Publications
David Houle
Full
texts (or abstracts) of most papers are online. Click on the authors names.
·
Tomaiuolo,
M., R. Bertram and D. Houle. 2008.
Enzyme isoforms may increase phenotypic robustness. Evolution 62:2868-2883.
We showed that having two forms of an enzyme can
increase the range of environments over which an individual functions
properly. This provides a novel
hypothesis for the divergence of gene function in evolution.
·
Hansen, T. F., and D. Houle. 2008.
Measuring and comparing evolvability and constraint in multivariate characters.
Journal of Evolutionary Biology 21:1201-1219. Corrected version of
Appendix 2. The published Appendix contains several errors. Thanks to John
Stinchcombe for pointing out the problem. We
derive measurements of the ability to evolve, the tendency for characters to slow the evolution of others,
and measures of differences among populations based on these measures.
·
Haag-Liautard,
C., N. Coffey, D. Houle, M. Lynch, B. Charlesworth and P. D. Keightley. 2008.
Direct estimation of the mitochondrial DNA mutation rate in D. melanogaster. PLOS
Biology 6:1706-1714. We showed that the spontaneous mutation rate of
mitochodria is higher than in the nuclear genome, and that there are peculiar
biases in the transition probabilities when a mutation occurs.
·
van der Linde, K. and D. Houle. 2008b.
Response to O’Grady et al.:
The potential and peril of the supertree approach. Insect
Systematics and Evolution
39:281-286. O’Grady et al. criticized the preceding paper for various reasons. We more fully explain the methods used, and
show that their criticisms are largely misunderstandings of what we did, or on
misconceptions about the nature of super-tree analyses.
·
van der Linde, K. and D.
Houle. 2008a. A phylogeny of the
genus Drosophila and some related
genera. Insect Systematics and Evolution
39:241-268. We use a supertree analysis to estimate the phylogeny
of the subfamily Drosophilinae, which includes the Drosophila melanogaster. Our
results suggest that the genus Drosophila is paraphyletic.
·
Houle,
D. 2007. A dispatch from the multivariate frontier. Journal of Evolutionary
Biology. 20:22-23.
·
Haag-Liautard, C., Dorris, X. Maside, S. Macaskill, L. Halligan,
D. Houle, D. Charlesworth, P. D. Keightley. 2007. Direct estimation of per
nucleotide and genomic deleterious mutation rates in Drosophila. Nature 445: 82-85. We
estimated the spontaneous mutation rate of the nuclear genome using mutation
accumulation lines from my lab.
·
Pélabon,
C., T. F. Hansen, A. J. R. Carter and D. Houle. 2006. Response of
fluctuating and directional asymmetry to selection on wing shape in Drosophila
melanogaster. Journal of Evolutionary Biology. 19:764-776.
·
van
der Linde, K., J. S. Birdsley, L. M. Alonso and D. Houle. 2006. First records
of Zaprionus indianus (Diptera, Drosophilidae), a potential
pest species, from Panama and the United States of America. Florida
Entomologist 89:402-404. We report the first records for this
species in North America. Z. indianus first appeared in south
Florida in July, and in Tallahassee, Florida between July and September
2005. This is a good opportunity for research on an invading
species. Contact me if you would like a stock.
·
Houle,
D. and Kondrashov, A.S. 2006. Mutation. Pp. 32-48 in Evolutionary
Genetics: Concepts and Case Studies, edited C.W. Fox and J. B. Wolf.
Oxford University Press.
·
Rifkin,
S. A., D. Houle, J. Kim, and K. P. White. 2005. A mutation accumulation assay
reveals a broad capacity for rapid evolution of gene expression. Nature
438:220-223. This study of mutation-accumulation lines revealed that
expression of 40% of the nearly 12,000 genes studied had been affected by
mutation. The rate of evolution between species is much lower than the
neutral expectation based on this variation, implicating stabilizing selection
on expression.
·
Fuller,
R. C., D. Houle, and J. Travis. 2005. Sensory bias as an explanation for
the evolution of mate preferences. American Naturalist 166:437-446. We place the
five major models for mate preference in the same quantitative genetic context,
revealing that much of the discussion of these models is misguided. In
particular, most workers do not understand the sensory bias model, and it has
therefore never been tested.
·
Mezey, J. G.,
D. Houle, and S. V. Nuzhdin. 2005. Naturally segregating quantitative trait
loci affecting wing shape of Drosophila melanogaster. Genetics
169:2101-2113. We confirmed that many genes have variation affecting wing
shape within our study population. Furthermore some of these show genetic
interactions with the hedgehog and decapentaplegic pathways.
·
Mezey,
J., and D. Houle. 2005. The dimensionality of genetic variation for wing
shape in Drosophila melanogaster. Evolution 59:1027-1038. We studied
the inheritance of 20 aspects of wing shape within a single population, and
were able to demonstrate genetic variation in at least 17 of these 20. This
suggests that the evolution of wing shape is not constrained by a lack of genetic
variation.
·
Hereford, J., T. F.
Hansen and D. Houle. 2004. Comparing strengths of directional selection:
how strong is strong? Evolution 58:2133-2143. Appendix giving references to
reviewed papers has been dropped from the Evolution web site. The strength of selection
standardized by the mean of the trait is directly comparable to the strength of
selection on fitness. Review of published estimates suggests that
selection is generally overestimated, but it is not possible to choose among
the many possible explanations for this.
·
McCune,
A.R., D. Houle, K. McMillan, R. Annable and A. S. Kondrashov. 2004. Two
classes of deleterious recessive alleles in a natural population of zebrafish, Danio
rerio. Proc. Roy. Soc. London B. 271:2025-2033. Inbreeding
depression in viability is due in part to recessive lethals that act early in
development, but also to later-acting smaller effect mutations.
·
Houle, D.
and S.V. Nuzhdin. 2004. Mutation accumulation and the effect of copia
insertions in Drosophila melanogaster. Genetical Research.
83:7-18.
·
Hansen,
T. F., and D. Houle. 2004. Evolvability, stabilizing selection,
and the problem of stasis. Pp. 130-150 in The Evolutionary Biology of Complex Phenotypes. M. Pigliucci and K.
Preston, Eds. Oxford University Press. We discuss possible explanations for
the frequently observed lack of evolutionary change over long periods of time.
The widely accepted idea that stabilizing selection is responsible seems
implausible, and is not supported by evidence. The alternative that there are
constraints on variation should be taken more seriously.
·
Houle, D., J.G. Mezey, P.
Galpern and A. Carter. 2003. Automated measurement of Drosophila wings. BMC
Evolutionary Biology. 3:25. This paper introduces our mostly
automated system for measuring Drosophila wings.
·
Mezey,
J. and D. Houle. 2003. Comparing G matrices: Are common principal
components informative? Genetics 165:411-425.
Proportional (or more similar) G matrices imply a modular organisation of
phenotypes, where each module affects a phenotypic subspace orthogonal to other
such modules. Powerful CPC analyses therefore can tell us something
fundamental about genotype-phenotype maps.
·
Worley,
A. C., D. Houle, and S. C. H. Barrett. 2003. Consequences of hierarchical
allocation for the evolution of life-history traits. American Naturalist
161:153-167. We use numerical calculations to investigate when trade-offs
can be revealed by selection in a multi-trade-off hierarchy.
·
Houle, D.,
and L. Rowe. 2003. Natural selection in a bottle. American Naturalist.
161:50-67. We
suggest that the study of natural selection in laboratory situations can
provide an essential test of our ability to understand and predict adaptation.
We present data on the fitness landscape for age at maturity of my laboratory
fly population.
·
Fuller,
R. C. and D. Houle. 2003. Inheritance of developmental instability.
Pp. 157-184 in Developmental Instability: Causes and Consequences,
edited by M. Polak. Oxford University Press. Traditional designs for
estimating genetic variation in fluctuating asymmetry have no power. Therefore,
the general lack of studies showing significant heritability of FA is not
informative.
·
Fuller,
R. C., and D. Houle. 2002. Detecting variation in developmental instability
by artificial selection on fluctuating asymmetry. Journal of Evolutionary
Biology. 15:954-960. We investigate the power of selection experiments to detect
genetic variation in the ability to produce a symmetrical body. Selection
for decreased symmetry, which is rarely performed, is much more powerful than
selection for increased symmetry.
·
Steppan,
S. J., P. C. Phillips, and D. Houle. 2002. Comparative quantitative genetics:
evolution of the G matrix. Trends in Ecology and Evolution 17:320-327. We review
approaches to the study of the additive genetic variance-covariance matrix,
concluding that proper analytical and statistical tools are just now becoming
available to test interesting hypotheses.
·
McCune,
A. R, R. C. Fuller, A. A. Aquilina, R. M. Dawley, J. M. Fadool, D. Houle, J.
Travis, and A. S. Kondrashov. 2002. Low number of genomic recessive lethals
in two fish species. Science 296:2398-2401. We show that
the average number of lethals carried in two outbred fish populations is
similar to the number carried by Drosophila, which has a much smaller
genome.
·
Houle, D, J.
Mezey. and Galpern, P. 2002. Interpretation of the results of partial
principal components analysis. Evolution 56:433-440. We show that
a popular new technique for comparing variance-covariance matrices gives
results that do not reflect biological intuition, and we urge caution in its
use.
·
Houle, D.
and A.S. Kondrashov. 2002. Coevolution of costly mate choice and
condition-dependent display of good genes. Proceedings of the Royal Society
of London, Biological Sciences, 269:97-104. We show that a relatively
simple good-genes model in which female choice is relative can explain even
extreme exaggeration of male traits by sexual selection.
·
Houle, D.
2001. The character problem in life history evolution. Pp. 109-140 in, The
Character Concept in Evolutionary Biology. G. P. Wagner,
ed. Academic Press. I argue that the most appropriate evolutionary definition of
a character is a biological process that integrates the effects of many genetic
loci. I argue that such processes are likely to exist and to form an
appropriate target for analysis intermediate to black box quantitative genetics
and fully detailed functional genomics. This idea forms the basis for the work
on wing variation that is my current research.
·
Houle, D.
2000. A simple model of the relationship between asymmetry and developmental
stability. Journal of Evolutionary Biology 13:720-730. I showed
that the standard model for the development of asymmetry of morphological
traits cannot readily explain the strong relationships between asymmetry and
fitness that some claim to have observed.
·
Houle, D. 2000. Is
there a ‘g’ factor for fitness? Pp. 149-159 in The Nature of Intelligence,
Novartis Foundation Symposium 233. John Wiley, London. I
investigated the idea that variation in fitness components covary positively,
as do the components of test-taking ability in humans. I conclude that the idea
is plausible but cannot be confirmed because suitable data are lacking.
·
Leung, B., M. R.
Forbes, and D. Houle. 2000. Fluctuating asymmetry as a bioindicator of
stress: comparing efficacy of analyses involving multiple traits. Am.
Nat. 155:101-115.
·
Pletcher, S.D.,
D. Houle, and J.W. Curtsinger. 1999. The evolution of age-specific
mortality rates in Drosophila melanogaster: divergence among unselected
lines. Genetics 153:813-823.
·
Lynch,
M., J. Blanchard, D. Houle, T. Kibota, S. Schultz, L. Vassilieva, and J.
Willis. 1999. Perspective: Spontaneous deleterious mutation. Evolution
53: 645-663.
·
Houle, D.
1998. High enthusiasm and low R-squared. Asymmetry, developmental
stability, and evolution, by A.P. Møller and J. P. Swaddle. Evolution
52:1872-1876.
·
Houle, D.
1998. How should we explain variation in the genetic variance of traits? Genetica,
102/103:241-253. I tested a series of hypotheses about the differences in
mean-standardized variation in traits. More genetically complex traits had
larger mutational inputs and more standing genetic variation. I really like
this paper.
·
Pletcher,
S.D., D. Houle, and J.W. Curtsinger. 1998. Age-specific properties
of spontaneous mutations affecting mortality in Drosophila melanogaster. Genetics,
148:287-303.
·
Houle, D., A. S. Kondrashov, L.
Yu. Yampolsky, S. Caldwell, and P. L. Steponkus. 1997. The effect of
cryopreservation on the lethal mutation rate in Drosophila melanogaster. Genetical
Research, 69:209-213.
·
Houle, D., K. A. Hughes, S.
Assimacopolous, and B. Charlesworth. 1997. The effects of spontaneous
mutation on quantitative traits. II. Dominance of mutations with effects on
life-history traits. Genetical Research, 70:27-34.
·
Houle, D. 1997. Comment on
"A meta-analysis of the heritability of developmental stability" by
Moller and Thornhill. J. Evol. Biol. 10:17-20.
·
Houle, D., B. Morikawa, and M.
Lynch. 1996. Comparing mutational variabilities. Genetics,
143:1467-1483.
·
Rowe, L. and D. Houle. 1996.
The lek paradox, condition dependence and genetic variance in sexually selected
traits. Proc. Roy. Soc. London B, 263:1415-1421.
·
Houle, D., K. A. Hughes, D. K.
Hoffmaster, J. Ihara, S. Assimacopolous, D. Canada, and B. Charlesworth. 1994.
The effects of spontaneous mutation on quantitative traits. I. Variance and
covariance of life history traits. Genetics, 138:773-785.
·
Kondrashov, A. S. and D. Houle.
1994. Genotype-environment interactions and the estimation of the genomic
mutation rate in Drosophila melanogaster. Proc. Roy. Soc. London B,
258:221-227.
·
Houle, D. 1994. Adaptive distance and the
genetic basis of heterosis. Evolution 48:1410-1417.
·
Houle, D. 1992. Comparing
evolvability and variability of quantitative traits. Genetics
130:195-204. Data set and references available here.
·
Houle, D., D. Hoffmaster, S.
Assimacopolous, and B. Charlesworth. 1992. The genomic mutation rate for
fitness in Drosophila. Nature 359:58-60. However, see Correction,
Nature, 371:358.
·
Houle, D. 1991. Genetic covariance of life
history traits: what genetic correlations are made of and why it matters. Evolution
45:630-648.
·
Zeng, Z.-B., D. Houle, and C. C.
Cockerham. 1990. How informative is Wright's estimator of the number of
genes affecting a quantitative character? Genetics 126:235-247.
·
Houle, D.
1989. Allozyme-associated heterosis in Drosophila melanogaster. Genetics
123:789-801.
·
Houle, D. 1989. The
maintenance of polygenic variation in finite populations. Evolution
43:1767-1780.
