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991.
992.
993.
Small mammal (rodents and lagomorphs) European biogeography from the Late Oligocene to the mid Pliocene 总被引:2,自引:0,他引:2
Olivier Maridet Gilles Escarguel Loïc Costeur Pierre Mein Marguerite Hugueney Serge Legendre 《Global Ecology and Biogeography》2007,16(4):529-544
Aim To analyse the fossil species assemblages of rodents and lagomorphs from the European Neogene in order to assess what factors control small mammal biogeography at a deep‐time evolutionary time‐scale. Location Western Europe: 626 fossil‐bearing localities located within 31 regions and distributed among 18 successive biochronological units ranging from c. 27 Ma (million years ago; Late Oligocene) to c. 3 Ma (mid Pliocene). Methods Taxonomically homogenized pooled regional assemblages are compared using the Raup and Crick index of faunal similarity; then, the inferred similarity matrices are visualized as neighbour‐joining trees and by projecting the statistically significant interregional similarities and dissimilarities onto palaeogeographical maps. The inferred biogeographical patterns are analysed and discussed in the light of known palaeogeographical and palaeoclimatic events. Results Successive time intervals with distinct biogeographical contexts are identified. Prior to c. 18 Ma (Late Oligocene and Early Miocene), a relative faunal homogeneity (high interregional connectivity) is observed all over Europe, a time when major geographical barriers and a weak climatic gradient are known. Then, from the beginning of the Middle Miocene onwards, the biogeography is marked by a significant decrease in interregional faunal affinities which matches a drastic global climatic degradation and leads, in the Late Miocene (c. 11 Ma), to a marked latitudinal pattern of small mammal distribution. In spite of a short rehomogenization around the Miocene/Pliocene boundary (6–4 Ma), the biogeography of small mammals in the mid Pliocene (c. 3 Ma) finally closely reflects the extant situation. Main conclusions The resulting biogeographical evolutionary scheme indicates that the extant endemic situation has deep historical roots corresponding to global tectonic and climatic events acting as primary drivers of long‐term changes. The correlation of biogeographical events with climatic changes emphasizes the prevalent role of the climate over geography in generating heterogeneous biogeographical patterns at the continental scale. 相似文献
994.
Amy L. Picard 《Ethology : formerly Zeitschrift fur Tierpsychologie》2005,111(9):799-809
Courtship in plethodontid salamanders includes the delivery of male courtship pheromones by two distinct modes. Within the eastern Plethodon clade of the tribe Plethodontini, members of the Plethodon cinereus species group use an ancestral ‘vaccination’ mode of delivery, while members of the P. glutinosus group use an olfactory delivery mode. In order to shed light on this transition in delivery mode, I observed courtship behavior in P. dorsalis, a species that is phylogenetically intermediate to the P. cinereus and P. glutinosus groups. My observations indicate that P. dorsalis also is intermediate to the P. cinereus and P. glutinosus species groups in terms of courtship behavior. The context of delivery of male courtship pheromones in P. dorsalis is similar to that of the P. cinereus species group; however, the mode of pheromone delivery in P. dorsalis is olfactory. Thus, a transition in the context of pheromone delivery underlies the more obvious change in pheromone delivery mode. I discuss these findings in terms of the evolution of courtship pheromone delivery across the eastern Plethodon clade. I also report the first observations of ‘premature’ spermatophore deposition by male plethodontids. 相似文献
995.
Florian Herry Frédéric Hérault David Picard Druet Amandine Varenne Thierry Burlot Pascale Le Roy Sophie Allais 《BMC genetics》2018,19(1):108
Background
The main goal of selection is to achieve genetic gain for a population by choosing the best breeders among a set of selection candidates. Since 2013, the use of a high density genotyping chip (600K Affymetrix® Axiom® HD genotyping array) for chicken has enabled the implementation of genomic selection in layer and broiler breeding, but the genotyping costs remain high for a routine use on a large number of selection candidates. It has thus been deemed interesting to develop a low density genotyping chip that would induce lower costs. In this perspective, various simulation studies have been conducted to find the best way to select a set of SNPs for low density genotyping of two laying hen lines.Results
To design low density SNP chips, two methodologies, based on equidistance (EQ) or on linkage disequilibrium (LD) were compared. Imputation accuracy was assessed as the mean correlation between true and imputed genotypes. The results showed correlations more sensitive to false imputation of SNPs having low Minor Allele Frequency (MAF) when the EQ methodology was used. An increase in imputation accuracy was obtained when SNP density was increased, either through an increase in the number of selected windows on a chromosome or through the rise of the LD threshold. Moreover, the results varied depending on the type of chromosome (macro or micro-chromosome). The LD methodology enabled to optimize the number of SNPs, by reducing the SNP density on macro-chromosomes and by increasing it on micro-chromosomes. Imputation accuracy also increased when the size of the reference population was increased. Conversely, imputation accuracy decreased when the degree of kinship between reference and candidate populations was reduced. Finally, adding selection candidates’ dams in the reference population, in addition to their sire, enabled to get better imputation results.Conclusions
Whichever the SNP chip, the methodology, and the scenario studied, highly accurate imputations were obtained, with mean correlations higher than 0.83. The key point to achieve good imputation results is to take into account chicken lines’ LD when designing a low density SNP chip, and to include the candidates’ direct parents in the reference population.996.
Eulalie Lasseaux Claudio Plaisant Vincent Michaud Perrine Pennamen Aurelien Trimouille Laetitia Gaston Solène Monfermé Didier Lacombe Caroline Rooryck Fanny Morice‐Picard Benoît Arveiler 《Pigment cell & melanoma research》2018,31(4):466-474
Albinism is a clinically and genetically heterogeneous disease characterized by variable degrees of hypopigmentation and by nystagmus, foveal hypoplasia, and chiasmatic misrouting of the optic nerves. The wide phenotypic heterogeneity impedes the establishment of phenotype–genotype correlations. To obtain a precise diagnosis, we screened the 19 known albinism genes in 990 index patients using targeted next‐generation sequencing (NGS) and high‐resolution comparative genomic hybridization. A molecular diagnosis was obtained in 72.32% of patients. A total of 243 new pathogenic variants were identified. Intragenic rearrangements represented 10.8% of all pathogenic alleles. NGS panel analysis allowed establishing a diagnosis for the rarest forms of the disease, which could not be diagnosed otherwise. Because of the clinical overlap between the different forms of the disease, diagnosis nowadays clearly relies on molecular grounds. 相似文献
997.
Peter N. Herbert Trudy M. Forte Richard S. Shulman Marguerite J. La Piana Elaine L. Gong Robert I. Levy 《Preparative biochemistry & biotechnology》2013,43(2):93-129
The effects of repetitive ultracentrifugation on the physical and chemical properties of very low density lipoproteins (VLDL) were investigated. VLDL recentrifuged one to seven times were characterized by chemical analyses, analytical ultracentrifugation and electron microscopy. The VLDL content of triglyceride was increased and the proportion of phospholipid decreased by ultracentrifugation. Recentrifugation of VLDL decreased the number of Sf o 20–100 particles and generated particles of Sf o > 400. The bulk of the material removed from VLDL by ultracentrifugation was lipoprotein having pre-g mobility on paper electrophoresis, flotation rates of Sf o 10–100 and a particle size of 300–400 Å. Two ultracentrifugations separated an average of 14% of the starting VLDL protein. Characterization of the apoproteins in this material by polyacrylamide gel electrophoresis, gel chromatography, immuno precipitation and amino acid analysis demonstrated a relatively high proportion of B-apoprotein and relatively little C-apoproteins. 相似文献
998.
J. G. Prunier B. Kaufmann S. Fenet D. Picard F. Pompanon P. Joly J. P. Lena 《Molecular ecology》2013,22(22):5516-5530
Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, that is, the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population‐based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic data sets to investigate the efficiency of an individual‐based sampling scheme (ISS) in detecting isolation‐by‐distance and isolation‐by‐barrier patterns. Provided that pseudo‐replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of interindividual measures of genotypic dissimilarity may efficiently replace interpopulation measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed. 相似文献
999.
Federico Carlini Karim Traore Nissem Cherouat Pierre Roubertoux Stéphane Buhler Martì Cortey Sophie Simon Ogobara Doumbo Jacques Chiaroni Christophe Picard Julie Di Cristofaro 《PloS one》2013,8(12)
The HLA-G molecule plays an important role in immunomodulation. In a previous study carried out on a southern French population our team showed that HLA-G haplotypes, defined by SNPs in the coding region and specific SNPs located in 5′URR and 3′UTR regulatory regions, are associated with differential soluble HLA-G expression (sHLA-G). Furthermore, the structure of these HLA-G haplotypes appears to be conserved in geographically distant populations.The aim of our study is to confirm these expectations in a sub-Saharan African population and to explore additional factors, such as HLA-A alleles, that might influence sHLA-G expression.DNA and plasma samples were collected from 229 Malians; HLA-G and HLA-A genotyping were respectively performed by the Snap Shot® method and by Luminex™ technology. sHLA-G dosage was performed using an ELISA kit. HLA-G and HLA-A allelic and haplotypic frequencies were estimated using an EM algorithm from the Gene[Rate] program. Associations between genetic and non genetic parameters with sHLA-G were performed using a non-parametric test with GRAPH PAD Prism 5.Our results reveal a good conservation of the HLA-G UTR haplotype structure in populations with different origins and demographic histories. These UTR haplotypes appear to be involved in different sHLA-G expression patterns. Specifically, the UTR-2 haplotype was associated with low sHLA-G levels, displaying a dominant negative effect. Furthermore, an allelic effect of both HLA-G and HLA-A, as well as non genetic parameters, such as age and gender possibly linked to osteogenesis and sexual hormones, also seem to be involved in the modulation of sHLA-G.These data suggest that further investigation in larger cohorts and in populations from various ethnical backgrounds is necessary not only to detect new functional polymorphism in HLA-G regulatory regions, but also to reveal the extent of biological phenomena that influence sHLA-G secretion and this might therefore have an impact on transplantation practice. 相似文献
1000.
Odin Goovaerts Wim Jennes Marguerite Massinga-Loembé Ann Ceulemans William Worodria Harriet Mayanja-Kizza Robert Colebunders Luc Kestens the TB-IRIS Study Group 《PloS one》2013,8(11)