The History and geography of the Y chromosome SNPs in Europe: an update

The knowledge of the evolution of the human genome is strictly dependent on the availability of appropriate genetic markers and their relative coverage of genetic variation which refine the phylogenetic reconstruction. While autosomal markers are particularly valuable for recognizing correspondence between genetic and geographic distances, markers on mitochondrial DNA (mtDNA) or Non Recombining Portion of Y Chromosome (NRY), because of their unilinear transmission, can effectively trace diachronical patterns of the human peopling. The maximum extent of polymorphism coverage has already been reached for the very small mitochondrial genome (about 16,5 Kbp), whereas the first studies based on RFLPs (Restriction Fragment Length Polymorphisms) (Cann et al., 1987) and on sequencing of the hypervariable regions (Vigliant et al., 1991), were then combined to get higher resolution (Torroni et al., 1996), and finally the complete genome sequencing is now routinely performed (Achilli et al., 2004, Pala et al., 2009), in order to detect the whole mtDNA variation. A similar approach cannot be used yet at population level for the by far larger nuclear genome. However, advances in genotyping technology have dramatically enhanced the resolution of the analysis at genome-wide level, and recent papers significantly improved the knowledge of the relationships among European populations, using 300 to 500 K SNPs (Single Nucleotide Polymorphisms) on microarrays chips (Tian et al., 2008; Novembre et al., 2008). As to the NRY, most of the studies before the year 2000 were performed using Alu insertion (Hammer, 1995) or STRs (Short Tandem Repeats) (De Knijff et al., 1997; Pritchard et al., 1999) with the known limitations due to recurrence and reversion of this kind of polymorphisms. Using D-HPLC (Denaturing High Performance Liquid Chromatography) technology, Underhill and coworkers (1997) discovered 22 new SNP biallelic markers, rapidly raising in number to 167 (Underhill et al., 2000), 242 (YCC, 2002), about 600 (Karafet et al., 2008), up to more than 725 presently listed in the Y-DNA SNP Index 2009, (www.isogg. org), and the knowledge of Y chromosome phylogeny and of the spread worldwide of human populations raised proportionally. The next goal of the research on Y chromosome will be the use of specific microarrays that can genotype a much higher number of SNPs than nowadays routinely performed, and, ultimately, the complete Y chromosome sequencing. Waiting for future developments, this short note reports the state of the art of the phylogenetic (“history”) and phylogeographic (“geography”) research on Y chromosome SNP analyses in Europe, updating the review published in this Journal by Francalacci & Sanna at the beginning of 2008

Mitochondrial DNA lineages of Italian Giara and Sarcidano horses

Giara and Sarcidano are 2 of the 15 extant native Italian horse breeds with limited dispersal capability that originated from a larger number of individuals. The 2 breeds live in two distinct isolated locations on the island of Sardinia. To determine the genetic structure and evolutionary history of these 2 Sardinian breeds, the first hypervariable segment of the mitochondrial DNA (mtDNA) was sequenced and analyzed in 40 Giara and Sarcidano horses and compared with publicly available mtDNA data from 43 Old World breeds. Four different analyses, including genetic distance, analysis of molecular variance, haplotype sharing, and clustering methods, were used to study the genetic relationships between the Sardinian and other horse breeds. The analyses yielded similar results, and the FST values indicated that a high percentage of the total genetic variation was explained by between-breed differences. Consistent with their distinct phenotypes and geographic isolation, the two Sardinian breeds were shown to consist of 2 distinct gene pools that had no gene flow between them. Giara horses were clearly separated from the other breeds examined and showed traces of ancient separation from horses of other breeds that share the same mitochondrial lineage. On the other hand, the data from the Sarcidano horses fit well with variation among breeds from the Iberian Peninsula and North-West Europe: genetic relationships among Sarcidano and the other breeds are consistent with the documented history of this breed

Mitochondrial DNA reveals genetic structuring of <i>Pinna nobilis</i> across the Mediterranean Sea

Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities have promoted the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. The aim of this study was to provide the first large broad-scale insight into the genetic variability of P. nobilis in the area that encompasses the western Mediterranean, Ionian Sea, and Adriatic Sea marine ecoregions. To accomplish this objective twenty-five populations from this area were surveyed using two mitochondrial DNA markers (COI and 16S). Our dataset was then merged with those obtained in other studies for the Aegean and Tunisian populations (eastern Mediterranean), and statistical analyses (Bayesian model-based clustering, median-joining network, AMOVA, mismatch distribution, Tajima’s and Fu’s neutrality tests and Bayesian skyline plots) were performed. The results revealed genetic divergence among three distinguishable areas: (1) western Mediterranean and Ionian Sea; (2) Adriatic Sea; and (3) Aegean Sea and Tunisian coastal areas. From a conservational point of view, populations from the three genetically divergent groups found may be considered as different management units

Genetic affinities within a large global collection of pathogenic <i>Leptospira</i>: implications for strain identification and molecular epidemiology

Leptospirosis is an important zoonosis with widespread human health implications. The non-availability of accurate identification methods for the individualization of different Leptospira for outbreak investigations poses bountiful problems in the disease control arena. We harnessed fluorescent amplified fragment length polymorphism analysis (FAFLP) for Leptospira and investigated its utility in establishing genetic relationships among 271 isolates in the context of species level assignments of our global collection of isolates and strains obtained from a diverse array of hosts. In addition, this method was compared to an in-house multilocus sequence typing (MLST) method based on polymorphisms in three housekeeping genes, the rrs locus and two envelope proteins. Phylogenetic relationships were deduced based on bifurcating Neighbor-joining trees as well as median joining network analyses integrating both the FAFLP data and MLST based haplotypes. The phylogenetic relationships were also reproduced through Bayesian analysis of the multilocus sequence polymorphisms. We found FAFLP to be an important method for outbreak investigation and for clustering of isolates based on their geographical descent rather than by genome species types. The FAFLP method was, however, not able to convey much taxonomical utility sufficient to replace the highly tedious serotyping procedures in vogue. MLST, on the other hand, was found to be highly robust and efficient in identifying ancestral relationships and segregating the outbreak associated strains or otherwise according to their genome species status and, therefore, could unambiguously be applied for investigating phylogenetics of Leptospira in the context of taxonomy as well as gene flow. For instance, MLST was more efficient, as compared to FAFLP method, in clustering strains from the Andaman island of India, with their counterparts from mainland India and Sri Lanka, implying that such strains share genetic relationships and that leptospiral strains might be frequently circulating between the islands and the mainland

Metodi topografici per la ricostruzione dettagliata della piezometria nelle aree costiere: il caso del Parco Regionale della Maremma (Toscana meridionale)

Una metodologia topografica è stata messa a punto all'interno del Parco Regionale della Maremma (Grosseto) con l’obbiettivo di conseguire una determinazione dei dati plano-altimetrici della locale rete di monitoraggio piezometrico tale da assicurare un’elevata accuratezza nella ricostruzione della rete di flusso ed una sufficiente velocità di esecuzione in modo da garantirne la sostenibilità di tempi e costi. I rilievi effettuati tramite strumentazione GNSS e livellazione geometrica “dal mezzo” hanno consentito un significativo miglioramento delle conoscenze sull'idrodinamica della falda ed in particolare sui lo-cali fenomeni di intrusione marina. La procedura proposta è da ritenersi pertanto conveniente in tutte le applicazioni idrogeologiche delle zone costiere caratterizzate dalla concomitanza tra un basso gradiente idraulico ed una significativa variazione della quota altimetrica, tipica casistica geomorfologica dei litorali italiani

Population structure of the <i>Monocelis lineata</i> (Proseriata, Monocelididae) species complex assessed by phylogenetic analysis of the mitochondrial Cytochrome c Oxidase subunit I (<i>COI</i>) gene

Monocelis lineate consists of a complex of sibling species, widespread in the Mediterranean and Atlantic Ocean. Previous genetic analysis placed in evidence at least four sibling species. Nevertheless, this research was not conclusive enough to fully resolve the complex or to infer the phylogeny/phylogeography of the group. We designed specific primers aiming at obtaining partial sequences of the mtDNA gene Cytochrome c Oxidase subunit I (COI) of M. lineate, and have identified 25 different haplotypes in 32 analyzed individuals. The dendrogram generated by Neighbor- Joining analysis confirmed the differentiation between Atlantic and Mediterranean siblings, as well as the occurrence of at least two Mediterranean sibling species. Thus validated, the method here presented appears as a valuable tool in population genetics and biodiversity surveys on the Monocelis lineate complex

Ancestral European roots of <i>Helicobacter pylori</i> in India

Background. The human gastric pathogen Helicobacter pylori is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of H. pylori mirror ancient human migrations. Ancestral origins of H. pylori in the vast Indian subcontinent are debatable. It is not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori. We tried to address these issues through mapping genetic origins of present day H. pylori in India and their genomic comparison with hundreds of isolates from different geographic regions. Results. We attempted to dissect genetic identity of strains by multilocus sequence typing (MLST) of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and phylogeographic analysis of haplotypes using MEGA and NETWORK software while incorporating DNA sequences and genotyping data of whole cag pathogenicity-islands (cagPAI). The distribution of cagPAI genes within these strains was analyzed by using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. All the isolates analyzed revealed European ancestry and belonged to H. pylori sub-population, hpEurope. The cagPAI harbored by Indian strains revealed European features upon PCR based analysis and whole PAI sequencing. Conclusion. These observations suggest that H. pylori strains in India share ancestral origins with their European counterparts. Further, non-existence of other sub-populations such as hpAfrica and hpEastAsia, at least in our collection of isolates, suggest that the hpEurope strains enjoyed a special fitness advantage in Indian stomachs to out-compete any endogenous strains. These results also might support hypotheses related to gene flow in India through Indo-Aryans and arrival of Neolithic practices and languages from the Fertile Crescent

Mendelian breeding units <i>versus</i> standard sampling strategies: mitochondrial DNA variation in southwest Sardinia

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits

Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample

Background: Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. Methods: DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. Results: From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. Conclusions: The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome

Why pelletizing hops? A comparison of physical-chemical properties between powder and pellets

Why was the work done: The use of pellets was introduced as a method to reduce volume and increase shelf-life of hop plants (Humulus lupulus). There is no evidence that pellets retain better hop qualities compared to powder. The objective of this study was to compare the physical-chemical properties of hops in flower, powder, and pellet forms. How was the work done: Hop species (Cascade, Northern Brewer, and Comet) were analyzed in triplicate using chromatography, conductometric titration, steam distillation, and gravimetry, for essential oil content, alpha-acid percentage, and humidity, respectively. &nbsp;What are the main findings: A consistent reduction in essential oil content, alpha-acid percentage, and humidity was observed as the degree of hop processing increased from flower to powder to pellet. (p&lt;0.0001, ANOVA and Tukey's post hoc test). Why is the work important: These results provide evidence that the pelleting process reduces key compounds like essential oils and alpha acids that contribute to hop quality for beer production when compared to the powder presentation. Eliminating the pelleting process could potentially reduce some production costs associated with hop processing. Pelleting requires additional equipment and energy, which contributes to overall production expenses