Past and present fish species recorded in the estuarine Lake Ichkeul,northern Tunisia

Lake Ichkeul in northern Tunisia is a Ramsar site, a MAB Biosphere Reserve and a UNESCO World Heritage Site. The system is one of the most important coastal wetlands in North Africa, especially as an over-wintering area for migratory birds, particularly Palaearctic waterfowl. The present study was aimed at diagnosing the status of fish species in Lake Ichkeul and documenting their annual and seasonal occurrence within the system. Fish samples were collected monthly at 22 sites from March 2011 to April 2012 using a variety of gears, including a dragnet, gillnet, trammelnet, frynet and beach-seine. Temperature and salinity measurements were taken at each site, while fishes were obtained from only 11 sites, representing mainly lacustrine stations. A total of 18 fish species belonging to 14 genera and 12 families were identified, with Mugilidae dominating with four species, followed by Syngnathidae with three species. This study represents a relative recovery in terms of fish species richness, since only 13 species were recorded here between 2003 and 2007. However, the numbers of fish caught, especially of the commercial taxa, seem to have declined in recent years, and the number of species currently present is much lower than that of several decades ago. Increasing human pressures, particularly reductions in catchment freshwater inputs, a breakdown in ecosystem connectivity, pollution and over-fishing appear to be the principal causes for the decline in fish abundance and diversity.     

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (R_ST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu R_ST = 0.96%, Andhra Pradesh R_ST = 0.77%) exceeds the estimate of variation between these geographically separated groups (R_ST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.     

A statistical approach for optimization of R-phycoerythrin extraction from the red algae Gracilaria verrucosa by enzymatic hydrolysis using central composite design and desirability function

The aim of this research is to statistically optimize enzymatic hydrolysis parameters for the production of R-phycoerythrin (RPE) from red algae Gracilaria verrucosa. Six independent variables, incubation temperature, incubation time, ratio of buffer to raw material, cellulase loading, xylanase loading, and pH, were selected for response surface methodology studies. A central composite design was employed to maximize RPE production. A mathematical model with high determination coefficient (R ²?=?0.86) was developed and could be employed to optimize RPE extraction. The optimal extraction conditions of RPE were determined as follows: incubation temperature (48°C), incubation time (6?h), ratio of buffer to raw material (20 w/v), cellulase loading (15%), xylanase loading (5%), and pH (6.5). Under this optimal condition, the experimental yield of RPE was 6.25?mg?g^?1. Based on the result of response surface methodology and desirability function approach study, total sugar, the main by-product in RPE extraction was considered as another response. A new optimal condition was predicted as follows: incubation temperature (30°C), incubation time (12?h), ratio of buffer to raw material (20, w/v), cellulase loading (15%), xylanase loading (5%), and pH (6). Under this condition, similar RPE levels were obtained while the concentration of total sugar decreased by 40%.     

A simulation study for the analysis of uncertain binary responses: Application to first insemination success in beef cattle

A simulation was carried out to investigate the methods of analyzing uncertain binary responses for success or failure at first insemination. A linear mixed model that included, herd, year, and month of mating as fixed effects; and unrelated service sire, sire and residual as random effects was used to generate binary data. Binary responses were assigned using the difference between days to calving and average gestation length. Females deviating from average gestation length lead to uncertain binary responses. Thus, the methods investigated were the following: (1) a threshold model fitted to certain (no uncertainty) binary data (M1); (2) a threshold model fitted to uncertain binary data ignoring uncertainty (M2); and (3) analysis of uncertain binary data, accounting for uncertainty from day 16 to 26 (M3) or from day 14 to 28 (M4) after introduction of the bull, using a threshold model with fuzzy logic classification. There was virtually no difference between point estimates obtained from M1, M3, and M4 with true values. When uncertain binary data were analyzed ignoring uncertainty (M2), sire variance and heritability were underestimated by 22 and 24%, respectively. Thus, for noisy binary data, a threshold model contemplating uncertainty is needed to avoid bias when estimating genetic parameters.     

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.Subject terms: Soil microbiology, Ecology     

Marcusenius desertus sp. nov. (Teleostei: Mormyridae), a mormyrid fish from the Namib desert

We critically compared Marcusenius specimens from the mouth of the Cunene River on the Namibia/Angola border, a harsh desert environment on the Atlantic Ocean coast virtually devoid of aerial insects with aquatic larvae which are an important food item, with Marcusenius multisquamatus Kramer & Wink, 2013 from the escarpment region of that same river, in a relatively rich and productive subtropical savannah environment. River mouth specimens were differentiated in morphology and electric organ discharges, as determined by ANOVA/MANOVA comparisons, principal component and discriminant analyses on morphological and electrophysiological characters, and genetics, including sequences of the mitochondrial cytochrome b gene, indicating reproductive isolation. Specimens from the river mouth differed from M. multisquamatus, their closest relatives, by having a shorter snout, a smaller eye diameter, and smaller nares separation. River mouth specimens were also differentiated from other, increasingly less-close relatives, such as M. altisambesi Kramer et al., 2007 from the Okavango River, Botswana, and from M. krameri Maake et al., 2014 from the Limpopo System, South Africa. We therefore designate the new species Marcusenius desertus sp. nov. for the Cunene River mouth population.     

Gene cloning and molecular characterization of the Talaromyces thermophilus lipase catalyzed efficient hydrolysis and synthesis of esters

A genomic bank from Talaromyces thermophilus fungus was constructed and screened using a previously isolated fragment lipase gene as probe. From several clones isolated, the nucleotide sequence of the lipase gene (TTL gene) was completed and sequenced. The TTL coding gene consists of an open reading frame (ORF) of 1083 bp encoding a protein of 269 Aa with an estimated molecular mass of 30 kDa. The TTL belongs to the same gene family as Thermomyces lanuginosus lipase (TLL, Lipolase®), a well known lipase with multiple applications. The promoter sequence of the TTL gene showed the conservation of known consensus sequences PacC, CreA, Hap2-3-4 and the existence of a particular sequence like the binding sites of Oleate Response Element (ORE) and Fatty acids Responsis Element (FARE) which are similar to that already found to be specific of lipolytic genes in Candida and Fusarium, respectively. Northern blot analysis showed that the TTL expression was much higher on wheat bran than on olive oil as sole carbon source. Compared to the Lipolase®, this enzyme was found to be more efficient for the hydrolysis and the synthesis of esters; and its synthetic efficiency even reached 91.6% from Waste Cooking Oil triglycerides.