How to Use Fewer Markers in Admixture Studies

Swiss Fleckvieh has been established from 1970 as a composite of Simmental and Red Holstein Friesian cattle. Breed composition is currently reported based on pedigree information. Information on ancestry informative molecular markers potentially provides more accurate information. For the analysis Illumina Bovine SNP50 Beadchip data for 495 bulls were used. Markers were selected based on difference in allele frequencies in the pure populations, using FST as an indicator. Performance of sets with decreasing number of markers was compared. The scope of the study was to see how much we can reduce the number of markers based on FST to get a reliability that is close to that with the full set of markers. On these sets of markers hidden Markov models (HMM) and methods used in genomic selection (BayesB, partial least squares regression, LASSO variable selection) were applied. Correlations of admixture levels were estimated and compared with admixture levels based on pedigree information. FST chosen SNP gave very high correlations with pedigree based admixture. Only when using 96 and 48 SNP with the highest FST, correlations dropped to 0.92 and 0.90, respectively

The Oxfordian–Kimmeridgian transition in the Boulonnais (France) and the onset of organic-rich marine deposits in NW Europe: a climatic control?

International audienceWe characterised the organic matter content of marine deposits at the Oxfordian–Kimmeridgian transition in the Boulonnais (France). Organic rich deposits in platform environments are evidenced in the uppermost Cymodoce and lowermost Mutabilis Zone (early late Kimmeridgian), associated with enhanced planktonic palaeoproductivity and/or developing dysoxia/anoxia. Similar organic rich intervals in early late Kimmeridgian are also evidenced in platformdeposits in Normandy and Charentes in France, and in basinal deposits from Yorkshire and Dorset in UK. This refined onsetof the organic rich bands (ORB), as described in NW Europe during the late Jurassic, is coeval with seawater warming. We propose that this seawater warming was an important trigger of the onset of the late Jurassic ORB deposition system in NW Europe, which began at the Cymodoce–Mutabilis boundary during the early late Kimmeridgian and lasted until the middle part of the Tithonian, over a time span of 6.8Myr

Thermal maturity of the Upper Triassic-Middle Jurassic Shemshak Group (Alborz Range, Northern Iran) based on organic petrography, geochemistry and basin modelling: implications for source rock evaluation and petroleum exploration.

International audienceOrganic petrography and geochemical analyses have been carried out on the shales, carbonaceous shales and coals of the Shemshak Group (Upper Triassic-Middle Jurassic) from fifteen localities along the Alborz Range of Northern Iran. Organic matter (OM) has been investigated using Rock-Eval pyrolysis, elemental analysis of kerogen, vitrinite reflectance (VRr) and Thermal Alteration Index (TAI). Reflectance of autochthonous vitrinite varies from 0.6 to 2.2 % indicating thermally early mature to over mature OM in the Shemshak Group, in agreement with other maturity parameters used. The shales of the Shemshak Group are characterized by poor to moderate residual organic carbon contents (0.25 to 8.5 %) and the presence of hydrogen-depleted OM, predominantly as a consequence of petroleum generation and of oxidation of OM. According to light-reflected microscopy results vitrinite/vitrinite-like macerals are dominant in the kerogens concentrated from the shaly facies. The coals and carbonaceous shales of the Shemshak Group show a wide range in organic carbon concentration (3.5 to 88.6 %) and composition (inertinite- and vitrinite-rich types), and thereby different petroleum potentials. Among the studied sections only the coals and carbonaceous shales of the Hive locality show good residual petroleum potential and may still generate oil. Thermal modelling results suggest that low to moderate paleo-heat flow, ranging from 47 to 79 mW.m-2 (57 mW.m-2 on average), affected the Central-Eastern Alborz. The maximum temperature which induced OM maturation of the Shemshak Group seems to be related to its deep burial rather than to a very strong heat flow related to an uppermost Triassic-Liassic rifting. The interval of petroleum generation in the most deeply buried part of the Shemshak Group (i.e., Tazareh section) corresponds to Late Jurassic-Early Cretaceous times. Exhumation of the Alborz Range during Late Neogene time, especially along the axis of the Central-Eastern Alborz, where maxima of VRr values are recorded, probably destroyed possible petroleum accumulations. However on the northern flank of the Central-Eastern Alborz, preservation of petroleum accumulations may be better. The northern part of the basin therefore seems the best target for petroleum exploration

Biomarker assemblages associated with the Eocene-Oligocene transition in lacustrine deposits of the Rennes Basin (France)

International audienceThe Eocene/Oligocene transition is one of the main climatic events to which more recent climate changes are often compared. Dated back to 34 Ma, it is remarkable because the Earth evolved from a greenhouse to icehouse state, permanent ice sheets appearing during the Late Eocene. In marine setting, it is marked by an increase in detrital input associated with an increase of primary productivity that resulted from well mixing of water masses (Peihzen et al., 2001). In terrestrial setting, this cooling led to major changes in animal and plant communities. For instance, palynology data show a vegetation shift from wet to dry taxa (Gregory and Chase, 1992) coincident with a large mammal turnover, the well-known "Grande coupure" (Stelhin, 1909). Although this transition is well documented in marine settings, the lack of data on lands - due to limited available outcrops - does not allow appreciating precisely its impacts on terrestrial ecosystems. Here, we have analysed the sediment infill of the Rennes Basin that consists of 300 m of organic-rich lacustrine deposits (laminated and massive) that encompass the Middle Eocene to Oligocene series, including the Eocene-Oligocene transition, the whole fully cored (CINERGY project, BRGM). About 100 samples were collected through the core enabling us to precisely decipher environmental changes that occurred during the studied interval and to focus on the Eocene/Oligocene transition. All samples were subjected to Rock-Eval and EA-irMS to measure bulk δ13C. Four over the 100 samples were analysed for their molecular content so far. For a preliminary test, we have chosen representative facies (a laminated and a massive Upper Eocene sample and a laminated and a massive Lower Oligocene sample). Lipids were extracted with an Automated Solvant Extractor (ASE200®, Dionex) using DCM:MeOH (9:1). The total extract was later separated into neutrals, acidic and polar compounds. The neutral compounds were further separated into aliphatic, aromatic, ethers and esters, ketones and alcohols. After addition of 5α-cholestane, each fraction was then analysed by Gas Chromatography-Mass spectrometry on a Trace GC Ultra gas chromatograph coupled to a TSQ Quantum XLS mass spectrometer equipped with an AS 3000 autosampler. The analysis of the different fractions of each sample revealed a high diversity of compounds that could partly be related to their source organisms or inform on the depositional environment. Hydrocarbon fraction is dominated by a series of n-alkanes that display a strong odd-over-even predominance, indicative of a good preservation. The dominance of long-chain homologues shows a strong higher plants contribution. This is confirmed by the presence of abundant and diversified higher plant pentacyclic triterpenes. These comprise angiosperms biomarkers such as oleanane, ursane and lupane, friedelin, onocerane I and diagenetic by-products (des-A-tritrepenes and aromatic derivatives). Fernene-type compounds could reveal an input from pteridophyts whereas tricyclic diterpenes indicate the presence of conifers. An algal influence is evidenced, for example, by the presence of 4-methylsteranes in the four samples. C27 to C32 hopanoids with α,β, β,β and β,α configurations show a substantial bacterial contribution. This is confirmed by high levels of hopane ketones in some beds. The comparison of angiosperm-derived biomarkers with gymnosperm-derived biomarkers indicates a stronger contribution of angiosperms in Upper Eocene samples than in Lower Oligocene samples (triterpenoids, aromatic, and rearranged-triterpenoids). This result is in agreement with palynological data (Bourdillon et al., 2012) and with the well-known cooling that is coeval with the Eocene/Oligocene transition. Reversely, the comparison between the two facies (massive and laminated) does not exhibit significant differences in the molecular assemblage. Based on this preliminary inventory of biomarkers and the richness in various biomarkers, we will proceed with the identification and quantitation on the remaining samples that cover the whole section. These preliminary results are also encouraging in the perspective of performing compound-specific isotopic analyses in order to depict, at high temporal resolution, the climatic evolution and the associated changes in plant communities during the Late Eocene and Early Oligocene and, more specifically, at the Eocene/Oligocene transition

Do soft sediment deformations in the Late Triassic and Early Jurassic of the UK record seismic activity during the break-up of Pangea?

The lagoonal and shallow marine sediments of the Penarth Group in the UK span the Triassic–Jurassic boundary. These sediments contain several disturbed levels with soft sediment deformations (SSDs), such as synsedimentary faults, injective domes, recumbent folds and slumps that are recognised in most basins from SW England and South Wales to NW Northern Ireland. Field observations, notably the close link of the SSDs to active faults, attest an earthquake origin of the SSDs. Fluids, faults, overpressure and lithology guided the style of the SSDs and their distribution in the sedimentary sections. Analysis of the directional data relating to SSDs in each disturbed level shows preferred orientations of deformation, which correspond to the local state of stress at the time. We favour a series of earthquakes, rather than a single mega-event as a trigger of the observed features. The active local extensional tectonic context was driven by the opening of the Permo-Triassic basins in Western Europe. The data from the SSDs in the UK suggest the development of a multi-directional, mosaic-style extensional context to occur during this early phase of the break-up of Pangea. Our integrated tectonic/sedimentary study suggests that directional data from faults, injective domes, recumbent folds and slumps preserved in sediments are reliable to reconstruct past seismic activity and basin geodynamics

Estimation of Breed Composition, Breed Heterosis and Epistatic Loss for Percent of Live Spermatozoa in Admixed Swiss Fleckvieh Bulls

The objective of this study was to estimate non-additive genetic effects of heterosis and epistatic loss on percent of live spermatozoa in admixed Swiss Fleckvieh bulls, a composite of Simmental and Holstein Friesian cattle. Heterosis is the additional gain in productivity or fitness of crossbred progeny over the mid purebred parents mean which arises from intra-locus gene interaction. Epistatic effects generally reduce productivity or fitness due to lack of gene interactions of genes from different breeds, which is called epistatic loss. Bovine SNP chip data of were used to predict locus specific breed origin of alleles along the autosomes of 815 admixed bulls as well as 147 Holstein Friesian and 207 Simmental bulls representing the parental breeds. The breed proportions for admixed bulls based on 32,899 SNP were used to calculate breed heterozygosity and epistatic loss, considering additive by additive effects for 1,000,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated to be 0.82. Results of fitting different linear mixed models showed that including breed heterozygosity and epistatic loss improved the model fitness (ΔAIC > 3). The heterosis effect and epistatic loss were estimated 2.5(±1.39) % and -0.65(±1.68) % of live spermatozoa, respectively. High correlation (0.97) between breed heterozygosity and epistatic loss values indicate strong confounding of these effects in the model, indicating that it is not possible to properly separate these effects

PREDICTION OF GLOBAL AND LOCAL SIMMENTAL AND RED HOLSTEIN FRIESIAN ADMIXTURE LEVELS IN SWISS FLECKVIEH CATTLE

In this study we estimated levels of local ancestry for individuals of the Swiss Fleckvieh dairy cattle population. It is a composite breed descending from two pure breeds, Simmental (SIM) and Red Holstein Friesian (RHF). Illumina BovineSNP50 Beadchip genotyping data for a total of 500 pure and admixed animals were used for the analysis. The global ancestries estimated by Hidden Markov model were 0.68 and 0.32 for RHF and SIM respectively. Local ancestry levels investigated along chromosomes 2, 3 and 13 indicated that there were some regions across the chromosomes exhibiting substantial fluctuations in admixture. On chromosome 2, in the range of 28 to 31, 41 to 46 and 54 to 56 Mb RHF ancestry is substantially higher than average (0.77-0.78). These regions on chromosome 2 are wide, indicating recent admixture. Along the segments on chromosome 2, many QTLs related to dairy, conformation, reproduction, health and carcass traits were found. We observed sharper excess in favour of SIM on chromosome 3, whereas different regions with excess of RHF and SIM were found out on Chromosome 13. At the first part of chromosome 13, an excess of RHF was observed. Moreover, in regions between 40 and 57 Mb excess of SIM, referred to recent admixture was detected. In respect of RHF chromosome segments in admixed animals, dairy, reproduction and health QTLs were found. In positions where more Simmental segments were detected, QTLs related to meat and carcass traits as well as udder health traits were found. In conclusion, the authors believe that estimation of local admixture levels in crossbred populations can add information to the composite breeds history of selection

Shallow-water marl-limestone alternations in the Late Jurassic of western France: Cycles, storm event deposits or both?

International audienceThe contribution of event deposits to various basin fills can be very significant, higher than 90% in some cases. Events may lead to the formation of marl–limestone alternations, which can also result from cyclic changes in sea level or climate, for example. The marl–limestone alternations of the Late Jurassic of western France contain abundant coarse-grained accumulations that resemble storm deposits described in other western European successions. The detailed analysis of facies evolution and hierarchical, high-frequency stacking pattern of depositional sequences of the Phare de Chassiron section (Ile d'Oléron, western France) allows the controls on marl–limestone formation to be defined. This section contains nearshore and shallow-marine mud deposits that were exposed to high-energy events. Elementary, small-, and medium-scale depositional sequences are defined. The stacking-pattern and the duration of these sequences suggest an orbital control on sedimentation. Precession (20 ka) cycles notably controlled the formation of elementary sequences that correspond to marl–limestone alternations. The deposition of marly or carbonate mud occurred in this storm-dominated system because of muddy sea beds, the gentle slope of the shelf, and the great amount of particles in suspension, which reduced water energy resulting from storms. Sediment supply was also sufficient to limit bioturbation and favour the preservation of numerous storm deposits. The production of carbonate mud was localised on positive structures and partly controlled by Milankovitch-scale sea-level cycles. Transport by storms of carbonate mud to the adjacent marly depressions during high carbonate production periods led to the formation of calcareous beds. Marl–limestone alternations in the Late Jurassic of western France therefore result from the combined effects of cyclic changes in carbonate production and high-energy, episodic events