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Wichman Lab: Publications

Wichman | Cantrell
 

 

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Dr. Holly A. Wichman

Bull, J.J., J. Millstein, J. Orcutt, and H.A. Wichman. (2006) Evolutionary feedback mediated through population density, illustrated with viruses in chemostats. Am. Nat. 167:E39-E51.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16670974

Pepin, K.M., M.A. Samuel, and H.A. Wichman. (2006) Variable pleiotropic effects from mutations at the same locus hamper prediction of fitness from a fitness component. Genetics 172:2047-2056.
http://www.genetics.org/cgi/content/full/172/4/2047

Rokyta, D.R., C.L. Burch, S.B. Caudle, and H.A. Wichman. (2006) Horizontal gene transfer and the evolution of microvirid coliphage genomes. J. Bacteriol. 188:1134-1142.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16428417

Scott, L., A. Kuroiwa, Y. Matsuda, and H.A. Wichman. (2006) X accumulation of LINE-1 retrotransposons in Tokudaia osimensis, a spiny rat with the karyotype XO. Cytogenet. Genome Res. 112:261-269.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16484782

Cantrell, M.A., M.M. Ederer, I.K. Erickson, V.J. Swier, R.J. Baker, and H.A. Wichman. (2005) MysTR: an endogenous retrovirus family in mammals undergoing recent amplifications to unprecedented copy numbers. J. Virol. 79:14698-14707.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16282470

Rokyta, D.R., P. Joyce, S.B. Caudle, and H.A. Wichman. (2005) An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat. Genet. 37:441-444.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15778707

Wichman, H.A., J. Millstein, and J.J. Bull. (2005) Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170:19-31.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15687276

Grahn, R.A., T.A. Rinehart, M.A. Cantrell, and H.A. Wichman. (2005) Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents. Cytogenet. Genome Res. 110:407-415. 
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16093693

Rinehart, T.A., R.A. Grahn, and H.A. Wichman. (2005) SINE extinction preceded LINE extinction in sigmodontine rodents: implications for retrotranspositional dynamics and mechanisms. Cytogenet. Genome Res. 110:416-425.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16093694

Bradley, R.D., R. Martinez, M. Maltbie, I. Tiemann-Boege, H.A. Wichman, and R.J. Baker. (2003) Rapidly evolving repetitive DNA in a karyotypically megaevolved genome: factors that affect chromosomal evolution. Occasional Papers No. 223. Museum of Texas Tech University.
http://www.nsrl.ttu.edu/publications/opapers.htm

Parish, D.A., H.A. Wichman, J.J. Bull, and R.J. Baker. (2002) Distribution of LINEs and other repetitive elements in the karyotype of the bat Carollia: implications for X-chromsome inactivation. Cytogent. Genome Res. 96:191-197.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12438798&dopt=Abstract

Bull, J.J. and H.A. Wichman. (2001) Applied evolution. Ann. Rev. Ecol. System. 16:183-217.
http://ecolsys.annualreviews.org/cgi/reprint/32/1/183.pdf

Cantrell, M.A., B.J. Filanoski, A. Ingermann, K. Olsson, N. DiLuglio, Z. Lister, H.A. Wichman (2001) An ancient retrovirus-like element contains hot spots for SINE insertion. Genetics 158:769-777.
http://www.genetics.org/cgi/content/full/158/2/769

Cantrell, M.A., R.A. Grahn, L.A. Scott, and H.A. Wichman. (2000) Isolation of markers from recently transposed LINE-1 retrotransposons. BioTechniques 29:1310-16.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11126134&dopt=Abstract

Wichman, H.A., C.D. Yarber, L.A. Scott, and J.J. Bull. (2000) Experimental evolution recapitulates natural evolution. Phil. Trans. R. Soc. Lond. B. 355:1677-1684.
http://www.journals.royalsoc.ac.uk/link.asp?id=9xtekg5a36blcy17

Bull, J. J., M.R. Badgett, and H.A. Wichman. (2000) Big-benefit mutations in a bacteriophage inhibited with heat. Mol. Biol. Evol. 17:942-50.
http://mbe.oupjournals.org/cgi/content/full/17/6/942

Casavant, N.C., L.A. Scott, M.A. Cantrell, L.E. Wiggins, R.J. Baker, and H.A. Wichman. (2000) The end of the LINE? Lack of recent L1 activity in a group of South American rodents. Genetics 154:1809-1817.
http://www.genetics.org/cgi/content/full/154/4/1809

Crill, W.D., H.A. Wichman, and J.J. Bull. (2000) Evolutionary reversals during viral adaptation to alternating hosts. Genetics 154: 27-37.
http://www.genetics.org/cgi/content/full/154/1/27

Wichman, H.A., M.R. Badgett, L.A. Scott, C.M. Boulianne, and J.J. Bull. (1999) Different trajectories of parallel evolution during viral adaptation. Science 285:422-424.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10411508&dopt=Abstract

Casavant, N.C., R.N. Lee, A.N. Sherman, and H.A. Wichman. (1998) Molecular evolution of two lineages of L1 (LINE-1) retrotransposons in the California mouse, Peromyscus californicus. Genetics 150:345-357.
http://www.genetics.org/cgi/content/full/150/1/345

Bull, J.J., M.R. Badgett, H.A. Wichman, J.P. Huelsenbeck, D.M. Hillis, A. Gulati, C. Ho, I.J. Molineaux. (1997) Exceptional convergent evolution in a virus. Genetics 147: 1497-1507.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9409816&dopt=Abstract

Sawby, R., and H.A. Wichman. (1997) Analysis of orthologous retrovirus-like elements in the white-footed mouse, Peromyscus leucopus. J. Mol. Evol. 44:74-80.
http://link.springer-ny.com/link/service/journals/00239/papers97/44n1p74.pdf

Casavant, N.C., A.N. Sherman, and H.A. Wichman. (1996) Two persistent LINE-1 lineages in Peromyscus have unequal rates of evolution. Genetics 142:1289-1298.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8846905&dopt=Abstract

Lee, R.N., J.C. Jaskula, R.A. Van Den Bussche, R.J. Baker and H.A. Wichman. (1996) Retrotransposon mys was active during evolution of the Peromyscus leucopus-maniculatus complex. J. Mol. Evol. 42:44-51.
http://link.springer-ny.com/link/service/journals/00239/papers/42n1p44.pdf

Clough, J.E., J.A. Foster, M. Barnett, and H.A. Wichman. (1996) Computer simulation of transposable element evolution: random template and strict master models. J. Mol. Evol. 42:52-58.
http://link.springer-ny.com/link/service/journals/00239/papers/42n1p52.pdf

Edwards, A.R., R.A. Van Den Bussche, H.A. Wichman, and C.S. Orser. (1994) Unusual pattern of bacterial ice nucleation gene evolution. Mol. Biol. Evol.11:911-920.
http://mbe.oupjournals.org/cgi/reprint/11/6/911.pdf

Bradley, R., and H.A. Wichman. (1994) Rapidly evolving repetitive DNA in a conservative genome: A test of factors that affect chromosomal evolution. Chromosome Res. 2:354-360.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7981939&dopt=Abstract

Van Den Bussche, R.A., R.J. Baker, H.A. Wichman, and M.J. Hamilton. (1993) Molecular phylogenetics of Stenodermatini genera: Congruence of data from nuclear and mitochondrial DNA. Mol. Biol. Evol. 10:944-959.
http://mbe.oupjournals.org/cgi/reprint/10/5/944.pdf

Janecek, L.L., J.L. Longmire, H.A. Wichman, and R.J. Baker. (1993) Organization of repetitive elements in the genome of the white-footed mouse, Peromyscus leucopus. Mamm. Genome 4:374-381.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8395263&dopt=Abstract

Wichman, H.A., and R.A. Van Den Bussche. (1992) In search of retrotransposons: Testing the potential of the polymerase chain reaction. BioTechniques 13:258-263.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1382466&dopt=Abstract

Hamilton, M.J., G. Hong and H.A. Wichman. (1992) Intragenomic movement and concerted evolution of satellite DNA in Peromyscus: Evidence from in situ hybridization. Cytogenet. Cell Genet. 60:40-44.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1582258&dopt=Abstract

Wichman, H.A., R.A. Van Den Bussche, M.J. Hamilton and R.J. Baker. (1992) Transposable elements and the evolution of genome organization in mammals. Genetica 86:287-293.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1334913&dopt=Abstract

Simmons, A.D., J.L. Longmire, T.W. Reeder, H.A. Wichman, and R.J. Baker. (1992) Restriction fragment length polymorphisms in heterochromatic DNA that distinguish chromosomal races of Peromyscus leucopus. Mol. Ecol. 1:251-254.

Wichman, H.A. and C.B. Lynch. (1991) Genetic variation for seasonal adaptation in Peromyscus leucopus: Non-reciprocal maternal effects in a population cross. J. Hered. 82:197-204.

Wichman, H.A., C.T. Payne, O.A. Ryder, M.J. Hamilton, M. Maltbie, and R.J. Baker. (1991) Genomic distribution of heterochromatic sequences in equids: implications to rapid chromosomal evolution. J. Hered. 82:367-377.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1658126&dopt=Abstract

Baker, R.J. and H.A. Wichman. (1990) Retrotransposon mys is concentrated on the sex chromosomes: implications for copy number containment. Evolution 44:2083-2088.

Wichman, H.A., S.S. Potter, and D.S. Pine. (1985) Mys, a family of mammalian transposable elements isolated by a phylogenetic screening procedure. Nature 317:77-81.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2993916&dopt=Abstract

Gram, W.D., H.W. Heath, H.A. Wichman, and G.R. Lynch (1982) Geographic variation in Peromyscus leucopus: Short day induced regression and spontaneous recrudescence. Biol. Reprod. 27:369-373.

Lynch, G.R., and H.A. Wichman (1981) Reproduction and thermoregulation in Peromyscus: Effects of chronic short days. Physiol. Behav. 26:201-205.

Bintz, G.L, H. Wichman Roesbery, and L.B. Bintz (1979) Glycogen levels in field and laboratory-acclimated Richardson ground squirrels. Comp. Biochem. Physiol. 62A:339-342.

Bintz, G.L., and H. Wichman Roesbery (1978) Evaporative water loss by control and starved laboratory rats and Spermophilus richardsoni. Comp. Biochem. Physiol. 59A:275-278.

Book chapters:

Joyce, P., L. Fox, N.C. Casavant, and H.A. Wichman. (1999) Linear estimators for the evolution of transposable elements. Pp. 207-220 in Statistics in Molecular Biology and Genetics. Seillier-Moiseiwitsch, F., ed. Institute of Mathematical Statistics, Hayward CA.

Baker, R.J., B. Albin, R.D. Bradley, J.J. Bull, J. Burns, K.A. Clark, G. Edson, R.E. Estrada, E. Farley, C.B. Fedler, B.M. Gharaibeh, R.L. Hammer, C. Jones, R. Monk, J.T. Montford, G. Moore, N.C. Parker, J. Rawlings, A. Sansom, D.J. Schmidly, R.W. Sims, H. Wichman, and F.D. Yancey. (1996) Natural science databases: resource management and public health. Pp. 10-20 in Organization of Fish and Wildlife Information Managers: Proceedings of the 4th Annual Conference.

Martin, S.L., and H.A. Wichman. (1993) Molecular approaches to mammalian retrotransposon isolation. Pp. 309-322 in Methods in Enzymology, Vol 224. Molecular Evolution: Producing the Biochemical Data. Zimmer, E.A., T.J. White, R.L. Cann, and A.C. Wilson, eds. Academic Press.

Wichman, H.A., R.A. Van den Bussche, M.J. Hamilton, and R.J. Baker. (1993) Transposable elements and the evolution of genome organization in mammals. Pp. 149-155 and Discussion. Wichman, pp 156-157 in Transposable Elements and Evolution. McDonald, J.F., ed. Sinauer Assoc. Inc., Sunderland MA.

Wichman, H.A., C.T. Payne, and T.W. Reeder. (1990) Intrageneric variation in repetitive sequences isolated by phylogenetic screening of mammalian genomes. Pp. 153-160 in Molecular Evolution. Clegg, M.T., and S.J. O'Brien, eds. Wiley-Liss, New York.

Other publications:

Bull, J.J. and H.A. Wichman. (1998) A revolution in evolution. Editorial. Science 1998:1959.

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