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Vale P.F.,CNRS Center of Evolutionary and Functional Ecology | Choisy M.,IRD Montpellier | Froissart R.,IRD Montpellier | Froissart R.,CIRAD - Agricultural Research for Development | And 3 more authors.
Evolution | Year: 2012

Adaptation depends greatly on the distribution of mutation fitness effects (DMFE), but the phenotypic expression of mutations is often environment dependent. The environments faced by multihost pathogens are mostly governed by their hosts and therefore measuring the DMFE on multiple hosts can inform on the likelihood of short-term establishment and longer term adaptation of emerging pathogens. We explored this by measuring the growth rate of 36 mutants of the lytic bacteriophage φX174 on two host backgrounds, Escherichia coli (EcC) and Salmonella typhimurium (StGal). The DMFE showed higher mean and variance on EcC than on StGal. Most mutations were either deleterious or neutral on both hosts, but a greater proportion of mutations were deleterious on StGal. We identified two mutations with beneficial fitness effects on EcC that were neutral on StGal. Host-specific differences in fitness were associated with particular functional classes of genes involved in the initial stages of infection in accordance with previous studies of host specificity. Overall, there was a positive correlation between the effects of mutations on each host, suggesting that most new mutations will have general, rather than host-specific fitness effects. We consider these results in light of simple fitness landscape models of adaptation and discuss the relevance of context-dependent DMFE for multihost pathogens. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution. Source

Tamames J.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | Tamames J.,CIBER ISCIII | Tamames J.,CSIC - National Center for Biotechnology | Abellan J.J.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | And 6 more authors.
BMC Microbiology | Year: 2010

Background. The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa. Results. We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB. Conclusions. This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina. © 2010 Tamames et al; licensee BioMed Central Ltd. Source

Cuevas J.M.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | Geller R.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | Garijo R.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | Lopez-Aldeguer J.,Hospital Universitario La Paz | And 3 more authors.
PLoS Biology | Year: 2015

Rates of spontaneous mutation critically determine the genetic diversity and evolution of RNA viruses. Although these rates have been characterized in vitro and in cell culture models, they have seldom been determined in vivo for human viruses. Here, we use the intrapatient frequency of premature stop codons to quantify the HIV-1 genome-wide rate of spontaneous mutation in DNA sequences from peripheral blood mononuclear cells. This reveals an extremely high mutation rate of (4.1 ± 1.7) × 10−3 per base per cell, the highest reported for any biological entity. Sequencing of plasma-derived sequences yielded a mutation frequency 44 times lower, indicating that a large fraction of viral genomes are lethally mutated and fail to reach plasma. We show that the HIV-1 reverse transcriptase contributes only 2% of mutations, whereas 98% result from editing by host cytidine deaminases of the A3 family. Hypermutated viral sequences are less abundant in patients showing rapid disease progression compared to normal progressors, highlighting the antiviral role of A3 proteins. However, the amount of A3-mediated editing varies broadly, and we find that low-edited sequences are more abundant among rapid progressors, suggesting that suboptimal A3 activity might enhance HIV-1 genetic diversity and pathogenesis. © 2015 Cuevas et al. Source

Bradwell K.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | Bradwell K.,University of Valencia | Combe M.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | Domingo-Calap P.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | And 2 more authors.
Genetics | Year: 2013

Genome sizes and mutation rates covary across all domains of life. In unicellular organisms and DNA viruses, they show an inverse relationship known as Drake's rule. However, it is still unclear whether a similar relationship exists between genome sizes and mutation rates in RNA genomes. Coronaviruses, the RNA viruses with the largest genomes (~30 kb), encode a proofreading 39 exonuclease that allows them to increase replication fidelity. However, it is unknown whether, conversely, the RNA viruses with the smallest genomes tend to show particularly high mutation rates. To test this, we measured the mutation rate of bacteriophage Qβ, a 4.2-kb levivirus. Amber reversion-based Luria-Delbrück fluctuation tests combined with mutant sequencing gave an estimate of 1.4 × 10-4 substitutions per nucleotide per round of copying, the highest mutation rate reported for any virus using this method. This estimate was confirmed using a direct plaque sequencing approach and after reanalysis of previously published estimates for this phage. Comparison with other riboviruses (all RNA viruses except retroviruses) provided statistical support for a negative correlation between mutation rates and genome sizes. We suggest that the mutation rates of RNA viruses might be optimized for maximal adaptability and that the value of this optimum may in turn depend inversely on genome size. © 2013 by the Genetics Society of America. Source

Jimenez-Peydro R.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva | Peris-Felipo F.J.,Instituto Cavanilles Of Biodiversidad Y Biologia Evolutiva
Journal of the Entomological Research Society | Year: 2014

The aim of the present work was to analyse the diversity of Opiinae (Hymenoptera) in three Spanish protected Mediterranean natural parks affected by bioclimatic conditions: La Font Roja, Las Lagunas de la Mata-Torrevieja and La Tinença de Benifassà. Sampling was conducted between 2004 and 2005. During this period, 226 specimens, belonging to 32 different species, were captured. Eleven species captured are new records for Spain: Ademon urinator, Biophthora rosica, Biosteres analis, Biosteres spinaciae, Eurytenes (Xynobiotenes) scutellatus, Opius (Agnopius) tirolensis, Opius (Misophthora) bulgaricus, Opius (Nosopoea) cingulatoides, Opius (Nosopoea) speciosus, Opius (Nosopoea) viennensis and Xynobius caelatus. Alpha, beta and gamma diversities, as well as the structure of the communities were subsequently analysed. Our results indicate that Tinença de Benifassà and Torrevieja have higher diversity than Font Roja. Based on analysis of structural models, the latter communities were observed to be unstable and are composed of only a few abundant species and a large number of rare species. Source

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