| H |
 |
 |
Hansen, T. F. and
E. P. Martins. 1996. Translating between microevolutionary process
and macroevolutionary patterns: A general model of the correlation
structure of interspecific data. Evolution 50:1404-1417.
Hardy GH. 1908. Mendelian proportions in a mixed population. Yale J Biol Med 1;76(2):79-80
Harshman, J. 1994. The effect of
irrelevant characters on bootstrap values. Syst. Zool. 43:419-424.
Hartl, D. L., A. R. Lohe, and
E. R. Lozovskaya. 1997. Modern thoughts on an ancyent marinere:
function, evolution, regulation. Annu Rev Genet. 31:337-358.
Hasegawa, M. and
H. Kishino. 1989a. Heterogeneity of tempo and mode of
mitochondrial DNA evolution among mammalian
orders. Jpn. J. Genet. 64:243-258.
Hasegawa, M. and
H. Kishino. 1989b. Confidence limits on the maximum-likelihood estimate of the hominoid tree from mitochondrial-DNA sequences. Evolution. 43:672-677.
Hasegawa, M. and
H. Kishino. 1994. Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree. Mol. Biol. Evol. 11:142-145.
Hasegawa, M., H. Kishino, and
T. Yano. 1985. Dating of the human-ape splitting by a molecular
clock of mitchondrial DNA. J. Mol. Evol. 22:160-174.
Heckman, D. S., D. M. Geiser, B. R.,
R. L. Stauffer, N. L. Kardos, S. B. Hedges. 2001. Molecular evidence
for the early colonization of land by fungi and plants. Science
293:1129-1133.
Hedges, S. B., P. H. Parker,
C. G. Sibley, and S. Kumar. 1996. Continental breakup and the
ordinal diversification of birds and
mammals. Nature. 381:226-229.
Heidelberg, J. F., J. A. Eisen,
W. C. Nelson, R. A. Clayton, M. L. Gwinn, R. J. Dodson, D. H. Haft,
E. K. Hickey, J. D. Peterson, L. Umayam, S. R. Gill, K. E. Nelson,
T. D. Read, H. Tettlelin, D. Richardson, M. D. Ermolaeva,
J. Vamathevan, S. Bass, H. Qin, I. Gragoi, P. Sellers, L. McDonald,
T. Utterback, R. D. Fleishmann, W. C. Niernam, O. White, S. L. Salzberg,
H. O. Smith, R. R. Colwell, J. J. Mekalamos, J. C. Venter and
C. M. Fraser. 2000. DNA sequence of both chromosomes of the
cholera pathogen Vibrio cholerae. Nature 406:477-484.
Hein, J. 1989. A new method that simultaneously aligns and reconstructs ancestral sequences for any
number of homologous sequence, when the phylogeny is given. Mol. Biol. Evol. 6:649-668.
Henikoff, S. 1998. Conspiracy of silence among repeated transgenes. Bioessays. 20:532-535.
Henikoff, S. and
J. G. Henikoff. 1992. Amino acid substitution matrices from
protein blocks. Proc. Natl. Acad. Sci. USA 89:10915-10919.
Hess, C. M., J. Gasper, H. E. Hoekstra, C. E. Hill, and S. V. Edwards. 2000. MHC class II pseudogene and genomic signature of a 32-kb cosmid in the house finch (Carpodacus mexicanus). Genome Res. 10:613-623.
Hey, J. and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760.
Hickson, R. E., C. Simon and
S. W. Perrey. 2000. The performance of several multiple-sequence
alignment programs in relation to secondary-structure features for an
rRNA sequence. Mol. Biol. Evol. 17:530-539.
Hill,
A. V. S., C. E. M. Allsopp, D. Kwiatowski, N. M. Anstey, P. Twumasi,
P. A. Rowe, S. Bennett, D. Brewster, A. J. McMichael and B. M. Greenwood.
1991. Common West African HLA antigens are associated with protection
from severe malaria. Nature 352:595-600.
Hillis, D. M. and J. J. Bull.
1993. An empirical test of bootstrapping as a method for assessing
confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
Hillis, D.M.,
J. P. Huelsenbeck and C. W. Cunningham. 1994. Application and
accuracy of molecular phylogenies. Science 264:671-677.
Hillis, D. M., Mable, B. K, and Moritz, C. 1996. Applications of molecular systematics: the state of the field and a look to the future. pp 515-543 in Molecular systematics 2nd ed., Hillis, D. M., Mable, B. K., and Moritz, C. (eds.). Sunderland.
Hirockika, H., H. Okamoto, and
T. Kakutani. 2000. Silencing of retrotransposons in arabidopsis
and reactivation by the ddm1 mutation. Plant Cell 12:357-369.
Hochbaum, D. S. and A. Pathria. 1997. Path costs in evolutionary tree reconstruction. J. Comput. Biol. 4:163-175.
Hoegg, S., Brinkmann, H., M. Taylor, J. and A. Meyer. 2004. Phylogenetic timing of the fish-specific genome duplication correlates with phenotypic and taxonomic diversification in fishes. Journal of Molecular Evolution 59:190-203.
Hoegg, S. and A. Meyer. 2005. Hox clusters as models for vertebrate genome evolution. Trends in Genetics 21:421?424.
Hoffmaster A, Ravel J, Rasko DA et al. (2004) Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc Natl Acad Sci U S A 101: 8449-54.
Hoffmaster A, Ravel J, Rasko DA et al. (2004) Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc Natl Acad Sci U S A 101: 8449-54.
Holder, M. T. and P. O. Lewis. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews Genetics 4:275-284.
Holmes, I. and W. J. Bruno. 2001. Evolutionary HMMs: a Bayesian approach to multiple alignments. Bioinformatics 17:803-820.
Hudson, R. R. 1987. Estimating the
recombination parameter of a finite population without selection.
Genet. Res. 50:245-250.
Hudson, R. R. 1990. Gene genealogies and
the coalescent process. In Oxford Surveys in Evolutionary Biology,
Volume 7, ed. D. Gutuyma and J. Antonovics, Oxford University Press,
Oxford.
Hudson, R. R. 1992. Gene trees, species trees and the segregation of ancestral alleles. Genetics 131:509-512.
Hudson, R. R., Kreitman, M., and M. Aguade. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
Huelsenbeck, J. P. 1995. The performance of phylogenetic methods in simulation. Systematic Biology 44:17-48
Huelsenbeck, J. P., and J. J. Bull. 1996. A likelihood-ratio test to detect conflicting phylogenetic signal. Systematic Biology 45:92-98.
Huelsenbeck, J. P. and
K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing
using maximum likelihood. Ann. Rev. Ecol. Syst. 28:437-466.
Huelsenbeck, J. P. and
K. A. Dyer. 2004. Bayesian estimation of positively selected sites. Journal of Molecular Evolution 58: 661-672.
Full Text
Huelsenbeck, J. P., B. Larget, and M. E. Alfaro. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain monte carlo. Mol. Biol. Evol. 21:1123-1133.
Huelsenbeck, J. P., Larget, B., Miller, R. E., and Ronquist, F. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51:673-688.
Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Syst. Biol. 52:131-158.
Huelsenbeck, J. P. and
B. Rannala. 1997. Phylogenetic methods come of age: testing
hypotheses in an evolutionary context. Science 276:227-232.
Huelsenbeck, J. P. and
B. Rannala. 2003. Detecting correlation between characters in a comparative analysis with uncertain phylogeny. Evolution 57:1237-1247.
Huelsenbeck, J. P. and
B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:905-913.
Huelsenbeck, J. P., B. Rannala,
and B. Larget. 2000. A Bayesian framework for the analysis of
cospeciation. Evolution 54:352-364.
Huelsenbeck, J. P., B. Rannala and
J. P. Masly. 2000. Accommodating phylogenetic uncertainty in
evolutionary studies. Science 288:2349-2350.
Huelsenbeck, J. P. and F.
Ronquist. 2001. MrBAYES: Bayesian inference of phylogenetic
trees. Bioinformatics 17:754-755.
Huelsenbeck, J. P., F. Ronquist,
R. Nielsen and J. P. Bollback. 2001. Bayesian inference of phylogeny
and its impact on evolutionary biology. Science 294:2310-2314.
Hurvich C. M. and C. -L. Tsai. 1989. Regression and time series model selection in small samples. Biometrika 76:297-307.
|