Ash dieback due to Hymenoscyphus fraxineus is threatening the Fraxinus excelsior species in most of its natural range in Europe and it is becoming obvious that other species in the Fraxinus genus are susceptible to the disease. The fungal pathogen apparently originates from Asia where it may act as an endophyte of local species like F. mandshurica. Previous studies reported significant levels of genetic variability for susceptibility in F. excelsior either in field or inoculation experiments. The present study was based on a field experiment planted in 1995, fifteen years before onset of the disease. Crown and collar status were monitored on 788 trees from 23 open-pollinated progenies originating from 3 French provenances. Susceptibility was modelled using a Bayesian approach where spatio-temporal effects were explicitly taken into account, thus providing accurate narrow-sense heritability estimates (h²). While moderate narrow-sense heritability estimates for Crown Dieback (CD, h² = 0.42 in this study) have already been reported in the literature, this study is first to show that Collar Lesions are also heritable (h² = 0.49 for prevalence and h² = 0.42 for severity) and that there is significant genetic correlation between the severities of both traits (r_spearman=0.40). Unexpectedly, their spatio-temporal dynamics followed almost opposite patterns. While no significant Provenance effect were detected for any trait, significant Family effects were found for both CD and CL. Moreover, the analysis strategy implemented here allowed to compute Individual Breeding Values (IBV) and to show that there is more genetic variability within families than between families. In agreement with previous reports, early flushing correlates with better crown status. Consequences of these results in terms of management and breeding are discussed.

Integrons recombine gene arrays and favor the spread of antibiotic resistance. However, their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – and used it to identify integrons in bacterial genomes with high accuracy and sensitivity. Some key taxa, such as α-Proteobacteria, lacked integrons suggesting they constitute deleterious genetic backgrounds for these elements. Integrons were much more frequent in intermediate size genomes, suggesting selection for compact gene acquisition. We used comparative genomics to quantify the differences between mobile and persistent integrons. The use of a covariance model to identify and align attC sites showed higher intrinsic variability in mobile integrons and a correlation between attC sites homogeneity and the number of integron cassettes. Surprisingly, numerous arrays of attC sites lacked nearby integrases (or pseudogenes of integrases), included many novel cassettes, and exhibited very diverse attC sites. These attC0 elements might provide incoming mobile integrons with a large unexplored pool of novel cassettes in genomes that currently lack integrons. They might also represent an intermediate step of the process of horizontal gene transfer following integron-capture and preceding definitive stabilization by loss of genetic mobility.

We present a type of agent-based model that uses off-lattice spheres to represent individual cells in a solid tumor. The model calculates chemical gradients and determines the dynamics of the tumor as emergent properties of the interactions between the cells. As an example, we present an investigation of cooperation among cancer cells where cooperators secrete a growth factor that is costly to synthesize. Simulations reveal that cooperation is favored when cancer cells from the same lineage stay in close proximity. The result supports the hypothesis that kin selection, a theory that explains the evolution of cooperation in animals, also applies to cancers.

ABSTRACT Background Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. Results This study of the largest worldwide collection (n = 215) of sequenced ST131 E. coli isolates to date demonstrates that clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of a blaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids, and chromosomal integration of blaCTX-M within sub-clusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed amongst ST131, the blaCTX-M-14/14-like group. Conclusions The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli. These data also highlight the global imperative to reduce specific antibiotic selection pressures, and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages.

Premise of the study: Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for maternal-excess crosses where the mother has a higher ploidy than the father. Here we investigate the evolutionary origins of Mimulus peregrinus, an allopolyploid recently derived from the triploid M. x robertsii, to determine whether reproductive asymmetry has shaped the formation of this new species. Methods: We used reciprocal crosses between the diploid (M. guttatus) and tetraploid (M. luteus) progenitors to determine the viability of triploid hybrids resulting from paternal- versus maternal-excess crosses. To investigate whether experimental results predict patterns seen in the field, we performed parentage analyses comparing natural populations of M. peregrinus to its diploid, tetraploid, and triploid progenitors. Organellar sequences obtained from pre-existing genomic data, supplemented with additional genotyping was used to establish the maternal ancestry of multiple M. peregrinus and M. x robertsii populations. Key results: We find strong evidence for asymmetric origins of M. peregrinus, but opposite to the common pattern, with paternal-excess crosses significantly more successful than maternal-excess crosses. These results successfully predicted hybrid formation in nature: 111 of 114 M. x robertsii individuals, and 27 of 27 M. peregrinus, had an M. guttatus maternal haplotype. Conclusion: This study, which includes assembly of the first Mimulus chloroplast genome, demonstrates the utility of parentage analysis through genome skimming. We highlight the benefits of complementing genomic analyses with experimental approaches to understand asymmetry in allopolyploid speciation.