(*Asterisks indicate student research)
*Hoissington, J. L., L. P. Waits, and J. Sullivan. 2012. Species limits and integrated taxonomy of the Idaho ground squirrel (Urocitellus brunneus): Genetic and ecological differentiation. Journal of Mammalogy. In Press.
Francia, M. E., S. Wicher, D. A. Pace, J. Sullivan, S. N. J. Moreno, and G. Arrizabalaga. 2011. A Toxoplasma protein with homology to intracellular type sodium hydrogen exchangers is required for osmotolerance and protein processing. Experimental Cell Research. 317:1382-1396.
*Reid, N., J. R. Demboski, and J. Sullivan. 2011. Phylogeny estimation of the radiation western American chipmunk (Tamias) in the face of introgression using reproductive protein genes. Systematic Biology. In Press. doi: 10.1093/sysbio/syr094.
*Evans, J. and J. Sullivan. 2011. Generalized mixture models for molecular phylogenetic estimation. Systematic Biology. In Press. doi: 10.1093/sysbio/syr093.
*Evans, J. and J. Sullivan. 2010. Approximating model probabilities in BIC and DT approaches to model selection in phylogenetics. Molecular Biology and Evolution. 28:343-349. doi:10.1093/molbev/msq195.
*Ripplinger, J. and J. Sullivan. 2010. Assessment of substitution-model adequacy using frequentist and Bayesian methods. Molecular Biology and Evolution. 27:2790- 2803. doi:10.1093/molbev/msq168.
*Ripplinger, J., Z. Abdo, and J. Sullivan. 2010. Effects of parameter estimation on maximum-likelihood bootstrap analysis. Molecular Phylogenetics and Evolution, 56: 642-648.
*Hird, S., N. Reid, J. R. Demboski, and J. Sullivan. 2010. Introgression at differentially aged hybrid zones in red-tailed chipmunks. Genetica, 138:869-883. doi:10.1007/s10709-010-9470-z.
*Reid, N., *S. Hird, A. Schulte-Hostedde, and J. Sullivan. 2010. Examination of nuclear loci across a zone of mitochondrial introgression between Tamias ruficaudus and T. amoenus. Journal of Mammalogy, 91:1389-1400. doi: 10.1644/09-MAMM-A-082.1
McPeek, M. A., D. L. DeAngelis, R. G. Shaw, A. J. Moore, M. D. Rausher, D. R. Strong, A. M. Ellison, L. Barrett, L. Reisberg, M. D. Breed, J. Sullivan, C. W. Osenberg, M. Holyoak, and M. A. Elgar. 2009. The golden rule of reviewing. The American Naturalist, 173: E155-E158.
Swofford, D. L. and J. Sullivan. 2009. Phylogenetic inference using parsimony and other methods using PAUP*. Pp. 260-312 In (P. Lemey, M. Salemi, A.M. Vandamme, eds.). The Phylogenetic Handbook, Second Edition. Cambridge University Press, Cambridge, UK.
*Hird, S., and J. Sullivan. 2009. Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus). Molecular Ecology. 18:3097-3109. DOI: 10.1111/j.1365-294X.2009.04196.x
*Ripplinger, J., and J. Sullivan. 2008. Does choice in model selection affect maximum likelihood analysis? Systematic Biology. 57:76-85.
*Good, J., *S. Hird, *N. Reid, J. Demboski, S. Steppan, and J. Sullivan. 2008. Ancient introgression and mtDNA capture in non-sister species of chipmunks (Tamias). Molecular Ecology. 17:1313-1327. DOI: 10.1111/j.1365-294X.2007.03640.x.
Nagler, J. J., T. Cavileer, J. Sullivan, D. G. Cyr, and C. Rexroad III. 2007. The complete estrogen receptor family in the rainbow trout: discovery of novel ER2 and both ER isoforms. Gene, 392:164-173.
*Nielson, M, K. Lohman, C. H. Daugherty, F. W Allendorf, K. L. Knudsen, and J. Sullivan. 2006. Allozyme and mitochondrial DNA variation in the tailed frog (Anura: Ascaphus): The influence of geography and gene flow. Herpetologica. 62:235-258.
Brunsfeld, S. J., and J. Sullivan. 2006. A multi-compartmented glacial refugium in the northern Rocky Mountains: Evidence from the phylogeography of Cardamine constancei (Brassicaceae). Conservation Genetics, 6:895-904.
*Carstens, B.C., J. R. Demboski, *J. M. Good, S. J. Brunsfeld, and J. Sullivan. 2005. The evolutionary history of the northern Rocky Mountain mesic forest ecosystem. Evolution. 59:1639-1652.
Sullivan, J. and P. Joyce. 2005. Model selection in phylogenetics. Annual Review of Ecology Evolution & Systematics, 36:445-466.
*Carstens, B.C., A. Bankhead III, P. Joyce, and J. Sullivan. 2005. Testing population genetic structure using parametric bootstrapping: The Migrate-n test of population structure. Genetica, 124:71-75.
*Steele, C. A., *B. C. Carstens, A. Storfer, and J. Sullivan. 2005. Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae). Molecular Phylogenetics and Evolution, 36:90-100.
Sullivan, J., *Z. Abdo, P. Joyce, and D. L. Swofford. 2005. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution, 22:1386-1392.
*Abdo, Z., V. Minin, P. Joyce, and J. Sullivan. 2005. Accounting for uncertainty in the tree topology has little effect on the decision theoretic approach to model selection in phylogeny estimation. Molecular Biology and Evolution, 22:691-703.
Sullivan, J. 2005. Maximum-likelihood estimation of phylogeny from DNA sequence data. In (E. Zimmer & E. Roalson, eds.) Molecular Evolution: Producing the Biochemical Data, Part B. Methods in Enzymology, 395:757-779.
*Carstens, B. C., *J. D. Degenhardt, *A. S. Stevenson, and J. Sullivan. 2005. Accounting for coalescent stochasticity in testing phylogeographic hypotheses: Testing models of Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology, 14:255-265.
*Carstens, B. C., *A. L. Stevenson, *J. D. Degenhardt, and J. Sullivan. 2004. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology, 53:781-792.
*Carstens, B. C, J. Sullivan, L. M. Davalos, P. A. Larsen, and S. C. Pedersen. 2004. Exploring population genetic structure in three species of Lesser Antillean bats. Molecular Ecology. 13:2557-2566.
*Minin, V., *Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology. 52:674-683.
*Good, J. M., J. Demboski, D. M. Nagorsen, and J. Sullivan. 2003. Phylogeography and introgressive hybridization: Chipmunks (Tamias) in the northern Rocky Mountains. Evolution, 57:1900-1916.
Swofford, D. L. and J. Sullivan. 2003. Phylogenetic inference using parsimony and maximum likelihood using PAUP*. Pp. 160-196 In (M. Salemi, A.M. Vandamme, eds.). The Phylogenetic Handbook. Cambridge University Press, Cambridge, UK.
Demboski, J., and J. Sullivan. 2003. Extreme differentiation among populations of Yellow-pine chipmunks, Tamias amoenus (Rodentia; Sciuridae). Molecular Phylogenetics and Evolution. 26:389-408.
*Winchell, C. J., J. Sullivan, C. B. Cameron, B. J. Swalla, and J. Mallatt. 2002. Evaluating hypotheses of deuterostome evolution with new LSU and SSU ribosomal DNA phylogenies. Molecular Biology and Evolution. 19: 48-761.
*Good, J. M., and J. Sullivan. 2001. Phylogeography of red-tailed chipmunks (Tamias ruficaudus), a northern Rocky Mountains endemic. Molecular Ecology, 10:2683-2696.
Brunsfeld, S., J. Sullivan, D. Soltis, and P. Soltis. 2001. Comparative phylogeography of northwestern North America: A synthesis. Pp. 319 – 339 In (J. Silvertown and J. Antonovics, eds.) Integrating ecological and evolutionary processes in a spatial context. Blackwell Science, Oxford.
Sullivan, J. and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know assumptions about among-site rate variation and nucleotide substitution pattern are violated? Systematic Biology, 50:723-729.
*Nielson, M. K., K. Lohman, and J. Sullivan. 2001. Phylogeography of the tailed frog (Ascaphus truei): Implications for biogeography of the Pacific Northwest. Evolution, 55:147-160.
Mallatt, J., J. Sullivan, and *C. J. Winchell. 2001. The relationship of lampreys to hagfishes: A spectral analysis of ribosomal DNA sequences. In: Major Events in Early Vertebrate Evolution: Palaeontology, Phylogeny, and Development. (P. E. Ahlberg, ed.). Pp. 106-118. Taylor and Francis, London.
*Harris, D. J., D. S. Rogers, and J. Sullivan. 2000. Phylogeography of Peromyscus furvus (Rodentia: Sigmodontinae) based on Cytochrome b sequences. Molecular Ecology, 9:2129 - 2136.
Sullivan, J., *E. A. Arellano, and D. S. Rogers. 2000. Comparative phylogeography of Mesoamerican highland rodents: Concerted versus independent responses to past climatic fluctuations. The American Naturalist, 155:755-768.
Steppan, S. J., and J. Sullivan. 2000. The emerging statistical perspective in systematic biology: A reply to Mares and Braun on the status of Andalgalomys (Rodentia: Sigmodontinae). Journal of Mammalogy, 81:260-270.
Waits, L., J. Sullivan, S. J. O’Brien, and R. Ward. 1999. Mitochondrial DNA phylogeny for bears: single region trees and combined data trees. Molecular Phylogenetics and Evolution, 13:82-92.
Sullivan, J., D. L. Swofford, and G. J. P. Naylor. 1999. The effect of taxon sampling on estimating rate-heterogeneity parameters of maximum-likelihood models. Molecular Biology and Evolution. 16:1347-1356.
Mallatt, J., and J. Sullivan. 1998. 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Molecular Biology and Evolution, 15:1706-1718.
Sullivan, J. and D. L. Swofford. 1997. Are guinea pigs rodents? The importnace of adequate models in molecular phylogenetics. Journal of Mammalian Evolution, 4:77-86.
Sullivan, J., J. A. Markert, and C. W. Kilpatrick. 1997. Phylogeography and molecular systematics of the Peromyscus aztecus group (Rodentia: Muridae) inferred using parsimony and likelihood. Systematic Biology, 46:426-440.
Frati, F., C. Simon, J. Sullivan, and D. L. Swofford. 1997. Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. Journal of Molecular Evolution, 44:145-158.
Sullivan, J. 1996. Combining data with different distributions of among-site rate variation. Systematic Biology, 45:375-380.
Simon, C., L. Nigro, J. Sullivan, A. Franke, A. Grapputo, A. Martin, and C. McIntosh. 1996. Large among-taxon differences in the 12S rRNA gene: Implications for the molecular clock. Molecular Biology and Evolution, 13:923-932.
Sullivan, J., K. E. Holsinger, and C. Simon. 1996. The effect of topology on estimates of among-site rate variation. Journal of Molecular Evolution, 42:308-312.
Hickson, R. E., C. Simon, A. J. Cooper, G. Spicer, J. Sullivan, and D. Penny. 1996. A refined secondary structure model, conserved motifs, and alignment for the third domain of animal 12S rRNA. Molecular Biology and Evolution, 13:150-169.
Sullivan, J., K. E. Holsinger, and C. Simon. 1995. Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents. Molecular Biology and Evolution, 12: 988-1001.
Sullivan, J. M. and C. W. Kilpatrick. 1991. Biochemical systematics of the Peromyscus aztecus assemblage. Journal of Mammalogy, 72:681-689.
Sullivan, J. M., C. W. Kilpatrick, and P. D. Rennert. 1991. Biochemical systematics of the Peromyscus boylii species group. Journal of Mammalogy, 72:681-696.
