Otolith formation,microstructure and daily increment validation in juvenile perch Perca fluviatilis

The otoliths of laboratory‐reared larval and juvenile perch Perca fluviatilis of known age were analysed to determine the age of otolith formation and validate the formation of daily increments. There was a linear relationship between number of increments and age in days post‐hatching, although by 82 days post‐hatching daily increment counts underestimated actual age by an average of 5 days. Otolith dimensions in relation to standard length indicated allometric growth of otoliths until completion of yolk absorption, and isometric growth thereafter, up to 82 days post‐hatching.     

Novel Rumen Bacterial Diversity in Two Geographically Separated Sub-Species of Reindeer

Svalbard reindeer (Rangifer tarandus platyrhynchus) live under austere nutritional conditions on the high-arctic archipelago of Svalbard, while semi-domesticated Norwegian reindeer (R. tarandus tarandus) migrate between lush coastal summer pastures and inland winter pastures with lichens on mainland Norway. Svalbard reindeer are known to have high rumen concentrations of cellulolytic bacteria, ranging from 15% of the viable population in summer to 35% in winter, compared to only 2.5% in Norwegian reindeer. Their rumen bacterial diversity was investigated through comparative analyses of 16S rRNA gene sequences (∼1.5 kb in length) generated from clone libraries (n = 121) and bacterial isolates (n = 51). LIBSHUFF comparisons of the composition of the two 16S rRNA libraries from Norwegian reindeer showed a significant effect of artificial feeding compared to natural pasture, but failed to yield significant differences between libraries from Norwegian reindeer and Svalbard reindeer. The combined sequences from reindeer were not significantly different from those reported in wild Thompson’s gazelle in Kenya but did differ from those reported in domestic cattle in Japan. A total of 90 distinct operational taxonomic units (OTUs) were identified by employing a criterion of 97% similarity, while the Chao1 index estimated the reindeer bacterial rumen population richness at 698 OTUs. The majority of the clone library sequences (92.5%) represented novel strains with <97% identity to any known sequence in the public database, most of them affiliated with the bacterial phylum Firmicutes (low G+C Gram-positives) related to the order Clostridiales (76.7%), while Gram-negative bacteria in the Bacteriodales (Prevotella–Bacteroides group) contributed to 22.5%. Also, six of the isolates were putatively novel strains, possibly representing new species in the Clostridium subphylum (cluster XIVa), Actinomyces and Butyrivibrio.     

Annual variation in maternal age and calving date generate cohort effects in moose (<Emphasis Type="Italic">Alces alces</Emphasis>) body mass

A general feature of the demography of large ungulates is that many demographic traits are dependent on female body mass at early ages. Thus, identifying the factors affecting body mass variation can give important mechanistic understanding of demographic processes. Here we relate individual variation in autumn and winter body mass of moose calves living at low density on an island in northern Norway to characteristics of their mother, and examine how these relationships are affected by annual variation in population density and climate. Body mass increased with increasing age of their mother, was lower for calves born late in the spring, decreased with litter size and was larger for males than for female calves. No residual effects of variation in density and climate were present after controlling for annual variation in mother age and calving date. The annual variation in adult female age structure and calving date explained a large part (71–75%) of the temporal variation in calf body mass. These results support the hypotheses that (a) body mass of moose calves are affected by qualities associated with mother age (e.g. body condition, calving date); and (b) populations living at low densities are partly buffered against temporal fluctuations in the environment.     

A Statistical Approach to Identify Ancient Template DNA

One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authentication of sequences obtained from ancient human remains is thought by many to be rather challenging. We propose a novel approach, based on the c statistic, that can be employed to help identify the sequence motif of an endogenous template, based on a sample of sequences that reflect the nucleotide composition of individual template molecules obtained from ancient tissues (such as cloned products from a PCR amplification). The c statistic exploits as information the most common form of postmortem damage observed among clone sequences in ancient DNA studies, namely, lesion-induced substitutions caused by cytosine deamination events. Analyses of simulated sets of templates with miscoding lesions and real sets of clone sequences from the literature indicate that the c-based approach is highly effective in identifying endogenous sequence motifs, even when they are not present among the sampled clones. The proposed approach is likely to be of general use to researchers working with DNA from ancient tissues, particularly from human remains, where authentication of results has been most challenging. [Reviewing Editor: Dr. Magnus Nordborg]     

Market-resource Links and Fish Vendor Livelihoods in the Upper Zambezi River Floodplains

This paper examines small-scale fish vending in a southern African floodplain from two perspectives: as a link between natural resource use and consumption, and as a livelihood in itself. We used a combination of observation, surveys and semistructured interviews in a market in Katima Mulilo, Namibia, to determine sources of fish, preferences and constraints to vending, average investment and profit, as well different routes into fish vending and perceptions regarding vending. Most vendors come from fishing households, but their stock is often an accumulation of purchases from other fishers. There is little evidence of formal arrangements between fishers and vendors, yet most adapt to the highly variable natural and social environments of the region. Although all vendors ranked selling fish as their most important livelihood activity, a wide range of investment and profit exists among individuals. Our findings indicate that fisheries management proposed for the area must be developed with a careful understanding of how changes in access and use will affect vending livelihoods.

Movements of undersized spotted grunter (<Emphasis Type="Italic">Pomadasys commersonnii</Emphasis>) in the Great Fish Estuary,South Africa: implications for fisheries management

The purpose of this study was to test the hypothesis that an estuarine species as the spotted grunter Pomadasys commersonnii is evenly distributed within the estuary and uniformly exploited by different groups of fishers. This was done by investigating the movements and area use of spotted grunter in relation to the fisheries. The position of 20 acoustically tagged fish was recorded during 36 days in February and March 2003, by manual tracking and automated data logging receivers. Information on the fisheries in the estuary was collected through visual registration of fishing effort and interviews. The spotted grunter moved on average 1.0 km (SD ± 0.7) between positional fixes. Most of the fish were positioned in the lower part of the 12 km long estuary, as 70% of the positional fixes were within the first 3 km, and 89% within the first 6 km. Approximately half (49%) of all the fixes were between 1.0 and 1.5 km from the estuary mouth. The spotted grunter used on average 4.9 km (SD ± 4.9) of the length of the estuary, and there was no significant relationship between the length of the estuary used and the body length of the fish (26–39 cm TL). Subsistence fishers accounted for 73% of fishing lines in the water, while recreational fishers accounted for the rest. Ninety-three percent of the lines were recorded within the first 6 km from the estuary mouth, of which 80% were recorded within the first 3 km. Almost 1/3 of the fishing effort was recorded between 1.0 and 1.5 km from the mouth. The hypothesis that the estuarine dependent species spotted grunter was evenly distributed within the estuary was rejected. However, there was a significant relationship between the distribution of the fishing effort of the subsistence fishers and the fish, indicating that the spotted grunter was uniformly exploited within the estuary by this group of fishers. In contrast, there was no relationship between the distribution of fish and recreational anglers.     

Intra-specific rDNA-ITS restriction site variation and an improved protocol to distinguish species and hybrids in the Daphnia longispina complex

A collaborative research effort was undertaken to evaluate the robustness of a recently developed genetic tool for species identification of members in the morphologically variable Daphnia longispina species complex. This genetic method, based on restriction fragment length polymorphism (RFLP) of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA (rDNA) with restriction enzymes Mwo I and Sau96 I [Billiones et al., 2004. Hydrobiologia 526: 43–53], was applied to many different European populations. Results were compared with two or more independently obtained characters (morphology, allozymes, mitochondrial DNA (mtDNA), or cloned rDNA-ITS sequences). Individuals of most taxa were readily identified, but unexpected ITS-RFLP patterns were found in many individuals indicated by other markers to be D. galeata or one of its hybrids. Among 43 investigated D. galeata populations (902 specimen analysed by ITS-RFLP), deviant RFLP fragment patterns occurred in 26 (i.e., more than half) of the populations. The deviant patterns could be attributed to the loss of one single restriction site in the ITS2 region. This loss made the distinction of D. galeata from other species unreliable, and F1 hybrids could not be identified. Future users should be aware of this shortcoming of the Billions et al. [2004. Hydrobiologia 526: 43–53] protocol. As a solution to this problem, we present an improved genetic identification protocol based on a simple double digestion of the rDNA-ITS region with the restriction enzymes BsrB I and EagI. Sequence analyses of rDNA-ITS clones and preliminary testing indicate that the new protocol is unaffected by the rDNA variation which troubled the Mwo I/Sau96 I protocol. Further, the new protocol identifies all European species of the D. longispina complex, as well as their F1 hybrids. However, a wider screening is required to verify its general utility for all species, since yet unknown variation may occur. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

Isolation and gene quantification of heterotrophic N2-fixing bacterioplankton in the Baltic Sea

Cyanobacteria are regarded as the main N(2)-fixing organisms in marine waters. However, recent clone libraries from various oceans show a wide distribution of the dinitrogenase reductase gene (nifH) originating from heterotrophic bacterioplankton. We isolated heterotrophic N(2)-fixing bacteria from Baltic Sea bacterioplankton using low-nitrogen plates and semi-solid diazotroph medium (SSDM) tubes. Isolates were analysed for the nitrogenase (nifH) gene and active N(2) fixation by nested polymerase chain reaction (PCR) and acetylene reduction respectively. A primer-probe set targeting the nifH gene from a gamma-proteobacterial isolate, 97% 16S rDNA similarity to Pseudomonas stutzeri, was designed for measuring in situ dynamics using quantitative real-time PCR. This nifH gene sequence was detected at two of 11 stations in a Baltic Proper transect at abundances of 3 x 10(4) and 0.8 x 10(3) copies per litre seawater respectively. Oxygen requirements of isolates were examined by cultivation in SSDM tubes where oxygen gradients were determined with microelectrodes. Growth, and thereby N(2) fixation, was observed as horizontal bands formed at oxygen levels of 0-6% air saturation. The apparent microaerophilic or facultative anaerobic nature of the isolates explains why the SSDM approach is the most appropriate isolation method. Our study illustrates how combined isolation, functional analyses and in situ quantification yielded insights into the oxygen requirements of heterotrophic N(2)-fixing bacterioplankton isolates, which were confirmed to be present in situ.