Pleistocene speciation and the mitochondrial DNA clock

Science

Volumn 282, Issue 5396, 1998, Pages

  Klicka, John ^a   Zink, Robert M ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80054775333     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.282.5396.1955a     Document Type: Note

References (31)

1. [J. Klicka and R. M. Zink, Science 277, 1666 (1997).
2. This widely accepted model of North American songbird diversification is derived in large part from the works of Mengel [R. M. Mengel, Living Bird 3, 9 (1964);
3. R. M. Mengel, Univ. Kansas Dept. Geol. Special Publ. 3, 279 (1970)]
4. [J. P. Hubbard, Living Bird 12, 155 (1973)].
5. We acknowledged [note 10 in (1)] many of the caveats surrounding the use of molecular clocks. A controversy receiving much recent attention is that of among-site nucleotide substitution rate variation [for example, J. Wakeley, J. Mol. Evol. 37, 613 (1993);
6. Z. Yang, N. Goldman, A. Friday, Mol. Biol. Evol. 11, 316 (1994);
7. [J. Sullivan and D. L. Swofford, J. Mamm. Evol. 4, 77 (1997)].
8. Several comments warrant mention. The true songbirds (oscine passerines) are a speciose group of some 4, 561 species [C. G. Sibley and B. L. Monroe Jr., Distribution and Taxonomy of Birds of the World, (Yale Univ. Press, New Haven, CT, 1990], nearly half of all known birds. Arbogast and Slowinski's test of the molecular clock using only 21 species (<1% overall species diversity) is dubious. Studies of molecular rates
9. 2 likelihood test for a molecular clock has been questioned
10. [N. Goldman, J. Mol. Evol. 36, 182 (1993)].
11. M. Nei, Molecular Evolutionary Genetics, (Columbia Univ. Press, New York, 1987);
12. A. Meyer, Trends Ecol. Evol. 9, 278 (1994);
13. [W. S. Moore and De Filippis, in Avian Molecular Systematics and Evolution, D. P. Mindell, Ed. (Academic Press, New York, 1997) pp. 83-119.
14. [C. Krajewski and D. G. King, Mol. Biol. Evol. 13, 21 (1996).
15. W. S. Moore, S. M. Smith, T. Prychitko, in Proc. 22 Int. Ornithol. Congr., N. Adams and Slowtow, Eds. (Univ. of Natal, Durban, South Africa), in press.
16. Levels of among-site rate heterogeneity vary widely among different genes, regions of genes, and organisms [D. L. Swofford et al., in Molecular Systematics, D. M. Hillis, C. Moritz, and B. K. Mable, Eds. (Sinauer, Sunderland, MA, 1996) pp. 407-514]. Our own work (unpublished) on various songbird data sets suggests that a single gamma estimate often is not applicable even to closely aligned taxonomic groups. Furthermore, gamma estimates for first and second codon positions are typically much lower than that for third position sites
17. [S. V. Edwards, in Avian Molecular Systematics and Evolution, D. P. Mindell, Ed. (Academic Press, New York, 1997) pp. 251-278;
18. G. Voelker, S. V. Edwards, Syst. Biol., in press]. Thus the maximum likelihood model used by Arbogast and Slowinski probably provides biased estimates of divergences at low levels. Also, because standard errors for gamma HKY85 distances are not given in the comment, the 95% confidence interval stated for the molecular rate of 5% is unknown.
19. E. Randi, Mol. Phylogenet. Evol. 6, 214 (1996).
20. [K. M. Helm Bychowski and A. C. Wilson, Proc. Natl. Acad. Sci. U. S. A. 83, 688 (1986).
21. D. M. Hillis, B. K. Mable, C. Moritz, in Molecular Systematics, D. M. Hillis, C. Moritz, B. K. Mable, Eds. (Sinauer, Sunderland, MA, ed. 2, 996) pp. 515-534.
22. R. C. Fleischer, C. E. McIntosh, C. L. Tarr, Mol. Ecol. 7, 533 (1998).
23. Arbogast and Slowinski do not account for the problem of among-lineage variation in substitution rates. Such variation may reflect differences in body size and correlates such as metabolic rate and generation time [C.-L. Wu and W.-H. Li, Proc. Natl. Acad. Sci. U. S. A. 82, 1741 (1985);
24. [A. P. Martin and S. R. Palumbi, Proc. Natl. Acad. Sci. U. S. A., 90, 4087 (1993);
25. P. Canatore et al., J. Mol. Evol. 39, 589 (1994);
26. A. P. Martin, Mol. Biol. Evol. 12, 1124 (1995)] as well as unique population histories (for example, bottleneck frequency) or phylogenetic constraints on mutation and fixation
27. [D. P. Mindell and C. E. Thacker, Ann. Rev. Ecol. Syst. 27, 279 (1996)]. We analyzed only North American oscine passerines (true songbirds) for this specific reason. Arbogast and Slowinski criticize our work for not testing for rate heterogeneity among songbird lineages, yet they assume that songbirds are evolving at the same rate as primates and Galliformes.
28. In earlier work on these birds [C. L. Tarr and R. C. Fleischer, Auk 110, 825 (1993)] a substitution rate of 2 to 2.4% was calculated from the entire mtDNA molecule using RFLP data. Fleischer et al. (18) attribute this difference to the fact that the cytochrome b gene evolves slightly below the genomewide rate.
29. The relevance of the difference in the distributions of divergence dates (figure 1 of the comment) is unclear. Because of variation accompanying genetic distance estimates we did not tabulate and compare exact numbers of Pleistocene versus Pliocene divergences. Arbogast and Slowinski do provide such an accounting. Traditionally, the Pleistocene-Pliocene boundary has been thought to correspond to a time of profound, worldwide climatic change [L. D. Martin, Inst. for Tertiary-Quaternary Studies Symp. Ser. 1, 33 (1985)]. The original framers of the LPO model [for example, see (2)] stated that the Pleistocene was one My in duration with only four glacial cycles. With new understanding of the paleoecological record, the value assigned to the Pleistocene-Pliocene boundary has increased. We now know that climatic oscillations sufficient to produce major changes in the biota are dated to well within the tertiary
30. [G. M. Hewitt, Biol. J. Linn. Soc. London 58, 247 (1996);
31. [T. Webb and P. J. Bartlein, Annu. Rev. Ecol. Syst. 23, 141 (1992)]. The 2-My date that Arbogast and Slowinski cite as a critical temporal reference point may be viewed instead as a relatively arbitrary point in time.