Key Words ancestral polymorphism, coalescence theory, maximum likelihood, molecular clock, sequence saturation s Abstract Molecular clocks have profoundly influenced modern views on the 1 In memoriam: Joseph Slowinksi passed away in September 2001 as the result of a snake bite he received while conducting fieldwork in Myanmar. He will be dearly missed by his friends and colleagues.

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.

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Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.

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Pleistocene glaciations have been suggested as major events influencing speciation rates in vertebrates. Avian paleontological studies suggest that most extant species evolved in the Pleistocene Epoch and that species' durations decreased through the Pleistocene because of heightened speciation rates. Molecular systematic studies provide another data base for testing these predictions. In particular, rates of diversification can be determined from molecular phylogenetic trees. For example, an increasing rate of speciation (but constant extinction) requires shorter intervals between successive speciation events on a phylogenetic tree. Examination of the cumulative distribution of reconstructed speciation events in mtDNA phylogenies of 11 avian genera, however, reveals longer intervals between successive speciation events as the present time is approached, suggesting a decrease in net diversification rate through the Pleistocene Epoch. Thus, molecular systematic studies do not indicate a pulse of Pleistocene diversification in passerine birds but suggest, instead, that diversification rates were lower in the Pleistocene than for the preceding period. Documented habitat shifts likely led to the decreased rate of diversification, although from molecular evidence we cannot discern whether speciation rates decreased or extinction rates increased.Temporal changes in rates of speciation and extinction result in variation in the net rate of organismal diversification through time (1). Documenting and explaining these rate changes represent major challenges in evolutionary biology. The Pleistocene Epoch presents such a challenge because of its marked environmental fluctuations and its recency, which permit detailed study of factors that influenced changes in species diversity. Many evolutionary biologists hypothesize accelerated vertebrate speciation in North America during the Pleistocene Epoch (2-5), owing to glacial advances and retreats that provided geographic barriers necessary for speciation (2, 3). Mayr (6) remarked, "Evolutionists agree on the overwhelming importance of Pleistocene barriers in the speciation of temperate zone animals." However, major Pleistocene extinctions are also known for some groups, including plants (7-9). The marked environmental effects of the Pleistocene Epoch clearly influenced rates of diversification, although the relative roles of speciation and extinction are unclear.The relatively high passerine bird diversity in modern fauna is often attributed to a burst of Pleistocene speciation (2, 3). Selander (2) also predicted that most extant bird species originated in the Pleistocene Epoch. A correlate of accelerated Pleistocene speciation concerns the average duration of bird species in the fossil record. Brodkorb (10) proposed that passerine bird species persisted for an average of three million yr in the Pliocene Epoch but only 500,000-1,000,000 yr in the Pleistocene Epoch. Thus, he predicted that species' durations decreased as the present time was approached. Although theseThe...

Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A 2 and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.