Evidence of coat color variation sheds new light on ancient canids.

International audienceWe have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling coat color, Mc1r (Melanocortin 1 Receptor) and CBD103 (canine-β-defensin), in respectively 15 and 19 ancient canids (dogs and wolf morphotypes) from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic) to ca. 4000 B.P. (Bronze Age). We provide evidence of a new variant (R301C) of the Melanocortin 1 receptor (Mc1r) and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus) on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant K(B) allele (CBD103), which causes melanism, and R301C (Mc1r), the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10 000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process

Island Grammar-based Parsing using GLL and Tom

International audienceExtending a language by embedding within it another language presents significant parsing challenges, especially if the embedding is recursive. The composite grammar is likely to be nondeterministic as a result of tokens that are valid in both the host and the embedded language. In this paper we examine the challenges of embedding the Tom language into a variety of general-purpose high level languages. Tom provides syntax and semantics for advanced pattern matching and tree rewriting facilities. Embedded Tom constructs are translated into the host language by a preprocessor, the output of which is a composite program written purely in the host language. Tom implementations exist for Java, C, C#, Python and Caml. The current parser is complex and difficult to maintain. In this paper, we describe how Tom can be parsed using island grammars implemented with the Generalised LL (GLL) parsing algorithm. The grammar is, as might be expected, ambiguous. Extracting the correct derivation relies on our disambiguation strategy which is based on pattern matching within the parse forest. We describe different classes of ambiguity and propose patterns for resolving them

Regional-scale paleofluid system across the Tuscan Nappe–Umbria–Marche Apennine Ridge (northern Apennines) as revealed by mesostructural and isotopic analyses of stylolite–vein networks

We report the results of a multiproxy study that combines structural analysis of a fracture–stylolite network and isotopic characterization of calcite vein cements and/or fault coating. Together with new paleopiezometric and radiometric constraints on burial evolution and deformation timing, these results provide a first-order picture of the regional fluid systems and pathways that were present during the main stages of contraction in the Tuscan Nappe and Umbria–Marche Apennine Ridge (northern Apennines). We reconstruct four steps of deformation at the scale of the belt: burial-related stylolitization, Apenninic-related layer-parallel shortening with a contraction trending NE–SW, local extension related to folding, and late-stage fold tightening under a contraction still striking NE–SW. We combine the paleopiezometric inversion of the roughness of sedimentary stylolites – that constrains the range of burial depth of strata prior to layer-parallel shortening – with burial models and U–Pb absolute dating of fault coatings in order to determine the timing of development of mesostructures. In the western part of the ridge, layer-parallel shortening started in Langhian time (∼15 Ma), and then folding started at Tortonian time (∼8 Ma); late-stage fold tightening started by the early Pliocene (∼5 Ma) and likely lasted until recent/modern extension occurred (∼3 Ma onward). The textural and geochemical (δ18O, δ13C, Δ47CO2 and 87Sr∕86Sr) study of calcite vein cements and fault coatings reveals that most of the fluids involved in the belt during deformation either are local or flowed laterally from the same reservoir. However, the western edge of the ridge recorded pulses of eastward migration of hydrothermal fluids (>140 ∘C), driven by the tectonic contraction and by the difference in structural style of the subsurface between the eastern Tuscan Nappe and the Umbria–Marche Apennine Ridge