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Downloadable Publications

Leducq, J.-B., *D. Sneddon, M. Santos, D. Condrain-Morel, G. Bourret, N. C. Martinez-Gomez, J. A. Lee, J. A. Foster, S. Stoylar, B. J. Shapiro, S. W. Kembrel, J. Sullivan, and C. J. Marx. 2022. Comprehensive phylogenomics of Methylobcterium reveals its complex evolution and diversity in the phyllosphere. Genome Biology and Evolution, Open Access.

Smith, M. L., J. Wallace, D. C. Tank, J. Sullivan, and B. C. Carstens. 2022. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Molecular Ecology, 31: (Download PDF).dio.org/10.1111/mec.16595.

Herrera, N. D., K. C. Bell, C. M. Callahan, E. Nordquist, B. A. J. Sarver, J. Sullivan, J. R. Demboski, and J. M. Good. 2022. Genomic resolution of cryptic species diversity in chipmunks. Evolution, Download PFD. doi.org/10.1111/evo.14546.

*Ruffley, M. R., M. L. Smith, A. Espindola, *D. Turck, *N. Mitchel, B. C. Carstens, J. Sullivan & D. C. Tank. 2022. Genomic evidence of an ancient Inland temperate rainforest. Molecular Ecology, (Open Access).

Leducq, J.-B., E. Seyer-Lamontagne, D. Condrain-Morel, G. Bourret, *D. Sneddon, J. Foster, C. Marx, J. Sullivan, J. Shapiro, and S. W. Kembel. 2022. Fine-scale adaptations to environmental variation and growth strategies drive phyllosphere Methylobacterium diversity. mBio, 13(1):e03175-21. (Open Access).

Duckett, D. J., J. Sullivan, S. Pirro, and B. C. Carstens. 2021. Genomic resources for the North American water vole (Microtus richardsoni) and the montane vole (Microtus montanus). Gigabyte, 1. (Open Access).

*Rankin, A., F. A. Anderson, S. Clutts, A. Espindola, B. C. Carstens, M. J. Lucid, and J. Sullivan. 2021, Comparative phylogeography of the widespread Anguispira kochi occidentalis and the narrow-range A. nimapuna, two Northern Rocky Mountain endemics. Biological Journal of the Linnean Society, 133:817-834. doi.org/10.1093/biolinnean/blab030. (Download PDF).

Lucid, M. K., S. Ehlers, L. Robinson, and J. Sullivan. 2021. Western toad (Anaxyrus boreas) cryptic diversity not detected in northern Idaho and Northeast Washington. Northwestern Naturalist, 102:89-93. doi.org/10.1898/1051-1733-102.1.89. (Download PDF).

*Sarver, B. A. J., N. D. Herrera, *D. Sneddon, S. H. Hunter, M. L. Settles, Z. Kronenberg, J. Demboski, J. M. Good, and J. Sullivan. 2021. Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains chipmunks (Sciuridae: Tamias). Systematic Biology, 70:908-921. doi.org/10.1093/sysbio/syaa085. (Download PDF).

Lucid, M. K., S. Cushman, L. Robinson, A. Kortello, D. Hausleitner, G. Mowat, S. Ehlers, S. Gillespie, L. Svancara, J. Sullivan, *A. Rankin and D. Paetkau. 2020. A species fracture zone delineated amongst genetically structured North American marten populations (Martes americana and Martes caurina). Frontiers in Genetics, 11:735. (Open Access).

Grond, K, K. C. Bell, J. R. Demboski, *M. Santos, J. Sullivan, and S. M. Hird. 2019. No evidence for phylosymbiosis in western chipmunk species. FEMS Microbiology Ecology, fiz182, doi.org/10.1093/femsec/fiz182. (Download PDF).

Tumendemberel, O., A. Zedrosser, M. Proctor, H. Reynolds, J. Adams, J. Sullivan, S. J. Jacobs, T. Khorloojay, T. Tserenbataa, M. Batmunkh, J. E. Swenson, L. P. Waits. 2019. Phylogeography, population genetic diversity, and recent connectivity of brown bear populations in central Asia. PLoS One, (Open Access).

*Rankin, A. M., T. Wilke, M. Lucid, W. Leonard, A. Espindola, M. L. Smith, *M. Ruffley, D. L. Tank, B. C. Carstens, and J. Sullivan. 2019. Biogeographic and evolutionary history of the Pacific Northwest: Jumping slugs (Hemphillia) as models. Biological Journal of the Linnean Society, 127: 876-889. doi.org/10.1093/biolinnean/blz040 (Download PDF).

*Sarver, B. A. J., M. W. Pennell, J. W. Brown, S. Keeble, K. M. Hardwick, J. Sullivan, & L. J. Harmon. 2019. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ. 7:e6334 (Open Access).

Lucid, M., *A. Rankin, J. Sullivan, L. Robinson, S. Ehlers, and S. Cushman. 2019. A carnivore's oasis? An isolated fisher (Pekania pennanti) population provides insight on persistence of a metapopulation. Conservation Genetics, 20:585-596. doi.org/10.1007/s10592-019-01160-w (Download PDF).

Sullivan, J., M. L. Smith, A. Espindola, *M. Ruffley, *A. Rankin, D. C. Tank, and B. C. Carstens. 2019. Integrating life history traits into predictive phylogeography. Molecular Ecology, 8:2062-2073. doi.org/10.1111/mec.15029. (Download PDF).

Pelletier, T. A., B. C. Carstens, D. C. Tank, J. Sullivan, and A. Espindola. 2018. Predicting plant conservation priorities on a global scale. Proceedings of the National Academy of Sciences, USA, 115:13027-13032. doi.org/10.1073/pnas.1804098115. (Download PDF).

Smith, M. L., *M. R. Ruffley, *A. Rankin, A. Espindola, D. C. Tank, J. Sullivan, and B. C. Carstens. 2018. Testing for the presence of cryptic diversity in tail-dropper slugs (Genus Prophysaon) using molecular data. Biological Journal of the Linnaean Society, 124:518-532. doi.org/10.1093/biolinnean/bly067. (Download PDF).

Lucid, M., *A. Rankin, A. Espindola, L. Chichister, S. Ehlers, L. Robinson, and J. Sullivan. 2018. Taxonomy and biogeography of Hemphillia (Gastropoda: Pulmonata: Arionidae) in North American rain forests, with a description of a new species (Hemphillia skadei sp. nov., Skade's slug). Canadian Journal of Zoology, 96:305-316. doi.org/10.1139/cjz-2017-0260. (Download PDF).

*Ruffley, M., M. L. Smith, A. Espindola, B. C. Carstens, J. Sullivan, and D. C. Tank. 2018. Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Molecular Ecology, 27:1012-1024. doi.org/10.1111/mec.14491. (Download PDF).

Smith, M., *M. Ruffley, A. Espindola, D. C. Tank, J. Sullivan, and B.C. Carstens. 2017. Demographic model selection using random forests and the site frequency spectrum. Molecular Ecology. 2017 26:4562-4573. (Download PDF).

*Sarver, B. A. J., J Demboski, J. M. Good, *N. Forshee, S. L. Hunter, and J. Sullivan. 2017. Comparative mitochondrial phylogenomic assessment of introgression among several species of chipmunks (Tamias). Genome Biology and Evolution. 9:7-19. doi.org/10.1093/gbe/evw254. (Open Access).

Espindola, A., *M. Ruffley, M. Smith, B. C. Carstens, D. C. Tank, and J. Sullivan. 2016. Predicting cryptic diversity from phylogeographic, climatic and taxonomic data. Proceedings of the Royal Society of London B. doi.org/10.1098/rspb.2016.1529. (Download PDF).

*Metzger, G., A., Espindola, L. P. Waits, and J. Sullivan. 2015. Genetic structure across broad spatial and temporal scales: Rocky Mountain tailed frogs (Ascaphus montanus; Anura: Ascaphidae) in the inland temperate rainforest. Journal of Heredity, 106:700-710. doi.org/10.1093/jhered/esv061. (Download PDF).

Sullivan, J., J. R. Demboski, K. C. Bell, S. Hird, *B. Sarver, N. Reid, and J. M. Good. 2014. Divergence-with-gene-flow within the recent chipmunk radiation (Tamias). Heredity. doi.org/10.1038/hdy.2014.27. (Download PFD).

Carstens, B. C., R. S. Brennan, V. Chua, C. V. Duffie, M. G. Harvey, R. A. Koch, C. D. McMahan, B. J. Nelsen, C. E. Newman, J. D. Satler, G., Seeholzer, K, Prosbic, D. C. Tank and J. Sullivan. 2013. Model selection as a tool for phylohgeographic inference: An example from the willow Salix melanopsis. Molecular Ecology, 22:4014-4028. doi.org/0.1111/mec.12347. (Download PDF).

*Sen, D., C. J. Brown, E. M. Top, and J. Sullivan. 2013. Inferring the evolutionary history of the IncP-1plasmids despite incongruence among backbone genes trees. Molecular Biology and Evolution, 30:154-166. doi.org/10.1093/molbev/mss210. (Download PDF).

*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. 93: 589-604. doi.org/10.1644/11-MAMM-A-021.1. (Download PDF).

*Reid, N., J. R. Demboski, and J. Sullivan. 2012. Phylogeny estimation of the radiation western American chipmunk (Tamias) in the face of introgression using reproductive protein genes. Systematic Biology, 61:44-62. doi.org/10.1093/sysbio/syr094. (Download PDF).

*Evans, J. and J. Sullivan. 2011. Generalized mixture models for molecular phylogenetic estimation. Systematic Biology, 61:12-21. doi.org/10.1093/sysbio/syr093. (Download PDF).

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. 317:1382-1386. doi.org/10.1016/j.yexcr.2011.03.020. (Link to Journal).

*Ripplinger, J. and J. Sullivan. 2010. Assessment of substitution-model adequacy using frequentist and Bayesian methods. Molecular Biology and Evolution, 27:2790- 2803. doi.org/10.1093/molbev/msq168. (Download PDF)

*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.org/10.1093/molbev/msq195. (Download PDF).

*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.org/10.1007/s10709-010-9470-z. (Download PDF).

*Ripplinger, J., Z. Abdo, and J. Sullivan. 2010. Effects of parameter estimation on maximum-likelihood bootstrap analysis. Molecular Phylogenetics and Evolution, 56: 642-648. (Download PDF).

*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. (Download PDF).

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. (Download PDF).

Ripplinger, J., and J. Sullivan. 2008. Does choice in model selection affect maximum likelihood analysis? Systematic Biology. 57:76-85. (Download PDF).

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. (Download PDF).

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 ER a2 and both ERB isoforms. Gene, 392: 164-173. (Download PDF).

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. ( Download PDF).

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. (Download PDF).

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. (Download PDF).

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 (Download PDF).

Sullivan, J. and P. Joyce. 2005. Model selection in phylogenetics. Ann. Rev. Ecol. Evol. Syst., 36:445-466. (Downlaod PDF) - Online Supplement (pdf)

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology, 52:674-683. ( Download PDF).

Good, J. M., J. Demboski, D. M. Nagorsen, and J. Sullivan. 2003. Phylogeography and introgressive hybridization: Chipmunks (genus Tamias) in the northern Rocky Mountains. Evolution, 57:1900-1916. (Download PDF).

Demboski, J., and J. Sullivan. 2003. Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America. Molecular Phylogenetics and Evolution, 26:389-408. (Download PDF).

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: 762-776. (Download PDF).

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. (Download PDF).

Good, J. M., and J. Sullivan. 2001. Phylogeography of red-tailed chipmunks (Tamias ruficaudus), a northern Rocky Mountains endemic. Molecular Ecology, 10:2683-2696. (Download PDF).

Brunsfeld, S., J. Sullivan, D. Soltis, and P. Soltis. 2001. Comparative phylogeography of northwestern North America: A synthesis. In (J. Silvertown and J. Antonovics, eds.) Integrating ecological and evolutionary processes in a spatial context. Pp. 319-339. Blackwell Science, Oxford. ( Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).

Sullivan, J. and D. L. Swofford. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. Journal of Mammalian Evolution, 4:77-86. (Download PDF).

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. (JSTOR Download).

Sullivan, J. 1996. Combining data with different distributions of among-site rate variation. Systematic Biology, 45:375-380. (JSTOR Download).

Simon, C., L. Nigro, J. Sullivan, A. Franke, A. Grapputo, A. Martin, C. McIntosh. 1996. Large among-taxon differences in the 12S rRNA gene: Implications for the molecular clock. Molecular Biology and Evolution, 13:923-932. (Download PDF).

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. (Download PDF).

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. (Download PDF).

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. (Download PDF).