Search results for "Evolutionary Genetics"
showing 7 items of 37 documents
Inferring heterozygosity from ancient and low coverage genomes
2016
Abstract While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here, we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage <1× of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence, except for the initial alignment of the sequencing data, and takes into account both variable sequencing errors and potential postmortem damage. It is thus also applicable to …
Mycobacterium tuberculosis molecular evolution in western Mediterranean Island of Sicily and Sardinia
2004
Abstract In this study, a total of 204 Mycobacterium tuberculosis DNAs from Sicily ( n = 144) and Sardinia ( n = 60) were studied by three genotyping methods. Results were analyzed both within and across islands, to define the phylogeographical specificities of the genotypes, look for their diversity and infer a molecular evolutionary scenario. A strong link between geography and tuberculosis genotypes was observed in Sardinia. The results were also matched against a world-wide genetic diversity database to compare the population structure of the tubercle bacilli in the islands. Eight common genotypes between Sicily, Sardinia and continental Italy were found which underlines the influences …
From foes to friends: Viral infections expand the limits of host phenotypic plasticity
2020
Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies hav…
The evolutionary genetics of the hobo transposable element in the Drosophila melanogaster complex.
1994
Hobo elements are a family of transposable elements found in Drosophila melanogaster and its three sibling species: D. simulans, D. mauritiana and D. sechellia. Studies in D. melanogaster have shown that hobo may be mobilized, and that the genetic effects of such mobilizations included the general features of hybrid dysgenesis: mutations, chromosomal rearrangements and gonadal dysgenis in F1 individuals. At the evolutionary level some hobo-hybridizing sequences have also been found in the other members of the melanogaster subgroup and in many members of the related montium subgroup. Surveys of older collected strains of D. melanogaster suggest that complete hobo elements were absent prior t…
Chapter 2 Fasciola, Lymnaeids and Human Fascioliasis, with a Global Overview on Disease Transmission, Epidemiology, Evolutionary Genetics, Molecular …
2009
Abstract Fascioliasis, caused by liver fluke species of the genus Fasciola, has always been well recognized because of its high veterinary impact but it has been among the most neglected diseases for decades with regard to human infection. However, the increasing importance of human fascioliasis worldwide has re‐launched interest in fascioliasis. From the 1990s, many new concepts have been developed regarding human fascioliasis and these have furnished a new baseline for the human disease that is very different to a simple extrapolation from fascioliasis in livestock. Studies have shown that human fascioliasis presents marked heterogeneity, including different epidemiological situations and…
A Novel Approach to Identify Candidate Prognostic Factors for Hepatitis C Treatment Response Integrating Clinical and Viral Genetic Data
2015
The combined therapy of pegylated interferon (IFN) plus ribavirin (RBV) has been for a long time the standard treatment for patients infected with hepatitis C virus (HCV). In the case of genotype 1, only 38%–48% of patients have a positive response to the combined treatment. In previous studies, viral genetic information has been occasionally included as a predictor. Here, we consider viral genetic variation in addition to 11 clinical and 19 viral populations and evolutionary parameters to identify candidate baseline prognostic factors that could be involved in the treatment outcome. We obtained potential prognostic models for HCV subtypes la and lb in combination as well as separately. We …
Data from: Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation
2018
D. montana gff fileGenome annotation file for D. montana genome (Accession number: LUVX00000000)D.mont_freeze_v1.4.gff.txt