1,721,128 research outputs found
Le popolazioni italiane della testuggine di Hermann (Testudo hermanni) puzzle ecologico e tassonomico per una strategia di conservazione
No full textTesting hypotheses on genetic variation and population structure: a general framework based on exact tests and combined p-values
No full textDuplication polymorphism at MHC class II DRB1 locus in the wild boar (Sus scrofa).
No full textAB The origin of allelic polymorphism in genes of the major histocompatibility complex represents a central topic in evolutionary genetics as it is probably the most polymorphic region in the nuclear genome of vertebrates. Accordingly, the analyses of genetic variability at these loci provide evidence complementary to the population genetics studies based on neutral loci. In this study, four wild boar populations, two from Italy (Florence region and Castelporziano Presidential Reserve, outside Rome) and one each from Hungary and Poland, were characterized at a highly polymorphic fragment including part of intron 1 and exon 2 of swine leukocyte antigen (SLA) class II DRB1 gene by direct sequencing and by cloning. Excluding the false alleles, a total of 18 different sequences were observed in 57 individuals. The high ratio of nonsynonymous (dN) vs synonymous (dS) substitution rates in the peptide-binding region supports the hypothesis that balancing selection is operating at this locus. A duplication event at the DRB1 gene was documented only in one Italian population with both copies being putatively active. This is the first evidence of a polymorphism for the number of copies of an SLA gene
DNA fingerprinting data and the analysis of population genetic structure by comparing band-sharing patterns
No full textEcology, IF=3.44
Identification of natural selection in genomic data with deep convolutional neural network
No full textBackground: With the increase in the size of genomic datasets describing variability in populations, extracting relevant information becomes increasingly useful as well as complex. Recently, computational methodologies such as Supervised Machine Learning and specifically Convolutional Neural Networks have been proposed to make inferences on demographic and adaptive processes using genomic data. Even though it was already shown to be powerful and efficient in different fields of investigation, Supervised Machine Learning has still to be explored as to unfold its enormous potential in evolutionary genomics. Results: The paper proposes a method based on Supervised Machine Learning for classifying genomic data, represented as windows of genomic sequences from a sample of individuals belonging to the same population. A Convolutional Neural Network is used to test whether a genomic window shows the signature of natural selection. Training performed on simulated data show that the proposed model can accurately predict neutral and selection processes on portions of genomes taken from real populations with almost 90% accuracy
Geographic 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.
Full text linkMicroRNAs (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
Small effective population size and fragmentation in Alpine populations of Bombina variegata: the combined effects of recent bottlenecks and postglacial recolonization
Full text linkAmphibians are experiencing population declines in all continents due to anthropogenic factors. Evidence of demographic reduction and local extinction have been reported also for the yellow-bellied toad, Bombina variegata, along all its distributional range, which includes the Italian Alps. Here we genotyped at the mtDNA cytb and at 11 nuclear microsatellites 200 individuals of B. variegata from 9 populations sampled in Trentino (north-eastern Italy). We investigated the fine-scale population structure and we tested for genetic traces of population decline using different methods. We found that all populations showed low level of genetic diversity in comparison with other studies, low estimates of effective population size, and clear evidence of demographic decline. When the age of the decline is estimated, contrasting results are found. Some methods suggest a recent reduction of population size possibly associated with anthropogenic environmental changes, and others support a more ancient bottleneck dating back to the postglacial recolonization of the Alps. We suggest that both demographic processes occurred in the evolutionary history of the yellow-bellied toad populations, and we are now testing this hypothesis by simulation
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