Multivariate methods in aquaculture research: case studies of tilapias in experimental and commercial systems

This volume documents the usefulness of multivariate methods û notably multiple regression, path analysis and canonical correlation û in the context of aquaculture, which has to date tended to neglect such methods, and hence to underutilize available data. All examples used here stem from experimental and/or commercial tilapia culture systems, and hence this book also represents an advance in the understanding of such systems.Aquaculture, Tilapia culture, Growth, Multivariate analysis Oreochromis

Genetic analysis of immunological traits in tilapia

The immunological response to handling stress of four tilapia species is evaluated.Polymorphism is examined in genes known to influence immune response in fish

DNA BARCODING OF FISH SPECIES FROM THE MEDITERRANEAN COAST OF ISRAEL

Accurately-classified genomic data in the Barcode of Life Data System (BOLD) database is vital to the protection and conservation of marine biodiversity in the Mediterranean Sea. The taxonomic classifications of 468 fish of 50 Mediterranean species were analyzed using the BOLD Identifier tool for variation in the cytochrome oxidase subunit I (COI) mitochondrial gene. Within species, nucleotide maximum composite likelihood was low with a mean of 0.0044±0.0008. Three presumptive species had significantly higher values e.g., Arnoglossus spp. (0.07), Torquigener flavimaculosus (0.013) and Boops boops (0.028). However, samples of Arnoglossus species were sub-classified into two groups that were finally identified as two different species e.g., Arnoglossus laterna and Arnoglossus thori. For the different species, BLAST searches against the BOLD database using our DNA barcoding data as the query sequences designated the most similar targets into groups. For each analyzed species, the similarity of the first and second threshold groups ranged from 95 to 99% and from 83 to 98%, respectively. Sequence based classification for the first threshold group was concordant with morphology-based identification. However, for 34 analyzed species (68%) overlaps of species between the two threshold groups hampered classification. Tree-based phylogeny analysis detected more than one cluster in the first threshold group for 22 out of 50 species, representing genetic subgroups and geographic origins. There was a tendency for higher conservation and lower number of clusters in the Lessepsian (Red Sea) migrant versus indigenous species

Linkage and Physical Mapping of Sex Region on LG23 of Nile Tilapia (Oreochromis niloticus)

Evidence supports that sex determination (SD) in tilapia is controlled by major genetic factors that may interact with minor genetic as well as environmental factors, thus implying that SD should be analyzed as a quantitative trait. Quantitative trait loci (QTL) for SD in Oreochromis niloticus were previously detected on linkage groups (LG) 1 and 23. Twenty-one short single repeats (SSR) of >12 TGs and one single nucleotide polymorphism were identified using the unpublished tilapia genome sequence on LG23. All markers showed two segregating alleles in a mapping family that was obtained by a cross between O. niloticus male (XY) and sex-reversed female (ΔXY) yielding 29 females (XX) and 61 males (XY and YY). Interval mapping analysis mapped the QTL peak between SSR markers ARO172 and ARO177 with a maximum F value of 78.7 (P < 7.6 × 10−14). Twelve adjacent markers found in this region were homozygous in females and either homozygous for the alternative allele or heterozygous in males. This segment was defined as the sex region (SR). The SR encompasses 1.5 Mbp on a single tilapia scaffold (no. 101) harboring 51 annotated genes. Among 10 candidate genes for SD that were tested for gene expression, anti-Müllerian hormone (Amh), which is located in the center of the SR, showed the highest overexpression in male vs. female embryos at 3 to 7 days postfertilization

Species-Specific Marker Discovery in Tilapia

Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations

Stochastic Resonance of Ensemble Neurons for Transient Spike Trains: A Wavelet Analysis

By using the wavelet transformation (WT), we have analyzed the response of an ensemble of $N$ (=1, 10, 100 and 500) Hodgkin-Huxley (HH) neurons to {\it transient} $M$-pulse spike trains ($M=1-3$) with independent Gaussian noises. The cross-correlation between the input and output signals is expressed in terms of the WT expansion coefficients. The signal-to-noise ratio (SNR) is evaluated by using the {\it denoising} method within the WT, by which the noise contribution is extracted from output signals. Although the response of a single (N=1) neuron to sub-threshold transient signals with noises is quite unreliable, the transmission fidelity assessed by the cross-correlation and SNR is shown to be much improved by increasing the value of $N$: a population of neurons play an indispensable role in the stochastic resonance (SR) for transient spike inputs. It is also shown that in a large-scale ensemble, the transmission fidelity for supra-threshold transient spikes is not significantly degraded by a weak noise which is responsible to SR for sub-threshold inputs.Comment: 20 pages, 4 figure

Cytogenetic and histological studies of the brook trout, Salvelinus fontinalis (Mitchill), and the Arctic char, S-alpinus (L.) hybrids

Although brook trout and the Arctic char hybrids are able to reproduce, individuals with decreased fertility or even fish that are unable to produce any gametes have been also described. Abnormal gonadal development and disturbances in the gamete production in the char hybrid offspring may be triggered by the odd chromosome number and disturbances in their pairing during meiosis. To verify this hypothesis, cytogenetic examination and the gonadal histology analysis of the brook trout x Arctic char hybrids were carried out. Diploid chromosome number in the studied char (F-1) hybrids varied from 82 to 84 (FN = 99-102). Among 28 hybrids, 12 males, three females, nine intersex individuals and two sterile specimens were described. In the case of two individuals, gonads were not found. Diploid chromosome numbers in the males and intersex individuals varied from 82 to 84. Chromosome numbers in the females were 82 and 83 chromosomes. Two sterile fish exhibited karyotypes composed of 82 and 84 chromosomes. Predominance of the ovarian component in the intersex gonads and gonadal sex ratio distortion towards the males suggested hybrid females had problems with gonadal differentiation. However, the lack of the clear relationship between chromosome number and gonadal development in the studied hybrids did not support our hypothesis that odd chromosome number may be responsible for such reproductive disturbances in the hybrid individuals. We have presumed that sterility and intersexual development of the gonads may be caused by interactions between brook trout and Arctic char genes on the sex chromosomes and autosomes rather than unpairing of the parental chromosomes.Polish National Science Center (NCN) [N N311 525240]info:eu-repo/semantics/publishedVersio

Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome

BACKGROUND: Automatic annotation of sequenced eukaryotic genomes integrates a combination of methodologies such as ab-initio methods and alignment of homologous genes and/or proteins. For example, annotation of the zebrafish genome within Ensembl relies heavily on available cDNA and protein sequences from two distantly related fish species and other vertebrates that have diverged several hundred million years ago. The scarcity of genomic information from other cyprinids provides the impetus to leverage EST collections to understand gene structures in this diverse teleost group. RESULTS: We have generated 6,050 ESTs from the differentiating testis of common carp (Cyprinus carpio) and clustered them with 9,303 non-gonadal ESTs from CarpBase as well as 1,317 ESTs and 652 common carp mRNAs from GenBank. Over 28% of the resulting 8,663 unique transcripts are exclusively testis-derived ESTs. Moreover, 974 of these transcripts did not match any sequence in the zebrafish or fathead minnow EST collection. A total of 1,843 unique common carp sequences could be stringently mapped to the zebrafish genome (version 5), of which 1,752 matched coding sequences of zebrafish genes with or without potential splice variants. We show that 91 common carp transcripts map to intergenic and intronic regions on the zebrafish genome assembly and regions annotated with non-teleost sequences. Interestingly, an additional 42 common carp transcripts indicate the potential presence of new splicing variants not found in zebrafish databases so far. The fact that common carp transcripts help the identification or confirmation of these coding regions in zebrafish exemplifies the usefulness of sequences from closely related species for the annotation of model genomes. We also demonstrate that 5' UTR sequences of common carp and zebrafish orthologs share a significant level of similarity based on preservation of motif arrangements for as many as 10 ab-initio motifs. CONCLUSION: Our data show that there is sufficient homology between the transcribed sequences of common carp and zebrafish to warrant an even deeper cyprinid transcriptome comparison. On the other hand, the comparative analysis illustrates the value in utilizing partially sequenced transcriptomes to understand gene structure in this diverse teleost group. We highlight the need for integrated resources to leverage the wealth of fragmented genomic data

Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean

The photosynthetic picocyanobacteria Prochlorococcus and Synechococcus are models for dissecting how ecological niches are defined by environmental conditions, but how interactions with bacteriophages affect picocyanobacterial biogeography in open ocean biomes has rarely been assessed. We applied single-virus and single-cell infection approaches to quantify cyanophage abundance and infected picocyanobacteria in 87 surface water samples from five transects that traversed approximately 2,200 km in the North Pacific Ocean on three cruises, with a duration of 2–4 weeks, between 2015 and 2017. We detected a 550-km-wide hotspot of cyanophages and virus-infected picocyanobacteria in the transition zone between the North Pacific Subtropical and Subpolar gyres that was present in each transect. Notably, the hotspot occurred at a consistent temperature and displayed distinct cyanophage-lineage composition on all transects. On two of these transects, the levels of infection in the hotspot were estimated to be sufficient to substantially limit the geographical range of Prochlorococcus. Coincident with the detection of high levels of virally infected picocyanobacteria, we measured an increase of 10–100-fold in the Synechococcus populations in samples that are usually dominated by Prochlorococcus. We developed a multiple regression model of cyanophages, temperature and chlorophyll concentrations that inferred that the hotspot extended across the North Pacific Ocean, creating a biological boundary between gyres, with the potential to release organic matter comparable to that of the sevenfold-larger North Pacific Subtropical Gyre. Our results highlight the probable impact of viruses on large-scale phytoplankton biogeography and biogeochemistry in distinct regions of the oceans

An online spike detection and spike classification algorithm capable of instantaneous resolution of overlapping spikes

For the analysis of neuronal cooperativity, simultaneously recorded extracellular signals from neighboring neurons need to be sorted reliably by a spike sorting method. Many algorithms have been developed to this end, however, to date, none of them manages to fulfill a set of demanding requirements. In particular, it is desirable to have an algorithm that operates online, detects and classifies overlapping spikes in real time, and that adapts to non-stationary data. Here, we present a combined spike detection and classification algorithm, which explicitly addresses these issues. Our approach makes use of linear filters to find a new representation of the data and to optimally enhance the signal-to-noise ratio. We introduce a method called “Deconfusion” which de-correlates the filter outputs and provides source separation. Finally, a set of well-defined thresholds is applied and leads to simultaneous spike detection and spike classification. By incorporating a direct feedback, the algorithm adapts to non-stationary data and is, therefore, well suited for acute recordings. We evaluate our method on simulated and experimental data, including simultaneous intra/extra-cellular recordings made in slices of a rat cortex and recordings from the prefrontal cortex of awake behaving macaques. We compare the results to existing spike detection as well as spike sorting methods. We conclude that our algorithm meets all of the mentioned requirements and outperforms other methods under realistic signal-to-noise ratios and in the presence of overlapping spikes