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- RESEARCH INTERISTS:
Fish Genetics and Reproduction
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RESEARCH SUMMARY:
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 loci, Mhc (major histocompatibility complex)
loci, and single nucleotide polymorphisms (SNPs). Projects related to
aquaculture include genetic and physical mapping of the rainbow trout
and Atlantic salmon genomes using fluorescence in situ hybridization (FISH)
and isolation of genes for traits important to aquaculture. Comparative
genomic mapping is being done between rainbow trout, chinook salmon, coho
salmon and zebrafish.
Our lab, the Salmonid
Genetics Research Laboratory at WSU Vancouver
The department
of biology WSU Vancouver
The faculty
page in the department at WSU Vancouver
REPRESENTATIVE PUBLICATIONS:
King, T.L., Verspoor, E., Spidle, A.P., Gross, R., Phillips,
R.B., Koljonen, M.L., Sanchez, J. A., and C.L. Morrison 2007.
Biodiversity and Population Structure. Chapter 5 In The Atlantic Salmon:
Genetics, Conservation and Management, edited by E. Verspoor, L. Stradmeyer
and J.L. Nielsen. Blackwell Publishing.
Williamson, KS, Phillips, RB and B May. 2008.Characterization
of a chromosomal rearrangement responsible for producing apparent XY female
fall chinook salmon in California (in press, Journal of Heredity).
Luckas MR, Hoestal H, Grimhjolt U, Beetz-Sargent M, Cooper GA, Reid L,
Baker HG, Phillips RB, Miller KM, Davidson WS and Koop
BF. 2007. Genomic organization of duplicated major histocompatbility class
I regions in Atlantic salmon (Salmo salar). BMC Genomics 8:251-8.
Yazawa, R., Cooper, GA, Hunt, P, Beetz-Sargent, Robb, A, Conrad, M, McKinnel,
So, S, Jantzen, S, Phillips, RB, Davidson, WS, and BF
Koop. 2007. Striking antigen recognition diversity in the Atlantic salmon
T-cell receptor alpha/delta locus. Developmental and Comparative Immunology
32:204-212.
Phillips, RB, JA DeKoning, MR Morasch, LK Park and
RH Devlin. Identification of the sex chromosome pair in chum salmon (Oncorhynchus
keta) and pink salmon (Oncorhynchus gorbuscha). 2007. Cytogenetics and
Genome Research 116:298- 304.
Laing, K.J., J.J. Zou, L.J. Purcell, R.B. Phillips,
C.J. Secombs, and J. D. Hansen. 2006. Evolution of the CD4 family: teleosts
possess two divergent forms of CD4 in addition to LAG3. Journal of Immunology
177:3939-3951.
Phillips, R.B., K.M Nichols, J.J. DeKoning, M.R. Morasch,
K.A. Keatley, C. Rexoad, S.
Gahr, R. G. Danzmann, R.E. Drew and G. H. Thorgaard. 2006. Assignment
of
rainbow trout linkage groups to specific chromosomes. Genetics 174: 1661–
1670.
Phillips, R.B. 2006. Application of fluorescence in
situ hybridization (FISH) to genome mapping in fishes. In Fish Cytogenetics,
edited by Eva Pisaro. Academic Press.
Landis, E.D., Y. Palti, J. J. DeKoning, R.B. Phillips, and J.
D. Hansen. 2006. Mapping and functional genomics of the TABP and TAPBPR
genes. Immunogenetics 58:56-59.
Bernard D., Riteau B., Hansen J.D., Phillips R.B., Michel F., Boudinot
P., Benmansour A..J. Immunol. 2006. Costimulatory receptors in a teleost
fish: typical CD28, elusive CTLA4. J. Immunology 176:4191-4200.
Phillips, R.B., A. Amores, M.R. Morasch, C. Wilson, and J. H. Postlethwait.
Assignment of the zebrafish linkage groups to chromosomes. 2006. Chromosome
Research 114:155-162.
DeKoning, J., Rhydderch, J., Noakes, M., Keatley, K., Phillips, R.,
and J. Janssen. 2006. Genetic analysis of wild lake trout embryos recovered
from Lake Michigan. Transactions of the American Fisheries Society 135:399-407.
Artieri, C.G., Ng, S, Mitchell, L., Danzmann, R.G., Phillips, R.B.,
Schein, J., Koop, B.F., and
W.S. Davidson. Identification of the sex-determining locus of Atlantic
salmon (Salmo
salar) on chromosome 2. 2006. Cytogenetics and Genome Research 112(1-2):152-9.
Thorgaard, G.H., K.M. Nichols, A. Felip, A.M. Zimmerman, K.H. Brown, R.E.
Drew, B.D. Robison, K. Sundin, J. Brunelli, R.B. Phillips, S.S.
Ristow and P.A. Wheeler, 2005. Fish genomics: from genetic manipulation
to genomic analyses. In: Proceedings of the 1st International Symposium
on Potential and Perspectives of Marine Bio-Manipulation. Graduate School
of Fisheries Science, Hokkaido University, Hakodate, Japan, pp. 4-17.
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.
Rexroad , Caird E. III, Rodriguez, Maria F., Coulibaly, Issa, Gharbi,
Karim, Danzmann, Roy G., DeKoning, Jenefer, Phillips, Ruth, and
Yniv Palti. 2005. Comparative mapping of expressed sequence tags containing
microsatellites in rainbow trout (Oncorhynchus
mykiss) BMC Genomics 2005, 6:54 (18 Apr 2005)
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 ofthe 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.
Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson
MM, Fjell CD, Hoyheim B, Jones SJ, de Jong PJ, Koop BF, Krzywinski MI,
Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto
SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H,
Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. 2005. A physical map of the
genome of Atlantic salmon, Salmo salar.Genomics.
86:396-404.
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? (in press, Cytogenetics and Genome Research).
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 RB, Zimmerman A, Noakes MA, Palti Y, Morasch MR, Eiben
L, Ristow SS, Thorgaard GH, Hansen JD. (2003) Physical and genetic mapping
of the rainbow trout major histocompatibility regions: evidence for duplication
of the class I region. Immunogenetics. 55(8):561-9.
Noakes MA, Reimer T, Phillips RB. (2003) Genotypic characterization
of an MHC class II locus in lake trout ( Salvelinus namaycush) from Lake
Superior by single-stranded conformational polymorphism analysis and reference
strand-mediated conformational analysis. Mar Biotechnol (NY). 5(3):270-8.
Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips
RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli
J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. (2003)
A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim
Genet. 34(2):102-15.
Phillips, R. B. and K. M. Reed. 2003. Chromosome Variation. In
Genetic Principles and Practices for Fisheries Scientists. American Fisheries
Society.
Shimizu, C., Shike, H., Malicki, DM, Breisch, E, Westerman,M, Buchanan,
J, Ligman, HR, Phillips, RB, Carlberg, JM, Van Olst, J, and JC
Burns. 2003. Characterization of a white Bass (Morone chrysops)
embryonic cell line with
epithelial features. In Vitro Cellular and Developmental Biology of Animals
39:29-35.
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.
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.
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.
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