Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.     

Mutation for Nonsyndromic Mental Retardation in the trans-2-Enoyl-CoA Reductase TER Gene Involved in Fatty Acid Elongation Impairs the Enzyme Activity and Stability,Leading to Change in Sphingolipid Profile

Very long-chain fatty acids (VLCFAs, chain length >C20) exist in tissues throughout the body and are synthesized by repetition of the fatty acid (FA) elongation cycle composed of four successive enzymatic reactions. In mammals, the TER gene is the only gene encoding trans-2-enoyl-CoA reductase, which catalyzes the fourth reaction in the FA elongation cycle. The TER P182L mutation is the pathogenic mutation for nonsyndromic mental retardation. This mutation substitutes a leucine for a proline residue at amino acid 182 in the TER enzyme. Currently, the mechanism by which the TER P182L mutation causes nonsyndromic mental retardation is unknown. To understand the effect of this mutation on the TER enzyme and VLCFA synthesis, we have biochemically characterized the TER P182L mutant enzyme using yeast and mammalian cells transfected with the TER P182L mutant gene and analyzed the FA elongation cycle in the B-lymphoblastoid cell line with the homozygous TER P182L mutation (TER^P182L/P182L B-lymphoblastoid cell line). We have found that TER P182L mutant enzyme exhibits reduced trans-2-enoyl-CoA reductase activity and protein stability, thereby impairing VLCFA synthesis and, in turn, altering the sphingolipid profile (i.e. decreased level of C24 sphingomyelin and C24 ceramide) in the TER^P182L/P182L B-lymphoblastoid cell line. We have also found that in addition to the TER enzyme-catalyzed fourth reaction, the third reaction in the FA elongation cycle is affected by the TER P182L mutation. These findings provide new insight into the biochemical defects associated with this genetic mutation.     

The excuse principle can maintain cooperation through forgivable defection in the Prisoner's Dilemma game

Reciprocal altruism describes a situation in which an organism acts in a manner that temporarily reduces its fitness while increasing another organism''s fitness, but there is an ultimate fitness benefit based on an expectation that the other organism will act in a similar manner at a later time. It creates the obvious dilemma in which there is always a short-term benefit to cheating, therefore cooperating individuals must avoid being exploited by non-cooperating cheaters. This is achieved by following various decision rules, usually variants of the tit-for-tat (TFT) strategy. The strength of TFT, however, is also its weakness—mistakes in implementation or interpretation of moves, or the inability to cooperate, lead to a permanent breakdown in cooperation. We show that pied flycatchers (Ficedula hypoleuca) use a TFT with an embedded ‘excuse principle’ to forgive the neighbours that were perceived as unable to cooperate during mobbing of predators. The excuse principle dramatically increases the stability of TFT-like behavioural strategies within the Prisoner''s Dilemma game.     

Silvicolous on a Small Scale: Possibilities and Limitations of Habitat Suitability Models for Small,Elusive Mammals in Conservation Management and Landscape Planning

Species distribution and endangerment can be assessed by habitat-suitability modelling. This study addresses methodical aspects of habitat suitability modelling and includes an application example in actual species conservation and landscape planning. Models using species presence-absence data are preferable to presence-only models. In contrast to species presence data, absences are rarely recorded. Therefore, many studies generate pseudo-absence data for modelling. However, in this study model quality was higher with null samples collected in the field. Next to species data the choice of landscape data is crucial for suitability modelling. Landscape data with high resolution and ecological relevance for the study species improve model reliability and quality for small elusive mammals like Muscardinus avellanarius. For large scale assessment of species distribution, models with low-detailed data are sufficient. For regional site-specific conservation issues like a conflict-free site for new wind turbines, high-detailed regional models are needed. Even though the overlap with optimally suitable habitat for M. avellanarius was low, the installation of wind plants can pose a threat due to habitat loss and fragmentation. To conclude, modellers should clearly state the purpose of their models and choose the according level of detail for species and environmental data.     

The Search for Significance: A Few Peculiarities in the Distribution of P Values in Experimental Psychology Literature

In this project I investigate the use and possible misuse of p values in papers published in five (high-ranked) journals in experimental psychology. I use a data set of over 135’000 p values from more than five thousand papers. I inspect (1) the way in which the p values are reported and (2) their distribution. The main findings are following: first, it appears that some authors choose the mode of reporting their results in an arbitrary way. Moreover, they often end up doing it in such a way that makes their findings seem more statistically significant than they really are (which is well known to improve the chances for publication). Specifically, they frequently report p values “just above” significance thresholds directly, whereas other values are reported by means of inequalities (e.g. “p<.1”), they round the p values down more eagerly than up and appear to choose between the significance thresholds and between one- and two-sided tests only after seeing the data. Further, about 9.2% of reported p values are inconsistent with their underlying statistics (e.g. F or t) and it appears that there are “too many” “just significant” values. One interpretation of this is that researchers tend to choose the model or include/discard observations to bring the p value to the right side of the threshold.     

Redox conditions during sedimentation of the Middle Jurassic (Upper Bajocian–Bathonian) clays of the Polish Jura (south-central Poland)

Depositional redox conditions of the uppermost Bajocian–Bathonian (Middle Jurassic) ore-bearing clays of the Gnaszyn/Kawodrza area in the Polish Jura have been determined using an integrated geochemical (Th/U and U/Th ratios, degree of pyritisation (DOP), sulphur stable isotopes, biomarker analysis) and petrographic approach (measurements of pyrite framboid diameters, and microfacies analysis). The Th/U and U/Th ratios indicate that oxic conditions prevailed on the sea-floor during this interval, and ³⁴S isotopes suggest open-system conditions. DOP values, however, are rather scattered, and may reflect oxic, dysoxic, or anoxic conditions. We consider that the DOP values result from reducing conditions within the sediment and the chemistry of the pore-waters, rather than true sea-floor redox conditions. Pyrite framboid populations also indicate that dysoxic conditions prevailed within the sediment, beneath an oxygenated water column. Biomarker data did not provide any evidence of water column stratification or anoxia during sedimentation of the Middle Jurassic clays.     

Taxonomy and palaeobiology of the Bathonian (Middle Jurassic) tulitid ammonite Morrisiceras

Taxonomic revision of a number of species belonging to the Middle Bathonian tulitid genus Morrisiceras (Morrisiceras Buckman - macroconchs and Holzbergia Torrens - microconchs) from the Polish Jura (south-central Poland) and England, shows that the genus is in fact represented by one, albeit morphologically very plastic (especially macroconchs), species Morrisiceras morrisi (Oppel). In the Polish Jura area, all of the previously described morphotypes of the macroconch, along with its microconch Holzbergia, are characterized by their identical stratigraphic ranges, both being confined to the Middle Bathonian Morrisi Zone. Much smaller microconchs (males) may have attained maturity earlier than their macroconchs (females). Morphologically very plastic macroconchs seem to have attained full maturity at various shell diameters. Such phenomenon is known in recent coleoids and similarly may be the result of changing environmental conditions. Palaeobiogeographically, the main area occupied by the species was confined to the epicratonic seas, which spread across what is now present-day central and North-West Europe, with some occurrences in western Asia (Turkmenistan/Uzbekistan) and sporadic occurrence in a deep-water facies of Apulia (Italy). Taphonomical observations suggest that Morrisiceras shells have not undergone significant post-mortem drifting or transport after deposition. The preservation of some of the Morrisiceras morphotypes, occurring as dorso-ventrally flattened specimens in the host clays, may indicate that they were quickly buried in life position after they have landed on the sea-floor.