Genetic divergence among native trout Salmo trutta populations from southern Balkans based on mitochondrial DNA and microsatellite variation

The genetic structure and the phylogenetic relationships among five Balkan populations of trout Salmo trutta that have been classified earlier into five different taxa were studied, using microsatellite and mitochondrial DNA (mtDNA) analyses. The pattern of population differentiation observed at microsatellites differed to that depicted by mtDNA variation, yet both methods indicated a very strong partitioning of the genetic variation among sampling locations. Results thus suggest that conservation strategies should be directed towards preserving the genetic integrity and uniqueness of each population.     

Dissecting Cell Lineage Specification and Sex Fate Determination in Gonadal Somatic Cells Using Single-Cell Transcriptomics

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Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

Background

RNA sequencing (RNA-seq) is the current gold-standard method to quantify gene expression for expression quantitative trait locus (eQTL) studies. However, a potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias gene quantifications and cause false positive eQTL associations. In this study, we analyze the effect of this allelic mapping bias in eQTL discovery.

Results

We simulate RNA-seq read mapping over 9.5 M common SNPs and indels, with 15.6% of variants showing biased mapping rate for reference versus non-reference reads. However, removing potentially biased RNA-seq reads from an eQTL dataset of 185 individuals has a very small effect on gene and exon quantifications and eQTL discovery. We detect only a handful of likely false positive eQTLs, and overall eQTL SNPs show no significant enrichment for high mapping bias.

Conclusion

Our results suggest that RNA-seq quantifications are generally robust against allelic mapping bias, and that this does not have a severe effect on eQTL discovery. Nevertheless, we provide our catalog of putatively biased loci to allow better controlling for mapping bias to obtain more accurate results in future RNA-seq studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0467-2) contains supplementary material, which is available to authorized users.     

Different degree of paternal mtDNA leakage between male and female progeny in interspecific Drosophila crosses

Maternal transmission of mitochondrial DNA (mtDNA) in animals is thought to prevent the spread of selfish deleterious mtDNA mutations in the population. Various mechanisms have been evolved independently to prevent the entry of sperm mitochondria in the embryo. However, the increasing number of instances of paternal mtDNA leakage suggests that these mechanisms are not very effective. The destruction of sperm mitochondria in mammalian embryos is mediated by nuclear factors. Also, the destruction of paternal mitochondria in intraspecific crosses is more effective than in interspecific ones. These observations have led to the hypothesis that leakage of paternal mtDNA (and consequently mtDNA recombination owing to ensuing heteroplasmy) might be more common in inter‐ than in intraspecific crosses and that it should increase with phylogenetic distance of hybridizing species. We checked paternal leakage in inter‐ and intraspecific crosses in Drosophila and found little evidence for this hypothesis. In addition, we have observed a higher level of leakage among male than among female progeny from the same cross. This is the first report of sex‐specific leakage of paternal mtDNA. It suggests that paternal mtDNA leakage might not be a stochastic result of an error‐prone mechanism, but rather, it may be under complex genetic control.     

Genetic characterization of brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) populations from the Southern Balkans using mtDNA sequencing and RFLP analysis

In the present study, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was used to survey variation in a 1450-bp mitochondrial DNA (mtDNA) segment which comprises part of the cytochrome oxidase III (COIII) and ATPase subunit VI genes in 8 brown trout (Salmo trutta L) populations from the southern Balkans. In addition, a 300 bp fragment at the 5′ end of the control region was sequenced from representatives of the populations studied providing the opportunity to assign PCR-RFLP haplotypes into major phylogenetic lineages (i.e. Atlantic, Danubian, marmoratus, Adriatic and Mediterranean). The level of polymorphism found in the 1450 bp segment suggests that this PCR-RFLP assay may be useful for future diagnostic analyses of mitochondrial DNA in brown trout populations. A reduced within-population genetic variability but considerable among-population differentiation was observed. The results are in accordance with previous data on phylogeography of Mediterranean brown trout suggesting that mitochondrial DNA haplotypes are distributed in a mosaic pattern as a consequence of a complex evolutionary history. The present study shows that brown trout populations from the Southern Balkans are highly divergent and possess a unique genetic profile that should be taken into account when establishing conservation management programs. Handling editor: C. Sturmbauer     

Medical confidentiality: legal and ethical aspects in Greece

Respect for confidentiality is firmly established in codes of ethics and law. Medical care and the patients' trust depend on the ability of the doctors to maintain confidentiality. Without a guarantee of confidentiality, many patients would want to avoid seeking medical assistance The principle of confidentiality, however, is not absolute and may be overridden by public interests. On some occasions (birth, death, infectious disease) there is a legal obligation on the part of the doctor to disclose but only to the appropriate authorities. Permissible disclosure can be granted by the patients' consent, for example, for the purpose of insurance they may wish to take out. Moreover, there are some ambivalent situations (such as criminal acts, or notification of sexual partner in case of a patient with AIDS) for which Greek law does not include relevant provisions, and the Codes of Medical Ethics do not offer clear guidelines. Therefore, the Greek doctor is called to estimate the situation and assume full responsibility for his decision. Finally, new considerations have arisen in the context of the recent advances in the field of telemedicine and electronic archiving. The paper discusses the current situation and legislation in Greece.     

Morphological variation between red mullet populations in Greece

Morphometric variation in 15 characters of the red mullet Mullus barbatus samples from seven Greek localities was examined using multivariate analysis. ANOVA, stepwise discriminant analysis and cluster analysis revealed a rather high morphological variability between the populations studied. The discriminant analysis revealed that about 80% of the examined fish could be correctly classified into the seven areas. This variability could be explained in terms of genetic structuring of the populations and/or environmental conditions prevailing in each geographic area in combination with fish migration and egg/larvae transportation from one area to another. The results suggest that multivariate analysis when combined with other important biological parameters of red mullet may have important implications for the management of the Greek demersal fish resources.