Search results for "Haplotypes"
showing 10 items of 295 documents
A minimalist macroparasite diversity in the round goby of the Upper Rhine reduced to an exotic acanthocephalan lineage.
2018
AbstractThe round goby, Neogobius melanostomus, is a Ponto-Caspian fish considered as an invasive species in a wide range of aquatic ecosystems. To understand the role that parasites may play in its successful invasion across Western Europe, we investigated the parasitic diversity of the round goby along its invasion corridor, from the Danube to the Upper Rhine rivers, using data from literature and a molecular barcoding approach, respectively. Among 1666 parasites extracted from 179 gobies of the Upper Rhine, all of the 248 parasites barcoded on the c oxidase subunit I gene were identified as Pomphorhynchus laevis. This lack of macroparasite diversity was interpreted as a loss of parasites…
Nucleotide Variability at the Acetyl Coenzyme A Carboxylase Gene and the Signature of Herbicide Selection in the Grass Weed Alopecurus myosuroides (H…
2004
Acetyl coenzyme A carboxylase (ACCase) is the target of highly effective herbicides. We investigated the nucleotide variability of the ACCase gene in a sample of 18 black-grass (Alopecurus myosuroides [Huds.]) populations to search for the signature of herbicide selection. Sequencing 3,396 bp encompassing ACCase herbicide-binding domain in 86 individuals revealed 92 polymorphisms, which formed 72 haplotypes. The ratio of nonsynonymous versus synonymous substitutions was very low, in agreement with ACCase being a vital metabolic enzyme. Within black grass, most nonsynonymous substitutions were related to resistance to ACCase-inhibiting herbicides. Differentiation between populations was stro…
Large Spatial Scale of the Phenotype-Environment Color Matching in Two Cryptic Species of African Desert Jerboas (Dipodidae: Jaculus)
2014
We tested the camouflage hypothesis, or the linkage between animal (Saharan rodent) and habitat coloration, on the largest geographical scale yet conducted. We aimed to determine whether phenotypic variation is explained by micro-habitat variation and/or genetic polymorphism to determine 1) the strength of linkage between fur color and local substrate color, and 2) the divergence in fur coloration between two genetic clades, representing cryptic species, throughout the complete range of the African desert jerboas (Jaculus jaculus). We used a combination of museum and field-collected specimens, remote sensing tools, satellite and digital photography and molecular genetic and phylogenetic met…
Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale.
2007
International audience; Genome reduction, a typical feature of symbiotic bacteria, was analyzed in the last stages of evolution of Buchnera aphidicola, the primary aphid endosymbiont, in two neutrally evolving regions: the pseudogene cmk and an intergenic region. These two regions were examined in endosymbionts from several lineages of their aphid host Rhopalosiphum padi, and different species of the same genus, whose divergence times ranged from 0.62 to 19.51 million years. Estimates of nucleotide substitution rates were between 4.3 and 6.7 x 10(-9) substitution/site/year, with G or C nucleotides being substituted around four times more frequently than A or T. Two different types of indel …
Colonisation and diversification of the Zenaida dove (Zenaida aurita) in the Antilles: phylogeography, contemporary gene flow and morphological diver…
2013
12 pages; International audience; Caribbean avifaunal biogeography has been mainly studied based on mitochondrial DNA. Here, we investigated both past and recent island differentiation and micro-evolutionary changes in the Zenaida Dove (Zenaida aurita) based on combined information from one mitochondrial (Cytochrome c Oxydase subunit I, COI) and 13 microsatellite markers and four morphological characters. This Caribbean endemic and abundant species has a large distribution, and two subspecies are supposed to occur: Z. a. zenaida in the Greater Antilles (GA) and Z. a. aurita in the Lesser Antilles (LA). Doves were sampled on two GA islands (Puerto Rico and the British Virgin Islands) and six…
Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity.
2013
This is the peer reviewed version of the following article: Eidesen, P.B., Ehrich, D., Bakkestuen, V., Alsos, I.G., Gilg, O., Taberlet, P. & Brochmann, C. (2013). Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity. New Phytologist, 200(3), 898-910. https://doi.org/10.1111/nph.12412, which has been published in final form at https://doi.org/10.1111/nph.12412. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. We provide the first comparative multispecies analysis of spatial genetic structure and diversity in the circumpolar Arctic using a common strategy for sam…
A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning
2020
ABSTRACT Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. F…
Fossorial but widespread: the phylogeography of the common spadefoot toad (Pelobates fuscus), and the role of the Po Valley as a major source of gene…
2007
International audience; Pelobates fuscus is a fossorial amphibian that inhabits much of the European plain areas. To unveil traces of expansion and contraction events of the species' range, we sequenced 702 bp of the mitochondrial cytochrome b gene. To infer the population history we applied phylogeographical methods, such as nested clade phylogeographical analysis (NCPA), and used summary statistics to analyse population structure under a neutral model of evolution. Populations were assigned to different drainage systems and we tested hypotheses of explicit refugial models using information from analysis of molecular variance, nucleotide diversity, effective population size estimation, NCP…
Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing
2019
Background The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. Results To better understand the origins of date palm cultivation we sequenced and analyzed ov…
IL10 promoter haplotypes may contribute to altered cytokine expression and systemic inflammation in celiac disease
2018
Celiac disease (CD) is an autoimmune/inflammatory condition triggered by dietary gluten intake in genetically predisposed individuals. Though associations with MHC class II HLA-DQ2 or -DQ8 are the primary and necessary genetic predisposition for CD, >97% of genetically predisposed individuals never develop CD. Cytokines were measured in the serum of CD patients and controls. Possible associations with IL10 promoter variants were investigated. Cytokine expression from PBMCs was monitored in response to gluten exposure, or CD3/TCR complex stimulation in the absence or presence of recombinant IL-10. Serum cytokines varied between patients with CD at the time of diagnosis, after dietary elimina…