Joseph B. Slowinski

MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF THE POLYTYPIC NORTH AMERICAN RAT SNAKE (ELAPHE OBSOLETA): A CRITIQUE OF THE SUBSPECIES CONCEPT

Abstract 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. Editor: B. Bowen

How Should Species Phylogenies Be Inferred from Sequence Data

levels as follows: (1) Separate gene trees are inferred from each linkage partition, and (2) the species phylogeny is then inferred from the set of gene trees. A method (Maddison, 1997; Page and Charleston, 1997a, 1997b; Slowinski et al., 1997) termed gene tree parsimony by Slowinski et al. (1997) is the appropriate method for implementing the second step. Gene tree parsimony operates by finding the species tree or trees that minimizes the number of hypothesized gene tree/ species tree conflict-producing events required to fit each gene tree to the species tree(s). Central to gene tree parsimony is the concept of fitting trees to other trees (Page, 1994a). Gene tree parsimony implements Doyle’s (1992) insightful concept that nucleotides are characters of gene trees, whereas gene trees are characters of species trees. An important caveat relates to the serious question raised by Maddison (1997) of just what a species phylogeny is meant to represent. The search for a species phylogeny assumes that such a diagram has some meaning. This is a difficult issue that we leave to other workers. Below, we briefly discuss the sources of conflict between gene and species trees, identify problems with previous methods for inferring species trees from molecular sequence data, define gene tree parsimony, and then illustrate the application of gene tree parsimony by using the computer program GeneTree (Page, 1998), which is free and available at http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html; it requires Mac OS 7.5 or later running on a PowerMac, or an Intel-based PC running Windows 95/NT 4.0 or later. The issues explored in this article bear directly on the controversial question of whether or not There are two levels of potential error in the inference of species phylogenies from molecular sequence data: (1) A gene tree (herein, we use the term gene for any contiguous block of nucleotides, regardless of whether it codes for a protein or not) for a set of molecular sequences will be incorrectly inferred if there is sufficient random or systematic error (Swofford et al., 1996), and (2) even if a gene tree is correctly inferred, the phenomena of deep coalescence, gene duplication, and horizontal gene transfer can produce a gene tree different from the true species tree (Goodman et al., 1979; Avise et al., 1983; Pamilo and Nei, 1988; Doyle, 1992; Maddison, 1996, 1997). The second level of error would be quite worrisome if all nucleotides of genomes were historically linked (as is generally true with organellar genomes). In this situation, there would only be one gene tree, which might not be the same as the true species tree. But happily, because of intraand interchromosomal recombination, the nuclear genome is composed of many historically linked sets of nucleotides with different histories. We call these linkage partitions (the cgenes of Doyle, 1992, 1997). Sequences sampled from several species and forming a single linkage partition are related by a unique, binary gene tree. Contrary to claims that natural data partitions do not exist (e.g., Kluge and Wolf, 1993; Siddall, 1997), linkage partitions are natural partitions of molecular sequence data and can be considered as independent estimators of the overlying species phylogeny. This strongly suggests that the molecular phylogenetic analysis of species by using 814 SYSTEMATIC BIOLOGY VOL. 48

Snake phylogeny: evidence from nuclear and mitochondrial genes

We constructed phylogenies of snakes from the c-mos and cytochrome b genes using conventional phylogenetic methods as well as the relatively new method of Bayesian inference. For all methods, there was excellent congruence between the c-mos and cytochrome b genes, implying a high level of support for the shared clades. Our results agree with previous studies in two important respects: first, that the scolecophidians and alethinophidians are monophyletic sister clades; and second, that the Colubroidea is a monophyletic group with the Acrochordidae as its sister clade. However, our results differ from previous studies in the finding that Loxocemus and Xenopeltis cluster with pythons. An additional noteworthy result from our data is that the genera Exiliboa and Ungaliophis, often placed with Tropidophis (and Trachyboa, not included in the present study) in the Tropidophiidae, are in reality boids.

Adaptive radiation and the topology of large phylogenies

The idea that some organisms possess adaptive features that make them more likely to speciate and/or less likely to go extinct than closely related groups, suggests that large phylogenetic trees should be unbalanced (more species should occur in the group possessing the adaptive features than in the sister group lacking such features). Several methods have been used to document this type of adaptive radiation. One problem with these attempts is that evolutionary biologists may overlook balanced phylogenies while focusing on a few impressively unbalanced ones. To overcome this potential bias, we sampled published large phylogenies without regard to tree shape. These were used to test whether or not such trees are consistently unbalanced. We used recently developed null models to demonstrate that the shapes of large phylogenetic trees: 1) are similar among angiosperms, insects, and tetrapods; 2) differ from those expected due to random selection of a phylogeny from the pool of all trees of similar size; and 3) are significantly more unbalanced than expected if species diverge at random, therefore, conforming to one prediction of adaptive radiation. This represents an important first step in documenting whether adaptive radiation has been a general feature of evolution.

A molecular approach to discerning the phylogenetic placement of the enigmatic snake Xenophidion schaeferi among the Alethinophidia

Maximum likelihood (ML) and Bayesian inference (BI) analyses of the complete nucleotide sequences of the cytochrome b gene (cytb) were used to examine the phylogenetic position of the rare snake Xenophidion schaeferi within the alethinophidian snakes. The cytochrome b sequence of this representative of the poorly known family Xenophiidae was compared with those of a large and comprehensive suite of alethinophidian taxa. The research presented here represents the first time all families of alethinophidian and caenophidian snakes have been included in a single molecular phylogenetic study. Results from ML and BI analyses suggest a possible sister taxon relationship between Xenophidion schaeferi and the Bolyeridae. Moreover, strong statistical support also indicates that Xenophiidae is a member of a clade that contains Pythonidae, Loxocemidae, Uropeltidae, Xenopeltidae and Bolyeriidae. Additionally, maximum parsimony and BI analyses of previously published morphological data revealed that these anatomical character states and potentially low taxonomic sampling produced little phylogenetic information valuable to understanding the relationship of Xenophiidae among the Alethinophidia.

Is the rate of molecular evolution inversely related to body size

The wealth of molecular data generated over the past two decades has led to the documentation of highly disparate rates of molecular evolution among different taxa. Among the more intriguing studies is that of Martin and Palumbi (1993), who presented data (their Table 2) derived from a variety of vertebrate taxa purporting to show that the rate of molecular evolution is inversely correlated with body size (and its correlates: metabolic rate, generation time, etc.). Their hypothesis has been cited as a possible ex? planation for variation in rate of molecular evolution among different taxa (e.g., Hafner et al., 1994; Rand, 1994; Stewart and Baker, 1994). We argue, however, that no such re? lationship is evidenced from Martin and Palumbis data and that the problem lies in the fact that their distance-based estimates for the rate of molecular evolution were un-