Back to Reading List

Reading List 9
The required readings are marked with two asterisks**. Highly recommended readings
are marked with one asterisk*; the rest are for background information and to allow
you an entrance into the literature.




***Crozier, R.H., Dunnett, L.J. and Agapow, P.M. 2005. Phylogenetic biodiversity assessment based on systematic nomenclature. Evolutionary Bioinformatics Online 2005:1 11-36.


Faith, D. P. 1992a. Conservation evaluation and phylogenetic diversity. Biological

Conservation 61:1-10.


Faith, D. P. 1992b. Systematics and conservation: on predicting the feature diversity of

subsets of taxa. Cladistics 8:361-373.


**Forey, P.L., C. J. Humphries and P. H. Williams. 1994. Systematics and conservation

evaluation, Systematics Association Special Volume No. 50. Clarendon Press, Oxford.

Mishler, B.D. 1995. Plant systematics and conservation: science and society. Madroņo

42: 103-113.


Moritz,C., J. L. Patton, C. J. Schneider, and T. B. Smith. 2000. DIVERSIFICATION OF

RAINFOREST FAUNAS: An Integrated Molecular Approach Annu. Rev. Ecol. Syst.

31: 533-563


Polhemus, D. A. (1997). “Phylogenetic analysis of the Hawaiian damselfly genus

Megalagrion (Odonata: Coenagrionidae): Implications for biogeography, ecology, and

conservation biology.” Pacific Science, 51(4), 395-412.


Tyler, H. A., Brown, K. S., Jr., and Wilson, K. H. (1994). “Swallowtail butterflies of the

Americas: A study in biological dynamics, ecological diversity, biosystematics, and



Vane-Wright, R. I., C. J. Humphries and P. H. Williams. 1991. What to protect? --

Systematics and the agony of choice. Biological Conservation 55:235-254.





Alroy, J. 1995. Continuous track analysis: a new phylogentic and biogeographic method.

Syt. Biol. 44(2):152-178.


Avise, J. C., J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb

and N. C. Saunders. 1987. Intraspecific phylogeography: the mitochondrial DNA

bridge between population genetics and systematics. Ann. Rev. Ecol. Syst.



Baldwin, B. G., D. W. Kyhos and J. Dvorak. 1990. Chloroplast DNA evolution and

adaptive radiation in the Hawaiian silversword alliance (Asteraceae-Madiinae).

Ann. Mo. Bot. Gard. 77:96-109.


Baldwin, B. G. and R. H. Robichaux. 1995. Historical biogeography and ecology of the

Hawaiian silversword alliance (Asteraceae): New molecular phylogenetic

perspectives.Pp. 259-287. In Wagner, W. L. and V. Funk (Eds.) Hawaiian

Biogeography, Evolution on a Hot Spot Archipelago. Smithsonian Institution Press,



Baldwin, B. G., and Sanderson, M. J. (1998). “Age and rate of diversification of the

Hawaiian silversword alliance (Compositae).” Proceedings of the National

Academy of Sciences of the United States of America, 95(16), 9402-9406.


Ball, I.R. 1976. Nature and formulation of biogeographical hypotheses. Syst. Zool.


**Brooks, D.R., & D. McLennan. 1991. Phylogeny, Ecology, and Behavior. University

of Chicago Press. pp 206-248


*Brooks, D. R. 1990. Parsimony analyisis in historical biogeography and coevolution:

Methodological and theoretical update. Syst. Zool. 39:14-30.


Carpenter, J M. Phylogeny and biogeography of Polistes. Turillazzi, S. and M. J. West-

Eberhard (Ed.). Natural history and evolution of paper-wasps; International

Workshop, Castiglioncello, Italy, October 4-7, 1993. xiv+400p. Oxford

University Press: Oxford, England, UK; New York, New York, USA. 1996. p.



Coscaron, M D C; Morrone, J J. Cladistics and biogeography of the assassin bug genus

Melanolestes Stal (Heteroptera: Reduviidae). Proceedings of the Entomological

Society of Washington, v.99, n.1, (1997): 55-59.


Cracraft, J. Cladistic analysis and vicariance biogeography. Slatkin, M. (Ed.). Exploring

evolutionary biology: Readings from American Scientist. iv+305p. Sinauer

Associates, Inc.: Sunderland, Massachusetts, USA. 1995. p. 104-112.


De Meyer, M. Cladistic and biogeographic analyses of Hawaiian Pipunculidae

(Diptera)revisited. Cladistics, v.12, n.4, (1996): 291-303.


Emerson, B C; Wallis, G P; Patrick, B H. Biogeographic area relationships in southern

New Zealand: A cladistic analysis of Lepidoptera distributions. Journal of

Biogeography, v.24, n.1, (1997): 89-99.


Enghoff, H. Historical biogeography of the Holarctic: Area relationships, ancestral areas,

and dispersal of non-marine animals. Cladistics, v.11, n.3, (1995): 223-263.


Evans, B J; Morales, J C; Picker, M D; Kelley, D B; Melnick, D J. Comparative

molecular phylogeography of two Xenopus species, X. gilli and X. laevis, in the

south-western Cape Province, South Africa. Molecular Ecology, v.6, n.4, (1997):



Grant, P. R. (1998). “Radiations, communities, and biogeography.” Evolution on islands,

P. R. Grant, ed., Oxford University Press, New York, New York, USA; Oxford,

England, UK, 196-209.


Gray, J. and A.J. Boucot (eds.). 1979. Historical Biogeography, Plate Tectonics, and the

Changing Environment, Oregon State University Press, Corvallis, Oregon.


Kluge, A. G. 1988. Parsimony in vicariance biogeography: a quantitative method and a

greater Antillean example. Syst. Zool. 37:315-328.


Linder, H P; Crisp, M D. Nothofagus and Pacific biogeography. Cladistics, v.11, n.1,

(1995): 5-32.

Lydeard, C. M.C. Wooten, and A. Meyer. 1995. Molecules, morphology and area

cladeograms: a cladistic and biogeographic analysis of Gambusia (Teleostei:

Poecilliiae) Syst. Biol. 44:221-236.


Minaka, N. Vicariance in historical biogeography: Analytical problems in reconstructing

area cladograms. Acta Phytotaxonomica et Geobotanica, v.44, n.2, (1993): 151-

184. Language: Japanese.


Morrone J.J. and Carpenter, J.M. 1994. In search of a method for cladistic biogeography -

an comparison of component analysis, brooks parsimony analysis, and three area

statements. Cladistics 10(2):99-153.


Nelson, G. 1985. A decade of challenge the future of biogeography. Earth Sciences

History 4(2):187-196.


Nelson, G. and N. Platnick. 1981. Systematics and biogeography. Cladistics and

vicariance. Columbia Univ. Press, New York.


Nelson, G. and Rosen, D.E. (eds.). 1981. Vicariance biogeography: a critique.

ColumbiaUniversity Press, New York. 593 pp.


Nelson, G; Ladiges, P Y. Paralogy in cladistic biogeography and analysis of paralogyfreesubtrees.

American Museum Novitates, n.3167, (1996): 1-58.


Page, R. D. M. 1989. Comments on component-compatibility in historical

biogeography.Cladistics 5: 167-182.


Page, R. D. M. 1994. Maps between trees and cladistic analysis of historical associations

among genes, organisms, and areas. Syst. Biol. 43: 58-77.


Page, R.D.M. 1994. Parallel phylogenies - reconstructing the history of host-parasite

assemblages. Cladistics 10(2): 155-173


Pielou, E. C. 1979. Biogeography. John Wiley and Sons; New York.

Rosen, D. E. 1975. A vicariance model of Caribbean biogeography. Syst. Zool. 24:431-



Rosen, D. E. 1978. Vicariant patterns and historical explanation in biogeography. Syst.

Zool. 27: 159-188.


Rosen, D. E. 1979. Fishes from the upland and intermontane basins of Guatemala:

revisionary studies and comparative geography. Bull. Amer. Mus. Nat. Hist. 162:



**Sanmartin, I.; Ronquist, F. New solutions to old problems: Widespread taxa, redundant distributions and missing areas in event-based biogeography. Animal Biodiversity and Conservation 25 (2) : 75-93 2002


Siddall, M E. Phylogenetic covariance probability: Confidence and historical

associations. Systematic Biology, v.45, n.1, (1996): 48-66.


Springer, V. G. 1982. Pacific plate biogeography, with special reference to shorefishes.

Smithsonian Contributions to Zoology 367:1-167.


Swenson, U. and K. Bremer. 1997. Pacific Biogeography of the Asteraceae genus

Abrotanella (Senecioneae, Belnnospermatinae). Systematic Botany 22: 493-508.


**van Veller, Marco G. P.; Brooks, D. R.; Zandee, M. Cladistic and phylogenetic biogeography: The art and the science of discovery. Journal of Biogeography 30 (3) : 319-329 March 2003


Vermeij, G. J. 1978. Biogeography and adaptation. Harvard University Press; Cambridge.


Wagner, W L. Hawaiian biogeography: Evolution on a hot spot archipelago. Wagner, W.

L. and V. A. Funk (Ed.). Hawaiian biogeography: Evolution on a hot spot

archipelago. xvii+467p. Smithsonian Institution Press: Washington, DC, USA;

London, England, UK. 1995.


Weston, P H; Crisp, M D. Cladistic biogeography of waratahs (Proteaceae:Embothrieae)

and their allies across the Pacific. Australian Systematic Botany, v.7, n.3,

(1994): 225-249.


Wiley, E. O. 1981. Phylogenetics: the theory and practice of phylogenetic systematics.

John Wiley and Sons, New York.



May 2: Macroevolution: patterns of diversification and extinction


Alroy, J. 2000. Understanding the dynamics of trends within evolving lineages.

Paleobiology 26: 319-329.


Brooks, D. R. and D. A. McLennan. 1993. Comparative study of adaptive radiations

with an example using parasitic flatworms (Platyhelminthes, Cercomeria). Am. Nat.

142: 755-778.


Charlesworth, B., R. Lande and M. Slatkin. 1982. A neo-Darwinian commentary on

macroevolution. Evol. 36:474-498.


Elbe, G. J. 2000. Contrasting evolutionary flexibility in sister groups: disparity and

diversity in Mesozoic atelostomate echinoids. Paleobiology 26: 56-79.


Gilinsky, N.L. and I.J. Good. 1991. Probabilities of origination, persistence, and

extinction of families of marine invertebrate life. Paleobiology 17(2):145-66


Gould, S. J. and N. Eldredge. 1977. Punctuated equilibria: the tempo and mode of

evolution reconsidered. Paleobiol. 3:115-151.


Gould, S.J., N.L. Gilinsky & R.Z. German 1987. Asymmetry and the direction of

evolutionary time. Science 236:1437-1441.


Gould, S.J. 1991. The disparity of the Burgess Shale arthropod fauna and the limits of

cladistic analysis: why we must strive to quantify morphospace. Paleobiology 17(4):



Hey, J. 1992. Using phylogenetic trees to study speciation and extinction. Evol. 46:



Jablonski, D., J.J. Sepkoski, Jr., D.J. Bottjer, and P.M. Sheehan. 1983. Onshore-offshore

patterns in the evolution of Phanerozoic shelf communities. Science 222: 1123-1125.


Jablonski, D. 1986. Background and mass extinctions: the alternation of

macroevolutionary regimes. Science 231: 129-133.


Jablonski, D. 1987. Heritability at the species level: Analysis of geographic ranges of

cretaceous mollusks. Science 238: 360-363.


Jablonski, D. 2000. Micro- and macroevolution: scale and heirarchy in evolutionary

biology and paleobiology. Paleobiology 26 (supplement to 4): 15-52.


Jeffery, C. H. 2001. Heart urchins at the Cretaceous/Tertiary boundary: a tale of two

clades. Paleobiology 27: 104-125.


Kubo, T. and I. Y. 1995. Inferring the rates of branching and extinction from molecular

phylogenies. Evol. 49: 694-704.


** Lemen, C.A. and P.W. Freeman. 1989. Testing macroevolutionary hypotheses with

cladistic analysis: evidence against rectangular evolution. Evolution 43:1538-1554.


Levington, J. S. and C. M. Simon. 1980. A critique of the punctuated equilibria model

and implications for the detection of speciation in the fossil record. Syst. Zool.



McShea, D. W. 2000. Trends, tools, and terminology. Paleobiology 26: 330-333.


** Mindell, D. P., J. W. Sites Jr. and D. Graur. 1989. Speciational evolution: A

phylogenetic test with allozymes in Sceloporus (Reptilia). Cladistics 5:49-61.


Norris, R.D. 1991. Biased extinction and evolutionary trends. Paleobiology 17:388-99.


Norris, R. D. 2000. Pelagic species diversity, biogeography, and evolution.

Paleobiology 26 (supplement to 4): 236-258.


Patterson, C. and A.B. Smith 1987. Is the periodicity of extinctions a taxonomic

artefact? [and reply by Sepkoski] Nature 330:248-252.


Raup, D.M. and J.J. Sepkoski 1986. Periodic extinction of families and genera. Science.



Robeck, H. E., C. C. Maley, and M. J. Donoghue. 2000. Taxonomy and temporal

diversity patterns. Paleobiology 26: 171-187.


Rohde, K. 1996. Robust phylogenies and adaptive radiations: a critical evaluation of

methods used to identify key innovations. Am. Nat. 148: 481-500.


Roopnarine, P. D., G. Byars, and P. Fitzgerald. 1999. Anagenetic evolution,

stratophenetic patterns and random walk models. Paleobiology 25: 41-57.


Schopf, T. M. J. 1981. Punctuated equilibria and evolutionary stasis. Paleobiol. 7:156-



Shubin, N. H. and C. R. Marshall. 2000. Fossils, genes, and the origin of novelty.

Paleobiology 26 (supplement to 4): 324-340.


Smith, A.B. & C. Patterson. 1988. The influence of taxonomic method on the perception

of patterns of evolution, Evol. Biol. 23:127-216.


Smith, A. B. 1994. Systematics and the fossil record: documenting evolutionary

patterns. Blackwell Scientific Publications, Oxford.


Smith, L. H. and B. S. Lieberman. 1999. Disparity and constraint in the olenelloid

trilobites and the Cambrian rasiation. Paleobiology 25: 459-470.


Stanley, S. M. 1982. Macroevolution and the fossil record. Evol. 36:460-473.


Stidd, B. M. 1985. Are punctuationists wrong about the modern synthesis? Phil. Sci.



Van Valen, L.M. and V.C. Maiorana. 1985. Patterns of origination. Evol. Theory 7:



Vrba, E.S. 1980. Evolution, species and fossils: how does life evolve? S. Afr. J. Sci. 76:



Wagner, P.J. 1995. Stratigraphic tests of cladistics hypotheses. Paleobiology 21(2): 153-



Wagner, P.J. 1995. Diversity patterns among early gastropds: contrasting taxonomic and

phylogenetic descriptions. Paloebiology 21(4):410-439.


Wagner, P. J. 1996. Contrasting the underlying patterns of active trends in

morphological evolution. Evolution 50: 990-1007.


Wagner, P. J. 2000. Exhaustion of morphologic character states among fossil taxa.

Evolution 54: 365-386.


Williamson, P. G. 1981. Paleontological documentation of speciation in Cenozoic

mollusks from Turkana Basin. Nature 293: 437-443. [see Biol. Journal Linn. Soc.,

Volume 26, Number 4, for several papers commenting on Williamson's work.]







Brooks, D.R., & D. McLennan. 1991. Phylogeny, Ecology, and Behavior. University of

Chicago Press.


Burt, A. 1989. Comparative methods using phylogenetically independent contrasts.

Oxford Surveys in Evolutionary Biology 6:33-53.


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.



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. London: Pion.


Coddington, J. 1988. Cladistic tests of adaptational hypotheses. Cladistics 4:3-22.

de Queiroz, K. 1996. Including the characters of interest during tree reconstruction and

the problems of circularity and bias in studies of character evolution. Am. Nat.

148: 700-708.


Donoghue, M.J. 1989. Phylogenies and analysis of evolutionary sequences, with

examples from seed plants. Evolution 43:1137-1156. (maddison’s test)

Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-



Funk, V.A. and D.R. Brooks. 1990. Phylogenetic systematics as the basis of comparative

biology. Smithsonian Institution Press.


Harvey, P.H. and M.D. Pagel. 1991. The comparative method in evolutionary

biology. Oxford University Press.


Martins, E. P. 1996. Phylogenies, spatial autoregression, and the comparative

method: A computer simulation test. Evolution, v.50, n.5, 1750-1765.


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.


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.


Sillin-Tullberg, B. 1988. Evolution of gregariousness in aposematic butterfly larvae: a

phylogenetic analysis. Evolution 42: 293-305. Sillin-Tullberg, B. 1988. Evolution

of gregariousness in aposematic butterfly larvae: a phylogenetic analysis.

Evolution 42: 293-305.


Vogl, C., and G. P. Wagner. 1990. Interspecific variability in randomly evolving clades:

models for testing hypotheses on the relative evolutionary flexibility of

quantitative traits. Sys. Zool. 39:109-123.149:646-667.