Comparative genomics: methods and applications

Interpreting the functional content of a given genomic sequence is one of the central challenges of biology today. Perhaps the most promising approach to this problem is based on the comparative method of classic biology in the modern guise of sequence comparison. For instance, protein-coding regions tend to be conserved between species. Hence, a simple method for distinguishing a functional exon from the chance absence of stop codons is to investigate its homologue from closely related species. Predicting regulatory elements is even more difficult than exon prediction, but again, comparisons pinpointing conserved sequence motifs upstream of translation start sites are helping to unravel gene regulatory networks. In addition to interspecific studies, intraspecific sequence comparison yields insights into the evolutionary forces that have acted on a species in the past. Of particular interest here is the identification of selection events such as selective sweeps. Both intra- and interspecific sequence comparisons are based on a variety of computational methods, including alignment, phylogenetic reconstruction, and coalescent theory. This article surveys the biology and the central computational ideas applied in recent comparative genomics projects. We argue that the most fruitful method of understanding the functional content of genomes is to study them in the context of related genomic sequences. In particular, such a study may reveal selection, a fundamental pointer to biological relevance.     

Epicuticular wax of large and small white butterflies,<Emphasis Type="Italic"> Pieris brassicae</Emphasis> and<Emphasis Type="Italic"> P. rapae crucivora</Emphasis>: qualitative and quantitative comparison between diapause and non-diapause pupae

We compared the quantity and quality of the epicuticular wax of diapause and non-diapause pupae in two closely related Pieris species, P. brassicae and P. rapae crucivora. Main components of their epicuticular wax were identified as hydrocarbons. In P. brassicae, more than 95% of hydrocarbons were saturated regardless of whether the pupae were in diapause or not. In P. rapae crucivora, 93% of hydrocarbons were saturated in non-diapause pupae whereas in diapause pupae 41% were saturated and 59% unsaturated. From measurements of body surface area by nuclear magnetic resonance microimaging, we calculated the average thickness of the wax layer. The thickness in diapause and non-diapause pupae of P. brassicae was 800 and 160 nm, respectively. In P. rapae crucivora, the thickness was 195 nm in diapause and 11 nm in non-diapause. This is the first report to clarify the compositional difference in epicuticular wax between diapause and non-diapause pupae.     

Closely associated theropod trackways from the Jurassic of Zimbabwe

Eighty-eight tracks of large theropod dinosaurs were found in the mid-Jurassic of Zimbabwe. Among the tracks, at least five adjacent trackways are recorded. The adjacent tracks were probably made by animals traveling as a group, given that they are in relatively close succession; that there are three overlapping tracks (among just 23) suggesting reasonably close associations of the animals; that all the tracks are apparently of the same ichnotaxon; that the preservational types of the tracks are similar; and that the tracks are all of animals traveling in one general direction closely associated in time (there are no returning tracks of the same animals or of those of other species; presence of such tracks would be highly probable if the tracks were made over a period of time of even several hours). Nearby, recently discovered giant sauropod tracks, the first in sub-Saharan Africa, indicate a realistic potential of predator/prey interactions between the two groups of dinosaurs.     

Mating success and fidelity to territories in a fallow deer lek: a female removal experiment

A lek is a clump of male territories that females visit only for mating; it is quite a rare mating system among mammals. As we wanted to investigate the role of past male mating success on their fidelity to lek territories, we displaced fallow deer females by a lek (Lek A), i.e. we removed the resources for rutting males. They moved to a new area followed by some of the territorial males (mobile males) where they established a new lek (Lek B). Other males (faithful males) stayed on Lek A. The former had lower mating success and dominance ranking in the early, undisturbed part of the rut. After disturbance, the MS of faithful males was much reduced, while that of mobile males was higher on Lek B than it had been on Lek A. We then disturbed Lek B. Females returned to Lek A, and the mating success of faithful males reverted to its original level. Past mating success was the main factor predicting whether a male was faithful or mobile. We illustrated for the first time the importance of past experience in promoting lek fidelity; this experiment gives an insight into the mechanisms leading to the traditional use of leks.     

Predatory behavior in a necrophagous bee<Emphasis Type="Italic"> Trigona hypogea</Emphasis> (Hymenoptera; Apidae,Meliponini)

Although most bees feed on nectar and pollen, several exceptions have been reported. The strangest of all is the habit found in some neotropical stingless bees, which have completely replaced pollen-eating by eating animal protein from corpses. For more than 20 years, it was believed that carrion was the only protein source for these bees. We report that these bees feed not only off dead animals, but on the living brood of social wasps and possibly other similar sources. Using well developed prey location and foraging behaviors, necrophagous bees discover recently abandoned wasps nests and, within a few hours, prey upon all immatures found there.     

European Atlantic: the hottest oil spill hotspot worldwide

Oil spills caused by maritime transport of petroleum products are still an important source of ocean pollution, especially in main production areas and along major transport routes. We here provide a historical and geographic analysis of the major oil spills (>700 t) since 1960. Spills were recorded from several key marine ecosystems and marine biodiversity hotspots. The past four decades have been characterized by an overall decrease in the number of accidents and tonnes of oil spilled in the sea, but this trend was less distinct in the European Atlantic area. Recent black tides from the Erika and Prestige vessels provided new evidence for the high risk of accidents with serious ecological impact in this area, which according to our analysis is historically the most important oil spill hotspot worldwide. The English Channel and waters around Galicia in Spain were the areas with most accidents. Maritime transport in European Atlantic waters has been predicted to continue increasing. Together with our own results this suggests that, in addition to measures for increased traffic safety, deployment of emergency capacities in the spill hotspot areas may be crucial for a sustainable conservation of sea resources and ecosystems.Electronic Supplementary Material  Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

A new C12 alcohol identified as a sex pheromone and a trail-following pheromone in termites: the diene (<Emphasis Type="Italic">Z</Emphasis>,<Emphasis Type="Italic">Z</Emphasis>)-dodeca-3,6-dien-1-ol

The diunsaturated C12 alcohol (Z,Z)-dodeca-3,6-dien-1-ol (dodecadienol) has been characterized by GC-MS and FTIR as a novel releaser pheromone in termites. This alcohol identified in Ancistrotermes pakistanicus (Termitidae, Macrotermitinae) possesses a double pheromonal function which again illustrates the chemical parsimony of termites compared with other social insects. In workers, dodecadienol elicits trail-following at a very low concentration (activity threshold at 0.1 pg/cm of trail); in male alates it induces trail-following at a low concentration (1–10 pg/cm) and sexual attraction at a higher concentration (about 1 ng). Traces of the monounsaturated C12 alcohol (Z)-dodec-3-en-1-ol (dodecenol), known as a trail pheromone of several Macrotermitinae, were also found in the sternal gland extracts of A. pakistanicus, although only dodecadienol was present at the surface of the sternal gland. Workers of A. pakistanicus are not sensitive to dodecenol, but they are as sensitive to dodecatrienol as to dodecadienol. However, in the study area (Vietnam), A. pakistanicus is living in sympatry only with those Macrotermitinae using dodecenol as a trail pheromone, the foraging populations therefore being well isolated through their respective trail pheromones. The presence of three types of unsaturated C12 alcohols as releaser pheromones in the only Macrotermitinae subfamily is discussed, and a possible biosynthetic pathway from linoleic acid is proposed for dodecadienol.     

The isostatic state of the southern Urals crust

The Uralide orogen, in Central Russia, is the focus of intense geoscientific investigations during recent years. The international research is motivated by some unusual lithospheric features compared with other collisional belts including the preservation of (a) a collisional architecture with an orogenic root and a crustal thickness of 55–58 km, and (b) large volumes of very low-grade and non-metamorphic oceanic crust and island arc rocks in the upper crust of a low–relief mountain belt. The latter cause anomalous gravity highs along the thickened crust and the isostatic equilibrium inside the Uralides lithosphere as well as the overthrust high-metamorphic rocks. The integrated URSEIS '95 seismic experiment provides fundamentally new data revealing the lithospheric architecture of an intact Paleozoic collisional orogen that allows the construction of density models. In the Urals' lithosphere different velocity structures resolved by wide-angle seismic experiments along both the URSEIS '95- and the Troitsk profile. They can be used to constrain lithospheric density models: a first model consists of a deep subducted continental lower crust which has been highly eclogitized at depths of 60–90 km to a density of 3550 kg/m³. The second model shows a slightly eclogitized lower crust underlying the Uralide orogen with a crustal thickness of 60 km. The eclogitized lower crust causes a too-small impedance contrast to the lithospheric mantle resulting in a lack of reflectors in the area of the largest crustal thickness. Both models fit the measured gravity field. Analyzing the isostatic state of the southern Urals' lithosphere, both density models are in isostatic equilibrium.     

The effects of predator abundance and habitat structural complexity on survival of juvenile sea urchins

We studied the effect of the abundance of predatory fishes and structural complexity of algal assemblages on the survival of juveniles of the sea urchin Paracentrotus lividus on Mediterranean infralittoral rocky bottoms. Post-settlement juveniles (2–10 mm) were placed on four distinct natural substrates with increasing structural complexity (coralline barren, algal turf, erect fleshy algal assemblages and small crevices) inside and outside the Medes Islands Marine Reserve. Predation on these sea urchins increased at greater abundance of predatory fishes, and decreased with greater structural complexity. The refuge provided by structural complexity, however, decreased with increasing size of sea urchin recruits. Predation on the smallest post-settlers was carried out almost exclusively by small fishes (<20 cm), mainly the labrid Coris julis, while the dominant predator of larger juveniles was the sparid Diplodus sargus. Our results demonstrate the cascading effects caused by the prohibition of fishing in marine reserves, and highlight the potential role of small predatory fishes in the control of sea urchin populations.Communicated by O. Kinne, Oldendorf/Luhe     

Parasites and headless chaetognaths in the Indian Ocean

Typhloscolecid polychaetes, assigned to the genera Typhloscolex (Typhloscolex muelleri) and Travisiopsis (Travisiopsis dubia), feeding on chaetognaths are reported for the first time from the Indian Ocean. These parasitic/predatory polychaetes cause decapitation in the chaetognath Flacisagitta enflata, either by eating the head or by causing injuries to the neck or body. Data from eastern Africa to western India showed a peak of polychaete infestation and decapitation of F. enflata in the Seychelles. A 5% peak occurrence (turnover rate is unknown) of decapitated individuals indicates that this parasitism/predation may have an important impact on local F. enflata populations. The harpacticoid copepod Microsetella norwegica was found feeding on the head and the reproductive organs of F. enflata. Therefore, this copepod may cause both decapitation and castration. Flatworm parasites are reported from the body cavity of F. enflata. Digeneans probably belonging to the genera Aphanurus, Parahemiurus, Accacladocoelium and Opechona, along with the accacoeliid Cercaria owreae and didymozoid metacercariae, were found. Cestode larvae were also recovered. No nematodes were found inside chaetognaths in this study.Communicated by O. Kinne, Oldendorf/Luhe