DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species

Birds are a taxonomically well-described group of animals, yet DNA barcoding, i.e., the molecular characterization of species using a standardized genetic marker, has revealed unexpected patterns of genetic divergences among North American birds. We performed a comprehensive COI (cytochrome c oxidase subunit I) barcode survey of 296 species of Scandinavian birds, and compared genetic divergences among 78 trans-Atlantic species whose breeding ranges include both Scandinavia and North America. Ninety-four percent of the Scandinavian species showed unique barcode clusters; the remaining 6% had overlapping barcodes with one or more congeneric species, which may reflect incomplete lineage sorting or a single gene pool. Four species showed large intra-specific divergences within Scandinavia, despite no apparent morphological differentiation or indications of reproductive isolation. These cases may reflect admixture of previously isolated lineages, and may thus warrant more comprehensive phylogeographic analyses. Nineteen (24%) of 78 trans-Atlantic species exhibited divergent genetic clusters which correspond with regional subspecies. Three of these trans-Atlantic divergences were paraphyletic. Our study demonstrates the effectiveness of COI barcodes for identifying Scandinavian birds and highlights taxa for taxonomic review. The standardized DNA barcoding approach amplified the power of our regional studies by enabling independently obtained datasets to be merged with the established avian barcode library.     

Direct observation of genomic heterogeneity through local haplotyping analysis

Background

It has been an abiding belief among geneticists that multicellular organisms’ genomes can be analyzed under the assumption that a single individual has a uniform genome in all its cells. Despite some evidence to the contrary, this belief has been used as an axiomatic assumption in most genome analysis software packages. In this paper we present observations in human whole genome data, human whole exome data and in mouse whole genome data to challenge this assumption. We show that heterogeneity is in fact ubiquitous and readily observable in ordinary Next Generation Sequencing (NGS) data.

Results

Starting with the assumption that a single NGS read (or read pair) must come from one haplotype, we built a procedure for directly observing haplotypes at a local level by examining 2 or 3 adjacent single nucleotide polymorphisms (SNPs) which are close enough on the genome to be spanned by individual reads. We applied this procedure to NGS data from three different sources: whole genome of a Central European trio from the 1000 genomes project, whole genome data from laboratory-bred strains of mouse, and whole exome data from a set of patients of head and neck tumors. Thousands of loci were found in each genome where reads spanning 2 or 3 SNPs displayed more than two haplotypes, indicating that the locus is heterogeneous. We show that such loci are ubiquitous in the genome and cannot be explained by segmental duplications. We explain them on the basis of cellular heterogeneity at the genomic level. Such heterogeneous loci were found in all normal and tumor genomes examined.

Conclusions

Our results highlight the need for new methods to analyze genomic variation because existing ones do not systematically consider local haplotypes. Identification of cancer somatic mutations is complicated because of tumor heterogeneity. It is further complicated if, as we show, normal tissues are also heterogeneous. Methods for biomarker discovery must consider contextual haplotype information rather than just whether a variant “is present”.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-418) contains supplementary material, which is available to authorized users.     

A retroviral vector for siRNA expression in mammalian cells

Utilization of RNA interference (RNAi) for knockdown of gene expression has become a standard tool for the study of gene function. Short hairpin RNAs (shRNAs) expressed from RNA polymerase III promoters are widely used to achieve stable knockdown of gene expression by RNAi. We have constructed a retroviral-based shRNA expression vector, pSiRPG, as a tool for shRNA-based functional genomic studies. This vector is based on a widely used shRNA expression system and was modified to harbor an enhanced green fluorescent protein (EGFP) and a puromycin selection marker. The functionality of the elements in the pSiRPG vector was validated. The H1(TetO₂) promoter in the vector facilitates doxycycline-inducible shRNA expression, which was demonstrated in cells expressing the Tet repressor (TetR). However, we also demonstrated limited efficiency of the inhibition of shRNA expression in an uninduced TetR-expressing cell line. This observation strongly indicates that the H1(TetO₂) promoter, which is used in a wide range of vectors, is not optimal for tightly regulated shRNA expression. Stable repression of the NDRG1 protein level was observed when introducing pSiRPG constructs expressing shRNAs targeting NDRG1 into two mammary epithelial cell lines by retroviral delivery. This vector should therefore facilitate functional studies in breast cell lines that are hard to transfect with conventional plasmid-based methods.     

Genetically distinct populations of northern shrimp,Pandalus borealis,in the North Atlantic: adaptation to different temperatures as an isolation factor

The large‐scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species’ range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: F_ST = ?0.0002 to 0.0475) with a highly significant average (F_ST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (F_ST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best‐fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5–4.7%) on large‐scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment.     

Negative impact of manganese on honeybee foraging

Anthropogenic accumulation of metals such as manganese is a well-established health risk factor for vertebrates. By contrast, the long-term impact of these contaminants on invertebrates is mostly unknown. Here, we demonstrate that manganese ingestion alters brain biogenic amine levels in honeybees and fruit flies. Furthermore, we show that manganese exposure negatively affects foraging behaviour in the honeybee, an economically important pollinator. Our findings indicate that in addition to its direct impact on human health, the common industrial contaminant manganese might also have indirect environmental and economical impacts via the modulation of neuronal and behavioural functions in economically important insects.     

Effect of low pass filtering on joint moments from inverse dynamics: implications for injury prevention

Analyses of joint moments are important in the study of human motion, and are crucial for our understanding of e.g. how and why ACL injuries occur. Such analyses may be affected by artifacts due to inconsistencies in the equations of motion when force and movement data are filtered with different cut-off frequencies. The purpose of this study was to quantify the effect of these artifacts, and compare joint moments calculated with the same or different cut-off frequency for the filtering of force and movement data. 123 elite handball players performed sidestep cutting while the movement was recorded by eight 240 Hz cameras and the ground reaction forces were recorded by a 960 Hz force plate. Knee and hip joint moments were calculated through inverse dynamics, with four different combinations of cut-off frequencies for signal filtering: movement 10 Hz, force 10 Hz, (10-10); movement 15 Hz, force 15 Hz; movement 10 Hz, force 50 Hz (10-50); movement 15 Hz, force 50 Hz. The results revealed significant differences, especially between conditions with different filtering of force and movement. Mean (SD) peak knee abduction moment for the 10-10 and 10-50 condition were 1.27 (0.53) and 1.64 (0.68) Nm/kg, respectively. Ranking of players based on knee abduction moments were affected by filtering condition. Out of 20 players with peak knee abduction moment higher than mean+1S D with the 10-50 condition, only 11 were still above mean+1 SD when the 10-10 condition was applied. Hip moments were very sensitive to filtering cut-off. Mean (SD) peak hip flexion moment was 3.64 (0.75) and 5.92 (1.80) under the 10-10 and 10-50 conditions, respectively. Based on these findings, force and movement data should be processed with the same filter. Conclusions from previous inverse dynamics studies, where this was not the case, should be treated with caution.     

Alanine radicals,part 4: relative amounts of radical species in alanine dosimeters after exposure to 6-19 MeV electrons and 10 kV-15 MV photons

The amino acid l-alpha-alanine can be used for high-precision dosimetry over a wide dose range, using EPR spectroscopy for monitoring radical concentrations. It is important, however, to understand the underlying composition of the observed EPR spectrum. In previous work, it was shown that the EPR signal from irradiated alanine consists of at least three different radical species, with the relative importance of each of these being almost independent of absorbed dose. However, it was not known whether the relative importance of each radical is independent of the radiation quality responsible for the EPR signal. In the present work, the relative contributions of the different radical species to the total EPR signal from alanine dosimeters irradiated with 6-19 MeV electrons and 10 kV-15 MV photons at a dose of 10 Gy were examined. By spectrum reconstruction using benchmark spectra generated from a simulation procedure, the relative amounts of the three different radical species were shown to be virtually independent of these radiation beam qualities.     

Radical formation in pyrimidine bases after X,proton and alpha-particle irradiation

Single crystals of anhydrous thymine (Ta) and cytosine monohydrate (Cm) were irradiated at room temperature using X rays, 20 MeV protons and 35 MeV alpha particles, and the relative distributions of the various radiation-induced stable radicals in the crystals were investigated. These two crystal systems were chosen because of systematic differences in their molecular packing and hydrogen-bonding network. The radicals stabilized in these systems have previously been identified and analyzed by several authors. Experimental EPR spectra could thus be reconstructed based on simulated benchmark spectra using a fitting procedure, yielding the relative amounts of the different radical species. It was found that the relative amounts of a given radical species varied with the type of radiation used, with differences being most prominent between alpha particles and protons or X rays. In Ta, an increased production of hydrogen addition or abstraction radicals was found after exposure to alpha particles. These radicals are believed to be formed predominantly from superexcited states, resulting from the higher density of ionizations along the track of the alpha particle. A corresponding reduction in radicals derived from proton transfer reactions was observed in comparison with exposure to protons or X rays. In Cm, the differences were smaller than for Ta. This is probably due to differences in the arrangement of the crystal lattice between the two systems, with Cm having an extended hydrogen-bonding network promoting fast proton transfers after ionization. Most interesting, however, was the observation that more than 50% of the radical population in Cm not could be accounted for by known radical species. The population with an unknown origin was represented with a broad singlet, having a line width of 1.5 mT and a g value of 2.0045, in the spectral reconstruction procedure.