Shell shape variation in Littorina saxatilis and L.arcana: a case of character displacement?

Variation in shape of the shell of Littorina saxatilis and Littorina arcana has been investigated using shells from four shores where the species co-occur and seven where the former only is present. Samples were taken from shores along the south-west and south coasts of Britain, between Cardigan Bay and Kent. Measurements of eight shell variables and of the operculum area were analysed using canonical variate analysis. The results of the analysis suggest that the shells can be separated into three groups, namely L. arcana, L. saxatilis where it is sympatric with L, arcana, and L. saxatilis where it is allopatric from L. arcana. The separation of the two groups of L. saxatilis is based primarily on their relative globosity, whereas the separation of L. saxatilis from L. arcana is based primarily on the relative size of the operculum and width of shell whorl one (the first above the body whorl). Sexual dimorphism has been considered and shown not to contribute significantly to the between-shore pattern of variation observed. The relationships between important variables were further investigated using ANCOVA, and the relationship of foot area to the shell variables was also analysed at four of the shores. It is concluded that there is evidence of character displacement in L. saxatilis, shown by an increase in globosity in the presence of L. arcana, and that this may partly explain the continuing uncertainty over the taxonomic and ecological identity of members of the rough periwinkle group

The Special Science Dilemma and How Culture Solves It

This is the final version of the article. It first appeared from Taylor & Francis via http://dx.doi.org/10.1080/00048402.2014.987149I argue that there is a tension between the claim that at least some kinds in the special sciences are multiply realized and the claim that the reason kinds are prized by science is that they enter into a variety of different empirical generalizations. Nevertheless, I show that this tension ceases in the case of ‘cultural homologues’–such as specific ideologies, religions, and folk wisdom. I argue that the instances of such special science kinds do have several projectable properties in common due to their shared history of reproduction, and that the social learning involved means we should also expect these kinds to be multiply realized

Cross-reactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies

Illumina DNA methylation arrays are a widely used tool for performing genome-wide DNA methylation analyses. However, measurements obtained from these arrays may be affected by technical artefacts that result in spurious associations if left unchecked. Cross-reactivity represents one of the major challenges, meaning that probes may map to multiple regions in the genome. Although several studies have reported on this issue, few studies have empirically examined the impact of cross-reactivity in an epigenome-wide association study (EWAS). In this paper, we report on cross-reactivity issues that we discovered in a large EWAS on the presence of the C9orf72 repeat expansion in ALS patients. Specifically, we found that that the majority of the significant probes inadvertently cross-hybridized to the C9orf72 locus. Importantly, these probes were not flagged as cross-reactive in previous studies, leading to novel insights into the extent to which cross-reactivity can impact EWAS. Our findings are particularly relevant for epigenetic studies into diseases associated with repeat expansions and other types of structural variation. More generally however, considering that most spurious associations were not excluded based on pre-defined sets of cross-reactive probes, we believe that the presented data-driven flag and consider approach is relevant for any type of EWAS

Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor

Respiration in the invertebrates

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