Prediction of whole-genome DNA-DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA-DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA-DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes recN, rpoA and thdF for the Pasteurellaceae, and determined if the sequences could be used for predicting DNA-DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, rpoB and infB gene-sequencing strategies in a multisequence-based phylogeny for the family Pasteurellaceae. It is proposed to use the three sequences as a taxonomic tool, replacing DNA-DNA hybridization.

Phylogenetic relationships of German heavy draught horse breeds inferred from mitochondrial DNA D-loop variation

We analysed a 610-bp mitochondrial (mt)DNA D-loop fragment in a sample of German draught horse breeds and compared the polymorphic sites with sequences from Arabian, Hanoverian, Exmoor, Icelandic, Sorraia and Przewalski's Horses as well as with Suffolk, Shire and Belgian horses. In a total of 65 horses, 70 polymorphic sites representing 47 haplotypes were observed. The average percentage of polymorphic sites was 11.5% for the mtDNA fragment analysed. In the nine different draught horse breeds including South German, Mecklenburg, Saxon Thuringa coldblood, Rhenisch German, Schleswig Draught Horse, Black Forest Horse, Shire, Suffolk and Belgian, 61 polymorphic sites and 24 haplotypes were found. The phylogenetic analysis failed to show monophyletic groups for the draught horses. The analysis indicated that the draught horse populations investigated consist of diverse genetic groups with respect to their maternal lineage.

New constraints on the gas age-ice age difference along the EPICA ice cores, 0-50 kyr

Gas is trapped in polar ice sheets at ~50–120 m below the surface and is therefore younger than the surrounding ice. Firn densification models are used to evaluate this ice age-gas age difference (Δage) in the past. However, such models need to be validated by data, in particular for periods colder than present day on the East Antarctic plateau. Here we bring new constraints to test a firn densification model applied to the EPICA Dome C (EDC) site for the last 50 kyr, by linking the EDC ice core to the EPICA Dronning Maud Land (EDML) ice core, both in the ice phase (using volcanic horizons) and in the gas phase (using rapid methane variations). We also use the structured 10Be peak, occurring 41 kyr before present (BP) and due to the low geomagnetic field associated with the Laschamp event, to experimentally estimate the Δage during this event. Our results seem to reveal an overestimate of the Δage by the firn densification model during the last glacial period at EDC. Tests with different accumulation rates and temperature scenarios do not entirely resolve this discrepancy. Although the exact reasons for the Δage overestimate at the two EPICA sites remain unknown at this stage, we conclude that current densification model simulations have deficits under glacial climatic conditions. Whatever the cause of the Δage overestimate, our finding suggests that the phase relationship between CO2 and EDC temperature previously inferred for the start of the last deglaciation (lag of CO2 by 800±600 yr) seems to be overestimated.

Provenance discrimination of Lower Cretaceous synrift sandstones (eastern Iberian Chain Spain) Constraints from detrital modes heavy minerals and geochemistry

Petrography, geochemical whole-rock composition, and chemical analyses of tourmaline were performed in order to determine the source areas of Lower Cretaceous Mora, El Castellar, and uppermost Camarillas Formation sandstones from the Iberian Chain, Spain. Sandstones were deposited in intraplate subbasins, which are bound by plutonic and volcanic rocks of Permian, Triassic, and Jurassic age, Paleozoic metamorphic rocks, and Triassic sedimentary rocks. Modal analyses together with petrographic and cathodoluminescence observations allowed us to define three quartz-feldspathic petrofacies and recognize diagenetic processes that modified the original framework composition. Results from average restored petrofacies are: Mora petrofacies = P/F >1 and Q(r)70 F(r)22 R(r)9; El Castellar petrofacies = P/F >1 and Q(r)57 F(r)25 R(r)18; and Camarillas petrofacies = P/F ∼ zero and Q(r)64 F(r)28 R(r)7 (P—plagioclase; F—feldspar; Q—quartz; R—rock fragments; r—restored composition). Trace-element and rare earth element abundances of whole-rock analyses discriminate well between the three petrofacies based on: (1) the Rb concentration, which is indicative of the K content and reflects the amount of K-feldspar modal abundance, and (2) the relative modal abundance of heavy minerals (tourmaline, zircon, titanite, and apatite), which is reproduced by the elements hosted in the observed heavy mineral assemblage (i.e., B and Li for tourmaline; Zr, Hf, and Ta for zircon; Ti, Ta, Nb, and their rare earth elements for titanite; and P, Y, and their rare earth elements for apatite). Tourmaline chemical composition for the three petrofacies ranges from Fe-tourmaline of granitic to Mg-tourmaline of metamorphic origin. The three defined petrofacies suggest a mixed provenance from plutonic and metamorphic source rocks. However, a progressively major influence of granitic source rocks was detected from the lowermost Mora petrofacies toward the uppermost Camarillas petrofacies. This provenance trend is consistent with the uplift and erosion of the Iberian Massif, which coincided with the development of the latest Berriasian synrift regional unconformity and affected all of the Iberian intraplate basins. The uplifting stage of Iberian Massif pluton caused a significant dilution of Paleozoic metamorphic source areas, which were dominant during the sedimentation of the lowermost Mora and El Castellar petrofacies. The association of petrographic data with whole-rock geochemical compositions and tourmaline chemical analysis has proved to be useful for determining source area characteristics, their predominance, and the evolution of source rock types during the deposition of quartz-feldspathic sandstones in intraplate basins. This approach ensures that provenance interpretation is consistent with the geological context.