Search results for "PHYLOGENY"
showing 10 items of 1398 documents
Shell palaeoproteomics: first application of peptide mass fingerprinting for the rapid identification of mollusc shells in archaeology.
2020
10 pages; International audience; Molluscs were one of the most widely-used natural resources in the past, and their shells are abundant among archaeological findings. However, our knowledge of the variety of shells that were circulating in prehistoric times (and thus their socio-economic and cultural value) is scarce due to the difficulty of achieving taxonomic determination of fragmented and/or worked remains. This study aims to obtain molecular barcodes based on peptide mass fingerprints (PMFs) of intracrystalline proteins, in order to obtain shell identification. Palaeoproteomic applications on shells are challenging, due to low concentration of molluscan proteins and an incomplete unde…
Early cave art and ancient DNA record the origin of European bison
2016
The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil re…
Aedes albopictus diversity and relationships in south-western Europe and Brazil by rDNA/mtDNA and phenotypic analyses: ITS-2, a useful marker for spr…
2021
AbstractBackgroundAedes albopictusis a very invasive mosquito, which has recently colonized tropical and temperate regions worldwide. Of concern is its role in the spread of emerging or re-emerging mosquito-borne diseases.Ae. albopictusfrom south-western Europe and Brazil were studied to infer genetic and phenetic diversity at intra-individual, intra-population and inter-population levels, and to analyse its spread.MethodsGenotyping was made by rDNA 5.8S-ITS-2 and mtDNAcox1 sequencing to assess haplotype and nucleotide diversity, genetic distances and phylogenetic networks. Male and female phenotyping included combined landmark-and outlined-based geometric morphometrics of wing size and sha…
Evolution of the immune system influences speciation rates in teleost fishes.
2016
Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outs…
Whole genome sequences reveal Vibrio hemicentroti Kim et al. 2013 as a later heterotypic synonym of Vibrio splendidus (Beijerinck 1900) Baumann et al…
2017
The synonymy between Vibrio hemicentroti Kim et al. 2013 and Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981 was suggested after a recent multilocus sequence analysis of the Splendidus clade, which included the type strains of both species. To clarify their status, we have determined genomic indexes from whole genome sequences of strains V. hemicentroti CECT 8714T and V. splendidus NCCB 53037T. Average Nucleotide Identities of 96.0–96.7 % and an in silico DNA–DNA hybridization value of 70.2 %, as well as similarity levels of selected housekeeping gene sequences support the consideration of V. hemicentroti as a later heterotypic synonym of V. splendidus .
Phylogeny of Syndermata (syn. Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monoph…
2015
Abstract A monophyletic origin of endoparasitic thorny-headed worms (Acanthocephala) and wheel-animals (Rotifera) is widely accepted. However, the phylogeny inside the clade, be it called Syndermata or Rotifera, has lacked validation by mitochondrial (mt) data. Herein, we present the first mt genome of the key taxon Seison and report conflicting results of phylogenetic analyses: while mt sequence-based topologies showed monophyletic Lemniscea (Bdelloidea + Acanthocephala), gene order analyses supported monophyly of Pararotatoria (Seisonidea + Acanthocephala) and Hemirotifera (Bdelloidea + Pararotatoria). Sequence-based analyses obviously suffered from substitution saturation, compositional …
Phylogenomics of Lophotrochozoa with Consideration of Systematic Error.
2015
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error. Here, we investigated why lophotrochozoan phylogeny has been such a difficult question to answer by identifying and reducing sources of sys…
Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA
2016
International audience; Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational taxonomic units distributed within 50 phylogenetic groups. Thus, microbial groups, such as Chlorophyta, Dinophyceae, Haptophyceae and Ciliophora, tha…
Microbial communities of polluted sub-surface marine sediments
2018
Abstract Microbial communities of coastal marine sediment play a key role in degradation of petroleum contaminants. Here the bacterial and archaeal communities of sub-surface sediments (5–10 cm) of the chronically polluted Priolo Bay (eastern coast of Sicily, Italy), contaminated mainly by n-alkanes and biodegraded/weathered oils, were characterized by cultural and molecular approaches. 16S-PCR-DGGE analysis at six stations, revealed that bacterial communities are highly divergent and display lower phylogenetic diversity than the surface sediment; sub-surface communities respond to oil supplementation in microcosms with a significant reduction in biodiversity and a shift in composition; the…
Genetic Diversity of O-Antigens in Hafnia alvei and the Development of a Suspension Array for Serotype Detection.
2016
Hafnia alvei is a facultative and rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. Although it has been more than 50 years since the genus was identified, very little is known about variations among Hafnia species. Diversity in O-antigens (O-polysaccharide, OPS) is thought to be a major factor in bacterial adaptation to different hosts and situations and variability in the environment. Antigenic variation is also an important factor in pathogenicity that has been used to define clones within a number of species. The genes that are required to synthesize OPS are always clustered within the bacterial chromosome. A serotyping scheme including 39 O-serotypes has…