Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient

Identification of loci with adaptive importance is a key step to understand the speciation process in natural populations, because those loci are responsible for phenotypic variation that affects fitness in different environments. We conducted an AFLP genome scan in populations of ocellated lizards (Lacerta lepida) to search for candidate loci influenced by selection along an environmental gradient in the Iberian Peninsula. This gradient is strongly influenced by climatic variables, and two subspecies can be recognized at the opposite extremes: L. lepida iberica in the northwest and L. lepida nevadensis in the southeast. Both subspecies show substantial morphological differences that may be involved in their local adaptation to the climatic extremes. To investigate how the use of a particular outlier detection method can influence the results, a frequentist method, DFDIST, and a Bayesian method, BayeScan, were used to search for outliers influenced by selection. Additionally, the spatial analysis method was used to test for associations of AFLP marker band frequencies with 54 climatic variables by logistic regression. Results obtained with each method highlight differences in their sensitivity. DFDIST and BayeScan detected a similar proportion of outliers (3–4%), but only a few loci were simultaneously detected by both methods. Several loci detected as outliers were also associated with temperature, insolation or precipitation according to spatial analysis method. These results are in accordance with reported data in the literature about morphological and life‐history variation of L. lepida subspecies along the environmental gradient.     

Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis)

Individuals in natural populations are frequently exposed to a wide range of pathogens. Given the diverse profile of gene products involved in responses to different types of pathogen, this potentially results in complex pathogen-specific selection pressures acting on a broad spectrum of immune system genes in wild animals. Thus far, studies into the evolution of immune genes in natural populations have focused almost exclusively on the Major Histocompatibility Complex (MHC). However, the MHC represents only a fraction of the immune system and there is a need to broaden research in wild species to include other immune genes. Here, we examine the evidence for natural selection in a range of non-MHC genes in a natural population of field voles (Microtus agrestis). We concentrate primarily on genes encoding cytokines, signalling molecules critical in eliciting and mediating immune responses and identify signatures of natural selection acting on several of these genes. In particular, genetic diversity within Interleukin 1 beta and Interleukin 2 appears to have been maintained through balancing selection. Taken together with previous findings that polymorphism within these genes is associated with variation in resistance to multiple pathogens, this suggests that pathogen-mediated selection may be an important force driving genetic diversity at cytokine loci in voles and other natural populations. These results also suggest that, along with the MHC, preservation of genetic variation within cytokine genes should be a priority for the conservation genetics of threatened wildlife populations.     

A small and compact genome in the marine cyanobacterium Prochlorococcus marinus CCMP 1375: lack of an intron in the gene for tRNA(Leu)(UAA) and a single copy of the rRNA operon

PCR-ribotying, a typing method based on polymorphism in the 16S-23S intergenic spacer region, has been recently used to investigate outbreaks due to Clostridium difficile. However, this method generates bands of high and close molecular masses which are difficult to separate on agarose gel electrophoresis. To improve reading of banding patterns of PCR-ribotyping applied to C. difficile, a partial sequencing of the rRNA genes (16S and 23S) and intergenic spacer region has been performed, then a new set of primers located closer to the intergenic spacer region has been defined. The new PCR gave reproducible patterns of bands easy to separate on agarose gel electrophoresis. Each of the 10 serogroups and 11 subgroups of serogroup A produced a different pattern. This typing method has evidenced major qualities such as easiness, rapidity and reproducibility. However, its discriminatory power has to be evaluated to validate its importance as a typing tool for C. difficile.     

Multitrait selection system using populations with a small number of interploid (4x-2x) hybrid seedlings in potato: Degree of high-parent heterosis for yield and frequency of clones combining quantitative agronomic traits

One of the most attractive features of the 4x-2x breeding scheme via unilateral sexual polyploidization (USP) is the possibility of obtaining heterotic clones with a combination of desirable traits based upon selection in a small number of hybrid seedlings. A set of experiments was carried out to verify this characteristic of the USP scheme using 42 families (with 20 plants each) derived from 2x Phureja-haploid Tuberosum or haploid Tuberosum-Solanum chacoense hybrids as male parents. These clones were 2n-pol-len-producers by either first-division restitution with crossing over (FDR-CO) or without crossing over (FDR-NCO). The 4x parents were eight cultivars of USA and European origin. A total of 168 out 840 clones was initially selected (four clones/family) based on general tuber appearance (GTA). An additional round of selection (not taking into account the parentage of the clone) for total tuber yield (TTY) reduced the sample to 96 clones. These selected clones and the original 4x parents were evaluated in two locations at Wisconsin (Hancock – E?1, and Rhinelander – E?2). The average high-parent heterosis values for TTY ranged from 27.8% (E?2) to 48% (E?1). The population of experimental clones also had a TTY range wider than that of the 4x parents. The best clone gave a yield of 101.6% and 63.2% over the best 4x parent at E?1 and E?2, respectively. For TTY, a significant genotype×environment (G×E) interaction for the experimental clones was found when a combined analysis of variance for both locations was carried out. However, the G×E interaction was not significant when only the 4x-parent group was considered. Clones derived from 4x European cultivars had higher GTA scores than clones derived from 4x USA cultivars. With two culling levels being set on the TTY≥4x parent group mean and the GTA≥three, about 56% (E?1) and 48% (E?2) of the clones would be retained for further evaluation. These percentages of selected clones are much higher than those reported using conventional 4x-4x crosses. Our results indicate that a USP strategy with 4x-2x (FDR) crosses would be more effective than intra-Tuberosum crosses in generating heterotic clones with a combination of desirable quantitative traits using populations with a small number of hybrid seedlings.