102,142 research outputs found
GEOGRAPHICAL STRUCTURING IN THE MTDNA OF ITALIANS
No full textGeographical patterns of mtDNA variation were studied in 12 Italian samples (1072 individuals) by two different spatial autocorrelation methods. Separate analyses of the frequencies of 12 restriction morphs show North-South dines, differences between Sardinia and the mainland populations, and the effects of isolation by distance. A recently developed autocorrelation statistic summarizing molecular similarity at all sites (AIDA; autocorrelation index for DNA analysis) confirms the presence of a clinal pattern; differences between random pairs of haplotypes tend to increase with their geographical distance. The partition of gene diversity, however, reveals that most variability occurs within populations, whereas differences between populations are minor (G(ST) = 0.057). When the data from the 12 samples are pooled, two descriptors of genetic variability (number of polymorphic sites and average sequence difference between pairs of individuals) do not behave as expected under neutrality, The presence of clinal patterns, Tajima's tests, and a simulation experiment agree in suggesting that population sizes in creased rapidly in Italy and Sicily but not necessarily so in Sardinia, The distribution of pairwise sequence differences in the Italian peninsula (excluding Sardinia) permits a tentative location of the demographic increase between 8000 and 20,500 years ago. These dates are consistent with archaeological estimates of two distinct;expansion processes, occurring, respectively, in the Neolithic and after the last glacial maximum in the Paleolithic, Conversely, there is no genetic evidence that such processes have had a major impact on the Sardinian population
4P: Fast computing of population genetics statistics from large DNA polymorphism panels
No full textMassive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations
Winter fattening strategies of two passerine species: Environmental and social influences
No full textWe studied the fattening strategies of two insectivorous passerines, the Robin Erithacus rubecula and the Wren Troglodytes troglodytes, during their wintering stage in a study area of the eastern Po valley (Northern Italy). We analysed the relationship between some environmental (temperature, photoperiod, rainfall) and social factors (density of migrant competitors, territoriality, home range size) on the one hand, and levels of fat reserve on the other. Although average body fat depots differed between the two species, both increased their daily fat stores as the photoperiod shortened with the progress of winter. The amount of fat accumulated by day was more than that required for overnight consumption. Both species also responded to short-term variations in weather conditions: fat depots were inversely related to the maximum temperature on the day of capture. The use of space and the social structure of the wintering populations seem to affect fattening strategies: fat reserves of resident Robins were negatively related to the density of conspecific migrants, early in the season. The same relationship was not observed for Wrens, which were dispersed in extensively overlapping home-ranges. In this species, the home-range size was positively, and fat reserves negatively, correlated with the body size of the bird
Le popolazioni italiane della testuggine di Hermann (Testudo hermanni) puzzle ecologico e tassonomico per una strategia di conservazione
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Testing hypotheses on genetic variation and population structure: a general framework based on exact tests and combined p-values
No full textGeographic homogeneity and non-equilibrium patterns of mtDNA sequences in Tuscany, Italy
No full textThe geographical distribution of 49 mtDNA sequences from 22 localities in Southern Tuscany, Italy, was studied by molecular analysis of variance, by a new spatial autocorrelation statistic specifically designed for sequence data and by reconstructing genealogies of haplotypes. All these methods indicated a high homogeneity of populations. Nevertheless, genetic variability showed significant departure from equilibrium expectations, in agreement with the predicted effects of a population expansion. We suggest that a past population expansion that was probably associated with a migrational wave and with local gene flow between localities prevented spatial structuring in Southern Tuscany
In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.
No full textMicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5′-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crop
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