. Whiting, and K. A. Crandall.	Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified.	Proceedings of the National Acedemy of Sciences, USA. 2008 105(36):13486-13491.
Crandall, K. A., H. W. Robison, and J. E. Buhay.	Avoidance of extinction through nonexistence: The use of museum specimens and molecular genetics to determine the taxonomic status of an endangered freshwater crayfish	Conservation Genetics.  In press 2008
Stacey, A., N. C. Sheffield, and K.A. Crandall.	Calculating expected DNA remnants from ancient founding events in human population genetics.	BMC Genetics. 2008 9:66 doi:10.1186/1471-2156-9-66.
Buhay, J. E. and K. A. Crandall	Taxonomic revision of cave crayfish in the genus Orconectes, subgenus Orconectes (Decapoda: Cambaridae) along the Cumberland Plateau, including a description of a new species - Orconectes barri	Journal of Crustacean Biology 28: 57-67
Egan AN, Crandall KA	Incorporating gaps as phylogenetic characters across eight DNA regions: Ramifications for North American Psoraleeae (Leguminosae)	Molecular Phylogenetics and Evolution, In Press
Pérez-Losada M, Harp M, Høeg JT, Achituv Y, Jones D, Watanabe H, Crandall KA	The tempo and mode of barnacle evolution	Mol Phylogenet Evol. 2008 Jan;46(1):328-46
Crandall, K. A. and J. E. Buhay	Global diversity of crayfish (Astacidae, Cambaridae, and Parastacidae – Decapoda) in freshwater	Hydrobiologia 595: 295-301

 

 

2007 Publications

Authors	Title	Reference	Data
Schultz, M. B., S. A. Smith, A. M. M. Richardson, P. Horwitz, K. A. Crandall, and C. M. Austin	Cryptic diversity in Engaeus Erichson 1846, Geocharax Clark 1936 and Gramastacus Riek 1972 (Decapoda: Parastacidae), revealed by mitochondrial 16S rDNA sequences.	Invertebrate Systematics 21:569-587.
Daniels SR, Hofmeyr MD, Henen BT, Crandall KA	Living with the genetic signature of Miocene induced change: Evidence from the phylogeographic structure of the endemic angulate tortoise Chersina angulata	Mol Phylogenet Evol. 2007 Dec;45(3):915-26
Leavitt DH, Bezy RL, Crandall KA, Sites JW Jr.	Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae).	Mol Ecol. 2007 Nov;16(21):4455-81
Bernardo J, Ossola RJ, Spotila J, Crandall KA	Interspecies physiological variation as a tool for cross-species assessments of global warming-induced endangerment: validation of an intrinsic determinant of macroecological and phylogeographic structure.	Biology Letters 3(6):695-698
Jobes DV, Daoust M, Nguyen VT, Padua A, Sinangil F, Pérez-Losada M, Crandall KA, Oliphant T, Posada D, Rambaut A, Fuchs J, Berman PW	Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial.	AIDS Res Hum Retroviruses. 2006 Oct;22(10):968-78. Erratum in: AIDS Res Hum Retroviruses. 2007 Jan;23(1):181
Jones, J. P. G., Andriahajaina, F. B., Hockley, N. J., Crandall, K. A. & Ravoahangimalala., O. R.	The ecology and conservation status of Madagascar's endemic freshwater crayfish (Parastacidae; Astacoides)	Freshwater Biology 52: 1820-1833
Rudolph, E. H., and K. A. Crandall	A new species of burrowing crayfish Virilastacus retamali (Decapoda: Parastacidae) from the southern Chile peatland.	Journal of Crustacean Biology 27(3):502-512.
Pérez-Losada, M., K. A. Crandall, J. Zenilman, R. P. Viscidi	Temporal trends in gonococcal population genetics in a high prevalence urban community.	Infection, Genetics, and Evolution 7(2):271-278.
Carvajal-Rodríguez, A., K. A. Crandall, and D. Posada	Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy.	Infection, Genetics, and Evolution 7(4):476-483
Pérez-Losada, M., K. A. Crandall, M. C. Bash, M. Dan, J. Zenilman, and R. P. Viscidi	Distinguishing importation from diversification of quinolone-resistant Neisseria gonorrhoeae by molecular evolutionary analysis.	BMC Evolutionary Biology 7:84
Pérez-Losada, M., M. Nolte, K. A. Crandall, and P. W. Shaw.	Testing hypotheses of population structuring in the NE Atlantic Ocean and Mediterranean Sea using the common cuttlefish Sepia officinalis.	Molecular Ecology 16(13):2667-2679.
Megan L. Porter, Thomas W. Cronin, David A. McClellan, and Keith A. Crandall	Molecular Characterization of Crustacean Visual Pigments and the Evolution of Pancrustacean Opsins	Mol. Biol. Evol. 24(1):253–268. 2007
Jennifer E. Buhay, Gerald Moni, Nathaniel Mann, Keith A. Crandall	Molecular taxonomy in the dark: Evolutionary history, phylogeography, and diversity of cave crayfish in the subgenus Aviticambarus, genus Cambarus	Molecular Phylogenetics and Evolution 42 (2007 435–448
Buhay, J.E., K.A. Crandall, and D. Posada	Nested Clade Analysis for Conservation Genetics. In press in Population Genetics for Animal Conservation.	Cambridge University Press, Cambridge, UK.
Marcos Pérez-Losada, Megan L. Porter, Loubna Tazi and Keith A. Crandall	New methods for inferring population dynamics from microbial sequences	Infection, Genetics and Evolution, Volume 7, Issue 1, January 2007, Pages 24-43

 

2006 Publications

Authors	Title	Reference	Data
David Posada, Keith A. Crandall and Alan R. Templeton	Nested clade analysis statistics	Molecular Ecology Notes (2006) 6, 590–593
Savel R. Daniels, Gavin Gouws and Keith A. Crandall	Phylogeographic patterning in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes) reveals the signature of historical climatic oscillations	Journal of Biogeography 33 (2006), pp. 1538–1549
Daniels, S. R., N. Cumberlidge, M. Pérez-Losada, S. A. E. Marijnissen, and K. A. Crandall	Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence	Molecular Phylogenetics and Evolution 40 (2006) pp. 227–235
Daniels, S. R., N. J. L. Heideman, M. G. J. Hendricks, and K. A. Crandall	Taxonomic subdivisions within the fossorial skink subfamily Acontinae Squamata: Scincidae) reconsidered: a multilocus perspective	Zoologica Scripta 35, (2006) pp. 353–362
Keith A. Crandall	Applications of Phylogenetics to issues in Freshwater Crayfish Biology	Bull. Fr. Pêche Piscic. (2006) 380-381 : 953-964
Cowlishaw, G., Crandall, K., Gittleman, J. L. & Milner-Gulland, E. J.	The Florida panther: an editorial perspective	Animal Conservation (2006) 9 (2), 113-113
Pérez-Losada, M., E. B. Browne, A. Madsen, T. Wirth, R. P. Viscidi, and K. A. Crandall	Population genetics of microbial pathogens estimated from Multilocs Sequence Typing (MLST) data	Infection, Genetics and Evolution 6(2006) pp. 97-112
Coulthart M. B., Posada D., Crandall K. A., Dekaban G. A	On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy.	Infection, Genetics and Evolution 6 (2006) 91-96
Mecham, J., M. Clement, T. Freestone, Q. Snell, K. Seppi, and K. A. Crandall	Jumpstarting phylogenetic analysis	International Journal of Bioinformatics Research and Applications :2(1) pp. 19-35 (2006)
Finlay, J.B., J.E. Buhay, and K. A. Crandall	Surface to subsurface freshwater connections: phylogeographic and habitat analyses of Cambarus tenebrosus, a facultative cave-dwelling crayfish	Animal Conservation 9 (2006) 375–387
Egan, A. N. and K. A. Crandall	Theory of Phylogenetic Estimation in Evolutionary Genetics: Concepts and Case Studies.	Oxford University Press, Oxford, England, pp. 426-446.
Sinclair, E. A., R. Scholl, R. L. Bezy, K. A. Crandall, and J. W. Sites Jr.	Isolation and characterization of di- and tetranucleotide microsatellite loci in the yellow-spotted night lizard Lepidophyma flavimaculatum (Squamata: Xantusiidae)	Molecular Ecology Notes (2006) 6, 233–236
Antonio Carvajal-Rodriguez, Keith A. Crandall, and David Posada	Recombination Estimation Under Complex Evolutionary Models with the Coalescent Composite-Likelihood Method	Mol. Biol. Evol. 23(4):817–827. 2006
Pérez-Losada, M., R. G. Christensen, D. A. McClellan, B. J. Adams, R. P. Viscidi, J. C. Demma, and K. A. Crandall	Comparing Phylogenetic Codivergence between Polyomaviruses and Their Hosts	Journal of Virology, June 2006, p. 5663–5669

 

2005 Publications

Authors	Title	Reference	Data
Jennifer E. Buhay and Keith A. Crandall	Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes	Molecular Ecology 14(2005): 4259-4273
Savel R. Daniels, Neil J.L. Heideman, Martin G.J. Hendricks, Mphalile E. Mokone,Keith A. Crandall	Unraveling evolutionary lineages in the limbless fossorial skink genus Acontias (Sauria: Scincidae): are subspecies equivalent systematic units?	Molecular Phylogenetics and Evolution 34(2005) 645-654
Porter, M. L., M. Perez-Losada, and K. A. Crandall	Model based multi-locus estimation of Decapod phylogeny and divergence times	Molecular Phylogenetics and Evolution 37 (2005): 355–369	Data
Schull, H. C., M. Pérez-Losada, D. Blair, K. Sewell, E. A. Sinclair, S. Lawler, M. Ponniah, and K. A. Crandall	Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA.	Molecular Phylogenetics and Evolution 37 (2005): 249–263
Rader, R. B., M. C. Belk, D. K. Shiozawa, and K. A. Crandall	Empirical tests for ecological exchangeability.	Animal Conservation (2005) 8: 239-247
Martin, D. P., C. Williamson, and D. Posada	RDP2: Recombination detection and analysis from sequence alignments.	Bioinformatics (2005) 21:260-262
Martin, D. P., D. Posada, K. Crandall, and C. Williamson	A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.	AIDS Research and Human Retroviruses (2005) 21:98-102
Carvajal-Rodríguez A, Crandall KA, Posada	Caracterización y modelado computacional de la recombinación en secuencias de ADN en el virus del SIDA (VIH-1)	Biojournal 2( May 2005) (http://www.biojournal.net)
Pérez-Losada, M., R. P. Viscidi, J. C. Demma, J. Zenilman, and K. A. Crandall	Population genetics of Neisseria gonorrhoeae in a high prevalence community using a hyper-variable outer membrane porB and thirteen slow-evolving housekeeping genes.	Molecular Biology and Evolution : 22(9):1887–1902. 2005
Sinclair, E. A., M. Pérez-Losada, and K. A. Crandall	Molecular phylogenetics for conservation biology.	In Phylogeny and Conservation(ed. J. L. Gittleman & A. Purvis), Pp. 19-56. Cambridge: Cambridge University Press.
Lewis-Rogers, N., K. A. Crandall, and D. Posada	Evolutionary analyses of genetic recombination	Pp. 49-78 in V. Parisi, V. De Fonzo, and F. Aluffi-Pentini, eds. Dynamical Genetics. Research Signpost, Kerala, India
Crandall, K. A., M. Pérez-Losada, R. G. Christensen, D. A. McClellan, and R. P. Viscidi	Phylogenomics and Molecular Evolution of Polyomaviruses.	In Polyomavirus and Human Diseases (Ed. Nasimul Ahsan), Pp. 1-13. Landes Biosciences, Georgetown, TX.

 

2004 Publications

Authors	Title	Reference	Data
Keith A. Crandall, Jennifer E. Buhay	Genomic Databases and the Tree of Life	Science 306: 1144-1145
Nicole Lewis-Rogers, Keith A. Crandall, David Posada	Evolutionary analyses of genetic recombination	Dynamical Genetics 2004:49-78
Rambaut, A., D. Posada, Crandall K. A.	The causes and consequences of HIV evolution	Nature Review Genetics 5:52-61
Sinclair, E. A., R. L. Bezy, K. Bolles, J. L. R. Camarillo, K. A. Crandall and J. W. Sites, Jr.	Testing species boundaries in an ancient species complex with deep phylogeographic history: genus Xantusia (Squamata: Xantusiidae)	American Naturalist 164(3):396-414
Tarjuelo, I., D. Posada, K. Crandall, M. Pascual, and X. Turon	Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigaster.	Molecular Ecology 13:3125-3136
Pérez-Losada M., G. Bond-Buckup, C. G. Jara, and K. A. Crandall	Molecular systematics and biogeography of the Southern South American Freshwater "crabs" Aegla (Decapoda: Anomura: Aeglidae) using multiple heuristic tree search approaches.	Systematic Biology 53(5):1-14
Sinclair, E. A., J. W. Fetzner, Jr., J. Buhay, and K. A. Crandall	Proposal to complete a phylogenetic taxonomy and systematic revision for freshwater crayfish (Astacida).	Freshwater Crayfish 14:21-29
Agapow, P. M., O.R.P. Bininda-Emonds, K. A. Crandall, J. L. Gittleman, G. M. Mace, J. C. Marshall, and A. Purvis	The impact of species concept on biodiversity studies.	Quarterly Review of Biology 79(2):161-179
Pérez-Losada M., Høeg J. T., Crandall K.A.	Unraveling the evolutionary radiation of the Thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches.	Systematic Biology 53(2):244-264
Devon E. Pearse and Keith A. Crandall	Beyond FST: Analysis of population genetic data for conservation	Conservation Genetics 5:585-602
Abdo Z, Crandall, K.A., Joyce P.	Evaluating the performance of likelihood methods for detecting population structure and migration	Molecular Ecology 13:837-851

 

2003 Publications

Authors	Title	Reference	Data
Jara, C. G., M. Pérez-Losada, Crandall K. A.	Aegla occidentalis (Crustacea: Decapoda: Aeglidae), a new species of freshwater crab from the Nahuelbuta Costal Range, Chile	Proceedings of the Biological Society of Washington 116(4):933-942
Sinclair, E.A., H.L. Black, Crandall K.A.	Population structure and paternity in an American Black Bear (Ursus americanus) population using microsatellite DNA	Western North American Naturalist 63(4)489-497
Porter, M.L., Crandall K.A.	Lost along the way: The significance of evolution in reverse.	Trends in Ecology and Evolution 18(10):541-547
Fetzner, J.W. Jr., Crandall K.A.	Linear habitats and the nested clade analysis: An empirical evaluatoin of geographic vs. river distances using an Ozark crayfish (Decapoda: Cambaridae).	Evolution 57(9):2101-2118
Pérez-Losada, M., Crandall K.A.	Can taxonomic richness be used as a surrogate for phylogenetic distinctness indices for ranking areas for conservation?	Animal Biodiversity and Conservation 26:77-84
Woolley, S., J. Johnson, M.J. Smith, K.A. Crandall, D.A. McClellan	TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees.	Bioinformatics 19:671-672

 

2002 Publications

Authors	Title	Reference	Data
Posada, D., , K.A. Crandall, E.C. Holmes	Recombination in Evolutionary genomics.	Annual Review of Genetics 36:75-97
Crandall, K. A.	Crayfish as model organisms.	Freshwater Crayfish 13:3-10
Perez-Losada, M., C.G. Jara, G. Bond-Buckup, M.L. Porter and K.A.Crandall	Anomuran Phylogenetic relationships: on the taxonomic positiosing of Aeglidae freshwater crabs	Journal of Crustacean Biology 22(3):670-676
Perez-Losada, M., J.T. Høeg, G.A. Kaolbasov, K.A. Crandall	Reanalysis of the relationships among the Cirripedia and the Ascothoracida and the phylogenetic position of the Facetotecta (Maxillopoda: Thecostraca) using 18srDNA sequences.	Journal of Crustacean Biology 22(3):661-669
Perez-Losada, M., C.G. Jara, G. Bond-Buckup, and K.A.Crandall	Phylogenetic relationships among the species of Aegla (Anomura: Aeglidae) freshwater crabs from Chile.	Journal of Crustacean Biology 22(2):304-313
Sinclair, E.A., Costello, B., Courtenay, J.M. and K.A. Crandall	Detecting a genetic bottleneck in Gilbert's Potoroo (Potorous gilbertii) (Marsupialia: Potoroidae), inferred from microsatellite and mitochondrial DNA sequnce data.	Conservation Genetics 3:191-196
Perez-Losada, M., C.G. Jara, G. Bond-Buckup and K.A. Crandall	Conservation phylogenetics of Chilean freshwater crabs Aegla (Anomura, Aeglidae): Assigining priorities for aquatic habitat protections	Biological Conservation 105:345-353
Posada, D., and Crandall, K.A.	The effect of recombination on the accuracy of phylogeny estimation.	Journal of Molecular Evolution 54:396-402
Crandall, K.A., Posada, D.	Phylogenetic Approaches to Molecular Epidemiology	The Molecular Epidemiolgy of Human Viruses Kluwer Academic Publishers
Crandall, K.A	Convergent and parallel evolution	Pp. 201-205 in Pagel (ed) Encyclopedia of Evolution.  Oxford University Press

 

2001 Publications

Author	Title	Reference	Data
Posada, D. and Crandall, K.A.	Evaluation of methods for detecting recombination from DNA sequences using computer simulations	PNAS 98(24):13757-13762.
Tarjuelo, I., Posada, D., Crandall, K.A., Pascual, M., and Turon, X.	Cryptic species of Clavelina (Ascidiacea) in two different habitats: harbours and rocky littoral zones in the northwestern Mediterranean.	Marine Biology 139:455-462
Posada, D., and Crandall, K.A.	A comparison of different strategies for selecting models of DNA subsitution.	Systematic Biology 50(4):580-601
Sinclair, E. A., Swenson, E., Bates, W., Choate, D., Wolf, M., and Crandall, K. A.	Gene flow estimates in Utah's cougars imply management beyond Utah.	Animal Conservation 4: 257-264.
Harris, D.M., J.C. Marshall, and K.A. Crandall	Squamate relationships based on C-Mos nuclear DNA sequences: increased taxon sampling improves bootstrap support.	Amphibia-Reptilia 22:235-242
Posada, D. and K.A. Crandall.	Selecting models of nucleotide substitution: An application to Human Immunodeficiency Virus 1 (HIV-1).	Molecular Biology and Evolution 18(6):897-906.
Posada, D. and K.A. Crandall.	Simple (wrong) models for complex trees: A case from the Retroviridae.	Molecular Biology and Evolution 18(2):271-275.
Imamichi, H., K. A. Crandall, V. Natarajan, M.K. Jiang, R. L. Dewar, S. Berg, A. Gaddam, M. Bosche, J. A. Metcalf, R. T. Davey, Jr., and H.C. Lane	Human Immunodeficiency Virus Type 1 quasi species that rebound after discontinuation of highly active antiretroviral therapy are similar to the viral quasi species present before Initiation of therapy.	The Journal of Infectious Diseases 183:36–50.
Posada, D. and K.A. Crandall.	Intraspecific gene genealogies: trees grafting into networks.	Trends in Ecology and Evolution 16(1):37-45.
Crandall, K.A.	Human Immunodeficiency Viruses (HIV).	Encyclopedia of Life Sciences NPG
Fetzner, J.W. Jr., Crandall, K.A.	Genetic Variation. In : Biology of freshwater crayfish, (ed. D.M. Holdich)	pp. 291-326. Blackwell Science, Oxford.
Posada, D. and K.A. Crandall.	Selecting models of nucleotide substitution: An application to Human Immunodeficiency Virus 1 (HIV-1).	Molecular Biology and Evolution 18(6):897-906
Posada, D. and K.A. Crandall and D.M. Hillis	Phylogenetics of HIV. In: Computational and Evolutionary Analysis of HIV Molecular Sequences	pp. 121-160. Kluwer Academic Publishers.
Vasco, D.A., K.A. Crandall and Y.X. Fu.	Molecular population genetics: coalescent methods based on summary statistics. In: Computational and Evolutionary Analysis of HIV Molecular Sequences	pp. 173-216. Kluwer Academic Publishers.
Sinclair, E. A.	Phylogeographic variation in the quokka, Setonix brachyurus (Marsupialia: Macropodiadae).	Animal Conservation 4:325-333
Engel, A.S., Porter, M.L., Kinkle, B.K., and Kane, T.C.	Ecological Assessment and Geological Significance of Microbial Communities from Cesspool Cave, Virginia	Geomicrobiology Journal 18:259-274
Crandall, K.A.	Phylogeny. In: Encyclopedia of Genetics (Brenner, S. & Miller J.H., eds)	pp.1465-1466. Academic Press, London
Sinclair, E.A.	Microgeographic variation in two relict island populations of the quokka, Setonix brachyurus (Macropodidae: Marsupialia), assessed by allozyme electrophoresis	JRSWA 84:111-116

 

2000 Publications

Authors	Title	Reference	Data
Matala, E., K.A. Crandall, R.C. Baker and N. Ahmad	Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission.	AIDS Research and Human Retroviruses 16:1481-1490.
Clement, M., D. Posada and K. A. Crandall.	TCS: a computer program to estimate gene genealogies.	Molecular Ecology 9:1657-1659.
Smith, K., K.A. Crandall, M.L. Kneissl and B.A. Navia	PCR detection of host and HIV-1 sequences from archival brain tissue.	Journal of Neurovirology 6:(2):164-171
Grandjean, F., Harris, D. J., Souty-Grosset, C. & Crandall, K. A.	Systematics of the European endangered crayfish species, Austropotamobius pallipes (Decapoda: Astacidae).	Journal of Crustacean Biology 20(3), 522-529.
Crandall, K. A., Harris, D. J. and Fetzner, J. W	The monophyletic origin of freshwater crayfishes estimated from nuclear and mitochondrial DNA sequences.	Proceedings of the Royal Society of London, Series B 267:1679-1686.	Data
Crandall, K. A., Fetzner, J. W., Jr., Jara, C. G. and Buckup, L	On the phylogenetic positioning of the South American freshwater crayfish genera (Decapoda: Parastacidae).	Journal of Crustacean Biology 20: 530-540.
Whiting, A.S., S.H. Lawler, P. Horwitz, & K.A. Crandall.	Biogeographic regionalization of Australia: assessing conservation priorities based on endemic freshwater crayfish phylogenetics.	Animal Conservation 3: 155-163.
Peters, A. A., M. B. Coulthart, J. J. F. Oger, D. J. Waters, K. A. Crandall, R. H. Ward and G. A. Dekaban.	HTLV-I and HTLV-II in British Columbia Amerindians: seroprevalence in the Nuu-Chah-Nulth and molecular characterisation of a Coast Salish HTLV-IIa isolate.	AIDS Research and Human Retroviruses 16(9):883-892.
Posada, D., K.A. Crandall, and A.R. Templeton.	GeoDis: A program for the cladistic nested analysis of the geographical distribution of genetic haplotypes.	Molecular Ecology 9: 487-488
Posada, D.K., K.A. Crandall, M. Nguyen, J.C. Demma, and R.P. Viscidi	Population genetics of the porB gene of Neisseria gonorrheae.	Molecular Biology and Evolution 17(3):423-436	Data
Crandall, K.A., O.R.P. Bininda-Emonds, G.M. Mace and R.K. Wayne.	Considering evolutionary processes in conservation biology.	Trends in Ecology and Evolution 15(7):290-295.	Data
Harris, D.J. and K.A. Crandall	Intra-genomic variation within ITS1 and ITS2 of crayfish (Decapoda: Cambaridae): implication for phylogenetic and microsatellite studies	Molecular Biology and Evolution 17(2)284-291
Harris, D. J., Maxson, L., Braithwaite, L. F. & Crandall, K. A.	Phylogeny of the Thoracican barnacles based on 18S rDNA sequences.	Journal of Crustacean Biology 20(2): 393-398.

 

1999 Publications 

Authors	Title	Reference	Data
Vilá, C., I.R. Amorim, J.A. Leonard, D. Posada, J. Castroviejo, F. Petrucci-Fonseca, K.A. Crandall, H. Ellegren, and R.K. Wayne.	Mitochondrial DNA phylogeography and population history of the Grey Wolf Canis lupus.	Molecular Ecology 8:2089-2103.
Fetzner, J.W., Jr. and K.A. Crandall.	Genetic Variability within and among Populations of the Golden Crayfish (Orconectes luteus): A comparison using amplified fragment length polymorphisms (AFLP) and mitocondrial 16s gene sequences.	Freshwater Crayfish 12: 396-412.
Harris, D. J., E. A. Sinclair, N. L. Mercader, J. C. Marshall and K. A. Crandall	Squamate relationships based on C-mos nuclear DNA sequences.	Herpetological Journal 9:147-151.
Crandall, K. A., Posada, D. & Vasco, D.	Effective population sizes: missing measures and missing concepts.	Animal Conservation 2:317-319.
Kelsey, C.R., K.A. Crandall, and A.F. Voevodin.	Different models, different trees: The geographic origin of PTLV-1.	Molecular Phylogenetics and Evolution. 13: 336-347.
Crandall, K.A., D.Vasco, D. Posada, and H. Imamichi.	Advances in understanding the evolution of HIV.	AIDS 13(Suppl A):S39-S47.
Shapshak, P., D.M. Segal, K.A. Crandall, B.T. Zhang, R.K. Fujimura, K. Goodkin, K.Q. Xin, K. Okuda, C.K. Petito, and C. E. Eisdorfer.	Independent Evolution of HIV Type 1 in Different Brain Regions AIDS	Research and Human Retroviruses. 15: 811-820.
Crandall, K.A., J.W. Fetzner Jr., S.H. Lawler, M. Kinnersley, and C. M. Austin.	Phylogenetic Relationships Among the Australian and New Zealand Genera of Freshwater Crayfish.	Australian Journal of Zoology. 47: 199-214.	Data
Crandall, K.A. and A.R. Templeton	The zoogeography and centers of origin of the crayfish subgenus Procericambarus (Decapoda: Cambaridae).	Evolution 53(1): 123-134.
Crandall, K.A. (Editor)	The Evolution of HIV.	Johns Hopkins Universtiy Press, Baltimore, MD
Crandall, K.A.	Uses of statistical parsimony in HIV analyses. Pp. In: Statistics in Molecular Biology, F. Seillier-Moiseiwitsch, ed. Institute of Mathematical Statistics and the American Mathematical Society, Hayward, CA.
Sinclair, E. A.	Morphological variation among populations of the quokka, Setonix brachyurus (Macropodidae: Marsupialia) in Western Australia.	Australian Journal of Zoology. 46: 439-449.

 

1998 Publications

Authors	Title	Reference	Data
Castilla, A. M., Fernandez-Pedrosa, V., Harris D. J., Gonzalez, A. Latorre, A. and Moya, A.	Mitochondrial DNA divergence suggest Podarcis hispanica atrata (Lacertidae) from the Columbretes Islands merits specific distinction.	Copeia 4:1037-1040.
Crandall, K.A.	Conservation phylogenetics of Ozark crayfishes: assigning priorities for aquatic habitat protection.	Biological Conservation 84:107-117.
Fujimura, R.K., P. Shapshak, D.M. Segal, K.A. Crandall, K. Goodkin, J.B. Page, R. Douyon, B.T. Zhang, K.Q. Xin, P. Rodriguez de la Vega, I. Nagano, and A. Sivastava.	Viral and host determinants of neurovirulence of HIV-1 infection.	Advances in Experimental Medicine and Biology, 437:241-253.
Goodkin, K., P. Shapshak, L.R. Metsch, C.B. McCoy, K.A. Crandall, M. Kumar, R.K. Fugimura, V. McCoy, B.T. Zhang, S. Reyblat, K.Q. Xin, A.M. Kumar.	Cocaine abuse and HIV-1 infection: Epidemiology and neuropathogenesis.	Journal of Neuroimmunology 83:88-101.
Lawler, S. H., and K. A. Crandall.	The relationship of the Australian freshwater crayfish genera Euastacus and Astacopsis.	Proceedings of the Linnean Society of New South Wales 119:1-8.
Posada, D., and K. A. Crandall.	Modeltest: Testing the model of DNA substitution.	Bioinformatics 14: 817-818.
Sinclair, E. A.	Morphological variation among populations of the quokka, Setonix brachyurus (Macropodidae: Marsupialia), in Western	Australia. Australian Journal of Zoology 46:439-449.

 

1997 Publications

Authors	Title	Reference	Data
Crandall, K. A.	The crayfish component to an endangered aquatic ecosystem of the Southeast United States.	Freshwater Crayfish 11:83-86.
Crandall, K. A.	Genetic variation within and among crayfish species.	Freshwater Crayfish 11:135-145
Crandall, K. A. and T. W. Cronin.	The molecular evolution of visual pigments of freshwater crayfishes (Decapoda: Cambaridae).	Journal of Molecular Evolution 45:524-534.
Crandall, K.A. and D.M. Hillis.	Rhodopsin evolution in the dark.	Nature 387:667-668.
Fetzner, J. W., Jr., R. J. Sheehan and L. W. Seeb.	Genetic implications of broodstock selection for crayfish aquaculture in the Midwestern United States.	Aquaculture 154:39-55
Annual Review of Ecology and Systematics 28:437-466.	Phylogeny estimation and hypothesis testing using maximum likelihood.	Annual Review of Ecology and Systematics 28:437-466.
Segal, D. M., P. Shapshak, B.-T. Zhang, K. A. Crandall, B. Page, R. Fujimura, K. Goodkin, R. Douyon, and C. B. McCoy.	Novel tetrameric tip motifs (APGK and VPGK) in the V3 loop of HIV type 12 envelope sequences in blood and brain from two injection drug users in Miami, Florida.	AIDS Research and Human Retroviruses 13:1643-1646.
Sinclair, E. A. and M. Westerman.	The molecular relationship of Gilbert's Potoroo (Marsupialia: Potoroidae).	Journal of Mammalian Evolution 4:147-161.
Sites, J. W. Jr., and K. A. Crandall.	Testing species boundaries in biodiversity studies.	Conservation Biology 11(6):1289-1297.
Vilá, C. J. Maldonado, I. R. Amorim, R. K. Wayne, K. A. Crandall, and R. L. Honeycutt.	Man and his dog.	Science 278:205-207.
Vila, C., P. Savolainen, J. E. Maldonado, I. R. Amorim, J. E. Rice, R. L. Honeycutt, K. A. Crandall, J. Lundeberg, and R. K. Wayne.	Multiple and ancient origins of the domestic dog.	Science 276:1687-1689.

 

1996 Publications

Authors	Title	Reference	Data
Crandall, K. A.	Identifying links between genotype and phenotype using marker loci and candidate genes.	The Impact of Plant Molecular Genetics Pp. 137-157. B. W. S. Sobral, ed. Birkhäuser, Boston.
Crandall, K. A.	Multiple Interspecies Transmissions of Human and Simian T-Cell Leukemia/Lymphoma Virus Type I Sequences.	Molecular Biology and Evolution 13(1):115-131.
Crandall, K. A. and T. W. Cronin.	Opsin evolution in crayfishes: Effects of functional constraints. Pp. 19-27. In: Current Issues in Molecular Evolution, M. Nei and N. Takahata, eds.	Institute of Molecular Evolutionary Genetics, The Pennsylvania State University.
Crandall, K. A. and J. F. Fitzpatrick, Jr.	Crayfish molecular systematics: Inferences using a combination of procedures to estimate phylogeny.	Systematic Biology 45(1):1-26.	Data
Crandall, K. A. and A. R. Templeton	Applications of intraspecific phylogenetics. Pp. 81-99. In: New Uses for New Phylogenies, P. H. Harvey, A. J. Leigh Brown, and J. Maynard Smith, eds.	Oxford University Press.
Fetzner, J. W., Jr.	Biochemical systematics and evolution of the crayfish genus Orconectes (Decapoda: Cambaridae).	Journal of Crustacean Biology 16(1): 111-141.
Shapshak, P., K. A. Crandall, K.-Q. Xin, K. Goodkin, R. Fujimura, W. Bradley, C. McCoy, I. Nagano, M. Yoshioka, C. Petito, N. Sun, A. Srivastava, N. Weatherby, R. Stewart, S. Delgado, A. Matthews, R. Douyon, K. Okuda, J. Yang, B. Zhang, X. Cao, S. Shatkovsky, J. Fernandez, S. Shah, and J. Perper.	HIV-1 neuropathogenesis and abused drugs: current views, problems, and solutions.	Advances in Experimental Medicine and Biology 402:171-186
Sinclair, E. A., Danks, A. and Wayne, A. F.	Rediscovery of Gilbert's Potoroo, Potorous tridactylus Western Australia.	Australian Mammalogy 19:69-72.
Sinclair, E. & K. Morris	Where have all the quokkas gone?	Landscope (Summer):49-53.
Sinclair, E. A., Webb, N. J., Marchant, A. D. and Tidemann, C. R	Determination of genetic variation in the Little Red Flying-fox, Pteropus scapulatus (Chiroptera: Pteropodidae): implications for management.	Biological Conservation 76:45-50.
Voevodin, A., K. A. Crandall, P. Seth, and S. A. Mufti.	HIV type 1 subtypes B and C from new regions of India and Indian and Ethiopian expatriates in Kuwait.	AIDS Research and Human Retroviruses 12(7):641-643

 

1995 Publications

Author	Title	Reference	Data
Chang, B. S. W., K. A. Crandall, J. P. Carulli, and D .L. Hartl.	Opsin phylogeny and evolution: Implications for wavelength regulation.	Molecular Phylogenetics and Evolution 4(1):31-43.
Crandall, K. A.	Intraspecific phylogenetics: Statistical support for dental HIV transmission.	Journal of Virology 69(4):2351-2356
Crandall, K. A.	Intraspecific cladogram estimation. Pp. 19-22. In: Proceedings of Phylogeny Workshop, Technical Report 95-48, S. Tavaré, ed.	DIMACS, New Jersey.
Crandall, K. A., S. H. Lawler, and C. Austin.	A preliminary examination of the molecular phylogenetic relationships of the crayfish genera of Australia (Decapoda: Parastacidae).	Freshwater Crayfish 10:18-30.
Shapshak, P., I. Nagano, K. Xin, W. Bradley, N. C. J. Sun, R. V. Stewart, M. Yoshioka, C. Petito, K. Goodbin, R. Douyon, A. K. Srivagtava, and K. A. Crandall.	HIV-1 Heterogeneity and Cytokines: Neuropathogenesis.	Advances in Experimental Medicine and Biology 373:225-238.
Start, T., A. Burbidge, E. Sinclair & A. Wayne	Lost and Found - Potoroos.	Landscope (Autumn): 28-33.
Thorpe, J.P., J. Smartt, A. L. Allcock, M. Chauvet, K. A. Crandall, D. R. Given, S.J.G. Hall, J.M. Iriondo, T.M. Lewinsohn, S.M. Lynch, G.M. Mace, A.M. Sole-Cava, E. Stackebrandt, A.R. Templeton, and P.C. Watts	"Genetic diversity as a component of biodiversity." Pp. 57-87. In: Global Biodiversity Assessment, V.H. Heywood and R. T. Watson, eds.	Cambridge University Press, Cambridge.
Xin, K-Q, X-H Ma, K. A. Crandall, H. Bukawa, Y. Ishigatsubo, S. Kawamoto, and K. Okuda.	Dual infection with HIV-1 Thai subtype B and E.	The Lancet 346:1372-1373.

 

1994 Publications

Author	Title	Reference	Data
Crandall K. A.	Intraspecific cladogram estimation: Accuracy at higher levels of divergence.	Systematic Biology 43(2): 222-235.
Crandall, K. A., A. R. Templeton, and C. F. Sing.	Intraspecific phylogenetics: Problems and solutions. Pp. 273-297 In: Models in Phylogeny Reconstruction (R.W. Scotland, D. J. Siebert, and D. M. Williams, eds.).	Systematics Association Special Volume, Clarendon Press, Oxford, England. (ASIN: 0198548249)
Krajewski, C. and J. W. Fetzner Jr.	Phylogeny of cranes (Gruiformes: Gruidae) based on cytochrome-b DNA sequences.	The Auk 111(2): 351-365
Krajewski, C. and J. W. Fetzner Jr.	Ancient DNA from the cuban sandhill crane.	The Ancient DNA Newsletter 1(2): 24-25

 

1993 Publications

Authors	Title	Reference	Data
Crandall, K. A. and A. R. Templeton.	Empirical tests of some predictions from coalescence theory.	Genetics 134:959-969.

 

1992 Publications

Authors	Title	Reference	Data
Templeton, A. R., K. A. Crandall, and C. F. Sing.	A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.	Genetics 132:619-633.