Population structure of mud flounder Paralichthys orbignyanus from the south-western Atlantic Ocean

The mud flounder Paralichthys orbignyanus (Pleuronectiformes, Paralichthyidae) inhabits shallow waters of low salinities and mud bottoms in the temperate marine coastal regions of the Bonaerensean Ecoregion of the Argentinean Biogeographic Province in the south-western Atlantic Ocean. Specimens of P. orbignyanus were collected from Lagoa dos Patos (LDP) (southern Brazil), Mar Chiquita (MCH) and Marisol (MAR) both located in Buenos Aires (Argentina), and San Antonio Oeste (SAO) in the San Matías Gulf, Rio Negro (Argentina). A fragment of the mitochondrial DNA of the Control Region and seven microsatellite loci were characterized. In the Control Region, P. orbignyanus showed high variability, low nucleotide diversity, mild population expansion and a coalescence time of 35,000 years before the present. Flounders provided evidence of a genetic structure between the sampling sites LDP, MCH, MAR vs. SAO. On the other hand, P. orbignyanus displayed a lower to moderate contemporary genetic structure among all samples except between LDP and MCH. With no evidence of isolation by distance, this analysis supports a model of limited gene flow that is likely to be associated with a consistent larvae retention in all sampling sites. In addition, the present connectivity is ascribed to a lower migration process from SAO in the San Matías Gulf congruent with the prevailing littoral drift.     

Bayesian tests for random mating in polyploids

Hardy–Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of the hwep R package on the Comprehensive R Archive Network https://cran.r-project.org/package=hwep .     

Poplar (Populus nigra L.) plants transformed with aBacillus thuringiensis toxin gene: insecticidal activity and genomic analysis

Insect-resistant poplar (Populus nigra L.) plants have been produced by infecting leaves withAgrobacterium tumefaciens strains carrying a binary vector containing different truncated forms of aBacillus thuringiensis (B.t.) toxin gene under a duplicated CaMV 35S promoter. Putative transgenic plants were propagated by cuttings at two experimental farms (in Beijing and Xinjiang, China). At 2–3 years after transformation, 17 of them were selected on the bases of insect-tolerance and good silvicultural traits, and evaluated for insect resistance, for the presence of theB.t. toxin DNA fragment (Southern blots and PCR) and for the expression of the transgene (western and northern blots). Somaclonal variation, as suggested by the appearance of permanent changes in the shape of the leaves, was also investigated with molecular tools (RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA) and microsatellite DNA).Bioassays withApochemia cineraius andLymantria dispar on the leaves of the selected clones showed different and, in some cases, high levels of insecticidal activity. The molecular analysis demonstrated integration and expression of the foreign gene. Somatic changes were correlated to extensive genomic changes and were quantified in dendrograms, in terms of genomic similarity. The analysis of control plants suggested that genomic changes were correlated to thein vitro culture step necessary forA. tumefaciens-mediated gene transfer, rather than to the integration of the foreign genes.Three transgenic clones (12, 153 and 192), selected for insect resistance, reduced morphological changes and promising silvicultural traits, are now under large-scale field evaluation in six different provinces in China.     

非放射性反相杂交法在HLA－DQA1位点基因分型中的应用

将遴选的经适当接尾的１２个ＨＬＡ－ＤＱＡ１序列特异性寡核苷酸固定在一张滤膜上,用生物素标记的ＤＱＡ１特异性扩增产物与滤膜上的序列特异性寡核苷酸在四甲基氯化铵杂交体系中杂交,然后经洗膜封膜,杂交信号用非放射性的碱性磷酸酶显色法检测,根据杂交斑点的显示结果分析标本的基因型。采用这种方法初步确定了ＨＬＡ－ＤＱＡ１位点８种单倍型等位基因：ＤＱＡ１０１０１、０１０２、０１０３、０２０１、０３０１１、０４０１、０５０１和０６０１．非放射性反相杂交法可对各种来源的杂合性标本进行ＨＬＡ－Ⅱ类基因快速分型,并适合在临床器官移植的组织分型配型、疾病易感性研究和法医鉴定等领城中应用。     

Repetitive DNA sequences located in the central region of the human mdr1 (multidrug resistance) gene may account for a gene fusion event during its evolution

The mdr1 gene, first member of the human multidrug-resistance gene family, is a major gene involved in cellular resistance to several drugs used in anticancer chemotherapy. Its product, the drug-excreting P-glycoprotein, shows a bipartite structure formed by two similar adjacent halves. According to one hypothesis, the fusion of two related ancestral genes during evolution could have resulted in this structure. The DNA sequence analysis of the introns located in the region connecting the two halves of the human mdr1 gene revealed a highly conserved poly(CA) · poly (TG) sequence in intron 15 and repeated sequences of the Alu family in introns 14 and 17. These repeated sequences most likely represent molecular fossils of ancient DNA elements which were involved in such a recombination event. Correspondence to: M. Pauly     

Characterization of six microsatellite markers in Trillium camschatcense using a dual‐suppression‐polymerase chain reaction technique

Trillium camschatcense is a herbaceous perennial plant distributed in Hokkaido and northern Honshu, Japan. Geographical variations in the breeding system (partial selfing or obligate outcrossing) are reported in the populations of Hokkaido. We isolated six polymorphic microsatellite loci from this species. The number of allele per locus ranged from four to 12, whereas the expected heterozygosities ranged from 0.69 to 0.83. These markers may allow further investigations to reveal the evolutionary and ecological processes of mating system in T. camschatcense.     

Genetic structure and differentiation of the Japanese extremely long-tailed chicken breed (Onagadori), associated with plumage colour variation: suggestions for its management and conservation

The Onagadori is a distinguished chicken breed that is characterized by an extremely long tail in the male. In this breed, three different plumage colour varieties have been developed (black-breasted white, black-breasted red and white) in which the black-breasted white is believed to be the original colour of the Onagadori, based on historical records. To establish a conservation strategy, 176 birds were genotyped for autosomal microsatellites. Significant genetic distinctness was found between the original (black-breasted white) and two derivative varieties ( F _ST = 0.091 and 0.093). At the same time, a Bayesian model-based clustering revealed that the majority of individuals belonging to the black-breasted red and white varieties had an extremely low proportion of the genome shared with the original type (black-breasted white). This suggests that derivative varieties were created by crossing with other breeds, with low introgression of the original-type genome. We propose that the three plumage colour varieties should be treated as separate genetic units in a conservation programme.     

Male mating success in an aquatically mating pinniped, the harbour seal (Phoca vitulina), assessed by microsatellite DNA markers

Similar to many other pinniped species, harbour seals ( Phoca vitulina ) mate exclusively at sea. Here we present the first attempt to measure male mating success in an aquatically mating pinniped. Male mating success was estimated by paternity analysis in two cohorts of pups born at Sable Island, Nova Scotia, Canada, using microsatellite DNA markers. The genotypes of 275 pups born in 1994 and 1995 were compared to those of 90 candidate males at six microsatellite loci using a likelihood approach to resolve paternity. Paternity could be assigned for two, 22, 40 and 85 pups at confidence levels of 95, 80, 65 and 50%, respectively. Most successful males were assigned the paternity of a single offspring, suggesting a low variance in male mating success relative to most pinniped species. The proportion of paternal half sibs within cohorts and between maternally related sibs estimated by maximum likelihood were not significantly different from zero. It is thus unlikely that most offspring were sired by a small number of highly successful unsampled males, and that female harbour seals do not usually exhibit fidelity to the same male in sequential breeding seasons. A low level of polygyny in Sable Island harbour seals is consistent with predictions based on their breeding ecology, as females are highly mobile and widely dispersed in the aquatic mating environment at Sable Island.