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Research Interests
The major emphasis of current research is
molecular genetics and genome evolution of salmonid fishes. Sequence
variation in nuclear and mitochondrial genes is being used for
phylogenetic analysis of the salmonid fishes world-wide and for
stock identification. The evolution of duplicate genes, the role of
chromosome rearrangements in speciation, and the evolution of sex
chromosomes in these ancestrally tetraploid species are being
investigated. Conservation questions at the population level are
being approached using variation at microsatellite and Mhc (major
histocompatibility complex) loci. Projects related to aquaculture
include genetic and physical mapping of the rainbow trout genome and
isolation of genes for traits important to aquaculture. A project on
comparative genomic mapping between zebrafish, an important
biomedical model, and salmonid fishes has been initiated using
fluorescence in situ hybridization (FISH) with large insert probes
and chromosome-specific paint probes made by chromosomal
microdissection.
Representative Publications
Hansen,
J.D., Landis, E.G. and Phillips, R.B. 2005.
Discovery of a new Ig heavy chain isotype in rainbow trout:
implications for a novel B cell developmental pathway in teleost
fish. Proceedings of the National Academy of Sciences
102:
6919-6924.
Phillips, R.B., Morasch, M.R., Park,
L.K., Naish, K.A., and R.H. Devlin. 2005.
Identification of the sex chromosome pair in coho salmon (Oncorhynchus
kisutch): lack of conservation of the sex linkage group with
chinook salmon (Oncorhynchus tschawytscha). Cytogenetics and
Genome Research.111:166-170.
Phillips, R.B . Morasch, M., Wheeler, P., and G. H.
Thorgaard. 2005.
Rainbow trout of Idaho and Alaskan origin (2n=58) share a chromosome
fusion relative to trout of California origin (2n=60). Copeia
2005-3:661-664.
Ohta, Y., Landis, E., Boulay, T., Phillips, R.B.,
Collet, B., Secombes, C.J., Flajnik, M. F., and Hansen, J.D.
2004. Homologs of CD83 from elasmobranch and teleost
fish. J. Immunology 173:4553-4560.
Phillips, R. B. 2004. Chromosome Morphology.
In Stock Identification Methods, edited by Kevin Friedland, John
Waldman and Steve Cadrin. Academic Press.
Phillips, R. B. 2004. Adaptive evolution or
genetic drift? Does genome complexity produce organismal complexity?
(Invited commentary paper) Heredity 93:122-123.
Phillips, R. B., Noakes, M.A., Morasch, M., Felip,
A. and G. H. Thorgaard. 2004. Does differential selection on the 5S
rDNA explain why the rainbow trout sex
chromosome heteromorphism is NOT linked to the SEX locus?
Cytogenetics and Genome Research 105:122-125..
Felip, A., Fujiwara, A., Young, W.P., Wheeler, P. A.,
Noakes, M., Phillips, R.B. and G.H. Thorgaard.
2004. Polymorphism and differentiation of rainbow trout
Y chromosomes (Genome, in press).
Phillips, R.
B., Zimmerman, A., Noakes, M., Palti,Y. Morasch, M., Eiben, L.,
Ristow, S. , Thorgaard, G. H. and J. D. Hansen. 2003. Physical and
genetic mapping of the rainbow trout major histocompatibility
regions: evidence for duplication of the class I region.
Immunogenetics 91:561-569.
Phillips, RB, MP Matsuoka,
NR Konkol, and S McKay. 2003. Molecular systematics and evolution
of the growth hormone introns in the Salmoninae. Environmental
Biology of Fishes 69:433-440.
Phillips, R. B.
and K. M. Reed. 2003. Chromosome Variation. In Genetic
Principles and Practices for Fisheries Scientists. American
Fisheries Society.
Noakes, M.
A. and Phillips, R. B. 2003. OtY1 is a Y-linked marker in chinook
salmon but not in rainbow trout.
Animal Genetics 34:156-157.
Nichols, KM,
Young, WP, Danzmann, RG, Robison, BD, Rexroad, C, Noakes, M,
Phillips, RB, Bentzen, P, Knudsen, K, Allendorf, F, Cunningham, B,
Brunelli, J, Ristow, S, Drew, R, Brown, KH, Wheeler, PA, and GH
Thorgaard. 2003. An updated genetic linkage map for rainbow trout.
Animal Genetics 134:102-115., in press.
Noakes, M.A., Reimer, T. R., and Phillips, R. B. 2003. Analysis of
an MHC Class II locus
in lake trout (Salvelinus namaycush) from Lake Superior by
single stranded conformational polymorphism (SSCP) analysis and
reference strand conformational analysis (RSCA). Marine
Biotechnology 5:1-9.,
in press.
Woram, R.A., Gharbi, K., Sakamoto, T., Hoyheim, B., Holm, Lars-Erik,
Naish, K., McGowan, C., Ferguson, M.M., Phillips, R. B., Stein, J.,
Guyomard, R, Ciarney, M, Taggart, J., Powell, R., Davidson, W, and
RG Danzmann. 2003. Comparative genome analysis of the primary sex
determining locus in salmonid fishes. Genome Research 13:272-280.
Stein, J. D.,
Reed, K. M., and Phillips R. B. 2002. Isolation and
characterization of a sex-linked microsatellite locus from the lake
trout Y chromosome. Environmental Biology of Fishes 64:211-216.
Phillips,
R. B., Matsuoka, M. P., and Reed, K. M. 2002. Characterization of
charr chromosomes using fluorescence in situ hybridization.
Environmental Biology of Fishes 64:223-228.
Westrich, K. M.,
Konkol, N. R., Matsuoka, M. P. and R. B. Phillips. 2002.
Interspecific relationships among charrs based on phylogenetic
analysis of nuclear growth hormone introns. Environmental Biology of
Fishes 64:217-222.
Phillips, R. B.,
N. R. Konkol, K. M. Reed, and J. D. Stein. 2001. Chromosome painting
supports independent evolution of sex chromosomes in Oncorhynchus,
Salmo and Salvelinus. Genetica 111:119-123 (invited
paper).
Phillips, R. B.
2001. Application of fluorescence in situ hybridization to
fish genetics and genome mapping. Marine Biotechnology 3:S145-S152.
(invited paper).
Phillips, R. B.
and P. Rab. 2001. Chromosome evolution in the Salmonidae (Pisces):
an update Biological Reviews 76:1-25.
Courses
Organic Evolution
(BIOL 405)
Introduction to
Genetics (BIOL 301)
Special Topics: Evolution of
Sex Chromosomes (BIOL 565)
Fish Genetics (BIOL 413)
Molecular Ecology (ES/RP 592) |
