We performed population genetic analyses on the American eel (Anguilla rostrata) with three main objectives. First, we conducted the most comprehensive analysis of neutral genetic population ...structure to date to revisit the null hypothesis of panmixia in this species. Second, we used this data to provide the first estimates of contemporary effective population size (Ne) and to document temporal variation in effective number of breeders (Nb) in American eel. Third, we tested for statistical associations between temporal variation in the North Atlantic Oscillation (NAO), the effective number of breeders and two indices of recruit abundance. A total of 2142 eels from 32 sampling locations were genotyped with 18 microsatellite loci. All measures of differentiation were essentially zero, and no evidence for significant spatial or temporal genetic differentiation was found. The panmixia hypothesis should thus be accepted for this species. Nb estimates varied by a factor of 23 among 12 cohorts, from 473 to 10 999. The effective population size Ne was estimated at 10 532 (95% CI, 9312–11 752). This study also showed that genetically based demographic indices, namely Nb and allelic richness (Ar), can be used as surrogates for the abundance of breeders and recruits, which were both shown to be positively influenced by variation during high (positive) NAO phases. Thus, long‐term genetic monitoring of American glass eels at several sites along the North American Atlantic coast would represent a powerful and efficient complement to census monitoring to track demographic fluctuations and better understand their causes.
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Freshwater eels Anguilla spp. are declining worldwide, and a major challenge is understanding why these panmictic species show contrasting patterns of intraspecific phenotypic variation and ...recruitment. We present results on studies of the American Eel A. rostrata to understand and discriminate the effects of origin and plasticity on growth and sex determination. We considered two separate growth and one length-at-age data sets. The first growth data set originated from a 34-month rearing experiment starting from the glass eel life stage to test the effects of origin, salinity, and density on growth and sex determination. The second growth data set originated from a shorter rearing experiment of 18 months starting at the yellow eel stage (around 3 years old) and compared transplanted individuals in Lake Ontario (LO) with natural migrants to the LO area. The third data set compared transplanted individuals in LO sampled by electrofishing with naturally migrating individuals. Sex ratios were identical for all origins and treatments in the long-term growth experiment (34–35% females). While male size distribution had little variability, certain female groups had a large variation in growth and presented fast- and slow-growing clusters. On the other hand, both cases of natural migrants to the LO area were consistent with being only slow-growing females. We found that wild individuals rearing in the LO area were nearly exclusively transplanted individuals and that males, as well as fast-growing females, were present. Even though the entire species is panmictic, these results support a role for spatially varying selection in explaining the phenotypic variation observed among regions and among individuals of the same region, and such factors must be considered for any successful management strategies of American Eel. Received December 17, 2013; accepted September 29, 2014
Class III Homeodomain Leucine Zipper (HD-Zip III) proteins have been implicated in the regulation of cambium identity, as well as primary and secondary vascular differentiation and patterning in ...herbaceous plants. They have been proposed to regulate wood formation but relatively little evidence is available to validate such a role. We characterised and compared HD-Zip III gene family in an angiosperm tree, Populus spp. (poplar), and the gymnosperm Picea glauca (white spruce), representing two highly evolutionarily divergent groups.
Full-length cDNA sequences were isolated from poplar and white spruce. Phylogenetic reconstruction indicated that some of the gymnosperm sequences were derived from lineages that diverged earlier than angiosperm sequences, and seem to have been lost in angiosperm lineages. Transcript accumulation profiles were assessed by RT-qPCR on tissue panels from both species and in poplar trees in response to an inhibitor of polar auxin transport. The overall transcript profiles HD-Zip III complexes in white spruce and poplar exhibited substantial differences, reflecting their evolutionary history. Furthermore, two poplar sequences homologous to HD-Zip III genes involved in xylem development in Arabidopsis and Zinnia were over-expressed in poplar plants. PtaHB1 over-expression produced noticeable effects on petiole and primary shoot fibre development, suggesting that PtaHB1 is involved in primary xylem development. We also obtained evidence indicating that expression of PtaHB1 affected the transcriptome by altering the accumulation of 48 distinct transcripts, many of which are predicted to be involved in growth and cell wall synthesis. Most of them were down-regulated, as was the case for several of the poplar HD-Zip III sequences. No visible physiological effect of over-expression was observed on PtaHB7 transgenic trees, suggesting that PtaHB1 and PtaHB7 likely have distinct roles in tree development, which is in agreement with the functions that have been assigned to close homologs in herbaceous plants.
This study provides an overview of HD-zip III genes related to woody plant development and identifies sequences putatively involved in secondary vascular growth in angiosperms and in gymnosperms. These gene sequences are candidate regulators of wood formation and could be a source of molecular markers for tree breeding related to wood properties.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Protecting freshwater biodiversity is considered an ultimate challenge but depends on reliable surveys of species distribution and abundance which eDNA metabarcoding (environmental DNA metabarcoding) ...may offer. To do so, a better understanding of the sources of temporal variation among species eDNA abundance and of data transformation in eDNA metabarcoding studies is needed. Here, we show that transformation based on relative abundance is critical to suitable analyses of eDNA metabarcoding data and that Hellinger transformation performed slightly better than other methods. Furthermore, we show that site localities significantly explain eDNA metabarcoding variation, while no variation is explained by time of sampling. This indicates that species communities vary more spatially than temporally within a dendritic system composed of small rivers. We then further documented the community structure in the St. Charles River (Québec City, Canada) and six of its tributaries. This revealed the existence of eight species communities explaining 82.1% of eDNA read variation within this river network. Moreover, variation in environmental variables among sites explained 53.0% of eDNA reads, while sampling events and temporal environmental variation explained no eDNA metabarcoding variation. Altogether, this supports the claim that eDNA metabarcoding is a powerful tool to document and monitor fish communities in watersheds composed of small river dendritic systems.
Protecting freshwater biodiversity is considered an ultimate challenge but depends on reliable surveys of species distribution. Our study supports the claim that eDNA metabarcoding is a powerful tool to document and monitor fish communities in watersheds composed of small river dendritic systems.
Variation in gene regulation may be involved in the differences observed for life history traits within species. American eel (Anguilla rostrata) is well known to harbor distinct ecotypes within a ...single panmictic population. We examined the expression of genes involved in the regulation of appetite as well as lipid and glycogen among glass eels migrating to different locations on the Canadian east coast and captured at two different periods of upstream migration. Gene expression levels of three reference and five candidate genes were analyzed by real-time PCR with Taqman probes in recently captured wild glass eels. All gene transcripts were detected in glass eels. Of the five candidate genes, bile salt activated and triacylglycerol lipases were respectively 7.65 and 3.25 times more expressed in glass eels from the St. Lawrence estuary than in those from Nova Scotia, and there was no effect related to the two-week difference in capture date. These two genes explained 82.41% of the dissimilarity between the two rivers. In contrast, glycogen phosphorylase, ghrelin, and leptin receptor genes showed no significant differences in gene transcription. These results confirmed at the molecular level an observation that was recently made at the phenotypic level that glass eels from the St. Lawrence estuary have a greater capacity to use lipid reserves to sustain their metabolic needs. These observations add to the body of evidence supporting the hypothesis that regional phenotypic variation observed in American eel is determined early in life and that part of this variation is likely under genetic control.
MHC class I-associated peptides (MAPs) define the immune self for CD8+ T lymphocytes and are key targets of cancer immunosurveillance. Here, the goals of our work were to determine whether the entire ...set of protein-coding genes could generate MAPs and whether specific features influence the ability of discrete genes to generate MAPs. Using proteogenomics, we have identified 25,270 MAPs isolated from the B lymphocytes of 18 individuals who collectively expressed 27 high-frequency HLA-A,B allotypes. The entire MAP repertoire presented by these 27 allotypes covered only 10% of the exomic sequences expressed in B lymphocytes. Indeed, 41% of expressed protein-coding genes generated no MAPs, while 59% of genes generated up to 64 MAPs, often derived from adjacent regions and presented by different allotypes. We next identified several features of transcripts and proteins associated with efficient MAP production. From these data, we built a logistic regression model that predicts with good accuracy whether a gene generates MAPs. Our results show preferential selection of MAPs from a limited repertoire of proteins with distinctive features. The notion that the MHC class I immunopeptidome presents only a small fraction of the protein-coding genome for monitoring by the immune system has profound implications in autoimmunity and cancer immunology.
Antibiotics are used to fight bacterial infections. However, a selective pressure gave rise to bacteria resistant to antibiotics. This leaves scientists worried about the danger to human and animal ...health. Some strategies can be borrowed to reduce the use of antibiotics in chicken farms. Much research has been carried out to look for natural agents with similar beneficial effects of growth promoters. The aim of these alternatives is to maintain a low mortality rate, a good level of animal yield while preserving environment and consumer health. Among these, the most popular are probiotics, prebiotics, enzymes, organic acids, immunostimulants, bacteriocins, bacteriophages, phytogenic feed additives, phytoncides, nanoparticles and essential oils.
These studies examined the concept of concentration and purification of several types of wastewater by freezing and thawing. The experiments demonstrated that freezing of contaminated liquid ...contributed to concentration of contaminants in solution as well as significant concentration and agglomeration of solid particles. A high degree of purification was achieved for many parameters. The results of comparative laboratory tests for single and multiple freezing are presented. It was found that there was a higher degree of concentration of pollutants in wastewater frozen as man-made snow than in bulk ice. Furthermore, the hypothesis that long storage time of liquid as snow and sufficient temperature gradient metamorphism allows for high efficiency of the concentration process was confirmed. It was reported that the first 30% of the melted liquid volume contained over 90% of all impurities. It gives great opportunities to use this method to concentrate pollutants. The results revealed that the application of this process in full scale is possible. Significant agglomeration of solid particles was also noted. Tests with clay slurry showed that repeated freezing and thawing processes significantly improve the characteristics of slurry for sedimentation and filtration.
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