Genome redundancy and plasticity within ancient and recent Brassica crop species

The crop species within the genus Brassica have highly replicated genomes. Three base 'diploid' species, Brassica oleracea , B. nigra and B. rapa , are likely ancient polyploids, and three derived allopolyploid species, B. carinata , B. juncea and B. napus , are created from the interspecific hybridization of these base genomes. The base Brassica genome is thought to have hexaploid ancestry, and both recent and ancient polyploidization events have been proposed to generate a large number of genome rearrangements and novel genetic variation for important traits. Here, we revisit and refine these hypotheses. We have examined the B. oleracea linkage map using the Arabidopsis thaliana genome sequence as a template and suggest that there is strong evidence for genome replication and rearrangement within the base Brassicas, but less evidence for genome triplication. We show that novel phenotypic variation within the base Brassicas can be achieved by replication of a single gene, BrFLC , that acts additively to influence flowering time. Within the derived allopolyploids, intergenomic heterozygosity is associated with higher seed yields. Some studies have reported that de novo genomic variation occurs within derived polyploid genomes, whereas other studies have not detected these changes. We discuss reasons for these different findings. Large translocations and tetrasomic inheritance can explain some but not all genomic changes within the polyploids. Transpositions and other small-scale sequence changes probably also have contributed to genomic novelty. Our results have shown that the Brassica genomes are remarkably plastic, and that polyploidy generates novel genetic variation through gene duplication, intergenomic heterozygosity and perhaps epigenetic change.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 665–674.     

Biological studies and phenology of the slug Deroceras reticulatum (Müller, 1774) (Pulmonata: Stylommatophora)

Summary

In the southeast of Buenos Aires Province (Argentina), slugs cause reductions in crop yield by killing seeds and seedlings, by destroying stems and growing points, and by reducing leaf area. Deroceras reticulatum (Müller, 1774) was introduced into Argentina a long time ago, but the biology and ecology of this species in this country are still unknown. The aim of this study was to determine how temperature affects growth rate, reproduction and survival of D. reticulatum and also to assess the seasonal phenology of this species. The life cycle of D. reticulatum was investigated at 12°C, 20°C and at a temperature which alternated between 12°C for 16 h and 20°C for 8 h. The light/dark regime during the experiment was LD: 8/16 h. Slug populations were sampled from grassland located at the Experimental Station of INTA Balcarce. Eggs hatched after 16.3 to 39.8 days and fertility varied between 83.9% and 91.1%. The mean time from hatching to oviposition was longer and fecundity lower at 20°C than 12°C and 12/20°C (p <0.05). The net reproductive rate was 1.49 to 70.53 and the mean generation time varied between the 27 and 30 weeks. In natural conditions, eggs of D. reticulatum were found from early winter until the end of the spring, when soil temperature was 8–15°C and humidity was above 15%. These results indicate that D. reticulatum has one generation per year, univoltine phenology, with peak densities of slugs from the beginning of winter to the end of spring, which coincides with the sowing and emergence of winter and summer crops.     

Spatio-temporal genetic variability in sea trout (Salmo trutta) populations from north-western Spain

1. Genetic variation at five microsatellite loci was investigated in six sea trout ( Salmo trutta ) populations to describe their spatio-temporal genetic variation in north-western Spain. We observed significant genetic variation between river basins, and isolation by distance with restricted gene flow between neighbouring rivers, which suggests an important homing behaviour.
2. Despite these populations suffering a serious demographic decline during 1998, we did not detect any reduction in their genetic variation, suggesting a reasonably high effective population size and temporal stability.
3. Genetic differences among rivers should be taken into account in future management activities. Given the high genetic variability and the temporal stability observed, we believe that no supportive breeding programmes are presently needed in these populations.     

Relationships between life-history strategies of European freshwater fish species and their habitat preferences

1. Focusing on the current environmental characteristics, the ‘habitat template’ theory proposes that life‐history strategies summarise how evolution has shaped species to cope with the temporal and spatial variability of their present environment. The hierarchical ‘landscape filters’ concept predicts that the distribution of species reflects their specific traits that allow them to pass through multiple habitat filters. Together, these theories showed the importance of identifying the functional relationships of species to selective habitat forces in order to predict the organisation and response of communities to the environment. 2. We test the relationships between life‐history traits of European freshwater fish species’ and their habitat preferences, to detect the strategies adopted by fish to cope with their current habitat. For this purpose, we use published data on species traits and habitat preferences (microhabitat hydraulics, temperature and oxygen level). We use multivariate analyses to classify fish species’ strategies and test the relationships between strategies and habitat preferences. 3. We identified a continuum of life‐history patterns between two extremes, with opportunistic and periodic species. Our study supports the idea that microhabitat hydraulics plays a more important role as a template for these species ecological strategies than temperature and oxygen level. Indeed, riffle habitats may select opportunistic species whereas weak relationships are found between species strategies and both their temperature and oxygen level preferences. In addition, the ratio between mortality and growth rate (dimensionless trait), reflecting a trade‐off between growth and survival, varied among species according to the use of their hydraulic habitat, with species using deep habitats exhibiting the highest values. 4. These general relationships between hydraulics and traits may be of importance in community ecology to develop predictive models to understand how fish communities change with the hydraulic environment.     

Ecological processes shaping Central Patagonian salt marsh landscapes

Plant zonation is one of the most conspicuous ecological features of salt marshes worldwide. In this work we used a combination of field transplant and greenhouse experiments to evaluate the importance of interspecific interactions and physical stress in the determination of the major plant zonation patterns in Central Patagonian salt marshes. There, Spartina alterniflora dominates the low marsh, and Sarcocornia perennis the high marsh. We addressed two questions: (i) What prevents Spartina alterniflora from colonizing the Sarcocornia perennis‐dominated high marsh zone? and (ii) What prevents Sarcocornia perennis from colonizing the Spartina alterniflora‐dominated low marsh zone? Our experimental transplants combined with neighbour exclusion treatments showed that the presence of Sarcocornia perennis negatively affects Spartina alterniflora, preventing it from surviving and/or spreading. Complementary field transplant and greenhouse experiments showed that Sarcocornia perennis did not survive the frequent tidal submersion by approximately 1.5 m of turbid seawater in the Spartina alterniflora zone, but its survival was independent of the presence of Spartina neighbours, and of the strong soil anoxia as well. Our results suggest that Spartina alterniflora is excluded by Sarcocornia perennis towards the low marsh, where frequent and prolonged submersion limit the survival of the latter. We provide and discuss key baseline information to facilitate the future design of ecophysiological experiments designed to accurately identify the exact mechanisms acting in every situation.     

Gliridae (Rodentia,Mammalia) with a simple dental pattern: a new genus and new species from the European Early and Middle Miocene

A new genus of Gliridae, Simplomys gen. nov. is proposed. It contains glirids with a simplified dental pattern from the European Early and Middle Miocene. Simplomys gen. nov. includes several species originally described as Pseudodryomys such as Simplomys simplicidens, Simplomys robustus, Simplomys julii, and Simplomys aljaphi. In addition, a new species, Simplomys meulenorum sp. nov. , is proposed from the Spanish Miocene. The species of this genus share not only a very reduced and simplified dental morphology, but also unique dental proportions that clearly separate them from any other genera of Gliridae. Simplomys gen. nov. is recorded in most of the fossil faunas from the Early and Middle Miocene of the Iberian Peninsula, and shows the maximum diversity in this area during Mammal Neogene Zones MN 3 and MN 4. The genus has been also recorded in other European countries such as France, Germany, and Switzerland, conferring to this very characteristic taxon an important role for biochronological correlations within the European continent. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 622–652.     

The D(-)lactic acid and acetoin/diacetyl as potential indicators of the microbial quality of vacuum-packed pork and meat products

The suitability of D(-)lactic acid and/or acetoin/diacetyl as indicators of spoilage of vacuum-packed meat and meat products has been studied. When pork was vacuum-packed, these substances reached measurable amounts after storage for only about 10 days. Although microbial counts stabilized from the 20th day of storage, the D(-)lactic acid and acetoin/diacetyl concentrations increased progressively. These substances could therefore be potential indicators of the storage time of vacuum-packed pork. From a survey carried out with several vacuum-packed meat products from the market, it was concluded that the D(-)lactic acid content could be used as an indicator of the storage time of these products. No consistent results were obtained with acetoin/diacetyl.     

The relationship between fruit production and primate abundance in Neotropical communities

Ecological models predict a positive correlation between fruit production and primate abundance in the Neotropics. To test this relationship, I compiled information on primate abundance and calculated different indexes of fruit production for 30 Neotropical sites. These indexes can be grouped in three categories: (1) Fruit production estimates based on fruit traps, (2) basal area of endozoochorous trees and (3) density of these trees. The first estimate was the best predictor of both primate biomass ( r ²= 0.80) and species richness ( r ²= 0.64). The advantage of using fruit trap estimates is that they take into account production rates (which is not the case for basal area or density estimates), while the advantage of using basal area over density estimates is that it includes some of the expected variation due to tree size. However, using both basal area and density indexes I found a positive correlation between the basal area index and primate biomass for frugivorous monkeys and small platyrhines, but there was no correlation for folivorous and seed predator primates. I also found a positive correlation between pitheciine biomass and the abundance of Eschweilera trees. The analyses gave little support to the importance of suggested keystone resources such as figs and palms. Finally, when including climatic, geographic and plant diversity variables, fruit production continued to be a good predictor of primate biomass in the Neotropics, but primate species richness was best predicted by latitudinal gradients and plant species richness.