|
*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: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: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: 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: 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: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: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: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: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).
|