Understanding the unique contributions of ecology and history to the distribution of species within communities requires an integrative approach. The Eastern Continental Divide in southwestern Virginia separates river drainages that differ in species composition: the more aquatic, predatory Desmognathus quadramaculatus is present only in the New River drainage (which drains to the Gulf of Mexico), while Desmognathus monticola is present in both the New River drainage and the James River drainage (which drains to the Atlantic Ocean). We investigated natural distributions, behavioral variation in experimental mesocosms, population genetic, and phylogenetic implications of community structure. The presence of D. quadramaculatus increased the terrestriality of D. monticola in natural and experimental situations but to different degrees in allopatric and sympatric populations. Our ecological data suggest that the degree of terrestriality in D. monticola is a result of a balance between the optimal aquatic habitat and risks of predation. Our genetic analyses suggest that D. monticola has experienced a recent range expansion and has only a recent history of association with D. quadramaculatus in Virginia. This is surprising given the strong behavioral variation that exists in populations experiencing unique community compositions over a scale of meters. This study demonstrates the need to combine both ecology and genetics toward an understanding of the factors affecting species distributions, behavioral variation between populations, and patterns of genetic variation across a landscape.

Many vertebrates, forest herbs, and trees exhibit both variable age at maturity and iteroparity as adaptations to uncertain environments. We analyze a stochastic model that combines these two life-history adaptations with density-dependent fertility. Results for a model with only iteroparity are consistent with previous work; environmental uncertainty favors adult survival over juvenile survival. This holds true even if there is a moderately strong convex trade-off between adult survival and fecundity, but the direction of selection can depend on which life-history trait is considered a random variable. A life history with only developmental delay favors juvenile survival in uncertain environments, consistent with previous models of seed banks. When both developmental delay and iteroparity are included in the model, both adaptations are favored in uncertain environments. Our simulations show that selection is not necessarily a runaway process in which either developmental delay or iteroparity is favored, as recently proposed by Tuljapurkar and Wiener, but rather that selection can favor both mechanisms. Invasion analysis shows that selective pressure on life-history delays increases as environmental variation increases. Reproductive delay and adult survival can be either adaptations or constraints. Natural-history studies that estimate model parameters can resolve this uncertainty.

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Abstract-RNA molecules are distinguished by their sequence composition and by their three-dimensional shape, called the secondary structure. The secondary structure of a pre-mRNA sequence may have a strong influence on gene splicing. In our previous work, we showed that a splice-site model employing sequence features built using our feature generation algorithm was very effective in predicting splice sites. The generated sequence features also contained biologically relevant features. In this paper, we extend the feature generation algorithm to construct secondary-structure features. These features capture the nucleotide pairing tendency in the splice-site neighborhood. We extend the splice-site model to include both pre-mRNA sequence and structure characteristics. The new model significantly outperforms the sequence-based features model. The identified secondary-structure features capture biologically relevant signals such as splicing silencers. We also found these signals to prefer specific regions around the splice-site neighborhood and we detail their preference.