There is increasing evidence for variation in rates of nucleotide substitution among divergent taxonomic groups. Here, we summarize published rate data and show a strong relationship between substitution rate and body size. For instance, rates of nuclear and mtDNA evolution are slow in whales, intermediate in primates, and fast in rodents. A similar relationship exists for poikilothermic vertebrates. However, these taxa have slower mtDNA substitution rates overall than do homeotherms ofsimilar size. A number of physiological and life history variables are highly correlated with body size. Of these, generation time and metabolic rate explain some patterns of rate heterogeneity equally well. In many cases, however, differences in metabolic rate explain important exceptions to the generation time model. Correlation between metabolic rate and nucleotide substitution may be mediated by (i) the mutagenic effects of oxygen radicals that are abundant by-products of aerobic respiration, and (it) increased rates of DNA synthesis and nucleotide replacement in organisms with higher metabolic rates. Both of these factors increase mutation rate by decreasing the "nucleotide generation time," the average length of time before a nucleotide is copied either through replication or repair. Reconsideration of the generation time hypothesis to include physiological effects such as metabolic rate improves the theoretical underpinnings of molecular evolution.reproduction, intrinsic rate of population increase, population size, and weight-specific metabolic rate (15). Traditionally, these variables have been related to a single, easily measurable biological attribute: body size (15). In the following, we show that when there are differences in rate of DNA substitution between taxa, high rates of DNA evolution often are associated with small body size.Body size probably does not control the rate of DNA substitution directly but serves as a convenient guidepost for understanding the biological correlates of molecular rate heterogeneity. We attempt to illuminate the underlying causes of the body size effect by separating the influence on evolutionary rate of some of the attributes correlated with body size. We primarily focus on generation time and metabolic rate because the effects of both on mutation have a sound mechanistic basis, have been suggested to play important roles in determining rates of molecular evolution, and represent factors for which large comparative data bases exist (6,11,13,14). Finally, we present an explanation for the influence of metabolic rate on silent substitutions that shows how generation-time effects should theoretically be affected by metabolic rate in just the fashion that we observe. Experimental Evidence for Body Size EffectsUnderstanding the factors that affect nucleotide substitution in DNA is central to evolutionary biology, population genetics, and mutation research. To explore such factors evolutionary rates are generally determined with reference to absolute or relative divergence time bet...

Diversity is the hard currency of ecologists. Various statistics have been developed for summarizing the diversity of an ecological community. A commonly adopted summary statistic is the Shannon-Weiner index: H ϭ Ϫ⌺p i lnp i , where p i is the frequency of the ith species. In addition, species richness (the number of different species) often is reported, and recent work emphasizes the importance of accurate estimates of species richness when ecological communities and processes that affect the composition of communities and the function of ecosystems are described (5). The significance of diversity is often inferred by comparing communities characterized from different environments. Typically, such comparisons rely on standard measures of overlap, including the percentage of species shared by two communities or similarity indices. One of the indices used is Sorensen's index: S ϭ S 12 /[0.5(S 1 ϩ S 2 )], where S 12 is the number of species common to both sites and S i is the number of species found at site i.A limitation of traditional statistics for describing and comparing diversity is that species (or operational taxonomic units [OTUs]) are defined inconsistently. For instance, Kroes et al. (6) defined an OTU as a 16S ribosomal DNA (rDNA) sequence group in which sequences differed by less than 1%. By contrast, the definition of McCaig et al. (11) included sequences that were less than 3% different, and other studies have used 5% as the magic number.

The finding that microbial communities are active under snow has changed the estimated global rates of biogeochemical processes beneath seasonal snow packs. We used microbiological and molecular techniques to elucidate the phylogenetic composition of undersnow microbial communities in Colorado, the United States. Here, we show that tundra soil microbial biomass reaches its annual peak under snow, and that fungi account for most of the biomass. Phylogenetic analysis of tundra soil fungi revealed a high diversity of fungi and three novel clades that constitute major new groups of fungi (divergent at the subphylum or class level). An abundance of previously unknown fungi that are active beneath the snow substantially broadens our understanding of both the diversity and biogeochemical functioning of fungi in cold environments.

Historical biogeography seeks to explain contemporary distributions of taxa in the context of intrinsic biological and extrinsic geological and climatic factors. To decipher the relative importance of biological characteristics vs. environmental conditions, it is necessary to ask whether groups of taxa with similar distributions share the same history of diversification. Because all of the taxa will have shared the same climatic and geological history, evidence of shared history across multiple species provides an estimate of the role of extrinsic factors in shaping contemporary biogeographic patterns. Similarly, differences in the records of evolutionary history across species will probably be signatures of biological differences. In this study, we focus on inferring the evolutionary history for geographical populations and closely related species representing three genera of primary freshwater fishes that are widely distributed in lower Central America (LCA) and northwestern Colombia. Analysis of mitochondrial gene trees provides the opportunity for robust tests of shared history across taxa. Moreover, because mtDNA permits inference of the temporal scale of diversification we can test hypotheses regarding the chronological development of the Isthmian corridor linking North and South America. We have focused attention on two issues. First, we show that many of the distinct populations of LCA fishes diverged in a relatively brief period of time thus limiting the phylogenetic signal available for tests of shared history. Second, our results provide reduced evidence of shared history when all drainages are included in the analysis because of inferred dispersion events that obscure the evolutionary history among drainage basins. When we restrict the analysis to areas that harbour endemic mitochondrial lineages, there is evidence of shared history across taxa. We hypothesize that there were two to three distinct waves of invasion into LCA from putative source populations in northwestern Colombia. The first probably happened in the late Miocene, prior to the final emergence of the Isthmus in the mid-Pliocene; the second was probably coincident with the rise of the Isthmus in the mid-Pliocene, and the third event occurred more recently, perhaps in the Pleistocene. In each case the geographical scale of the dispersion of lineages was progressively more limited, a pattern we attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins. Thus, the fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages.