What free‐ranging animals do at the zoo: a study of the behavior and habitat use of opossums (Didelphis virginiana) on the grounds of the St. Louis Zoo

Studies of urban wildlife are important because they can give us insight into both how animals adapt to novel environments and how some species survive and prosper in human‐dominated landscapes. Urban zoological institutions provide an ideal setting for research on such species. We report on a study of the behavior and ecology of opossums (Didelphis virginiana) on the grounds of the St. Louis Zoological Park. We used radio tracking to investigate the movement patterns and den site use of opossums on the grounds of the zoo and compared the results to data available for opossums elsewhere. We find that urban opossums in the St. Louis zoo have smaller home ranges and move shorter distances than their rural counterparts. We suggest that increased food availability and decreased risk of predation might explain such differences, and we suspect that conditions are even more favorable to opossums in a zoological setting than in cities in general. Our findings illustrate that there is much to be learned from scientific study of the free‐living animals found on zoological park grounds. Zoo Biol 00:1–17, 2005. © 2005 Wiley‐Liss, Inc.     

ArchAlign: coordinate-free chromatin alignment reveals novel architectures

To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html.     

The role of geography and ecological opportunity in the diversification of day geckos (Phelsuma)

We examine the effects of ecological opportunity and geographic area on rates of species accumulation and morphological evolution following archipelago colonization in day geckos (genus Phelsuma) in the Indian Ocean. Using a newly generated molecular phylogeny for the genus, we present evidence that these geckos likely originated on Madagascar, whereas colonization of three archipelagos in the Indian Ocean, the Seychelles, Mascarene, and Comoros Islands has produced three independent monophyletic radiations. We find that rates of species accumulation are not elevated following colonization but are roughly equivalent on all three isolated archipelagos and on the larger island of Madagascar. However, rates of species accumulation have slowed through time on Madagascar. Rates of morphological evolution are higher in both the Mascarene and Seychelles archipelagos compared to rates on Madagascar. This negative relationship between rate of morphological evolution and island area suggests that ecological opportunity is an important factor in diversification of day gecko species.     

From low to high gear: there has been a paradigm shift in our understanding of evolution

Experimental studies of evolution performed in nature and the associated demonstration of rapid evolution, observable on a time scale of months to years, were an acclaimed novelty in the 1980–1990s. Contemporary evolution is now considered ordinary and is an integrated feature of many areas of research. This shift from extraordinary to ordinary reflects a change in the perception of evolution. It was formerly thought of as a historical process, perceived through the footprints left in the fossil record or living organisms. It is now seen as a contemporary process that acts in real time. Here we review how this shift occurred and its consequences for fields as diverse as wildlife management, conservation biology, and ecosystems ecology. Incorporating contemporary evolution in these fields has caused old questions to be recast, changed the answers, caused new and previously inconceivable questions to be addressed, and inspired the development of new subdisciplines. We argue further that the potential of contemporary evolution has yet to be fulfilled. Incorporating evolutionary dynamics in any research program can provide a better assessment of how and why organisms and communities came to be as they are than is attainable without an explicit treatment of these dynamics.     

Listeria monocytogenes: a foodborne pathogen.

Listeriosis, caused by Listeria monocytogenes, appears to be increasing in incidence worldwide. The disease is of great concern to the food industry. A recent outbreak in California was linked to the consumption of Mexican-style soft cheese and involved more than 300 cases, 30% of which were fatal. L. monocytogenes can be found in a variety of dairy products, leafy vegetables, fish and meat products. It can grow in refrigerated foods and is more heat resistant than most vegetative microbes. The epidemiologic features of listeriosis are poorly understood, and the minimum infectious dose is unknown. Those predisposed to listeriosis include immunocompromised people and pregnant women and their fetuses. Meningitis, spontaneous abortion and septicemia are the primary manifestations of the disease. Early recognition is critical for successful treatment, and ampicillin is the preferred drug. Listeriosis should be considered in any febrile patient with neurologic symptoms of unknown origin, as well as in women with unexplained recurrent miscarriages, premature labour or fetal death. A food source should be the prime suspect if any isolated case or outbreak occurs.     

A PHYLOGENETIC ANALYSIS OF CHARACTER DISPLACEMENT IN CARIBBEAN ANOLIS LIZARDS

Twenty-seven islands in the Lesser Antilles contain either one or two species of Anolis lizards. On nine of the ten two-species islands, the species differ substantially in size; 16 of the 17 one-species islands harbor an intermediate-sized species. Two processes could produce such a pattern: size adjustment (or character displacement), in which similar-sized species evolve in different directions in sympatry; and size assortment, in which only different-sized species can successfully colonize the same island together. Previous analyses implicitly have assumed that size is evolutionarily plastic and determined solely by recent ecological conditions, and consequently have tested the hypothesis that character displacement has occurred on each of the ten two-species islands. Other studies have focused only on size assortment. By analyzing such patterns in a phylogenetic context, I explicitly consider historical effects and can distinguish between size adjustment and size assortment. Using a minimum evolution algorithm, I assess evidence for size adjustment by partitioning changes in size along branches of the phylogenetic tree. Size evolution appears rare (a minimum of 4-7 instances of substantial size evolution). In the northern (but not the southern) Lesser Antilles, size change was significantly greater when a descendant taxon occurred on a two-species island and its hypothetical ancestor occurred on a one-species island, thus supporting the size adjustment hypothesis, though size adjustment might have occurred only once. The relative rarity of size evolution suggests that size assortment might be responsible for nonrandom patterns. In both the northern and southern Lesser Antilles, a null model of no size assortment is convincingly rejected. Closely related taxa, however, are usually similar in size, and hybridization between species has been reported. Consequently, similar-sized species might not coexist because they interbreed and coalesce into one gene pool. A null model that only allows species from different “clades” to co-occur is rejected for the northern Lesser Antilles, but is ambiguous with regard to the southern Lesser Antilles. Thus, competitive exclusion is probably responsible for the pattern of size assortment in the northern Lesser Antilles; both competitive exclusion and interbreeding of closely related species of similar size might be responsible for the patterns evident in the southern Lesser Antilles.     

The glucose transport system of the hyperthermophilic anaerobic bacterium Thermotoga neapolitana

The glucose transport system of the extremely thermophilic anaerobic bacterium Thermotoga neapolitana was studied with the nonmetabolizable glucose analog 2-deoxy-D-glucose (2-DOG). T. neapolitana accumulated 2-DOG against a concentration gradient in an intracellular free sugar pool that was exchangeable with external source of energy, such as pyruvate, and was inhibited by arsenate and gramicidin D. There was no phosphoenolpyruvate-dependent phosphorylation of glucose, 2-DOG, or fructose by cell extracts or toluene-treated cells, indicating the absence of a phosphoenolpyruvate:sugar phosphotransferase system. These data indicate that D-glucose is taken up by T. neapolitana via an active transport system that is energized by an ion gradient generated by ATP, derived from substrate-level phosphorylation.