Thermal plasticity in Drosophila melanogaster: A comparison of geographic populations

BACKGROUND: Populations of Drosophila melanogaster show differences in many morphometrical traits according to their geographic origin. Despite the widespread occurrence of these differences in more than one Drosophila species, the actual selective mechanisms controlling the genetic basis of such variation are not fully understood. Thermal selection is considered to be the most likely cause explaining these differences. RESULTS: In our work, we investigated several life history traits (body size, duration of development, preadult survival, longevity and productivity) in two tropical and two temperate natural populations of D. melanogaster recently collected, and in a temperate population maintained for twelve years at the constant temperature of 18°C in the laboratory. In order to characterise the plasticity of these life history traits, the populations were grown at 12, 18, 28 and 31.2°C. Productivity was the fitness trait that showed clearly adaptive differences between latitudinal populations: tropical flies did better in the heat but worse in the cold environments with respect to temperate flies. Differences for the plasticity of other life history traits investigated between tropical and temperate populations were also found. The differences were particularly evident at stressful temperatures (12 and 31.2°C). CONCLUSION: Our results evidence a better cold tolerance in temperate populations that seems to have been evolved during the colonisation of temperate countries by D. melanogaster Afrotropical ancestors, and support the hypothesis of an adaptive response of plasticity to the experienced environment

Mannose-Binding Lectin 2 Gene and Risk of Adult Glioma

Collection of specimens in this study, including funding: JMG JM MS SST DJH CAC. Selection of genes and SNPs to include in the analysis: FCFC MES. Manuscript editing: DMB DGC MS SST CAC ATP. Conceived and designed the experiments: DSM ATP. Performed the experiments: AS. Analyzed the data: DSM AS DGC. Wrote the paper: DSM.Background and AimsThe immune system is likely to play a key role in the etiology of gliomas. Genetic polymorphisms in the mannose-binding lectin gene, a key activator in the lectin complement pathway, have been associated with risk of several cancers.MethodsTo examine the role of the lectin complement pathway, we combined data from prospectively collected cohorts with available DNA specimens. Using a nested case-control design, we genotyped 85 single nucleotide polymorphisms (SNPs) in 9 genes in the lectin complement pathway and 3 additional SNPs in MBL2 were tested post hoc). Initial SNPs were selected using tagging SNPs for haplotypes; the second group of SNPs for MBL2 was selected based on functional SNPs related to phenotype. Associations were examined using logistic regression analysis. All statistical tests were two-sided. Nominal p-values are presented and are not corrected for multiple comparisons.ResultsA total of 143 glioma cases and 419 controls were available for this analysis. Statistically significant associations were observed for two SNPs in the mannose-binding lectin 2 (ML2) gene and risk of glioma (rs1982266 and rs1800450, test for trend p = 0.003 and p = 0.04, respectively, using the additive model). One of these SNPs, rs1800450, was associated with a 58% increase in glioma risk among those carrying one or two mutated alleles (odds ratio = 1.58, 95% confidence interval = 0.99–2.54), compared to those homozygous for the wild type allele.ConclusionsOverall, our findings suggest that MBL may play a role in the etiology of glioma. Future studies are needed to confirm these findings which may be due to chance, and if reproduced, to determine mechanisms that link glioma pathogenesis with the MBL complement pathway.Yeshttp://www.plosone.org/static/editorial#pee

HR-snps

The genotype of the second cross (HR) in Linkage format

HP genotype

The genotype of the first cross (HP) in LINKAGE data forma

HR SNP IDs

SNP IDS corresponding to the first cross (HR) genotype file. The IDs are in the exact same order as in the genotype file

RAD fragments and SNPs

A list of 41 bp fragments names and in which base of the fragment we genotyped the SN

HP SNPs IDs

The P. pungitius SNP IDs for the first cross (HP) corresponding, and in the exact same order, as the HP genotype data file

First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species

BACKGROUND: Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world's poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. This is an important step towards knowing if the species should be managed separately or as a single stock. Population structure is important for fisheries management, yet understudied for many African freshwater species. We hypothesize that distinct stocks of S. tanganicae could be present due to the large size of the lake (isolation by distance), limnological variation (adaptive evolution), or past separation of the lake (historical subdivision). On the other hand, high mobility of the species and lack of obvious migration barriers might have resulted in a homogenous population. RESULTS: We performed a population genetic study on wild-caught S. tanganicae through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (83 individuals). Samples were collected at five locations along a north-south axis of Lake Tanganyika. The mtDNA data had low global FST and, visualised in a haplotype network, did not show phylogeographic structure. RAD sequencing yielded a panel of 3504 SNPs, with low genetic differentiation (FST = 0.0054; 95% CI: 0.0046-0.0066). PCoA, fineRADstructure and global FST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (FST = 0.1338 95% CI: 0.1239,0.1445), which do not correspond to sampling locations. Autocorrelation analysis showed a slight increase in genetic difference with increasing distance. No outlier loci were detected in the RADseq data. CONCLUSION: Our results show at most very weak geographical structuring of the stock and do not provide evidence for genetic adaptation to historical or environmental differences over a north-south axis. Based on these results, we advise to manage the stock as one population, integrating one management strategy over the four riparian countries. These results are a first comprehensive study on the population structure of these important fisheries target species, and can guide fisheries management.status: publishe