101 research outputs found
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
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
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
First insights on the mitochondrial genetic variability of Lightiella magdalenina (Crustacea), the sole Mediterranean cephalocarid species
Background: Here we report the first insight into the mitochondrial (Cytochrome c Oxidase subunit I - COI and Cytochrome b - Cyt b) genetic variation of the only Mediterranean cephalocarid Lightiella magdalenina. Findings: COI sequences provide a scenario of low intraspecific variability, while significant genetic divergence occurs between L. magdalenina and L. incisa. Interestingly, Cyt b sequences reveal a higher degree of intraspecific variability, with no shared haplotypes between the sites considered. Conclusions: In the future, COI and Cyt b molecular markers could be used as valuable tools to shed new light into the extant species within the genus Lightiella thus providing molecular support to the taxonomical identifications carried out on a morphological basis
Worldwide variation of the COL14A1 gene is shaped by genetic drift rather than selective pressure
Background: The aim of this study is to analyze the worldwide distribution of SNP rs4870723 in COL14A1 gene to check if there are significant genetic differences among different populations and to test if the gene is a trait under selection. Methods: Genomic DNA was extracted from 69 unrelated individuals from Sardinia and genotyped for SNP rs4870723. Data were compared with 26 different populations, clustered in 5 super-populations, from the public 1000 genomes database. Allele frequency and heterozygosity were calculated with Genepop. The Hardy–Weinberg equilibrium and pairwise population differentiation through analysis of molecular variance (AMOVA FST) were determined with Arlequin. Results: Allele frequencies of COL14A1 rs4870723 were compared in 27 populations clustered in 5 super-populations. All populations were in the Hardy–Weinberg equilibrium. In almost all populations, allele C was the most frequent allele, reaching the highest values in East Asia. The 27 populations showed an appreciable structure, with significant differences observed between European, African, and Asian populations. Conclusion: Significant differences were observed in the rs4870723 SNP distribution among the populations studied. However, we found no evidence for a selective pressure. Rather, the differentiation among the populations is likely the result of founder effect, genetic drift, and cultural factors, all events known to establish and maintain genetic diversity between populations
Mitochondrial DNA Variation among Dogs of Mongolian, Tuvinian and Altaic Nomads
Dogs originated from the domestication of Eurasian grey wolves. From a genetic viewpoint, they can be grouped into two main clusters: the first is represented by several breeds obtained by artificial selection, whereas the second is of dogs that adapted to
a human commensal lifestyle. Here we have provided a molecular survey aimed to infer on the genetic variability of dogs from nomadic camps in Mongolia, and the Republics of Tuva and Altai belonging to the Russian Federation. The results provided evidence of typical marks of expanding populations with multiple origins. Such a scenario could be the result of genetic exchanges among dogs from different camps, that were likely mediated by nomads
Surname analysis of the Corsican population reveals an agreement with geographical and linguistic structure
The surname is a cultural trait that is extremely useful for historical and linguistic studies and can effectively be used as a genetic marker. In many human populations the surname is inherited in the paternal lineage, and can therefore be considered a marker for the Y chromosome. In this study, surnames were recorded from the white pages of telephone directories in current use in Corsica in 1993. All surnames present in thirteen villages scattered over the whole island and covering the main historical regions were transcribed. Surname variability was found to be higher in coastal villages, and lower in more isolated communities. The isonymy detected among the thirteen villages allowed the calculation of kinship values, visualized in a tree showing two main clusters, one referring to the northern villages and one encompassing the villages of the south. The pattern reflects the administrative division of the island, with the exception of Vico, which belongs to the southern administrative region but is geographically close to the northern villages, and Ghisoni, which belongs to the northern district but is more similar to the village of Bastelica in the southern district. The data presented here show a structure in the surname distribution that is in substantial agreement with the geographical patterns. The kinship values are consistent with a moderated gene flow among villages producing a surname structure according to the geographic features of the territory
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
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
Ancestral European roots of Helicobacter pylori in India
<p>Abstract</p> <p>Background</p> <p>The human gastric pathogen <it>Helicobacter pylori </it>is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of <it>H. pylori </it>mirror ancient human migrations. Ancestral origins of <it>H. pylori </it>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 <it>H. pylori</it>. We tried to address these issues through mapping genetic origins of present day <it>H. pylori </it>in India and their genomic comparison with hundreds of isolates from different geographic regions.</p> <p>Results</p> <p>We attempted to dissect genetic identity of strains by multilocus sequence typing (MLST) of the 7 housekeeping genes (<it>atp</it>A, <it>efp</it>, <it>ure</it>I, <it>ppa</it>, <it>mut</it>Y, <it>trp</it>C, <it>yph</it>C) and phylogeographic analysis of haplotypes using MEGA and NETWORK software while incorporating DNA sequences and genotyping data of whole <it>cag </it>pathogenicity-islands (<it>cag</it>PAI). The distribution of <it>cag</it>PAI genes within these strains was analyzed by using PCR and the geographic type of <it>cag</it>A phosphorylation motif EPIYA was determined by gene sequencing. All the isolates analyzed revealed European ancestry and belonged to <it>H. pylori </it>sub-population, hpEurope. The <it>cag</it>PAI harbored by Indian strains revealed European features upon PCR based analysis and whole PAI sequencing.</p> <p>Conclusion</p> <p>These observations suggest that <it>H. pylori </it>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.</p
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