My research program continues to have two major foci: theoretical systematics and empirical rodent systematics.

Phylogenetic Methodology

Our understanding of the processes of nucleotide substitution (DNA sequence evolution) has been expanding greatly over the last 10 years. Furthermore, it has become apparent that ignoring such processes as heterogeneity of base composition, substitution pattern, and rate variation among nucleotide sites can compromise attempts to estimate phylogeny from DNA sequence data. Therefore, model-based analyses of DNA sequence data have become increasingly wide spread because such approaches afford the investigator the opportunity to account for such processes explicitly. This is especially true when a maximum-likelihood framework is adopted.

Unfortunately, however, such methods require vast computational power. Thus, given the finite computational capacities most researchers face, it is critical to develop approximate methods of model-based analyses that may be applied to relatively large data sets. One approximate method that has been rather widely used is based on an iterative search strategy in which one alternates between estimating model parameters and topology. While this method appears very useful, it needs to be tested more rigorously than has been possible. We are conducting such tests using multiple networked alpha-powered workstations running in parallel. This work entails examination of several real data sets as well as large simulated data sets, and is being conducted in collaboration with Dr. David L. Swofford.

Comparative Phylogeography

Our current empirical research is centered on comparative phylogeography, the phylogenetic study of the historical processes that have influenced geographic distributions in multiple, codistributed taxa. Two regions are being examined: the highlands of Middle America and northwestern North America. Both these areas have been under-examined, and both are subject to intense, but very differently motivated exploitation and degradation of forest ecosystems. The general objectives of this research are to assess the influence of past geological and climatic events on the geographic structure of genetic variation in several codistributed highland forest species. The degree to which geographic patterns of genetic variation are correlated across taxa will provide insight regarding the degree to which conservation strategies aimed at maintaining genetic diversity in one species will protect genetic diversity in other codistributed species.

Middle American Highlands. Several murid rodent species complexes are being examined from Middle America. Two of these have almost perfectly congruent widespread distributions, the Peromyscus aztecus/P. hylocetes complex, and the Reithrodontomys sumichrasti complex. Analyses of mtDNA data indicate that there are strong similarities between the phylogeographies of the two complexes; in both complexes, populations from each of several mountain ranges represent monophyletic assemblages of haplotypes, and the Isthmus of Tehuantepec is a strong phylogeographic barrier. However there are also instances of strong phylogeographic incongruence. These mixed results indicate that these two taxa have responded to Pleistocene climatic neither completely independently, as would be predicted by the current paradigm in historical biogeography, nor in a completely concerted fashion.

Northwestern North America. Three broad distributional patterns characterize northwestern North American endemics across kingdoms; widespread in the northwest; restricted to the northern Rocky Mountains; and disjunct, with populations in the coastal ranges and separate populations in the Northern Rockies. We are currently conducting research on the comparative phylogeography of several species representing each of these distributional patterns.

Jeff Good is a Master's student conducting research of Red-tailed chipmunks (Tamias ruficaudus). This species is restricted to the northern Rockies and contains two subspecies; these have been suggested to actually distinct species based on differences in male genital bone (baculum) morphology. We have identified two mtDNA haplotype clades (among ca. 200 chipmunks sequenced) that correspond only roughly to the bacular morphotypes, and there appears to be differential introgression of mtDNA across the contact zone. We are beginning to use microsatellite loci to assess transgression of nuclear genes across the contact zone. Future plans are to examine mtDNA phylogeography for other species restricted to the northern Rockies, including the Couer d'Alene salamander (Plethodon idahoensis), Rocky Mountain giant salamander (Dicamptodon aterimus), and Columbian ground squirrel (Spermophilus columbianus).

Two widespread taxa endemic to northwestern North America, Montane voles (Microtus montanus) and Yellow-pine chipmunks (T. amoenus) are also being examined. Dr. John Demboski, a postdoc in my lab, is collecting sequence data for these two species. The mtDNA sequence data for T. amoenus indicates remarkable levels of genetic structuring. Some monophyletic assemblages of haplotypes are found across a relatively large portion of the range, whereas others are quite localized. For example a well-differentiated clade of haplotypes occurs only in the Purcell and Selkirk Mountains, and is the only haplotype we've found there. Similarly, a differentiated clade occurs only in the Blue Mountains. We are beginning to assess differentiation at microsatellite loci to ascertain if the differentiation we've observed in the mtDNA is also present in the nuclear genome.

The Water vole (M. richardsoni) has a disjunct distribution, with populations in the coastal ranges and separate populations in the northern Rockies. Dr. Demboski is also collecting data on this species, and it appears that the inland populations may have arisen via dispersal along the retreating glacial front at the close of the Pleistocene. A second taxon with this disjunct distribution is the Tailed frog (Ascaphus truei). Master's student Marylin Nielson has collected mtDNA sequence data for this species. These data indicate that there are two extremely well differentiated haplotypes that support the persistence of a mesic-forest refugium in the northern Rockies throughout the Pleistocene. This is particularly interesting because paleobotanical data supporting such a refugium is lacking. This disjunct distribution occurs in over 150 other species, including invertebrates, plants and fungi, and we are forming collaborations with botanists to examine the genetics of many of these disjunct plant species.

Courses

• Comparative Vertebrate Anatomy (BIOL 324)
• Principles of Systematic Biology (BIOL 445)
• Mammalogy (BIOL 483)

Selected Publications

for PDF links go to the Lab Website

*Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. In Press. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology. In Press.

*Good, J. M., J. Demboski, D. M. Nagorsen, and J. Sullivan. 2003. Phylogeography and introgressive hybridization: Chipmunks (Tamias) in the northern Rocky Mountains. Evolution, In Press.

Swofford, D. L. and J. Sullivan.  2003.  Phylogenetic inference using parsimony and maximum likelihood using PAUP*. 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. 19:748-761.

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.

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

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.

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. American Naturalist, 155:755-768.

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.

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. OBrien, 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 utility of 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 44:154-158.

 Sullivan, J. (1996). Combining data with different distributions of among-site rate variation. Systematic Biology 43:375-380.

 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.

 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.

* indicates a current or former graduate student