Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees

Systematic Biology

Volumn 57, Issue 1, 2008, Pages 160-166

  Heath, Tracy A ^a   Zwickl, Derrick J ^a,c   Kim, Junhyong ^b   Hillis, David M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; PHYLOGENY; SAMPLE SIZE; SPECIES DIFFERENTIATION; SPECIES EXTINCTION;

COMPUTER SIMULATION; EXTINCTION, BIOLOGICAL; GENETIC SPECIATION; MODELS, BIOLOGICAL; PHYLOGENY; SAMPLE SIZE;

EID: 47749095118     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150701884640     Document Type: Review

References (57)

1. Ackerly, D. D. 2000. Taxon sampling, correlated evolution, and independent contrasts. Evolution 54:1480-1492.
2. Agapow, P. M., and A. Purvis. 2002. Power of eight tree shape statistics to detect nonrandom diversification: A comparison by simulation of two models of cladogenesis. Syst. Biol. 51:866-872. (Pubitemid 36111101)
3. Blum,M.G. B.,andO. Francios. 2006.Whichrandomprocesses describe the Tree of Life? A large-scale study of phylogenetic tree imbalance. Syst. Biol. 55:685-691.
4. Cunningham, S. A. 1995. Problems with null models in the study of phylogenetic radiation. Evolution 49:1292-1294.
5. DeBry, R. W. 2005. The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony. Syst. Biol. 54:432-440.
6. Dial, K. P., and J. M. Marzluff. 1989. Nonrandom diversification within taxonomic assemblages. Syst. Zool. 38:26-37.
7. Dodd, M. E., J. Silvertown, and M. W. Chase. 1999. Phylogenetic analysis of trait evolution and species diversity variation among angiosperm families. Evolution 53:732-744. (Pubitemid 29332406)
8. Fusco, G., and Q. C. B. Cronk. 1995. A new method for evaluating the shape of large phylogenies. J. Theor. Biol. 175:235-243.
9. Good-Avila, S. V., V. Souza, B. S. Gaut, and L. E. Eguiarte. 2006. Timing and rate of speciation in Agave (Agavaceae). Proc. Natl. Acad. Sci. USA 103:9124-9129. (Pubitemid 43904340)
10. Gould, S. J., D. M. Raup, J. J. Sepowski, and T. J. M. Schopf. 1977. The shape of evolution: A comparison of real and random clades. Paleobiology 3:23-40.
11. Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17. (Pubitemid 128449782)
12. Guyer, C., and J. B. Slowinski. 1991. Comparisons of observed phylogenetic topologies with null expectations among 3 monophyletic lineages. Evolution 45:340-350.
13. Guyer, C., and J. B. Slowinski. 1993. Adaptive radiation and the topology of large phylogenies. Evolution 47:253-263.
14. Heard, S. B. 1992. Patterns in tree balanceamongcladistic, phenetic, and randomly generated phylogenetic trees. Evolution 46:1818-1826.
15. Heard, S. B., and A. O. Mooers. 1996. Imperfect information and the balance of cladograms and phenograms. Syst. Biol. 45:115-118.
16. Heard, S. B., and A. O. Mooers. 2002. Signatures of random and selective mass extinctions in phylogenetic tree balance. Syst. Biol. 51:889- 897. (Pubitemid 36111103)
17. Hedtke, S. M., T. M. Townsend, and D. M. Hillis. 2006. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 55:522-529.
18. Hendy, M. D., and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
19. Hillis, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
20. Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
21. Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126. (Pubitemid 36300065)
22. Holman, E.W. 2005. Nodes in phylogenetic trees: The relation between imbalance and number of descendent species. Syst. Biol. 54:895-899.
23. Huelsenbeck, J. P., and M. Kirkpatrick. 1996. Do phylogenetic methods produce trees with biased shapes? Evolution 50:1418-1424. (Pubitemid 26351006)
24. Huelsenbeck, J. P., and K. M. Lander. 2003. Frequent inconsistency of parsimony under a simple model of cladogenesis. Syst. Biol. 52:641- 648. (Pubitemid 37365045)
25. Huelsenbeck, J. P., B. Larget, and D. Swofford. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879- 1892. (Pubitemid 30211265)
26. Kim, J. 1998. Large-scale phylogenies and measuring the performance of phylogenetic estimators. Syst. Biol. 47:43-60. (Pubitemid 128449785)
27. Kirkpatrick, M., and M. Slatkin. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47:1171-1181.
28. Kishino, H., J. L. Thorne, and W. J. Bruno. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18:352-361. (Pubitemid 32225084)
29. McPeek, M. A., and J. M. Brown. 2007. Clade age and not diversification rate explains species richness among animal taxa. Am. Nat. 169:E97- E106.
30. Mitter, C., B. Farrell, and B.Wiegmann. 1988. The phylogenetic study of adaptive zones - Has phytophagy promoted insect diversification. Am. Nat. 132:107-128. (Pubitemid 19324041)
31. Mooers, A. O. 1995. Tree balance and tree completeness. Evolution 49:379-384.
32. Mooers, A. O., and S. B. Heard. 1997. Evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72:31-54. (Pubitemid 127681333)
33. Mooers, A. O., R. D. M. Page, A. Purvis, and P. H. Harvey. 1995. Phylogenetic noise leads to unbalanced cladistic tree reconstructions. Syst. Biol. 44:332-342. (Pubitemid 126005883)
34. Nee, S., E. C. Holmes, R. M. May, and P. H. Harvey. 1994. Extinction rates can be estimated from molecular phylogenies. Philos. Trans. R Soc. Lond. B Biol. Sci. 344:77-82.
35. Poe, S. 2003. Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods. Syst. Biol. 52:423- 428. (Pubitemid 36844329)
36. Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300. (Pubitemid 129522963)
37. Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671. (Pubitemid 35180695)
38. Purvis, A., and P. M. Agapow. 2002. Phylogeny imbalance: Taxonomic level matters. Syst. Biol. 51:844-854. (Pubitemid 36111099)
39. Purvis, A., A. Katzourakis, and P. M. Agapow. 2002. Evaluating phylogenetic tree shape: Two modifications to Fusco & Cronk's method. J. Theor. Biol. 214:99-103. (Pubitemid 34946995)
40. Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. Roy. Soc. B 267:2267-2272.
41. Pybus, O. G., A. Rambaut, E. C. Holmes, and P. H. Harvey. 2002. New inferences from tree shape: Numbers of missing taxa and population growth rates. Syst. Biol. 51:881-888. (Pubitemid 36111102)
42. Rambaut, A. 2002. Phyl-o-gen: Phylogenetic tree simulator package v1.1. http://evolve.zoo.ox.ac.uk/software.html?id=phylogen.
43. Rannala, B., J. P. Huelsenbeck, Z. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702- 710. (Pubitemid 128370907)
44. Raup, D. M., S. J. Gould, T. J. M. Schopf, and D. S. Simberloff. 1973. Stochastic-models of phylogeny and the evolution of diversity. J. Geol. 81:525-542.
45. Ricklefs, R. E. 2006. Global variation in the diversification rate of passerine birds. Ecology 87:2468-2478. (Pubitemid 44885960)
46. Robinson, M., M. Gouy, C. Gautier, and D. Mouchiroud. 1998. Sensitivity of the relative-rate test to taxonomic sampling. Mol. Biol. Evol. 15:1091-1098. (Pubitemid 28394944)
47. Rosen, D. E. 1978. Vicariant patterns and historical explanation in biogeography. Syst. Zool. 27:159-188.
48. Salisbury, B. A., and J. Kim. 2001. Ancestral state estimation and taxon sampling density. Syst. Biol. 50:557-564.
49. Sanderson, M. J., and M. J. Donoghue. 1994. Shifts in diversification rate with the origin of angiosperms. Science 264:1590- 1593.
50. Savage, H. M. 1983. The shape of evolution - Systematic tree topology. Biol. J. Linn. Soc. 20:225-244.
51. Savolainen, V., S. B. Heard, M. P. Powell, T. J. Davies, and A. O. Mooers. 2002. Is cladogenesis heritable? Syst. Biol. 51:835-843. (Pubitemid 36111098)
52. Shao, K. T., and R. R. Sokal. 1990. Tree balance. Syst. Zool. 39:266-276.
53. Stam, E. 2002. Does imbalance in phylogenies reflect only bias? Evolution 56:1292-1295. (Pubitemid 34793528)
54. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
55. Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647- 1657. (Pubitemid 28550989)
56. Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analyses of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin. Available at www.bio.utexas.edu/faculty/ antisense/garli/Garli.html.
57. Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598. (Pubitemid 35180690)