Integrative Biology 200B Spring 2007
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION"
Most important recommended readings are
in bold face; required readings also have two asterisks
Feb
8 - 15; Feb 27 :
QUANTITATIVE CHARACTER EVOLUTION WITHIN A CLADOGRAM
Abouheif E. 1998. Random trees and
the comparative method: a cautionary tale. Evolution 52:1197-1204
Abouheif, E. 1999. A method
for testing the assumption of phylogenetic independence in comparative data.
Evol.
Ecol. Res. 1:895-909.
Ackerly,
Ackerly,
Ackerly,
Ackerly,
Ackerly,
Archie,
J. 1989. Homoplasy excess ratios: New indices for
measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index. SystZool.
38:253-269.
Archie,
J. 1996. Measures of homoplasy.
Pages 153-188 in M.
J. Sanderson and L. Hufford, editors. Homoplasy: the recurrence of similarity in evolution.
Academic Press,
Armstrong
D, Westoby M. 1993. Seedlings from large seeds
tolerate defoliation better: a test using phylogenetically
independent contrasts. Ecology 74:1092-1100
Bauwens D,
Bjorklund, M.
1994. The independent contrast method in comparative biology. Cladistics 10(4): 425-433.
Broughton, R. E., S. E. Stanl;ey, and R. T. Durrett. 2000. Quantification of homoplasy
for nucleotide transitions and transversions and a
reexamination of assumptions in weighted phylogenetic analysis. Systematic Biology 49: 617-627.
Burt, A. 1989. Comparative methods
using phylogenetically independent contrasts.
Burt,
B. B. 2001. Evolutionary stasis, constraint and other
terminology describing evolutionary patterns. Biol. J. Linn. Soc.
72:509-517.
Cheverud, J., and M.
Dow. 1985. An autocorrelation analysis of the effect of
lineal fission on genetic variation among social groups. Amer. J.
Phys. Anthropol. 67:113-121.
Cheverud, J. M., M. M. Dow, and
W. Leutenegger. 1985. The quantitative assessment of phylogenetic
constraints in comparative analyses:
Sexual dimorphism in body weight among primates. Evolution,
39, 1335-1351.
Cliff, A. D., and Ord, J. K. 1973. Spatial Autocorrelation.
Coddington, J. 1994. The roles of homology and convergence in studies of adaptation.
Pages 53-78 in P. Eggleton and R. Vane-Wright, editors. Phylogenetics
and ecology. Academic Press,
Cunningham
CW, Omland K, Oakley TH. 1998. Reconstructing
ancestral character states: a critical reappraisal. TREE 13:361-366
de Queiroz, K.
1996. Including the characters of interest during tree
reconstruction and the problems of circularity and bias in studies of character
evolution. AmerNat. 148:700-708.
Desdevises, Y., P. Legendre, L. Azouzi, and S. Morand.
2003. Quantifying phylogenetically structured
environmental variation. Evolution 57:2647-2652.
Diaz-Uriarte R,
Dîaz-Uriarte, R. and T. Garland.
1998. Effects of branch-length
errors on the performance of phylogenetically
independent contrasts. Syst. Biol. 47: 654-672.
Diniz-Filho, J. A. F., C. E. Ramos de Sant'Ana,
and L. M. Bini. 1998. An eigenvector
method for estimating phylogenetic inertia. Evolution 52:1247-1262.
Donoghue, M. J., and
Farris,
J. 1989. The retention index and the rescaled consistency
index. Cladistics 5:417-419.
Farris, J.
S. 1999.
Likelihood and Inconsistency. Cladistics 15: 199-204.
** Felsenstein, J.
1985. Phylogenies and the
comparative method. Am. Nat. 125:1-15.
Freckleton RP. 2000. Phylogenetic tests
of ecological and evolutionary hypotheses: checking for phylogenetic
independence. Func. Ecol. 14:129-134
Freckleton, R. P., P. H. Harvey, and M. Pagel.
2002. Phylogenetic analysis and comparative data: a test and review of the
evidence. Amer. Nat. 160:712-726.
Friday, A. 1987. Models of evolutionary
change and the estimation of evolutionary trees.
Gittleman, J., and H.-K. Luh. 1992. On comparing
comparative methods. Ann. Rev. Ecol. gittSyst.
23:383-404.
Gittleman, J., and H.-K. Luh. 1994. Phylogeny,
evolutionary models and comparative methods: a simulation study. Pages 103-122 in P. Eggleton and R. Vane-Wright, editors. Phylogenetics
and ecology. Academic Press,
Gittleman, J., and M. Kot.
1990. Adaptation: statistics and a null model for estimating phylogenetic
effects. Syst. Zool.
39:227-241.
Givnish, T. 1997. Adaptive
radiation and molecular systematics: issues and
approaches. Pages 1-54 in
T. J. Givnish and K. J. Sytsma,
editors. Molecular evolution and adaptive radiation.
Goldman, N., J. P. Anderson, A. G.
Rodrigo. 2000. Likelihood-based tests of topologies in phylogenetics.
Systematic Biology 49: 652-670.
Grafen, A. 1989. The phylogenetic
regression. Phil. Trans. Royal Soc.
Hansen, T. F., and S. H. Orzack.
2005. Assessing current adaptation and phylogenetic inertia as explanations of
trait evolution: The need for controlled comparisons. Evolution 59:2063-2072
Hansen, T. F. and E. P. Martins. 1996.
Translating between micorevolutionary process
and macroevolutionary patterns: the correlation
structure of interspecific data. Evol. 50: 1404-1417.
Harris, M. A., and Steudel, K. (1997). "Ecological correlates of hind-limb length in the Carnivora." Journal of Zoology (
Harvey, P. H., and T. H. Clutton-Brock.
1985. Life history variation in primates. Evolution 39:559-581.
Harvey, P., A. Read, and S. Nee.
1995. Further remarks on the role of phylogeny in comparative ecology. JEcol.
83:733-734.
Harvey, P., A. Read, and S. Nee.
1995. Why ecologists need to be phylogenetically
challenged. JEcol. 83:000-000.
Henry, C. S., M. L. M. Wells, and C. M. Simon. 1999. Convergent evolution of courtship songs among cryptic species of the Carnea group of lacewings (Neuroptera: Chrysopidae: Chrysoperla). Evolution 53: 1165-1179.
Högland, J., and B. Sillén-Tullberg. 1994. Does lekking
promote the evolution of male-biased size dimorphism in birds? On the use of comparative approaches. Amer. Nat.
144:881-889.
Hormiga, G., N. Scharff, and J. A. Coddington. 2000. The phylogenetic basis of sexual size dimorphism in orb-weaving spiders. Systematic Biology 49: 435-462.
Housworth, E. A., and E. P. Martins. 2001. Random sampling of
constrained phylogenies: Conducting phylogenetic analyses when the phylogeny is
partially known. Syst. Biol. 50:628-639.
Huelsenbeck, J. P. and R. Nielsen. 1999.
Effect of nonindependent substitution on phylogentic accuracy.
Systematic Biology 48: 317-328.
Huelsenbeck,
J. P., and B. Rannala.
2003. Detecting correlation between characters in a comparative analysis with
uncertain phylogeny. Evolution 57:1237-1247.
Huey, R.B. and A.F.
Bennett. 1987.
Phylogenetic studies of co-adaptation: preferred temperature versus optimal
performance temperatures of lizards. Evolution 41: 1098-115.
Huey, R.B.
1987. Phylogeny, history, and the
comparative method. Pp. 76-101 in Feder, M.E., A.F. Bennett, W.W. Burggren,
R.B. Huey (eds). New Directions in
Ecological Physiology.
Irschick, D. J. and J. B. Losos. 1998. A
comparative analysis of the ecological significance of maximal locomotor performance in
Jackman, T. R., A. Larson, K. de Queiroz, J. B. Losos. 1999.
Phylogenetic relationships and tempo of early diversification of Anolis lizards. Systematic Biology 48: 254-285.
Johnson, s. G. and E.
Bragg. 1999.
Age and polyphyletic origins of hybrid and spontaneous parthenogenic Campeloma (Gastropoda: Viviparidae) from the southeastern
Knowles, L. L. 2000.
Test of Pleistocene speciation in montane
grasshoppers (Genus Melanoplus)
from the
Kochmer, J., and S. Handel. 1986. Constraints and
competition in the evolution of flowering phenology. EcolMonogr.
56:303-325.
Leroi, A. M., M. R. Rose, and G. V. Lauder.
1994. What does the comparative method reveal about adaptation? Amer. Nat.
143:381-402.
Lord,
J., M. Westoby, and M. Leishman.
1995. Seed size and phylogeny in six temperate floras:
constraints, niche conservatism, and adaptation. Amer. Nat. 146:349-364.
Losos, J. B. 1994. An
approach to the analysis of comparative data when a phylogeny is unavailable or
incomplete. Syst. Biol. 43:117-123.
Losos, J. B.
1996. Phylogenies and comparative
biology, Stage II: Testing causal hypotheses derived from phylogenies with data
from extant taxa. Syst.
Biol. 45: 259-260. [Introduction to a
symposium -- several relevant papers here]
Losos J. 1999. Commentaries
: Uncertainty in the reconstruction of ancestral character states and
limitations on the use of phylogenetic comparative methods. Animal Behaviour 58:1319-1324
Maddison W. 1991. Squared-change
parsimony reconstructions of ancestral states for continuous-valued characters on
a phylogenetic tree. Syst. Zool.
40:304-314
Martins, E. P. 1994. Estimating
the rate of phenotypic evolution from comparative data. Amer. Nat.
144:193-209.
Martins, E. P. 1996. Conducting
phylogenetic comparative studies when the phylogeny is not known.
Evolution 50:12-22.
Martins,
E. P. 1996. Phylogenies, spatial autoregression,
and the comparative method: a computer simulation test. Evol. 50: 1750-1765.
Martins EP. 1999. Estimation of
ancestral states of continuous characters: a computer simulation study. Syst. Biol. 48:642-650
Martins, E.P. and T.
Garland, Jr. 1991.
Phylogenetic analyses of
the correlated evolution of continuous characters: a simulation
study. Evolution 45: 534-557.
Martins, E., and T. Hansen.
1996. A microevolutionary link between phylogenies
and comparative data. Pages 273-288 in P. Harvey, A. Leigh
Brown, J. Maynard Smith, and S. Nee, editors. New uses
for new phylogenies.
Martins, E. P., and
Hansen, T. F. 1997.
Phylogenies and the comparative method:
A general approach to incorporating phylogenetic information into the
analysis of interspecific data. Am. Nat.
McKitrick, M. C. 1993. Phylogenetic
constraint in evolutionary theory: Has it any explanatory power? Ann. Rev.
Ecol. Syst. 24:307-330.
McPeek, M. A.
1995. Testing hypotheses about
evolutionary change on single branches of a phylogeny using evolutionary
contrasts. Am. Nat. 145: 686-703.
**
Miles, D. B. and A. E. Dunham.
1993. Historical perspectives in
ecology and evolutionary biology: the use of phylogenetic comparative
analyses. Ann. Rev. Ecol. Syst. 24: 587-619.
Morales, E. 2000.
Estimating phylogenetic inertia in Tithonia (Asteraceae):
a comparative approach. Evolution 54:
475-484.
Oakley
TH, Cunningham CW. 2000. Independent contrasts succeed where ancestral
reconstruction fails in a known bacteriophage
phylogeny. Evolution 54:397-405
Oakley, T. H. and C. W. Cunningham.
2000. Independent contrasts succeed
where ancestor reconstruction fails in a known bacteriophage
phylogeny. Evolution 54: 397-405.
*O'Meara,
B., C. M. Ane, M. J. Sanderson, and P. Wainwright.
2005. Testing for different rates of continuous trait evolution in different
groups using likelihood. Evolution 60:922-933.
Orzack, S. H., and E.
Sober. 2001. Adaptation, phylogenetic inertia, and the method
of controlled comparisons. Pages 45-63 in S. H. Orzack
and E. Sober, editors. Adaptationism and optimality.
Pagel, M. D. 1992. A method
for the analysis of comparative data. J. Theor.
Biol. 156:431-442.
Pagel M. 1993. Seeking the
evolutionary regression coefficient: an analysis of what comparative methods
measure. JTheorBiol. 164:191-205
Peterson, A. T., J. Soberon, and
V. Sanchez-Cordero. 1999. Conservatism of ecological niches
in evolutionary time. Science 285:1265-1267.
Polly
PD. 2001. Paleontology and the comparative method: ancestral node
reconstructions versus observed node values. Amer. Nat. 157:596-609
Price
T. 1997. Correlated evolution and independent contrasts. Phil. Trans. Roy. Soc.
Lond. Ser. B 352:519-529
Purvis
A, Rambaut A. 1995. Comparative analysis by
independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Comp. Appl.
Bios. 11:247-251
Rees,
M. 1995. EC-PC comparative analyses. JEcol.
83:891-892.
Renner, S. S., D. B.
Foreman, and D. Murray. 2000.
Timing transantarctic disjunctions in the Atherospermataceae (Laurales):
Evidence from coding and noncoding chroloplast sequences.
Systematic Biology 49: 579-591.
Ricklefs RE, Starck
JM. 1996. Applications of phylogenetically
independent contrasts: a mixed progress report. Oikos
77:167-172
Ridley,
M. 1992.
Sanderson,
M. 1991. In search of homoplastic tendencies: Statistical inference of topological
patterns in homoplasy. Evolution 45:351-358.
Schluter D, Price T, Mooers A, Ludwig D. 1997. Likelihood of ancestor states in
adaptive radiation. Evolution 51:1699-1711
Schultz
T, Cocroft R, Churchill G. 1996. The
reconstruction of ancestral character states. Evolution 50:504-511
Siddall, M. E.
1996. Phylogenetic covariance
probability: confidence and historical associations. Syst. Biol. 45:
48-66.
Silvertown, J., and Dodd, M.
(1996).
"Comparing plants and connecting traits." Philosophical Transactions
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J. B. Slowinski and B. S. Abrogast.
1999. Is the rate of molecular
evolution inversely related to body size?
Systematic Biology: 396-399.
Starck, J. 1998. Non-independence
of data in biological comparisons a critical appraisal of current concepts
assumptions and solutions. Theory Biosci.
117:109-138.
Stearns, S. C. 1984.
The influence of size and phylogeny on patterns of covariation
in the life history traits of lizards and snakes. Am. Nat. 123: 56-72.
Steppan, S. J.
1997. Phylogenetic analysis of
phenotypic covariance structure. I. Contrasting results from matrix correlation
and common principle components analysis.
Evol. 51: 571-586.
Steppan, S. J., M. R. Akhverdyan,
E. A. Lyapunova, D. G. Fraser, N. N. Vorontsov, R. S. Hoffman, M. J. Braun. Molecular phylgoeny
of the marmots (Rodentia: Sciuridae):
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hypotheses. Systemaitc
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Swofford DL, Maddison
WP. 1987. Reconstructing ancestral states under Wagner parsimony. Math. Biosci. 87:199-229
Symposium on
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Voelker, G.
1999. Dispersal, vicariaence, and clocks: historical biogeography and
speciation in a cosmopolitan passerine genus (Anthus: Motacillidae). Evolution 53: 1536-1552.
Waddell, P. J., Y. Cao,
M. Hasegawa, D. P. Mindell. 1999.
Assessing the Cretaceous superordinal
divergence times within birds and mammals by using whole mitochondrial protein
sequences and an extended statistical framework. Systematic Biology 48: 119-137.
Wanntorp, H.-E. 1983. Historical
constraints in adaptation theory: traits and non-traits. Oikos
41:157-160.
Webster
AJ, Purvis A. 2002. Testing the accuracy of methods for
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Westoby, M., M. Leishman, and J. Lord.
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Westoby, M., M. Leishman, and J. Lord.
1995. Issues of interpretation after relating comparative datasets to
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Westoby, M., M. Leishman, and J. Lord.
1995. On misinterpreting the "phylogenetic correction". JEcol.
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