[Show abstract][Hide abstract] ABSTRACT: Factors affecting the rate and pattern of the mutational process are being identified for human autosomes, but the same relationships for the male specific portion of the Y chromosome (MSY) are not established. We considered 3,390 mutations occurring in 19 sequence bins identified by sequencing 1.5 Mb of the MSY from each of 104 present-day chromosomes. The occurrence of mutations was not proportional to the amount of sequenced bases in each bin, with a 2-fold variation. The regression of the number of mutations per unit sequence against a number of indicators of the genomic features of each bin, revealed the same fundamental patterns as in the autosomes. By considering the sequences of the same region from two precisely dated ancient specimens, we obtained a calibrated region-specific substitution rate of 0.716 × 10-9 /site/year. Despite its lack of recombination and other peculiar features, the MSY then resembles the autosomes in displaying a marked regional heterogeneity of the mutation rate. An immediate implication is that a given figure for the substitution rate only makes sense if bound to a specific DNA region. By strictly applying this principle we obtained an unbiased estimate of the antiquity of lineages relevant to the genetic history of the human Y chromosome. In particular, the two deepest nodes of the tree highlight the survival, in Central Western Africa, of lineages whose coalescence (291 ky, 95% C.I. 253–343) predates the emergence of anatomically modern features in the fossil record.
PLoS ONE 07/2015; 10(7). DOI:10.1371/journal.pone.0134646 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade
within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared to the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to 5 new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a SNP-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 kya. Time frames, phylogenetic structuring and socio-geographic distribution of E-V1515 and its subclades are consistent with a multi-step demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to sub-equatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry- informative markers.
[Show abstract][Hide abstract] ABSTRACT: The proportion of Europeans descending from Neolithic farmers ∼10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ∼2.1-4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.
[Show abstract][Hide abstract] ABSTRACT: Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51 ×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analysing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of non-synonymous variants in 15 MSY single-copy genes.
[Show abstract][Hide abstract] ABSTRACT: We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg) A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.
PLoS ONE 04/2014; 9(4):e95969. DOI:10.1371/journal.pone.0095969 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Two gene clusters are tightly linked in a narrow region of chromosome 22q11.23: the macrophage migration inhibitory factor (MIF) gene family and the glutathione S-transferase theta class. Within 120 kb in this region, two 30-kb deletions reach high frequencies in human populations. This gives rise to four haplotypic arrangements, which modulate the number of genes in both families. The variable patterns of linkage disequilibrium (LD) between these copy number variants (CNVs) in diverse human populations remain poorly understood. We analyzed 2469 individuals belonging to 27 human populations with different ethnic origins. Then we correlated the genetic variability of 22q11.23 CNVs with environmental variables. We confirmed an increasing strength of LD from Africa to Asia and to Europe. Further, we highlighted strongly significant correlations between the frequency of one of the haplotypes and pigmentation-related variables: skin color (R(2)=0.675, P<0.001), distance from the equator (R(2)=0.454, P<0.001), UVA radiation (R(2)=0.439, P<0.001), and UVB radiation (R(2)=0.313, P=0.002). The fact that all MIF-related genes are retained on this haplotype and the evidences gleaned from experimental systems seem to agree with the role of MIF-related genes in melanogenesis. As such, we propose a model that explains the geographic and ethnic distribution of 22q11.23 CNVs among human populations, assuming that MIF-related gene dosage could be associated with adaptation to low UV radiation.European Journal of Human Genetics advance online publication, 26 March 2014; doi:10.1038/ejhg.2014.47.
European journal of human genetics: EJHG 03/2014; 23(1). DOI:10.1038/ejhg.2014.47 · 4.35 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background: The APOE gene has received much attention due to the remarkable spatial variation patterns of some of its genotypes and alleles in human populations and to its relevance in biomedicine. Aim: This work was addressed to investigate the extent of APOE polymorphism between autochthonous Andalusians originating from Huelva and Granada provinces. No data on this marker in these southern Spanish coastal populations are available up to date. Subjects and methods: This study used genomic DNA from healthy, unrelated Andalusians of both sexes (n ¼ 322). All samples were genotyped for two SNPs, rs429358 and rs7412, which determine the three APOE alleles: "2, "3 and "4. For analyses, a TaqMan-based technique was applied using a RT-PCR. Comparisons with other Mediterranean populations were performed based on multivariate analysis. Results: A relatively high frequency of "4 in Granada (eastern Andalusia), as well as a low "2 frequency in Huelva (western Andalusia) were observed. The finding that "4 allele in Southern Spain and Portugal is higher than expected given its geographical location poses an interesting question for this study, given the well-established APOE-"4 gradient in Europe. Conclusion: This population study may represent useful information for further prospective anthropological and molecular genetic studies focused on unravelling the relationship between population genetic composition and specific human diseases.
Annals of Human Biology 02/2014; 4460:1464-5033. DOI:10.3109/03014460.2013.877966 · 1.27 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region.
The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population.
The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements from eastern Africa and southwestern Asia.
[Show abstract][Hide abstract] ABSTRACT: To clarify the population history of dentatorubropallidoluysian atrophy (DRPLA) in Italy and to date back the introduction of the mutation, we reconstructed extended haplotypes flanking the CAG repeat in 10 patients of Italian ancestry, analyzing their similarity/dissimilarity as a function of distance from the CAG repeat. Our aim was to compare the hypothesis of a single, recent genealogy connecting all the observed haplotypes with the alternative hypothesis of multiple introductions by more distantly related haplotypes from outer sources. Polymorphic DNA markers were chosen to cover a region of 153 kb flanking the CAG repeat, that is, informative for dating the age of the DNA segment unaffected by recombination. In all patients, an expansion of the ATN1 CAG segment was confirmed residing onto the same narrow haplotype described to be associated with the CAG expansion in the Japanese and Portuguese populations. We also observed the disruption of the DRPLA haplotype at longer distances, on both sides of the CAG. Our results are compatible with a single founder in the last 600 years, most likely before the last 270 years. These estimates for the Sicilian population largely overlap a period in which the Japanese haplotype with the DRPLA mutation could have been introduced by the Portuguese maritime travelers.Journal of Human Genetics advance online publication, 9 January 2014; doi:10.1038/jhg.2013.137.
Journal of Human Genetics 01/2014; 59(3). DOI:10.1038/jhg.2013.137 · 2.46 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The phylogeography of the paternally-inherited MSY has been the subject of intense research. However, sequence diversity and the ages of the deepest nodes of the phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next generation sequencing, including 18 deep-rooting ones, and identified 2,386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY a large proportion of newly arisen alleles have survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our MSY tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: 1) patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; 2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; 3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e. a period of our evolution which had been previously considered to be poorly accessible with paternally-inherited markers.
Genome Research 01/2014; 24(3). DOI:10.1101/gr.160788.113 · 14.63 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The green turtle (Chelonia mydas) is an occasional visitor of Italian waters. Nonetheless, its presence has been recorded in all Italian seas during the past decades. Genetic analysis coupled with satellite tracking of green turtles foraging in Italian waters has never been carried out, so far. We report here preliminary data about three individuals found dead or severely weakened on North Adriatic and South Tyrrhenian coasts in recent years (2006, 2011 and 2012). When analyzed for a 817 bp long fragment of the mitochondrial D-loop region, all of them turned out to carry haplotype CM-A13.1. This is indicative of an eastern-Mediterranean origin, narrowing the area of provenance of the three turtles to Turkey and Cyprus. Collection data indicated that active swimming juveniles (mean CCL of the animals: 45.67 ± 20.07 cm) frequent Italian coastal waters in warm periods, probably to feed on seagrass beds. The turtle stranded at Cetraro (Cosenza, South-Tyrrhenian Sea) has been rescued, rehabilitated and released after having been equipped with a satellite transmitter. The route followed by this juvenile, together with data from fishery bycatch, pointed to the Messina Strait as a strategic area for migrations and foraging of sea turtles. In addition, the importance of the North Adriatic for small and large Mediterranean individuals of Caretta caretta seems in part extendable also to C. mydas. Finally, the causes of death and injury observed for the green turtles here analyzed seem to be attributable to human coastal activities, as fishing and boat traffic.
II Congresso “Testuggini e tartarughe”, organizzato dalla SHI (Societas Herpetologica Italica), Chieti (Italy); 09/2013
[Show abstract][Hide abstract] ABSTRACT: Huntington's disease (HD) is a neurodegenerative disorder characterized by motor, cognitive, and behavioral disturbances. It is caused by the expansion of the HTT CAG repeat, which is the major determinant of age at onset (AO) of motor symptoms. Aberrant function of N-methyl-D-aspartate receptors and/or overexposure to dopamine has been suggested to cause significant neurotoxicity, contributing to HD pathogenesis. We used genetic association analysis in 1,628 HD patients to evaluate candidate polymorphisms in N-methyl-D-aspartate receptor subtype genes (GRIN2A rs4998386 and rs2650427, and GRIN2B rs1806201) and functional polymorphisms in genes in the dopamine pathway (DAT1 3' UTR 40-bp variable number tandem repeat (VNTR), DRD4 exon 3 48-bp VNTR, DRD2 rs1800497, and COMT rs4608) as potential modifiers of the disease process. None of the seven polymorphisms tested was found to be associated with significant modification of motor AO, either in a dominant or additive model, after adjusting for ancestry. The results of this candidate-genetic study therefore do not provide strong evidence to support a modulatory role for these variations within glutamatergic and dopaminergic genes in the AO of HD motor manifestations.
[Show abstract][Hide abstract] ABSTRACT: A putative hybrid sea turtle juvenile was evaluated with discriminant DNA markers. When compared with standard values for sea turtles, the general morphological features assigned the specimen to Caretta caretta, while the shape and coloration of the head and the beak profile fell within the Eretmochelys imbricata range; the front flippers were instead like those of a Chelonia mydas. Moreover, prefrontal scale number was outside the putative parental species' ranges. The mitochondrial D-loop sequence was from C. caretta, and matched haplotype CC-A2.1, the most common in the Mediterranean. Sequence profiles at three nuclear loci with species-specific substitutions (Cmos, BDNF and R35) revealed only C. caretta variants, thus excluding that the individual was an F1 hybrid. This study highlights the importance of integrating different methodological approaches to understand reproductive animal biology and to set the boundaries for specific morphological traits. In particular, we propose the genetic analysis of a new combination of mitochondrial and nuclear markers as a standard procedure which can be adopted in the identification of sea turtle hybrids.
[Show abstract][Hide abstract] ABSTRACT: Huntington's disease (HD) is an inherited neurodegenerative disorder characterized by motor, cognitive and behavioral disturbances, caused by the expansion of a CAG trinucleotide repeat in the HD gene. The CAG allele size is the major determinant of age at onset (AO) of motor symptoms, although the remaining variance in AO is highly heritable. The rs7665116 SNP in PPARGC1A, encoding the mitochondrial regulator PGC-1α, has been reported to be a significant modifier of AO in three European HD cohorts, perhaps due to affected cases from Italy. We attempted to replicate these findings in a large collection of (1,727) HD patient DNA samples of European origin. In the entire cohort, rs7665116 showed a significant effect in the dominant model (p value = 0.008) and the additive model (p value = 0.009). However, when examined by origin, cases of Southern European origin had an increased rs7665116 minor allele frequency (MAF), consistent with this being an ancestry-tagging SNP. The Southern European cases, despite similar mean CAG allele size, had a significantly older mean AO (p < 0.001), suggesting population-dependent phenotype stratification. When the generalized estimating equations models were adjusted for ancestry, the effect of the rs7665116 genotype on AO decreased dramatically. Our results do not support rs7665116 as a modifier of AO of motor symptoms, as we found evidence for a dramatic effect of phenotypic (AO) and genotypic (MAF) stratification among European cohorts that was not considered in previously reported association studies. A significantly older AO in Southern Europe may reflect population differences in genetic or environmental factors that warrant further investigation.
Human Genetics 07/2012; 131(12). DOI:10.1007/s00439-012-1205-z · 4.82 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Huntington's disease is a neurodegenerative disorder caused by an expanded CAG trinucleotide repeat whose length is the major determinant of age at onset but remaining variation appears to be due in part to the effect of genetic modifiers. GRIK2, which encodes GluR6, a mediator of excitatory neurotransmission in the brain, has been suggested in several studies to be a modifier gene based upon a 3' untranslated region TAA trinucleotide repeat polymorphism. Prior to investing in detailed studies of the functional impact of this polymorphism, we sought to confirm its effect on age at onset in a much larger dataset than in previous investigations. We genotyped the HD CAG repeat and the GRIK2 TAA repeat in DNA samples from 2,911 Huntington's disease subjects with known age at onset, and tested for a potential modifier effect of GRIK2 using a variety of statistical approaches. Unlike previous reports, we detected no evidence of an influence of the GRIK2 TAA repeat polymorphism on age at motor onset. Similarly, the GRIK2 polymorphism did not show significant modifier effect on psychiatric and cognitive age at onset in HD. Comprehensive analytical methods applied to a much larger sample than in previous studies do not support a role for GRIK2 as a genetic modifier of age at onset of clinical symptoms in Huntington's disease.
Biochemical and Biophysical Research Communications 07/2012; 424(3):404-8. DOI:10.1016/j.bbrc.2012.06.120 · 2.30 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Age at onset of diagnostic motor manifestations in Huntington disease (HD) is strongly correlated with an expanded CAG trinucleotide repeat. The length of the normal CAG repeat allele has been reported also to influence age at onset, in interaction with the expanded allele. Due to profound implications for disease mechanism and modification, we tested whether the normal allele, interaction between the expanded and normal alleles, or presence of a second expanded allele affects age at onset of HD motor signs.
We modeled natural log-transformed age at onset as a function of CAG repeat lengths of expanded and normal alleles and their interaction by linear regression.
An apparently significant effect of interaction on age at motor onset among 4,068 subjects was dependent on a single outlier data point. A rigorous statistical analysis with a well-behaved dataset that conformed to the fundamental assumptions of linear regression (e.g., constant variance and normally distributed error) revealed significance only for the expanded CAG repeat, with no effect of the normal CAG repeat. Ten subjects with 2 expanded alleles showed an age at motor onset consistent with the length of the larger expanded allele.
Normal allele CAG length, interaction between expanded and normal alleles, and presence of a second expanded allele do not influence age at onset of motor manifestations, indicating that the rate of HD pathogenesis leading to motor diagnosis is determined by a completely dominant action of the longest expanded allele and as yet unidentified genetic or environmental factors.
[Show abstract][Hide abstract] ABSTRACT: Age at the onset of motor symptoms in Huntington disease (HD) is determined largely by the length of a CAG repeat expansion in HTT but is also influenced by other genetic factors. We tested whether common genetic variation near the mutation site is associated with differences in the distribution of expanded CAG alleles or age at the onset of motor symptoms. To define disease-associated single-nucleotide polymorphisms (SNPs), we compared 4p16.3 SNPs in HD subjects with population controls in a case:control strategy, which revealed that the strongest signals occurred at a great distance from the HD mutation as a result of "synthetic association" with SNP alleles that are of low frequency in population controls. Detailed analysis delineated a prominent ancestral haplotype that accounted for ∼50% of HD chromosomes and extended to at least 938 kb on about half of these. Together, the seven most abundant haplotypes accounted for ∼83% of HD chromosomes. Neither the extended shared haplotype nor the individual local HTT haplotypes were associated with altered CAG-repeat length distribution or residual age at the onset of motor symptoms, arguing against modification of these disease features by common cis-regulatory elements. Similarly, the 11 most frequent control haplotypes showed no trans-modifier effect on age at the onset of motor symptoms. Our results argue against common local regulatory variation as a factor influencing HD pathogenesis, suggesting that genetic modifiers be sought elsewhere in the genome. They also indicate that genome-wide association analysis with a small number of cases can be effective for regional localization of genetic defects, even when a founder effect accounts for only a fraction of the disorder.
The American Journal of Human Genetics 03/2012; 90(3):434-44. DOI:10.1016/j.ajhg.2012.01.005 · 10.93 Impact Factor