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.     

疏浚物中有机锡的生物累积效应研究

于1998年6月在塘沽港附近水域采集贻贝（Mytilus edulis），经试验室培养驯化后作为试验材料，研究了三丁基氯化锡（TBTC0和三苯基氯化锡（TPTC）的累积效应及其对贻贝的毒性影响。结果表明，在累积效应试验中，TBTC及TPTC对贻贝的半致死浓度LC50分别为3．5μg/dm^3和5．0μg/dm^3，当TBTC浓度达2．0μg/dm^3时，贻贝的成活率开始降低，实验还表明，TPT对贻贝的毒性效应与TBT相近。     

Portrait of an Asian stalk-eyed fly

Diopsid flies have eyes set on stalks which are in some cases so long that the distance between the eyes exceeds the body length. These conspicuous structures have given rise to much speculation about their adaptive value, but there are very few actual observations by which to judge these hypotheses.Cyrtodiopsis whitei Curran lives in the tropical rainforest of Malaysia. We describe a number of aspects of its morphology and biology, some functional properties of the eye, and the ritualized fights between males, by which harems are acquired. The evolutionary significance of the eyestalks is discussed: they represent structures subjected to a double selection pressure; they are an adaptation by which a sensory system is better matched to the special problems encountered in a densely structured habitat (in that the field of view is extended and the ability to estimate distance and size and to identify objects at a large distance is improved), also they act as key stimulus for species recognition and as releaser for intraspecific behaviour.     

A unique strategy of host colony exploitation in a parasitic ant: workers of<Emphasis Type="Italic"> Polyrhachis lama</Emphasis> rear their brood in neighbouring host nests

The formicine ant Polyrhachis lama is a social parasite, exploiting its ponerine host ant species Diacamma sp. In most social parasitic associations, the parasitic species are closely related to their host species group, evolving directly from independent ancestors of the host species. However, in the Polyrhachis lama–Diacamma sp. association, the associated species belong to different ant subfamilies. Based on preliminary field surveys, we had presumed that P. lama might have given up its reproductive division of labour, i.e. workers would be able to produce males as well as workers and females parthenogenetically. In this study, this hypothesis was disproved: Polyrhachis lama workers cannot be fertilized and are only able to produce males. In the host–parasite association originating from nests possessing a P. lama queen, workers penetrate surrounding Diacamma sp. nests, carrying brood for rearing within these satellite nests. In this peculiar way, a single P. lama colony is able to exploit several Diacamma sp. colonies simultaneously.     

An approach and preliminary model of integrating ecological and economic constraints of environmental quality in the Guayas River estuary, Ecuador

We describe conceptual and simulation models of land use within the intertidal zone of the Guayas River estuary to quantify the contribution of mangrove wetlands to maintaining environmental quality of a tropical estuary. The goal of this exercise is to demonstrate the important consideration of ecological constraints in determining economic and management decisions; and how modeling can be used to quantify impacts of land use such as loss of mangrove wetlands on environmental quality. Our conceptual model treats solar energy, river flow, and tides as forcing functions that control the properties of estuarine ecosystems, but also describes market forces and cultural policies as constraints on properties of socioeconomic systems. The controversy of coastal resource management in Ecuador centers around the relative impacts of shrimp pond construction and management as negative feedbacks to the environmental quality of the Guayas River estuary. Unique oceanographic processes and land use changes contribute to complex issues of water and habitat quality in this tropical estuary, the largest estuarine complex on the Pacific coast of South America. A dynamic box model was developed for the estuary and calibrated with data collected from a 14 month survey of water quality parameters throughout the estuary. Scenarios included conversion of mangroves to shrimp ponds in three regions of the estuary, and the construction of a dam by varying three different rates of river discharge at 100, 50 and 10% of 1989 base flow. Good water quality is maintained by the low residence time of water in the estuary (11 d) because of seasonally high river flow and tidal exchange. With a 90% reduction of mangrove forests in the estuary caused by shrimp pond construction, total nitrogen concentrations increased 5 fold. However, as river discharge decreased to 10%, the same construction caused a 60 fold increase in nitrogen concentrations to 250 μM. Increases in nitrogen concentrations were higher in the upper estuary region, with much less change in the lower estuary. Thus the sensitivity of environmental quality to changes in land use in the intertidal and upland zone are linked to the hydrography of the estuary and is site specific. In the future, the combinations of these ecological models together with economic analyses of the goods and services of mangroves may provide better techniques to evaluate the economic impacts of specific coastal zone management decisions.     

The influence of serum screening on the amniocentesis rate in women of advanced maternal age

We investigated the effect of maternal serum screening on the amniocentesis (AC) rate in women of advanced maternal age. The AC rate after maternal serum screening was compared in two groups of women with a singleton pregnancy, 855 women of 30–35 years and 98 of 36 years and older. In our population, 34·1 per cent of the women of 36 years or older were ‘screen-positive’ for Down syndrome. Only 41·2 per cent of these women chose to undergo AC as opposed to 88·2 per cent in the younger age group. Within the older age group, the tendency to avoid AC increased with increasing age. Maternal serum screening led to a significant decrease in the AC rate in the older women. In this group, a comparison between the ‘a priori’ and the calculated risk might have had more influence on the decision to undergo AC than being screen-positive or screen-negative as such. We conclude that maternal serum screening had a major effect on the AC rate in women of advanced maternal age. This is of importance in a society in which the average maternal age is steadily increasing.     

Feeding ecology of the three juvenile phases of the spiny lobster<Emphasis Type="Italic"> Panulirus argus</Emphasis> in a tropical reef lagoon

The three juvenile phases of the spiny lobster Panulirus argus (algal phase: 5-15 mm carapace length, CL; postalgal phase: 15-45 mm CL, and subadults: 45-80 mm CL) occur in the reef lagoon at Puerto Morelos, Mexico. The algal phase abounds in this lagoon, which is covered by extensive seagrass-algal meadows, but the density of postalgal and subadult juveniles is low, owing to the scarcity of crevice-type shelters suitable for these phases. The feeding ecology of the three juvenile phases was investigated to examine whether spatial or temporal differences in food intake, diet composition, or nutritional condition occurred among phases and could partially account for the low abundance of the larger juveniles. Juveniles were collected by divers at night, from January to November 1995, throughout the mid-lagoon and back-reef zones. Percent stomach fullness, relative weight of the digestive gland (RWDG, an index of nutritional condition), percent frequency of occurrence and percent volume of food categories in the diet were compared between sexes, juvenile phases, molt stages (postmolt, intermolt, premolt), seasons, and sampling zones (mid-lagoon and back-reef zones). Significant differences in stomach fullness occurred only among molt stages, mainly because postmolt individuals had emptier stomachs. The main food categories in all juvenile phases were crustaceans (mostly hermit crabs and brachyurans) and gastropods, but the food spectrum was wide, including many other animal taxa as well as plant matter. In June 1995, the epibenthic macrofauna was sampled in five sites in the lagoon that differed in their amount of vegetation. The most abundant taxa in all sites were decapods and gastropods, but density and diversity measures showed that the distribution of these potential prey taxa for juvenile P. argus was rather patchy. Diet overlap in juvenile lobsters was high between sexes, juvenile phases, sampling zones, seasons, and molting stages, indicating that all juveniles fed on the same general food categories throughout time. The only factor that affected the RWDG was the juvenile phase. RWDG was significantly lower in subadults than in algal and postalgal phases, suggesting a poorer nutritional condition in the largest juveniles. This may be related to the scarcity of suitable shelters for large juveniles throughout the lagoon, which may preclude subadults from exploiting food resources in areas of the lagoon where shelter is limited.     

Zooplankton biomass and indices of grazing and metabolism during a late winter bloom in subtropical waters

The development of the so-called late winter bloom in subtropical water was studied in an oceanic area north of the Canary Islands from January to May 2000. Zooplankton was sampled at short-term intervals (1–4 days) during the bloom (January–March), and biomass, indices of grazing (gut fluorescence) and metabolism (electron transfer system activity, ETS) were measured in four different size fractions (100–200, 200–500, 500–1000 and >1000 µm). During the bloom, ETS activity and gut fluorescence increased before the development of zooplankton biomass. At the end of February, the presence of an impressive cloud of dust formed in the Sahara desert was related to an increase in chlorophyll and small zooplankton a week later. The increments in biomass were the consequence of consumption by zooplankton as inferred from the indices of grazing and metabolism. Estimated grazing from gut fluorescence and gut evacuation rates during the period of study accounted for 55% of the assessed total ingestion from respiration and normal values of assimilation, showing the importance of the non-pigmented food in the diet of zooplankton in these waters. In contrast, the sharp decreases in zooplankton biomass observed during the bloom appeared during the dark period of the moon, the days in which the diel vertical migrants reach the shallower layers, in agreement with previous works in the area. Thus, the development of the late winter bloom in this region is suggested to be driven by the interplay between resource and consumer controls.Communicated by S.A. Poulet, Roscoff     

Ontogeny of the digestive capacity of Senegalese sole (<Emphasis Type="Italic">Solea senegalensis</Emphasis>), with respect to digestion,absorption and metabolism of amino acids from<Emphasis Type="Italic"> Artemia</Emphasis>

Ontogenetic changes in the capacity of Senegalese sole (Solea senegalensis Kaup, 1858) larvae to digest and metabolise Artemia protein and amino acids (AA) were studied using 12, 22 and 35 days after hatching (DAH) larvae that were fed Artemia metanauplii radiolabelled with a [U-¹⁴C] protein hydrolysate. About 82% and 18% of the label was incorporated into the Artemia trichloroacetic acid (TCA) precipitate (mostly protein) and soluble (mainly free AA) fractions, respectively. The digestibility of Artemia was high at all tested ages, with label absorption varying between 77% and 83% at 24 h after feeding (HAF). A rapid digestion, absorption and catabolism of Artemia AA were noted, with most of the absorption into the body occurring during the first 3 HAF. Traces of label were already found in the metabolic-CO₂ trap at 1 HAF. Furthermore, label was largely and almost immediately incorporated into the TCA precipitate fraction (mostly protein) of gut and body tissues. Slight differences were noted in diet utilization between larvae at different ages. At 12 DAH larvae had a lower catabolism and evacuation of the label, as well as the highest accumulation in the gut. However, except for the amount of catabolised label, the results were not significantly different from those for 35 DAH larvae. Moreover, no significant differences were found in the amount of label incorporated into the body, although it seemed to be higher in 12 DAH larvae. Taken together, these results reveal a higher absorption and a significantly higher retention of the absorbed label in 12 DAH larvae. In addition, 12 DAH larvae appeared to have a slower absorption of the label, which, in continuously feeding larvae, might result in overall lower food absorption efficiency. Therefore, it seems that young larvae have the ability to compensate for a possible lower digestive capacity with higher body retention of absorbed AA. This study confirms that sole larvae, even young stages, have a high capacity for digesting live preys.Communicated by O. Kinne, Oldendorf/Luhe