PUBLICATIONS
C. WILLIAM BIRKY, JR.
(List does not include abstracts or letters.)
Birky, C. W., Jr., 1964 Studies on the physiology and
genetics of the rotifer Asplanchna. I. Methods and physiology.
J. Exp. Zool. 155:273-292.
Birky, C. W., Jr., 1965 Studies on the physiology and
genetics of the rotifer Asplanchna. II. The genic basis of
a case of male sterility. J. Exp. Zool. 158:349-356.
Birky, C. W., Jr., and Bonnie Field, 1966 Nuclear number
in the rotifer Asplanchna: Intraclonal variation and environmental
control. Science 151:585-587.
Koehler, James K. and C. W. Birky, Jr., 1966 An electron
microscope study of the dimorphic spermatozoa of Asplanchna
(Rotifer). II. the development of "atypical spermatozoa." Zeit.
Zellforsch. 70:303-321.
Birky, C. W., Jr., 1967 Studies on the physiology and
genetics of the rotifer Asplanchna. III. Results of outcrossing,
selfing, and selection. J. Exp. Zool. 164:105-116.
Birky, C. W., Jr., 1967 Rotifers. pp. 245-255. In: Methods
in Developmental Biology, Edited by Fred Wilt and Norman Wessels.
Thomas Y. Crowell Co., New York.
Birky, C. W., Jr., Rossana Zito Bignami, and Sister M.
Jacinta Bentfeld, 1967 Nuclear and cytoplasmic DNA synthesis in adult and
embryonic rotifers. Biol. Bull. 133:502-509.
Birky, C. W., Jr., 1969 The developmental genetics of
polymorphism in the rotifer Asplanchna. I. Dietary vitamin
E control of mitosis and morphogenesis in embryos. J. Exp. Zool. 169:205-210.
Birky, C. W., Jr., and Judith A. Power, 1969 The developmental
genetics of polymorphism in the rotifer Asplanchna. II. A method
for quantitative analysis of changes in morphogenesis induced by vitamin
E, and the short-term inheritance of the effects of vitamin E. J. Exp. Zool.
170:157-168.
Birky, C. W., Jr., 1969 The developmental genetics of
polymorphism in the rotifer Asplanchna. III. Quantitative modification
of developmental responses to vitamin E, by the genome, physiological state,
and population density of responding females. J. Exp. Zool. 170:437-448.
Gilbert, John J., and C. W. Birky, Jr., 1971 Sensitivity
and specificity of the Asplanchna response to dietary a-tocopherol.
J. Nutrit. 101:113-126.
Birky, C. William, Jr., and John J. Gilbert, 1971 Parthenogenesis
in rotifers: the control of sexual and asexual reproduction. Am. Zoologist
11:245-266.
Birky, C. W., Jr., and John J. Gilbert, 1972 Vitamin
E as an extrinsic and intrinsic signal controlling development in the rotifer
Asplanchna: Uptake, transmission and localization of [3H]a-tocopherol.
J. Embryol. Morph. 27:103-120.
Birky, C. W., Jr., 1973 On the origin of mitochondrial
mutants: Evidence for intracellular selection of mitochondria in the origin
of antibiotic-resistant cells in yeast. Genetics 74:421-432.
Perlman, Phillip S., and C. William Birky, Jr., 1974
Mitochondrial genetics in bakers' yeast: A molecular mechanism for recombinational
polarity and suppressiveness. Proc. Nat. Acad. Sci. USA 71:4612-4616.
Birky, C. William, Jr., 1975 Mitochondrial genetics in
fungi and ciliates. pp. 182-224. In: Genetics and Biogenesis of Mitochondria
and Chloroplasts, Edited by C. W. Birky, Jr., P. S. Perlman, and
T. J. Byers. Ohio State University Press, Columbus.
Birky, C. W. Jr., 1975 Effects of glucose repression
on the transmission and recombination of mitochondrial genes in yeast (Saccharomyces
cerevisiae). Genetics 80:695-709.
Birky, C. W., Jr., 1975 Zygote heterogeneity and uniparental
inheritance of mitochondrial genes in yeast. Mol. Gen. Genet. 141:41-58.
Birky, C. Ww., Jr., 1976 The inheritance of genes in
mitochondria and chloroplasts. BioScience 26:26-33.
Birky, C. W., Jr., and Russell V.. Skavaril, 1976 Maintenance
of genetic homogeneity in systems with multiple genomes. Genet. Res. 27:249-265.
Perlman, P. S., C. W. Birky, Jr., C. A. Demko, and R.
L. Strausberg, 1976 Confirmations and exceptions to the phage analogy model:
Input bias, bud position effects, zygote homogeneity, and uniparental inheritance.
pp. 405-414. In: Genetics and Biogenesis of Chloroplasts and Mitochondria,
Edited by Th. Bücher, W. Neupert, W. Sebald, and S. Werner. North-Holland
Publishing Company, Amsterdam, pp. 405-414.
Skavaril, Russell V., C. William Birky, Jr., Richard
E. Duhrkopf, and Jeffrey A. Knight, 1976 The use of CAI to provide problems
for students in introductory genetics. J. Computer-Based Instruction 3:13-20.
Birky, C. William, Jr., Robert L. Strausberg, Philip
S. Perlman, and Jean L. Forster, 1978 Vegetative segregation of mitochondria
in yeast: Estimating parameters using a random model. Molec. Gen. Genet.
158:251-261.
Birky, C. W., Jr., 1978 Transmission genetics of mitochondria
and chloroplasts. Ann. Rev. Genet. 12:471-512.
Birky, C. W. Jr., Catherine A. Demko, Philip S. Perlman,
and Robert L. Strausberg, 1978 Uniparental inheritance of mitochondrial
genes in yeast: Dependence on input bias of mitochondrial DNA and preliminary
investigations of the mechanism. Genetics 89:615-651.
VanWinkle-Swift, Karen P., and C. William Birky, Jr.,
1978 The non-reciprocality of organelle gene recombination in Chlamydomonas
reinhardtii and Saccharomyces cerevisiae. Molec. Gen.
Genet. 166:193-209.
Perlman, Philip S., C. William Birky, Jr., and Robert
L. Strausberg, 1979 Segregation of mitochondrial markers in yeast. Methods
in Enzymology: Biomembranes 56:139-154.
Gilbert, John J., C. William Birky, Jr., and Elizabeth
S. Wurdak, 1979 Taxonomic relationships of Asplanchna brightwelli,
A. intermedia, and A. sieboldi. Arch. Hydrobiol. 87:224-242.
Strausberg, Susan L., and C. William Birky, Jr., 1979
Recombination of yeast mitochondrial DNA does not require mitochondrial
protein synthesis. Curr. Genet. 1:21-31.
Thrailkill, Kathryn M., C. William Birky, Jr., Gudrun
Lückemann, and Klaus Wolf, 1980 Intracellular population genetics:
Evidence for random drift of mitochondrial allele frequencies in Saccharomyces
cerevisiae and Schizosaccharomyces pombe. Genetics 96:237-262.
Treat, Lynda G., and C. William Birky, Jr., 1980 Early
vegetative segregation of mitochondrial genes in Saccharomyces cerevisiae.
Plasmid 4:261-275.
Tilney-Bassett, R. A. E., and C. W. Birky, Jr., 1981
The mechanism of the mixed inheritance of chloroplast genes in Pelargonium:
Evidence from gene frequency distributions among the progeny of crosses.
Theoret. Appl. Genet. 60:43-53.
Birky, C. William, Jr., Karen P. VanWinkle-Swift, Barbara
B. Sears, John E. Boynton, and Nicholas W. Gillham, 1981 Frequency distributions
for chloroplast genes in Chlamydomonas zygote clones: Evidence
for random drift. Plasmid 6:173-192.
Birky, C. w., Jr., Arlene R. Acton, Rosemary Dietrich,
and Maureen Carver, 1982 Mitochondrial transmission genetics: Replication,
recombination, and segregation of mitochondrial DNA and its inheritance
in crosses. pp. 333-348. In: Mitochondrial Genes, Edited by
G. Attardi, P. Borst, and P. P. Slonimski. Cold Spring Harbor Laboratory,
New York.
Waxman, Michael F., and C. William Birky, Jr., 1982 Partial
pedigree analysis of the segregation of yeast mitochondrial genes during
vegetative reproduction. Curr. Genet. 5:171-180.
Birky, C. W. Jr., 1982 Endosymbiosis vs. autogeny. Science
215:495-497. (Essay review of Origins and Evolution of Eukaryotic
Intracellular Organelles, Edited by Jerome F. Frederick. New York
Academy of Sciences, New York, 1981.)
Birky, C. W., Jr., 1983 The partitioning of cytoplasmic
organelles at cell division. Int. Rev. Cytol, Suppl. 15:49-89.
Birky, C. W., Jr., Takeo Maruyama, and Paul Fuerst, 1983
An approach to population and evolutionary genetic theory for genes in mitochondria
and chloroplasts, and some results. Genetics 103:513-527.
Birky, C. W., Jr., 1983 Relaxed cellular controls and
organelle heredity. Science 222:468-475.
Treat-Clemmons, Lynda G., and C. William Birky, Jr.,
1983 Persistent heteroplasmic cells for mitochondrial genes in Saccharomyces
cerevisiae. Curr. Genet. 7:489-492.
Birky, C. William, Jr., Pamela Katko, and Maureen Lorenz,
1984 Cytological demonstration of chloroplast DNA behavior during gametogenesis
and zygote formation in Chlamydomonas reinhardtii. Curr. Genet.
8:1-7.
Lewis, J. E., and C. William Birky, Jr., 1984 Homoplasmic
mutant yeast cells contain no selectable "hidden" mitochondrial
alleles. Curr. Genet. 8:81-84.
Birky, C. William, Jr., and Russell V. Skavaril, 1984
Random partitioning of cytoplasmic organelles at cell division: The effect
of organelle and cell volume. J. Theoret. Biol. 106:441-447.
Hennis, Annette S., and C. William Birky, Jr., 1984 Stochastic
partitioning of chloroplasts at cell division in the alga Olisthodiscus,
and compensating control of chloroplast replication. J. Cell Sci. 70:1-15.
Backer, James S. and C. William Birky, Jr., 1985 The
origin of mutant cells: Mechanisms by which Saccharomyces cerevisiae
produces cells homoplasmic for new mitochondrial mutants. Curr. Genet. 9:627-640.
Banks, Jo Ann, and C. William Birky, Jr., 1985 Chloroplast
DNA diversity is low in a wild plant, Lupinus texensis. Proc.
Nat. Acad. Sci. USA 82:6950-6954.
Birky, C. William, Jr., 1987 The partitioning of cytoplasmic
organelles at cell division. pp. 43-56. In: Spatial Organization in
Eukaryotic Microbes, Edited by R. K. Poole and A. P. J. Trinci. Society
for General Microbiology Special Publications, Vol. 23, IRL Press, Oxford.
Birky, C. W., Jr., 1988 Evolution and variation in plant
chloroplast and mitochondrial genomes. pp. 23-53. In: Plant Evolutionary
Biology,, Edited by Leslie D. Gottlieb and Subodh K. Jain. Chapman
& Hall, Ltd., London.
Birky, C. W., Jr., and J. Bruce Walsh, 1988 Effects of
linkage on rates of molecular evolution. Proc. Nat. Acad. Sci. USA 85:6414-6418.
Birky, C. W., Jr., Paul Fuerst and Takeo Maruyama, 1989
Organelle gene diversity under migration, mutation, and drift: Equilibrium
expectations, approach to equilibrium, effects of heteroplasmic cells, and
comparison to nuclear genes. Genetics 121:613-627.
Vernon-Kipp, Dawne, Steve A. Kuhl, and C. William Birky,
Jr., 1989 Molecular evolution of Polytoma, a non-green chlorophyte.
pp. 284-286 In: Physiology, Biochemistry, and Genetics of Nongreen
Plastids, Edited by C. D. Boyer, J. C. Shannon, and R. C. Hardison.
The American Society of Plant Physiologists.
Birky, C. William, Jr., 1989 Organelle evolution. Genome
31(Supplement 2):1095-1097. (Summary of a workshop conducted by CWB at the
XIth International Congress of Genetics.)
Birky, C. W., Jr., 1991 Evolution and population genetics
of organelle genes: Mechanisms and models. In: Evolution at the Molecular
Level, Edited by R. K. Selander, A. G. Clark, T. S. Whittam. Sinauer,
Sunderland, Mass.
Maruyama, Takeo and C. William Birky, Jr., 1991 Effects
of periodic selection on gene diversity in organelle genomes and other systems
without recombination. Genetics 127:449-451.
Birky, C. William, Jr. and J. Bruce Walsh, 1992 Biased
gene conversion, copy number, and apparent mutation rate differences within
chloroplast and bacterial genomes. Genetics 130:677-683.
Birky, C. William, Jr., 1994 Relaxed and stringent genomes:
Why cytoplasmic genes don't obey Mendel's laws. J. Hered. 85:355-365.
Gordon, Julie, Robert Rumpf, Samuel L. Shank, Dawne Vernon,
and C. William Birky, Jr., 1995 Sequences of the Rrn18 genes of Chlamydomonas
humicola Luksch and C. dysosmos Moewus are identical, in agreement with
their combination in the species C. applanata Pringshein (Chlorophyta).
J. Phycol. 31:312-313.
Birky, C. William, Jr., 1995 Uniparental inheritance
of mitochondria and chloroplast genes: mechanisms and evolution. Proc.
Nat. Acad. Sci. USA 92:11331-11338. Birky95UPI.pdf
Rumpf, Robert, Dawne Vernon, David Schreiber, and C.
William Birky, Jr., 1996 Evolutionary consequences of the loss of photosynthesis
in Chlamydomonadaceae: Phylogenetic analysis of Rrn18 (18S rDNA) in 13 Polytoma
strains (Chlorophyta). J. Phycol. 32:119-126.
Birky, C. William, Jr., 1996 Heterozygosity, heteromorphy,
and phylogenetic trees in asexual eukaryotes. Genetics 144:427-437.
Birky96Heterozygosity.pdf
Birky, C. William, Jr., 1999 Inheritance of Mitochondrial
Mutations. In: Keshav K. Singh (ed.) Mitochondrial Mutations in Aging, Disease
and Cancer, RG Landes Company.
Birky, C. William, Jr., 1999 An even broader perspective
on sex and recombination. J. Evol. Biol. 12:1013-1016. Birky99BroaderPerspective.pdf
Birky, C. William, Jr., 2001 The inheritance of genes
in mitochondria and chloroplasts: Laws, mechanisms, and models. Annu.
Rev. Genet. 35:125-148. Birky01AnnRevGenet.pdf
Vernon, Dawne, Robin Gutell, Jaime Cannone, Robert Rumpf,
and C. William Birky, Jr., 2001. Accelerated evolution of functional plastid
rRNA and elongation factor genes due to reduced protein synthetic load after
the loss of photosynthesis in the chlorophyte alga Polytoma.. Mol. Biol.
Evol. 18:1810-1822. Vernon01PolyRates.pdf
Maughan, H., C. W. Birky,Jr, W. L. Nicholson, W. D. Rosenzweig,
and R. H. Vreeland, 2002. "The paradox of the 'ancient' bacterium which
contains 'modern' protein-coding genes. Mol. Biol. Evol. 19:1637-1639.
Maughan02BacillusPermians.pdf
Lizhi Yu, C.. William Birky, Jr., and Rodney D. Adam,
2002 "The two nuclei of Giardia each have complete copies of
the genome as demonstrated by fluorescence in situ hybridization.
Eukaryotic Cell 1:191-199. Yu02Giardia.pdf
Birky, C. William, Jr., 2002 "Non-Mendelian Mitochondrial
Inheritance: Evolutionary Origin and Consequences." Encyclopedia
of the Human Genome, entry 1129, Nature Publishing Group.
Birky, C. William, Jr., 2002 "Extrnuclear Inheritance."
In Robinson, Richard (ed)., Genetics. New York, MacMillan Reference
USA.
Barraclough, Timothy G., C. William Birky, Jr., and Austin
Burt, 2003 "Diversification in sexual and asexual organisms."
Evolution 57:2166-2172. BarraBirkyBurt2003.pdf
Birky, C. William, Jr. (2004) Bdelloid rotifers revisited.
Proceedings of the National Academy of Sciences USA 101:2651-2652.
Birky04BdelloidsRevisited.pdf
Birky, C. William, Jr. (2005) Sex: Is Giardia
doing it in the dark? Current Biology 15:R56-58. Birky05SexInGiardia?.pdf
Birky, C. William, Jr., Cynthia Wolf, Heather Maughan,
Linnea Herbertson, Elena Henry (2005) Speciation and selection without sex.
Hydrobiologia 546:29-45.
Birky, C. William, Jr. (2005) Sex: Is Giardia
doing it in the dark? Current Biology 15:R56-58
Maughan, Heather., Victoria Callicotte, Adam Hancock, C. William Birky, Jr., Wayne L. Nicholson, Joanna Masel (2006) The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis. Evolution 60:686-695.
Maughan,
Heather, Joanna Masel, C. William Birky Jr, Wayne L. Nicholson (2007)
The roles of mutation accumulation and selection in loss of sporulation
in experimental populations of Bacillus subtilis. Genetics 177:937-948,
Birky, C. William, Jr. (2007) Barcoded DNA: Application
to rotifer phylogeny, evolution, and systematics. Hydrobiologia 593:175-183.
Birky, C. William, Jr. (2008) Uniparental inheritance of organelle genes. Current Biology 18 (16):R1-R4.
Maughan, Heather, C. William Birky Jr, Wayne L. Nicholson (2009) Transcriptome divergence and the loss of plasticity in Bacillus subtilis after 6,000 generations of evolution under relaxed selection for sporulation. Journal of Bacteriology 191:428-433.
Birky, C. William, Jr. (2009) Sex and Evolution in Eukaryotes. In: Encyclopedia of Life Support Systems (EOLSS), Developed under the Auspices of the UNESCO, EoLSS Publishers, Oxford ,UK, [http://www.eolss.net].
Birky, C. William, Jr., Timothy G. Barraclough (2009)
Asexual Speciation. pp. 201-216. In: Lost Sex. The Evolutionary Biology of Parthenogenesis.
Isa Schön, Koen Martens, Peter Van Dijk (eds.) Springer.
Birky, C. William, Jr. (2010) Positively negative evidence for asexuality. Journal of Heredity 101(supp1):S42-S45.
Birky,
C. William, Jr., Joshua Adams, Marlea Gemmel, Julia Perry(2010) Using
population genetic theory and DNA sequences for species detection and
identification in asexual
organisms PLoS One 5:e10609
Birky,
C. William, Jr., Claudia Ricci, Giulio Melone, Diego Fontaneto (2011)
Integrating DNA and traditional taxonomy to describe diversity in
poorly studied microscopic animals: new species of the genus Abrochtha
Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae). Zoological Journal of the Linnean Society 161:723-734 (DOI: 10.1111/j.1096-3642.2010.00674.x).
Schön, Isa,
Ricardo L. Pinto, Stuart Halse, Alison J. Smith, Koen Martens & C.
William Birky, Jr. (2012) Cryptic species in putative ancient asexual
darwinulids (Crustacea, Ostracoda). PLoS One 7(7):e39844 (doi:10.1371/journal.pone.0039844).
Birky,
C. William, Jr. (2013) Species detection and identification in sexual
organisms using population genetic theory and DNA sequences. PLoS One
8(1):e52544.
Morgan,
M.J., Bass, D., Bik, H., Birky, C.W., Blaxter, M., Crisp, M.D.,
Derycke, S., Fitch, D., Fontaneto, D., Hardy, C.M., King, A.J.,
Kiontke, K.C., Moens, T., Pawlowski, J.W., Porazinska, D., Tang, C.Q.,
Thomas, W.K., Yeates, D.K., Creer, S. 2014 A critique of Rossberg et
al.: noise obscures the genetic signal of meiobiotal ecospecies in
ecogenomic datasets. Proc. Roy. Soc. B 281:20133076.
Manuscripts in preparation or submitted
Birky,
C. William, Jr. (2014) Species detection and identification in bacteria
using population genetic theory and DNA sequences. In
preparation for submission to PLoS One.
Through 1980, I gave graduate students who worked with a substantial degree
of independence the option of publishing their thesis research as sole authors.
The resulting papers were:
Brodie, Ann E., 1970 Development of the cuticle in the
rotifer, Asplanchna brightwelli. Z. Zellforsch. 105:515-525.
Brodie, Ann E., 1971 Localization of streptomycin at
the ciliary membrane region of the rotifer, Asplanchna brightwelli.
Exp. Cell Res. 68:157-162.
Bentfeld, Mary E., 1971 Studies of oogenesis in the rotifer,
Asplanchna. I. Fine structure of the female reproductive system.
Z. Zellforsch. 115:165-183.
Bentfeld, Mary E., 1971 Studies of oogenesis in the rotifer,
Asplanchna. II. Oocyte growth and development. Z. Zellforsch.
115:184-195.
Knight, Jeffrey A., 1980 New antibiotic resistance loci
in the ribosomal region of yeast mitochondrial DNA. Genetics 94:69-92.
Berrill, N. J. 1961 Growth, Development, and Pattern
W. H. Freeman & Company, San Francisco. Reviewed inThe American
Biology Teacher 23:534 (1960).
Grun, Paul 1977 Cytoplasmic Genetics and Evolution
Columbia University Press, New York. Reviewed in American Scientist
65:232 (1977).
Gillham, N. W. 1978 Organelle Heredity Raven
Press, New York. Reviewed in Science 204:761 (1979).
Boffey, S. A. and Lloyd, D. (eds.) 1988 Division
and Segregation of Organelles Cambridge University Press, Cambridge.
Reviewed in Trends in Genetics 5:385-386 (1989).
Bogorad, Lawrence and Indra K. Vasil (eds.) 1991 The
Molecular Biology of Plastids. Academic Press, San Diego. Reviewed
in Science 255:95-96 (1992).
Dyer, Betsey Dexter and Obar, Rovert Alan 1994 Tracing
the History of Eukaryotic Cells. The Enigmatic Smile. Columbia University
Press, New York. Reviewed in Science 266:309-310.
