HEATHER D. BRACKEN, ALICIA TOON, DARRYL L. FELDER, JOEL W. MARTIN,MAEGAN FINLEY, JENNIFER RASMUSSEN, FERRAN PALERO & KEITH A. CRANDALL.  "The Decapod Tree of Life: Compiling the Data and Moving toward a Consensus of Decapod Evolution."  Arthropod Systematics & Phylogeny.  2009. 

JENS T. HØEG, MARCOS PÉREZ-LOSADA, HENRIK GLENNER,GREGORY A. KOLBASOV & KEITH A. CRANDALL.  "Evolution of Morphology, Ontogeny and Life Cycles within the Crustacea Thecostraca."  Arthropod Systematics & Phylogeny.  2009. 

Keith A. Crandall, E Henry W. Robison, and Jennifer E. Buhay.  "Avoidance of extinction through nonexistence: the use of museum specimens and molecular genetics to determine the taxonomic status of an endangered freshwater cray
sh."  Conservative Genetics.  2009. 

Nicole Lewis-Rogers, Matthew L. Bendall, and Keith A. Crandall.  "Phylogenetic Relationships and Molecular Adaptation Dynamics of Human Rhinoviruses."  Molecular Biological Evolution.  Jan. 2009. 

M. Perez-Losada, G Bond-Buckup, C. G. Jara, and K. A. Crandall.  "Conservation Assessment of Southern South American Freshwater Ecoregions on the Basis of the Distribution and Genetic Diversity of Crabs from the Genus Aegla."  Conservation Biology.  Sep. 2009. 

Marcos Pérez-Losada, Jens T. Høeg and Keith A. Crandall.  "Remarkable convergent evolution in specialized parasitic Thecostraca (Crustacea)."  BMC Biology.  Apr. 2009.  <website>

Marcos Perez-Losada, David Posada, Miguel Arenas, David V. Jobes, Faruk Sinangil, Phillip W. Berman, and Keith A. Crandall.  "Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial."  Retrovirology.  July 2009.  <website>

Ferran Palero, Keith A. Crandall, Pere Abello, Enrique Macpherson, Marta Pascual.  "Phylogenetic relationships between spiny, slipper and coral lobsters (Crustacea, Decapoda, Achelata)."  Molecular Phylogenetics and Evolution.  Oct. 2009.  <website>

Mark B. Shultz, Sarah A. Smith, Pierre Horwitz, Alastair M.M. Richardson, Keith A. Crandall, Christopher M. Austin.  "Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater cray
sh (Decapoda: Parastacidae) with particular focus on Engaeus Erichson."  Molecular Phylogenetics and Evolution.  Nov. 2009.  <website>

Jiawu Xu, Marcos Perez-Losada, Carlos G. Jara, and Keith A. Crandall.  "Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia."  Molecular Ecology.  Nov. 2009. 

Buhay, J. E., and K. A. Crandall.  "Taxonomic revision of cave crayfishes 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.  28.1 (2008): 57-67. 

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 (2008): 267-273. 

Crandall, K. A. and J. E. Buhay.  "Global diversity of crayfish (Astacidae, Cambaridae, and Parastacidae - Decapoda) in freshwater."  Hydrobiologia.  595 (2008): 295-301. 

Pérez-Losada, M., M. Harp, J. T. Høeg, Y. Achituve, D. Jones, H. Watanabe, and K. A. Crandall.  "The tempo and mode of barnacle evolution."  Molecular Phylogenetics and Evolution.  46.1 (2008): 328-346. 

Antonio Carvajal-Rodríguez,*§ Keith A. Crandall, § and David Posada.  "Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy."  Infection, Genetics, and Evolution.  7.4 (2008): 271-278. 

Pérez-Losada M, Crandall KA, Zenilman J, and Viscidi RP.  "Temporal Trends in Gonococcal Population Genetics in a High Prevalence Urban Community."  Infection, Genetics, and Evolution.  7.4 (2008): 476-483. 

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 (2008): 2667-2679. 

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 (2008): 502-512. 

Egan, A. N., and K. A. Crandall.  "Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae)."  Molecular Phylogenetics and Evolution.  46.2 (2008): 532-546. 

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.  8 (2008): 110-120. 

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.  82.11 (2008): 5548-5561. 

Woolley, S. M., D. Posada, and K. A. Crandall.  "A comparison of phylogenetic network methods using computer simulation."  PLoS One.  3.4 (2008): 1-12. 

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.  9 (2008): 907-916. 

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 Academy of Sciences, USA.  105.36 (2008): 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.  10.1007/s10592-008-9546-9 (2008). 

Lewis-Rogers, N., D. A. McClellan, and K. A. Crandall.  "The evolution of foot-and-mouth disease virus: Impacts of recombination and selection."  Infection, Genetics and Evolution.  8 (2008): 786-798. 

Stacey, A., N. C. Sheffield, and K.A. Crandall.  "Calculating expected DNA remnants from ancient founding events in human population genetics."  BMC Genetics.  9.66 (2008): doi:10.1186/1471-2156-9-66. 

Schram, F. R., S. T. Ahyong, K. A. Crandall, F. Gherardi, M. J. Grygier, K. L. Lavalli, G. Poore, D. C. Rogers, G. Scholtz, T. Simon, S. Tamone, M. Wicksten.  "Publication in the Journal of Crustacean Biology."  Journal of Crustacean Biology.  28.2 (2008): 197-202. 

Schultz, M.B., D.A. Ierodiaconou, S. A. Smith, P. Horwitz, A.M.M. Richardson, K.A. Crandall, C.M. Austin.  "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.  17 (2008): 5291-5314. 

Egan, A.N. and K.A. Crandall.  "Divergence and diversification in North American Psoraleeae (Fabaceaae) due to climate change."  BMC Biology.  6.55 (2008). 

Buhay, J. E., G. Moni, N. Mann, and K. 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.  42.2 (2007): 435-448. 

Porter, M. L., T. W. Cronin, D. A. McClellan, K. A. Crandall.  "Molecular characterization of crustacean visual pigments and the evolution of Pancrustacean opsins."  Molecular Biology and Evolution.  24.1 (2007): 253-268. 

Pérez-Losada, M., M. L. Porter, L. Tazi, and K. A. Crandall.  "New methods for inferring population dynamics from microbial sequences."  Infection, Genetics, and Evolution.  7 (2007): 24-43. 

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.  7.2 (2007): 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 (2007): 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 (2007): 476-483. 

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 (2007): 2667-2679. 

Jones, J. P. G., F. B. Andriahajaina, N. J. Hockley, K. A. Crandall, O. R. Ravoahangimalala.  "The ecology and conservation status of Madagascars endemic freshwater crayfish (Parastacidae: Astacoides)."  Freshwater Biology.  52.9 (2007): 1820-1833. 

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 (2007): 1-10. 

Bernardo, J., R. J. Ossola, J. Spotila, and K. A. Crandall.  "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 (2007): 695-698. 

Leavitt, D. H., R. L. Bezy, K. A. Crandall, and J. W. Sites, 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)."  Molecular Ecology.  16 (2007): 4455-4481. 

Daniels, S. R., M. D. Hofmeyr, B. T. Henen, K. A. Crandall.  "Living with the genetic signature of Miocene induced change: Evidence from the phylogeographic structure of the endemic angulate tortoise Chersina angulata."  Molecular Phylogenetics and Evolution.  45.3 (2007): 915-926. 

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."  Molecular Phylogenetics and Evolution.  21 (2007): 569-587. 

Jesse Mecham, Mark Clement, Quinn Snell, Todd Freestone, Kevin Seppi, and Keith Crandall.  "Jumpstarting phylogenetic analysis."  International Journal of Bioinformatics Research and Applications.  2.1 (2006): 19-35. 

Elizabeth A. Sinclair, Rebecca Scholl, Robert L. Bezy, Keith A. Crandall, and Jack 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.  6 (2006): 233-236. 

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): 97-112. 

Coulthart, M. B., D. Posada, K. A. CRANDALL, and G. A. Dekaban.  "On the phylogenetic placement of the human T cell leukemia virus type 1 sequences associated with an Andean mummy."  Infection, Genetics and Evolution.  6 (2006): 91-96. 

Antonio Carvajal-Rodriguez, Keith A. Crandall, David Posada.  "Recombination Estimation Under Complex Evolutionary Models with the."  Molecular Biology and Evolution.  23.4 (2006): 817-827.  <website>

Finlay, J., J.E. Buhay, K.A. Crandall.  "Surface and subsurface connectivity: phylogeographic and habitat analyses of stygophilic freshwater crayfish species."  Animal Conservation.  9 (2006): 375-387. 

D. Posada, K. A. CRANDALL, A. R. Templeton.  "Nested clade analysis statistics."  Molecular Ecology Notes.  6 (2006): 590-593. 

Ryan L. Parr, Gabriel D. Dakubo, KEITH A. CRANDALL, Jennifer Maki, Brian Reguly, Andrea Aguirre, Roy Wittock, Kerry Robinson, Jude S. Alexander, Mark A. Birch-Machin, Mamdouh Abdel-Malak, M. Kent Froberg, Eleftherios P. Diamandis, and Robert E. Thayer.  "Somatic Mitochondrial DNA Mutations in Prostate Cancer and Normal Appearing Adjacent Glands in Comparison to Age-Matched Prostate Samples without Malignant Histology."  Journal of Molecular Diagnostics.  8.3 (2006): 312-319. 

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.  33.9 (2006): 1538-1549. 

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.  80.12 (2006): 5663-5669. 

Daniels, S. R., N. J. Heideman, M. G. Hendricks, and K. A. Crandall.  "Taxonomic subdivisions within the fossorial skink subfamily Acontinae (Squamata: Scincidae) reconsidered: a multilocus perspective."  Zoologica Scripta.  35 (2006): 353-362. 

Daniels, S. R., N. Cumberlidge, M. Pérez-Losada, S. A. E. Marijnissen, K. A. Crandall.  "Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence."  Molecular Phylogenetics and Evolution.  40 (2006): 227-235. 

Crandall, K. A.  "Applications of phylogenetics to issues in freshwater crayfish biology."  Bulletin Francais De La Peche Et De La Protection Des Milieux Aquatiques.  380-381 (2006): 953-964. 

Jobes, D.V., M. Daoust, V. T. Nguyen, A. Padua, F. Sinangil, M. Pérez-Losada, K. A. Crandall, T. Oliphant, D. Posada, A. Rambaut, J. Fuchs, and P. W. Berman.  "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 trail."  AIDS Research and Human Retroviruses.  22.10 (2006): 1014-1021. 

Daniels, S. R., N. Heideman, M. Hendricks, M. E. Mokone, and K. 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. 

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.  21.21 (2005): 98-102. 

Rader, R. B., M. C. Belk, D. K. Shiozawa, and K. A. CRANDALL.  "Empirical tests for ecological exchangeability."  Animal Conservation.  8.8 (2005): 239-247. 

Bahir, M. M., P. K. L. Ng, K. CRANDALL, R. Pethiyagoda.  "A conservation assessment of the freshwater crabs of Sri Lanka."  The Raffles Bulletin of Zoology.  Supplement No. 12 (2005): 121-126. 

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 (2005): 1887-1902. 

Rudolph, E.H. and K. A. CRANDALL.  "A new species of burrowing crayfish Virilastacus rucapihuelensis (Crustacea, Decapoda, Parastacidae) from southern Chile."  Proceedings of the Biological Society of Washington.  118.4 (2005): 765-776. 

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.  <website>

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): 355-367. 

CRANDALL, K. A., M. Pérez-Losada, R. G. Christensen, D. A. McClellan, and R. P. Viscidi.  "Phylogenomics and Molecular Evolution of Polyomaviruses."  Polyomaviruses and Human Diseases.  July 2005: 1-13.  <website>

Sinclair, E. A., M. Pérez-Losada, and K. A. CRANDALL.  "Molecular phylogenetics for conservation biology."  Phylogeny and Conservation.  Oct. 2005: 19-56. 

Buhay, J.E., and K. A. CRANDALL.  "Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes."  Molecular Ecology.  14 (2005): 4259-4273.  <website>

Sinclair E.A., Scholl R., Bezy R.L., CRANDALL K.A., Sites J.W., Jr.  "Isolation and characterization of di- and tetranucleotide microsatellite loci in the Yellow-spotted Night Lizard Lepidophyma flavimaculatum (Squamata: Xantusiidae)."  Molecular Ecology Notes.  2005. 

Rambaut, A., D. Posada, K. A. Crandall, and E. C. Holmes.  "The causes and consequences of HIV evolution."  Nature Review Genetics.  2004: 52-61. 

Abdo Z, Crandall, K. A., Joyce P.  "Evaluating the performance of likelihood methods for detecting population structure and migration."  Molecular Ecology.  2004: 837-851.  <website>

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 (2004): 244-264. 

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 (2004): 161-179. 

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 (2004): 1-9. 

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 (2004): 767-780. 

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 (2004): 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 (2004): 3125-3136. 

Crandall, K. A. and J. Buhay.  "Genomic databases and the Tree of Life."  Science.  306 (2004): 1144-1145.  <website>

Pearse, D. E., and K. Crandall.  "Beyond Fst: Analysis of population genetic data for conservation."  Conservation Genetics.  5.5 (2004): 585-602. 

Lewis-Rogers, N., K. A. CRANDALL, and D. Posada.  "Evolutionary analyses of genetic recombination."  Dynamical Genetics.  Oct. 2004: 49-78. 

Woolley, S., J. Johnson, M. J. Smith, K. A. Crandall, and D. A. McClellan.  "TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees."  Bioinformatics.  19 (2003): 671-672. 

Pérez-Losada, M., and K. A. Crandall.  "Can taxonomic richness be used as a surrogate for phylogenetic distinctness indices for ranking areas for conservation?."  Animal Biodiversity and Conservation.  26 (2003): 77-84. 

Fetzner, J. W., Jr., and K. A. Crandall.  "Linear habitats and the nested clade analysis: An empirical evaluation of geographic vs. river distances using an Ozark crayfish (Decapoda: Cambaridae)."  Evolution.  57.9 (2003): 2101-2118. 

Porter, M. L., and K. A. Crandall.  "Lost along the way: The significance of evolution in reverse."  Trends in Ecology and Evolution.  18.10 (2003): 541-547. 

Sinclair, E. A., H. L. Black, and K. A. Crandall.  "Population structure and paternity in an American Black Bear (Ursus americanus) population using microsatellite DNA."  Western North American Naturalist.  63.4 (2003): 489-497. 

Jara, C. G., M. Pérez-Losada, and K. A. Crandall.  "Aegla occidentalis (Crustacea: Decapoda: Aeglidae), a new species of freshwater crab from the Nahuelbuta Coastal Range, Chile."  Proceedings of the Biological Society of Washington.  116.4 (2003): 933-942. 

Pérez-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 protection."  Biological Conservation.  105 (2002): 345-353. 

Sinclair, E. A., Costello, B., Courtenay, J. M. and Crandall, K. A.  "Detecting a genetic bottleneck in Gilbert's Potoroo (Potorous gilbertii) (Marsupialia: Potoroidae), inferred from microsatellite and mitochondrial DNA sequence data."  Conservation Genetics.  3 (2002): 191-196. 

Pérez-Losada, M., C. G. Jara, G. Bond-Buckup and K. A. Crandall.  "Phylogenetic relationships maong the species of Aegla (Anomura: Aeglidae) freshwater crabs from Chile."  Journal of Crustacean Biology.  22.2 (2002): 304-313. 

Pérez-Losada, M., J. T. Høeg, G. A. Kaolbasov and K. A. Crandall.  "Reanalysis of the relationships among the Cirripedia and the Ascothoracida and the phylogenetic position of the Facetotecta (Maxillopoda: Thecostraca) using 18S rDNA sequences."  Journal of Crustacean Biology.  22.3 (2002): 661-669. 

Pérez-Losada, M., C. G. Jara, G. Bond-Buckup, M. L. Porter and K. A. Crandall.  "Anomuran phylogenetic relationships: on the taxonomic positioning of Aeglidae freshwater crabs."  of Crustacean Biology.  22.3 (2002): 670-676. 

.  "Crayfish as model organisms."  Freshwater Crayfish.  13 (2002): 3-10. 

Posada, D., K. A. Crandall and E. C. Holmes.  "Recombination in evolutionary genomics."  Annual Review of Genetics.  36 (2002): 75-97. 

Posada, D., and Crandall, K. A.  "The effect of recombination on the accuracy of phylogeny estimation."  Journal of Molecular Evolution.  54 (2002): 396-402. 

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 (2001): 235-242. 

Sinclair, E. A., Swenson, E., Wolfe, M. L., Choate, D. C., Bates, B. and Crandall, K. A.  "Estimating gene flow in Utah's mountain lions."  Animal Conservation.  4.3 (2001): 257-264. 

Posada, D. and Crandall, K. A.  "A comparison of different strategies for selecting models of DNA substitution."  Systematic Biology.  50.4 (2001): 580-601. 

Tarjuelo, I., Posada, D., Crandall, K. A., Pascual, M. and Turon, X.  "Cryptic species of Clavelina (Ascidiacea: Aplousobranchiata, Polycitoridae) in two different habitats: harbours and rocky littoral in the northwestern Mediterranean."  Marine Biology.  139 (2001): 455-462. 

Posada, D. and K. A. Crandall.  "Evaluation of methods for detecting recombination from DNA sequences using computer simulations."  Proceedings of the National Academy of Sciences, U.S.A.  98.24 (2001): 13757-13762. 

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 (2001): 897-906. 

Imamichi, H., Crandall, K. A., Natarajan, V., Jiang, M. K., Dewar, R. L., Berg, S., Gaddam, A., Bosche, M., Matcalf, J. A., Davey, R. T. & Lane, H. C.  "The viral quasispecies of HIV-1 rebounding following discontinuation of HAART are similar to the viral quasispecies present prior to the initiation of therapy."  Journal of Infectious Disease.  183 (2001): 36-50. 

Posada, D. & Crandall, K. A.  "Simple (wrong) models for complex trees: A case from Retroviridae."  Molecular Biology and Evolution.  18 (2001): 271-275. 

Posada, D. and K. A. Crandall.  "Intraspecific gene genealogies: trees grafting into networks."  Trends in Ecology and Evolution.  16 (2001): 37-45. 

Clement, M., Posada, D. and Crandall, K. A.  "TCS: a computer program to estimate gene genealogies."  Molecular Ecology.  9 (2000): 1657-1659. 

Matala, E., Crandall, K. A., Baker, R. C. and Ahmad, N.  "Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission."  AIDS Research and Human Retroviruses.  16 (2000): 1481-1490. 

Crandall, K. A., Bininda-Emonds, O. R. P., Mace, G. M. and Wayne, R. K.  "Considering evolutionary processes in conservation biology: returning to the original meaning of evolutionary significant units."  Trends in Ecology and Evolution.  15.7 (2000): 290-295. 

Harris, D. J. and Crandall, K. A.  "Intra-genomic variation within ITS1 and ITS2 of crayfish (Decapoda: Cambaridae): Implications for phylogenetic and microsatellite studies."  Molecular Biology and Evolution.  17 (2000): 284-291. 

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 (2000): 530-540. 

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 (2000): 1679-1686. 

Harris, D. J., Maxson, L., Braithwaite, L. F. and Crandall, K. A.  "Phylogeny of the thoracican barnacles based on 18S rDNA sequences."  Journal of Crustacean Biology.  20 (2000): 393-398. 

Peters, A. A., Coulthart, M. B., Oger, J. J. F., Waters, D. J., Crandall, K. A., Baumgartner, A. A., Ward, R. H. and Dekaban, G. A.  "HTLV type I/II in British Columbia Amerindians: a seroprevalence seroprevalence study and sequence characterization of an HTLV type IIa isolate."  AIDS Research and Human Retroviruses.  16 (2000): 883-892. 

Posada, D., Crandall, K. A. and Templeton, A. R.  "GeoDis: A program for the cladistic nested analysis of the geographical distribution of genetic haplotypes."  Molecular Ecology.  9 (2000): 487-488. 

Smith, K. M., Crandall, K. A., Kneissl, M. L. and Navia, B. A.  "PCR detection of host and HIV-1 sequences from archival brain tissue."  Journal of Neurovirology.  6 (2000): 164-171. 

Whiting, A. S., Lawler, S. H., Horwitz, P. and Crandall, K. A.  "Biogeographic regionalisation of Australia: Assigning conservation priorities based on endemic freshwater crayfish phylogenetics."  Animal Conservation.  3 (2000): 155-163. 

Posada, D., Crandall, K. A., Nguyen, M., Demma, J. C. and Viscidi, R. P.  "Population genetics of the porB gene of Neisseria gonorrheae."  Molecular Biology and Evolution.  2000: 423-436. 

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 (2000): 522-529. 

Vila, C., Amorim, I. R., Leonard, J. A., Posada, D., Castroviejo, J., Petrucci-Fonseca, F., Crandall, K. A., Ellegren, H. and Wayne, R. K.  "Mitochondrial DNA phylogeography and population history of the Gray Wolf Canis lupus."  Molecular Ecology.  8 (1999): 2089-2103. 

Kelsey, C. R., Crandall, K. A. and Voevodin, A. F.  "Different models, different trees: The geographic origin of PTLV-I."  Molecular Phylogenetics and Evolution.  13 (1999): 336-347. 

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 (1999): 147-151. 

Fetzner, J.W., and K.A. Crandall.  "Genetic variability within and among populations of the golden crayfish (Orconectes luteus): A comparison using amplified fragment length polymorphisms (AFLP's and mitochondrial 16s gene sequences."  Freshwater Crayfish.  12 (1999): 396-412. 

Posada, D., K.A. Crandall.  "Modeltesst: Testing the model of DNA substitution."  Bioinformatics.  14.9 (1998): 817-818. 

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 (1998): 1-8. 

K.A. Crandall.  "Conservation phylogenetics of Ozark crafishes: assigning priorities for aquatic habitat protection."  Biological Conservation.  84 (1998): 107-117. 

Vila, C., J. Maldonado, I.R. Amorim, R.K. Wayne, K.A. Crandall, and R.L. Honeycutt.  "Man and his dog."  Science.  278 (1997): 205-207. 

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 (1997): 1643-1646. 

K.A. Crandall and T.W. Cronin.  "The molecular evolution of visual pigments of freshwater crayfishes (Decapoda: Cambaridae)."  Journal of Molecular Evolution.  45 (1997): 524-534. 

K.A. Crandall.  "Genetic variation within and among crayfish species."  Freshwater Crayfish.  11 (1997): 135-145. 

K.A. Crandall.  "The crayfish component to an endangered aquatic ecosystem of the Southeast United States."  Freshwater Crayfish.  11 (1997): 83-86. 

Sites, J.W. Jr., K.A. Crandall.  "Testing species boudaries in biodiversity studies."  Conservation Biology.  11.6 (1997): 1289-1297. 

Huelsenbeck, J.P., and K.A. Crandall.  "Phylogeny estimation and hypothesis testing using maximum likelihood."  Annual Review of Ecology and Systematics.  28 (1997): 437-466. 

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 for the domestic dog."  Science.  276 (1997): 1687-1689. 

Crandall, K.A., and D.M. Hillis.  "Rhodopsin evolution in the dark."  Science.  387 (1997): 667-668. 

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,.  "HIV-1 neropathogenesis and abused drugs: Current views, problems, and solutions."  Advances in Experimental Medicine and Biology.  402 (1996): 171-186. 

Voevodin, A., K.A. Crandall, P. Seth, S.A. Mufti.  "HIV type 1 subtype B and C from new regions of India and Indian and Ethiopian expatriates in Kuwait."  AIDS Research and Human Retroviruses.  12.7 (1996): 641-643. 

Crandall, K.A. and J.F. Fitzpatrick, Jr.  "Crayfish molecular systematics: Inferences using a combination of procedures to estimate phylogeny."  Systematic Biology.  45.1 (1996): 1-26. 

Crandall, K.A.  "Muliple Interspecies Transmissions of Human and Simian T-Cell Leukemia/Lymphoma Virus Type I Sequences."  Molecular Biology and Evolution.  13.1 (1996): 115-131. 

Xin, K-G, X-H Ma, K. A. Crandall, H. Bukawa, Y. Ishigatsubo, S. Kawamoto, and K. Okuda.  "Dual infection with HIV-I Thai subtype and B and E."  The Lancet.  346 (1995): 1372-1373. 

Shapskak, 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 (1995): 225-238. 

Crandal, 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 (1995): 18-30. 

Crandall, K. A.  "Intraspecific phylogenetics: Statistical support for dental HIV transmission."  Journal of Virology.  69.4 (1995): 2351-2356. 

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 (1995): 31-43. 

Crandall, K. A.  "Intraspecific cladogram estimation: Accuracy at higher levels of divergence."  Systematic Biology.  43.2 (1994): 222-235. 

Crandall, K. A. and A. R. Templeton.  "Empirical tests of some predictions from coalescence theory."  Genetics.  134 (1993): 619-633. 

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 sequnece data. III. Cladogram estimation."  Genetics.  132 (1992): 619-633. 

JESSE BREINHOLT, MARCOS PEREZ-LOSADA & KEITH A. CRANDALL.  The Timing of the Diversi
cation of the Freshwater Cray
shes.  2009. 

Keith A. Crandall, Megan L. Porter, and Marcos Pérez-Losada.  Crabs, shrimps, and lobsters (Decapoda).  Jan. 2009. 

Marcos Pérez-Losada, Jens T. Høeg and Keith A. Crandall.  Stalked and acorn barnacles (Thoracica).  2009. 

Kit J. Menlove, Mark Clement, and Keith A. Crandall.  Similarity Searching Using BLAST.  2009. 

Crandall, K. A., and M. Pérez-Losada.  "Epidemiological and evolutionary dynamics of pathogens."  Evolutionary Biology of Bacterial and Fungal Pathogens.  Ed. F. Baquero, C. Nombela, G. H. Cassell, and J. A. Gutiérrez-Fuentes.  Washington, DC: ASM Press, Dec. 2008. 

Crandall, K.A., and J. Lagergren.  Algorithms in Bioinformatics.  Berlin, Germany: Springer-Verlag, Oct. 2008.  <website>

Buhay, J. E., K. A. Crandall, D. Posada.  "Population Genetics for Animal Conservation."  Nested Clade Analysis for Conservation Genetics.  Cambridge, UK: Cambridge University Press, Sep. 2008. 

Pérez-Losada, M., M. Porter, and K. A. Crandall.  "Methods for analyzing viral evolution."  Plant Virus Evolution.  Ed. M. J. Roosinck.  Berlin, Germany: Springer-Verlag, Sep. 2008. 

.  "Astacoides (Freshwater crayfishes, orana, orambanonga, orambato, oramboro)."  The Natural History of Madagascar.  Ed. Goodman, S. & Benstead, J.  Chicago: University of Chicago Press, 2003. 

.  "Reticulate Evolution."  Encyclopedia of Evolution.  Ed. Pagel, M.  New York: Oxford University Press, 2002. 

.  "Astacoides (Freshwater crayfishes, orana, orambanonga, orambato, oramboro)."  The Natural History of Madagascar.  Ed. Goodman, S. & Benstead, J.  Chicago: University of Chicago Press, 2002. 

Crandall, K. A. and D. Posada.  "Phylogenetic approaches to molecular epidemiology."  The Molecular Epidemiology of Human Viruses.  Ed. Leitner, T.  Dordrecht, The Netherlands: Kluwer Academic Publishers, 2002. 

Fetzner, J.W. Jr & Crandall, K.A.  "Genetic variation."  Biology of Freshwater Crayfish.  Ed. D. M. Holdich.  Oxford: Blackwell Science, 2001. 

Crandall, K.A.  "Human Immunodeficiency Viruses (HIV)."  Encyclopedia of Life Sciences.  London: Nature Publishing Group, 2001. 

Crandall, K.A.  "Phylogeny."  Encyclopedia of Genetics.  Ed. Brenner, S. & Miller, J. H.  London: Academic Press, 2001. 

Posada, D., Crandall, K. A. and Hillis, D. M.  "Phylogenetics of HIV."  Computational and Evolutionary Analysis of HIV Molecular Sequences.  Ed. Rodrigo, A. G. & Learn, G. H., Jr.  Dordrecht. The Netherlands: Kluwer Academic Publishers, 2001. 

Vasco, D. A., Crandall, K. A. and Fu, Y.-X.  "Molecular population genetics: coalescent methods based on summary statistics."  Computational and Evolutionary Analysis of HIV Molecular Sequences.  Ed. Rodrigo, A. G. & Learn, G. H., Jr.  Dordrecht. The Netherlands: Kluwer Academic Publishers, 2001. 

Crandall, K.A.  The Evolution of HIV.  Baltimore, MD: The Johns Hopkins University Press, 1999. 

Crandall, K.A.  "Uses of statistical parsimony in HIV analyses."  Statistics in Molecular Biology and Genetics.  Ed. F. Seillier-Moiseiwitsch.  Hayward, CA: Institute of Mathematical Statistics and the American Mathematical Society, 1999. 

Crandall, K. A. & Templeton, A. R.  "Statistical methods for detecting recombination."  The Evolution of HIV.  Ed. K. A. Crandall.  Baltimore, MD: The Johns Hopkins University Press, 1999. 

Crandall, K. A.  The Evolution of HIV.  Baltimore: Johns Hopkins University Press, 1999. 

Crandall, K.A. and A.R. Templeton.  "Applications of intraspecific phylogenetics."  New Uses for New Phylogenies.  Oxford University Press, Oct. 1996. 

Crandall, K.A. and T.W. Cronin.  "Opsin evolution in crayfishes: Effects of functional constraints."  Current Issues in Molecular Evolution.  Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, July 1996. 

Crandall, K.A.  "Identifying links between genotype and phenotype using marker loci and candidate genes."  The Impact of Plant Molecular Genetics.  Boston: Birkhauser, Apr. 1996. 

Crandall, K. A.  "Intraspecific cladogram estimation."  Proceedings of Phylogeny Workshop.  New Jersey: DIMACS, 1995. 

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 componenet of biodiversity."  Global Biodiversity Assessment.  Ed. V. H. Heywood and R. T. Watson.  Cambridge: Cambridge University Press, 1995. 

Crandall, K. A.  "Molecular Markers, Natural History and Evolution by John C. Avise."  Systematic Biology.  1995. 

Crandall, K. A., A. R. Templeton, and C. F. Sing.  "Intraspecific cladogram estimation: Problems and solutions."  Models in Phylogeny Reconstruction.  Ed. R. W. Scotland, D. J. Siebert, and D. M. Williams.  Oxford: Clarendon Press, 1994. 

Crandall, K. A. and K. L. Shaw.  "The Comparative Method in Evolutionary Biology by P.H. Harvey and M.D. Pagel."  Bulletin Of Mathematical Biology.  1993.