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CURRICULUM VITAE
John M. (Jack) Sullivan
Department
of Biological Sciences, Box 443051,
University of Idaho, Moscow, ID 83844-3051
Office Phone: (208) 885-9049 Lab Phone: (208) 885-8062 Fax: 208-885-7905
e-mail: jacks@uidaho.edu
Date of Birth: 9/18/63
Married to D. Brandy Sullivan, Children: Connor J. Sullivan,
Terra S. Sullivan
Education
1995 Ph.D. Ecology
& Evolutionary Biology, University of Connecticut (Christine
M. Simon)
1990 M.S. Zoology, University of Vermont (C.
William Kilpatrick)
1985 B.A. Zoology, University of Vermont
Academic Positions
Professor of Biological Sciences, Department of Biological Sciences, University
of Idaho. July, 2008 - Present.
Director, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho. July, 2015 - 2018.
Associate Professor of Zoology, Department of Biological Sciences, University
of Idaho. July, 2002 - June, 2008.
Assistant Professor of Zoology, Department of Biological Sciences, University
of Idaho. July, 1997 - June, 2002.
Postdoctoral Fellow, Laboratory of Molecular Systematics, Smithsonian
Institution. January, 1996 - July, 1997.
Research Interests
Theoretical systematics; Comparative phylogeography and cryptic diversity;
Rodent systematics and evolution, especially chipmunk speciation;
Conservation genetics.
Early Research Experience
Graduate Research Assistant, 1993-1995; Ecology & Evolutionary Biology,
University of Connecticut. Evolution of 12S rRNA in sigmodontine
rodents.
Graduate Research Assistant, Summer, 1992; Ecology & Evolutionary Biology,
University of Connecticut. mtDNA sequence variation in New Zealand
cicadas.
Graduate Research Assistant, Summer, 1991; Ecology & Evolutionary Biology,
University of Connecticut. Allozyme and mtDNA sequence variation
in Magicicada.
Lab Technician,
Fall, 1990; Department of Zoology, University of Vermont. DNA-DNA
hybridization in sigmodontine rodents.
Field Technician,
Summer, 1990; Department of Zoology, University of Vermont. Collection
of sigmodontine rodents of Mexico.
Courses
Mammalogy, Phylogenetics
Publications (*Asterisks indicate student research.)
Total Citations: 7287 (as of July 2022) h-index: 44 i10 index: 63
Tumendemberel, O., S. A. Hendricks, P. A. Hohenlohe., J. Sullivan, A. Zedrosser,
M. Saebo, M. F. Proctor, J. L. Koprowski, and L. P. Waits. 2023. Range-wide
evolutionary relationships and historical demography of brown bears (Ursus arctos)
revealed by whole-genome genome sequencing of isolated central Asian populations.
Molecular Ecology, Open Access.
Kelt, D. A., A. A. Coppeto, D. H. Van Vuren, J. Sullivan, J. A. Wilson, and N. Reid. 2023.
Nice conservatism versus niche differentiation in sympatric chipmunks in the northern Sierra
Nevada, Journal of Mammalogy, (Download PDF).
doi.org/10.1093/jmammal/gyad048.
Smith, M. L., C. Lang, *D. Sneddon, J. Wallace, *A. M. Rankin, A. Espindola, D. C.
Tank, J. Sullivan, and B. C. Carstens. 2023. Comparative phylogeography of
leaf-litter dwelling invertebrates from the Pacific Northwest. Northwest Science,
96:117-132. (Download PDF). doi.org/10.3955/046.096.0108.
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., C. Lang, *D. Sneddon, J. Wallace, *A. M. Rankin, A. Espíndola, D. C.
Tank, J. Sullivan, and B. C. Carstens. 2022. Comparative phylogeography of
leaf-litter dwelling invertebrates from the Pacific Northwest. Northwest Science,
Accepted.
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, 31:4402-4416. (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, 76:2004-2019. Download PDF.
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. (https://doi.org/10.46471/gigabyte.19.) 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. Carnivore contact: A species fracture
zone delineated amongst genetically structured North American marten populations (Martes
americana and Martes caurina). Frontiers in Genetics, 11:735. doi.org/10.3389/fgene.2020.00735
(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, doi.org/10.1371/journal.pone.0220746
(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/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. doi.org/10.1111/mec.14223/full. (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/evx034. (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: 10.1098/rspb.2016.1529.
(Download PDF).
*Metzger, G., A. Espíndola, 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: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, 113: 185-194.
doi:10.1038/hdy.2014.27. (Download PDF).
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 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-1 plasmids despite incongruence
among backbone genes trees. Molecular Biology and Evolution. 30:154-166.
(Published on-line August, 2012). 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,
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).
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.
*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.
(Download 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 maximum-likelihood phylogeny
estimation. Molecular Biology and Evolution, 22:1386-1392.
(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).
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 proofs).
*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).
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.
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. (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).
Good, J. A., 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. Pp. 319-339 In (J. Silvertown and
J. Antonovics, eds.) Integrating ecological and evolutionary
processes in a spatial context. Blackwell Science, Oxford.
(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).
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).
Mallatt, J., J. Sullivan, and C. J. Winchell.
2000. The relationship of lampreys to hagfishes: A spectral analysis
of ribosomal DNA sequences. Pp. 106-118. In: Major Events
in Early Vertebrate Evolution: Palaeontology, Phylogeny, and
Development. (P. E. Ahlberg, ed.). Taylor and Francis.
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).
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. (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).
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).
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. 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).
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.
Solicited Book Reviews
Sullivan, J. 2014. Review of Mammalogy:
6th edition. (T. A. Vaughan, J. M. Ryan, and N. J. Czaplewski, authors).
Journal of Mammalogy, In Press.
Sullivan, J. 1998. Review of Molecular
Evolution. (W.-H. Li, author). Systematic Biology, 47:173-175.
Invited Symposia and Workshops
2013 - Society of Systematic Biologists Presidential
Address, Snowbird Utah. Systematic biology two decades after Snowbird 1993,
and w(h)ither the species tree?
2007 - NSF Sponsored Workshop on Biogeography, Las Vegas Nevada.
2006 - Annual Meetings, Society of Systematic Biologists,
Symposium on Species Delimitation: New Approaches for Discovering Diversity -
Detecting Hybridization and Species Limits with Phylogeographic Data: Tamias.
2006 - Annual Meetings of the Idaho Academy of Sciences,
Plenary Session - Genetics and Evolution of the Inland Mesic Forest Ecosystem.
2001 - University of Southern Illinois,
Systematic Biology Symposium, Keynote Speaker. Statistical
Tests in Comparative Phylogeography: Methods and Examples from
the Pacific Northwest and Middle American Highlands.
1997 - International Theriological Congress
VII, Symposium on Systematics and Biogeography of Montane Rodents
of Southeastern Mexico and Northern Central America. Phylogeography
and Molecular Systematics the Peromyscus aztecus complex.
1997 - International Theriological Congress
VII, Symposium on Molecular Systematics of Peromyscine Rodents.
The Importance of Adequate Models in the Molecular Systematics
of Rodents.
1996 - Annual Meetings, Italian Society
of Zoologists, Plenary Session - Advances in Molecular Systematics:
Examining Conflict between Molecular and Classical Data Sets.
1995 - Annual Meetings, Society of Systematic
Biologists, Symposium on Incorporating Molecular Evolution into
Molecular Phylogenetic Analyses. Accommodating Among-Site
Rate Variation in Phylogenetic Analyses.
1994 - New England Molecular Evolution
Meetings. Gene Tree/Species Tree Symposium. Congruence and
Conflict in Peromyscus Systematics.
Invited Departmental Seminars
2021 University of Idaho, Department of Biological Sciences
2018 University of Montana, Division of Biological Sciences
2018 Washington State University, School of Biological Sciences
2014 University of Maryland, Graduate Program in Behavior, Ecology, Evolution and Systematics
2014 The Washington Area Phylogenetics Consortium (Smithsonian Institution)
2012 Eastern Washington University, Darwin Day Lecture
2010 University of Vermont, Department of Biological Sciences
2010 Massey University, Department of Ecology
2010 Massey University, School of Molecular Biosciences
2010 Massey University, Alan Wilson Center for Molecular Evolution and Ecology
2009 Texas Tech University, Department of Biological Sciences
2009 University of Idaho, Fish & Wildlife Resources
2009 Louisiana State University, Systematics, Ecology, & Evolution
2007 Portland State University, Department of Biology
2005 University of Texas, Integrative Biology
2004 University of Illinois at Urbana-Champaign, Integrative Biology
2004 University of Vermont, Department of Biology
2003 University of Washington; Department of Biology
2003 Boise State University; Department of Biology
2001 University of Nevada, Las Vegas; Department of Biological
Sciences
2000 University of Connecticut; Department of Ecology and
Evolutionary Biology
1999 University of Nevada, Reno; Ecology, Evolution, and
Conservation Biology
1998 University of Idaho; Departments of Statistics and
Computer Science
1998 Washington State University; Department of Zoology
1997 University of Idaho; Department of Fisheries and Wildlife
Resources
1997 Brigham Young University; Department of Zoology
1996 George Washington University; Department of Biological
Sciences
1996 National Museum of Natural History; Vertebrate Zoology
1996 San Francisco State University; Biology Department
1996 University of Idaho; Department of Biological Sciences
Contributed Talks/Posters
2018 SSB Satellite Annual Meeting (1 talk).
2017 SSE/SSB/ASN Annual Meetings (2 talks).
2017 Annual Meeting of the American Society of Mammalogists (1 talk).
2016 SSE/SSB/ASN Annual Meetings (3 talks).
2013 SSE/SSB/ASN Annual Meetings (1 talk, 2 posters).
2011 SSE/SSB/ASN Annual Meetings (1 talk).
2010 Annual New Zealand Phylogenetics Conference (1 talk).
2009 SSE/SSB/ASN Annual Meetings (3 talks).
2008 SSE/SSB/ASN Annual Meetings (2 talks).
2006 SSE/SSB/ASN Annual Meetings (1 talk, 2 posters).
2005 NSF/DFG Understanding Species Diversity on Earth (poster).
2004 SSE/SSB/ASN Annual Meetings (1 talk, 1 poster).
2003 SSE/SSB/ASN Annual Meetings (1 talk, 1 poster).
2002 SSE/SSB/ASN Annual Meetings (1 talk, 1 poster).
2001 Annual Meeting of the American Society of Mammalogists
(3 talks).
2000 SSE/SSB/ASN Annual Meetings (2 talks, 1 poster).
2000 Northwestern Regional Meetings, Wildlife Society.
1999 SSE/SSB/ASN Annual Meetings.
1998 SSE/SSB/ASN Annual Meetings.
1997 SSE/SSB/ASN Annual Meetings.
1996 SSE/SSB/ASN Annual Meetings.
1995 Annual Meeting of the American Society of Mammalogists.
1994 SSE/SSB/ASN/SMBE Annual Meetings.
1994 Eastern Great Lakes Molecular Evolution Meetings.
1993 SSE/SSB/ASN/SMBE Annual Meetings.
1993 New England Molecular Evolution Meetings.
1993 University of Connecticut Graduate Student Symposium.
1992 University of Connecticut Graduate Student Symposium.
1991 University of Connecticut Graduate Student Symposium.
1990 Annual Meeting of the American Society of Mammalogists.
Grants and Awards
2018 – NSF Dimensions of Biodiversity DEB-1831838.
$1,777,713. January 2019 - December 2022. Dimensions: An inordinate fondness
for Methylobacterium - roles of phylogeny, genome content, and functional
performance traits in the evolution and assembly of a diverse community.
(PI: Chris Marx; Sullivan is Co-PI.).
2015 - NSF Biodiversity Discovery and Analysis DEB-1457726.
$622,614. May 2015 - April 2019. Collaborative Research: A Comparative
Phylogeographic Approach to Predicting Cryptic Diversity - The Inland Temperate
Rainforest as a Model System. David Tank is CoPI, UofI is the lead institution,
and collaborator Bryan Carstens (Ohio State University) also received $284,000
for his activities on the same project.
2014 - National Geographic Society Committee for Research
and Exploration. $12,865. July 2014 - May 2016. A Comparative Phylogeographic
Approach to Predicting Cryptic Diversity: Inland Northwest Rainforests as a
Model Ecosystem. CoPIs are David Tank and Bryan Carstens.
2012 - NSF BEACON Project Grant, $20,945. September 2012
- August 2013. An Integrated Approach to Testing the Divergence with Gene Flow Model of Speciation;
Empirical Genomics, Simulation, and in silico Evolution. This is a collaboration among
Sullivan, James Foster, & David Hillis.
2011 - NSF BEACON Project Funding. $96,949. August 2011 - July 2012.
An Integrated Approach to Testing the Divergence with Gene Flow Model of Speciation;
Empirical Genomics, Simulation, and in Silico Evolution. This is a collaboration among
Sullivan, James Foster, & David Hillis (University of Texas, who received an
additional $55,527).
2010 - Outstanding Alumnus Award, University of Vermont, Department of Biology.
2008 - NIH Centers of Biomedical Research Excellence (COBRE) (PI: Larry Forney); $9,800,000 total, Sullivan is one of 9 participating faculty; February, 2008 - January, 2013. Center for Research on Evolutionary Processes. This is an IBEST grant (see Synergistic Activities).
2007 - NSF Systematic Biology & Biodiversity
Inventories DEB-0717426. $200,000. August, 2007 - July, 2011.
Collaborative Research: A Comprehensive Multigene Phylogeny of Chipmunks
(Rodentia: Tamias): Testing Divergence with Gene Flow. UofI is
the lead institution, and collaborator John Demboski (Denver Museum of
Nature and Science) also received $200,000 for his activities on the same project.
2006 - NSF Microbial Genome Sequencing. $360,000.
November 2006 - October 2008. The Genetic Diversity of Broad Host-Range Plasmids in Prokaryotes.
(Eva Top, PI; Sullivan is Senior Personnel).
2005 - Idaho State Board of Education.
Center for Research on Invasive Species & Small Populations;
$102,200. April 2006 - March 2008. Temporal and Spatial Patterns
of Genetic Variation in Small Populations of Plants and Animals
Found in one of Idaho's Major Biodiversity Hotspots.
2003 - Idaho Department of Fish & Game
State Wildlife Conservation Grant; $5,000. June 2003 - August
2003. Population Survey of Idaho Giant Salamanders (Dicamptodon
aterrimus).
2002 - NSF EPSCoR REU Fellowship for
Jeremiah Degenhardt; $2,250
2002 - NIH Centers of Biomedical Research
Excellence (COBRE) (PI: Larry Forney); $10,200,000 total, $58,000
per year to Sullivan; February, 2002 January, 2007; Center
for Research on Evolutionary Processes.
2001 - Alumni Award for Faculty Excellence,
University of Idaho Alumni Association.
2000 - NSF EPSCoR EPS-0080935 (PI: James
A. Foster); $249,993 total, $41,078 to Sullivan; August 2000
July 2002. Multidisciplinary Studies in Bioinformatics
and Evolutionary Studies.
1999 - NSF Systematic Biology Panel
DEB-9974124; $128,976; August 1999 July, 2002. Testing
Iterative Search Strategies for Maximum-likelihood Estimation
of Phylogeny from DNA Sequence Data. David L. Swofford, Co-PI.
1999 - NSF EPSCoR EPS-9720634; $120,000;
February 1999 - June 2001. Comparative Phylogeography of Northern
Rocky Mountain Conifer-dwelling Rodents.
1998 - University of Idaho
Research Council Seed Grant; $6,000; July 1998 - June 1999. Molecular
Systematics and Population Genetics of Red-tailed Chipmunks (Tamias
ruficaudus): An Initial Assessment of Genetic Structure in
Northern Rocky Mountain Forest-dwelling Species.
1996 - Smithsonian Institution Molecular
Evolution Post Doctoral Fellowship; $36,500; January, 1996- July,
1997. Sampling Properties of Model Parameters in Phylogenetic
Analyses of DNA Sequence Data.
1995 - Outstanding Student Presenter. American
Society of Mammalogists.
1994 - Edwin V. Gant Award for Excellence
in Graduate Studies; $1,500; University wide competition in academic
performance, professional potential, service, and integrity.
1994 - Ecology and Evolutionary Biology
Award for Excellence in Graduate Student Teaching, University
of Connecticut.
1993 - Graduate Research Traineeship in
the Evolution, Ecology, and Conservation of Biodiversity; $14,000;
NSF Sponsored fellowship, awarded through the EEB Department,
University of Connecticut.
1993 - University of Connecticut Research
Foundation Grant; $10,000; January- December, 1993. Among-site
rate variation and phylogenetic analyses of DNA sequence data
in sigmodontine rodents.
Synergistic Activities
Past President, Society of Systematic Biologists. 2013
President, Society of Systematic Biologists. 2012
President-elect, Society of Systematic Biologists. 2011
Editor-elect and Editor-in-Chief, Systematic Biology. 2007-2010.
Founding member of IBEST (Initiative
for Bioinformatics and Evolutionary Studies), a collaboration among University
of Idaho biologists, computer scientists, and mathematicians designed to
foster interdisciplinary research in bioinformatics and evolution. This effort
includes a team-taught seminar course, development and administration of a
computational biology facility, and acquisition of center-based grants (see Grants and Awards).
Founder of PEES
(Palouse Ecology, Evolution and Systematics), a group of biologists from the
University of Idaho and Washington State University. The primary function of
this group is to meet one evening a month for a talk on members’ research.
This group was initiated to provide faculty and graduate students from five
departments at the two universities with an intellectually invigorating
environment and to provide a forum to present research at various stages of
completion.
Graduate Students Supervised
Daniel J. Harris, PhD Student:
Deceased
Marilyn M. Nielson, MS: Graduated December, 2000
Jeffrey M. Good, MS: Graduated May, 2002
Bryan C. Carstens, PhD: Graduated December, 2004
Jessica Hosington (Co-advised), MS: Graduated December, 2007
Sarah Hird (Co-advised), MS: Graduated June, 2008
Noah Reid, MS: Graduated August, 2008
Jason Evans, PhD: Graduated December, 2010
Jennifer Ripplinger, PhD: Graduated December, 2010
Brice Sarver, PhD: Graduated May 2014
Genevieve Metzger, PhD Student: Graduated December 2016
Megan Ruffley, PhD Student: Graduated May 2020
Andrew Rankin, PhD Student: Due to graduate May 2021
Malia Santos, PhD Student: Due to graduate May 2022
David Sneddon, PhD Student: Due to graduate May 2024
Undergraduate Research Supervised
Kyle Grunwald 2015 - 2016
Bethany Hammerston 2015 - 2016
Elizabeth Musser 2015 - 2016
William Gentry 2015 - 2016
Lauren Goss 2015 - 2016
Lauren Blenn 2014
Jacob Brigham 2014
Jessica Giffords 2014
Audra Borden 2013 - 2014
Nick Forshee 2010 - 2012
Tara Potter 2006 - 2007
Javan Bauder 2004 - 2006
Karina Villa Romero 2003-2004
Angela Stevenson 2002 - 2005
Jeremiah Degenhardt (REU Fellowship) 2002 - 2005
Stacey M. Gregory 1998-2001
Jeffrey M. Good 1998-1999
Graduate Committees (*Students whom have finished).
Zaid Abdo* - University of Idaho, Bioinformatics & Computational Biology
Patryce Avsharian* - University of Idaho, Department of Biological Sciences
Kerry Barnowe-Meyer* - University of Idaho, Department of Biological Sciences
Justin Bohling* - University of Idaho, Department of Fish & Wildlife Resources
Frances Bonier* - University of Idaho, Department of Biological Sciences
Ike Brown* University of Idaho, Department of Biological Sciences
Celeste Brown* - University of Idaho, Department of Mathematics and Statistics
Amie-June Brumble* -University of Idaho, Department of Forest Resources
Daniel Caetano* - University of Idaho, Department of Biological Sciences
Matthew Carling* - University of Idaho, Department of Biological Sciences
Christine Cegelski* - University of Idaho, Department of Fish & Wildlife Resources
Brooke Christensen University of Idaho, Department of Biological Sciences
Andrew Duckett The Ohio State University, Department of EEOB.
Isaac Erikson* - University of Idaho, Department of Biological Sciences
Harpo Faust - University of Idaho, Department of Biological Sciences
Ryan Garrick* - La Trobe University (Australia), School of Molecular Sciences
Ian Gilman* - University of Idaho, Department of Biological Sciences
Andrew Giordano* - Washington State University, School of Biological Sciences
William Godsoe* - University of Idaho, Department of Biological Sciences
Robert Grahn* - University of Idaho, Department of Biological Sciences
Lukas Grossfurthner University of Idaho, Bioinformatics & Computational Biology
Travis Hagey* - University of Idaho, Department of Biological Sciences
James Harper* - University of Idaho, Department of BiologicalSciences
Nathanael Herrera - University of Montana, Division of Biological Sciences, OBEE
Sarah Jacobs* - University of Idaho, Department of Biological Sciences
Martyna Leukascewicz - University of Idaho, Bioinformatics & Computational Biology
Kevin Lewallen - University of Idaho, Department of Biological Sciences
Hanna Marx* - University of Idaho, Bioinformatics & Computational Biology
Samuel McCauley* - University of Idaho, Department of Biological Sciences
Craig Miller* - University of Idaho, Department of Fish & Wildlife Resources
Terry Miller* - University of Idaho, Department of Forest Resources
Diego Morales-Briones* - University of Idaho, Department of Biological Sciences
Sebastian Mortimer - University of Idaho, Department of Biological Sciences
Matt Pennell* - University of Idaho, Department of Biological Sciences
Kimberly Peppin* - University of Idaho, Department of Biological Sciences
Matthew Rain* - University of Idaho, Department of Biological Sciences
Darrin Rokyta* - University of Idaho, Bioinformatics & Computational Biology
Janneke Schwaner - University of Idaho, Department of Biological Sciences
Diya Sen* - University of Idaho,Bioinformatics & Computational Biology
Katherine Shine* - University of Idaho, Department of Biological Sciences
Steven Spears* - Washington State University, School of Biological Sciences
Craig Steele* - Washington State University, School of Biological Sciences
Todd Steury* - University of Idaho, Department of Fish & Wildlife Resources
Angela Streit* - Washington State University, School of Biological Sciences
Smitha Surakanti* - University of Idaho, Bioinformatics & Computational Biology
Dan Turck University of Idaho, Department of Biological Sciences
Simon Uribe-Convers* - University of Idaho, Department of Biological Sciences
Chris Winchell* - Washington State University, School of Biological Sciences
Jeremy Yoder* - University of Idaho, Department of Biological Sciences
Li Zheng* - University of Idaho, Department of Mathematics and Statistics
Postdoctoral Fellow Supervised
Dr. Jean-Baptiste Luducq: August, 2020 - July 2023
Dr. Anahi Espindola: May, 2012 - May, 2018
Dr. Christopher Drummond: April, 2006 - May, 2008
Dr. Roland Fleissner: September, 2003 - August, 2004
Dr.
Kari Segraves: August, 2003 - July, 2005: NSF Interdisciplinary
Informatics Postdoc
Dr. John R. Demboski: August, 1999 - July, 2001
Professional Societies
American
Society of Mammalogists
Society
for the Study of Evolution
Society for
Molecular Biology and Evolution
Society of
Systematic Biologists
Intramural Service
Research Council, College of Science Representative, 2013 - present.
Departmental Review Committee of Chair, 2018.
University Search Committee for EPSCoR Director, 2018.
Re-imagining Program Prioritization (REAPP), 2018.
University Program Prioritization Design Team, 2018
College of Science Faculty Council, 2012 - 2016.
University Faculty Appeals Hearing Board, 2013 - present.
Research Oversight Team, Institute of Bioinformatics and Evolutionary Studies, 2012 - present.
Chair, Departmental Curriculum Committee, 2015 - present.
Departmental Graduate Affairs Committee, 2013 - present.
Departmental Curriculum Committee, 2011 - 2014.
Chair, Departmental Tenure Review Committee for Dr. David Tank, 2013.
Chair, Departmental Promotion Review Committee for Dr. Scott Nuismer, 2012.
Chair, Departmental Tenure Review Committee for Dr. Luke Harmon, 2011.
Chair, Departmental 3rd Year Review Committee for Dr. Erica Bree Rosenblum, 2009.
Chair, Departmental 3rd Year Review Committee for Dr. Luke Harmon, 2008.
University Budget and Finance Committee, 2008 - 2009.
College of Science Representative to Faculty Senate, 2007 - 2009.
Institutional Animal Care and Use Committee, 2006 - 2009.
Chair, Departmental Graduate Affairs Committee, 2002 - 2009.
Herbarium Task Force, 2006 - 2007.
College of Science Representative to the Graduate Council, 2003 - 2006.
Vice Chair, Arboretum Advisory Board, 2002 - 2006.
University Promotions Review Committee, AY 2004/2005.
College of Science Promotion & Tenure Committee, 2003.
Arboretum Advisory Board, 2000 - 2002.
Departmental Strategic Planning Committee, 1999 - 2002.
Departmental Search Committees (10)
IBEST Search Committees (2)
Extramural Service
Past President, Society of Systematic Biologists, 2013.
Chair, Publications Committee, Society of Systematic Biologists 2011-2014.
President, Society of Systematic Biologists, 2012.
Review Panel, PLoS - Tree of Life, 2010 - 2111.
President-Elect, Society of Systematic Biologists, 2011.
Editor-in-Chief, Systematic Biology, 2008-2010.
Editor-Elect, Systematic Biology 2007.
Elected to Governing Council, Society of Systematic Biologists, 2005 - 2008.
Ernst Mayer Award Judge, Society of Systematic Biologists, 2005.
External Member of Search Committee, WSU Animal Molecular Phylogeny Position, 2003.
Nominating Committee: Society of Systematic Biologists, 2003.
Associate Editor: Systematic Biology, 2001 - 2006.
Editorial Board: Systematic Biology, 1996 - 2000.
NSF Panelist: 2001, 2003, 2008, 2012, 2013, 2014, 2015, 2016.
External Peer Review for Promotion and Tenure - Massey University, Louisiana State University, University of Connecticut,
University of Kansas, Humboldt State University, Portland State University,
Southern Illinois State University, Texas A&M University,
University of California-Berkeley, University of California-Los-Angeles,
University of Memphis, University of Wisconsin, University of Alabama.
Reviewer for:
American Zoologist,
Annals Entomological Society of America,
Bioinformatics,
BioTechniques,
Biological Journal of the Linnean Society,
Biological Conservation,
BMC-Evolutionary Biology,
Evolution,
Copeia,
Italian Journal of Zoology,
Journal of Biogeography,
Journal of Heredity,
Journal of Mammalian Evolution,
Journal of Mammalogy,
Journal of Molecular Evolution,
Mammalian Genome,
Molecular Biology and Evolution,
Molecular Ecology,
Molecular Phylogenetics and Evolution,
National Science Foundation,
PLoS Evolutionary Biology,
Proceedings of the National Academy of Sciences,
Science,
Transactions in Computational Biology and Bioinformatics,
Trends in Ecology and Evolution,
The American Naturalist
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