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1.
Hum Mol Genet ; 32(1): 65-78, 2023 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-35921243

RESUMEN

The human MSY ampliconic region is mainly composed of large duplicated sequences that are organized in eight palindromes (termed P1-P8), and may undergo arm-to-arm gene conversion. Although the importance of these elements is widely recognized, their evolutionary dynamics are still nuanced. Here, we focused on the P8 palindrome, which shows a complex evolutionary history, being involved in intra- and inter-chromosomal gene conversion. To disclose its evolutionary complexity, we performed a high-depth (50×) targeted next-generation sequencing of this element in 157 subjects belonging to the most divergent lineages of the Y chromosome tree. We found a total of 72 polymorphic paralogous sequence variants that have been exploited to identify 41 Y-Y gene conversion events that occurred during recent human history. Through our analysis, we were able to categorize P8 arms into three portions, whose molecular diversity was modelled by different evolutionary forces. Notably, the outer region of the palindrome is not involved in any gene conversion event and evolves exclusively through the action of mutational pressure. The inner region is affected by Y-Y gene conversion occurring at a rate of 1.52 × 10-5 conversions/base/year, with no bias towards the retention of the ancestral state of the sequence. In this portion, GC-biased gene conversion is counterbalanced by a mutational bias towards AT bases. Finally, the middle region of the arms, in addition to intra-chromosomal gene conversion, is involved in X-to-Y gene conversion (at a rate of 6.013 × 10-8 conversions/base/year) thus being a major force in the evolution of the VCY/VCX gene family.


Asunto(s)
Cromosomas Humanos Y , Conversión Génica , Humanos , Conversión Génica/genética , Cromosomas Humanos Y/genética , Mutación , Evolución Molecular
2.
Hum Mol Genet ; 30(23): 2272-2285, 2021 11 16.
Artículo en Inglés | MEDLINE | ID: mdl-34244762

RESUMEN

About one-quarter of the euchromatic portion of the male-specific region of the human Y chromosome consists of large duplicated sequences that are organized in eight palindromes (termed P1-P8), which undergo arm-to arm gene conversion, a proposed mechanism for maintaining their sequence integrity. Although the relevance of gene conversion in the evolution of palindromic sequences has been profoundly recognized, the dynamic of this mechanism is still nuanced. To shed light into the evolution of these genomic elements, we performed a high-depth (50×) targeted next-generation sequencing of the palindrome P6 in 157 subjects belonging to the most divergent evolutionary lineages of the Y chromosome. We found 118 new paralogous sequence variants, which were placed into the context of a robust Y chromosome phylogeny based on 7240 SNPs of the X-degenerate region. We mapped along the phylogeny 80 gene conversion events that shaped the diversity of P6 arms during recent human history. In contrast to previous studies, we demonstrated that arm-to-arm gene conversion, which occurs at a rate of 6.01 × 10 -6 conversions/base/year, is not biased toward the retention of the ancestral state of sequences. We also found a significantly lower mutation rate of the arms (6.18 × 10-10 mutations/base/year) compared with the spacer (9.16 × 10-10 mutations/base/year), a finding that may explain the observed higher inter-species conservation of arms, without invoking any bias of conversion. Finally, by formally testing the mutation/conversion balance in P6, we found that the arms of this palindrome reached a steady-state equilibrium between mutation and gene conversion.


Asunto(s)
Cromosomas Humanos Y , Evolución Molecular , Conversión Génica , Secuencias Invertidas Repetidas , Mutación , Mapeo Cromosómico , Variación Genética , Humanos , Masculino , Tasa de Mutación , Filogenia
3.
BMC Biol ; 17(1): 3, 2019 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-30674303

RESUMEN

BACKGROUND: Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America. RESULTS: Our analyses of 1.5 Mb of 152 Y chromosomes, 34 re-sequenced in this work, support a "coastal and inland routes scenario" for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand years ago (kya), followed by a period of constant population size from 8 to 3 kya, after which a secondary sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainly revealed by haplogroup Q-Z780, suggest an entrance in South America prior to 15 kya. During the global constant population size phase, local South American hints of growth were registered by different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steady population growth and a single cohesive culture diffusion as it occurred in Europe. CONCLUSIONS: We established and dated a detailed haplogroup Q phylogeny that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.


Asunto(s)
Cromosomas Humanos Y , Variación Genética , Haplotipos , Indígenas Norteamericanos/genética , Polimorfismo de Nucleótido Simple , Población Blanca/genética , Américas , Europa (Continente) , Genética de Población , Humanos , Filogenia
4.
Hum Genet ; 136(5): 605-619, 2017 05.
Artículo en Inglés | MEDLINE | ID: mdl-28303348

RESUMEN

The presence of large and near-identical inverted repeat sequences (called palindromes) is a common feature of the constitutively haploid sex chromosomes of different species. Despite the fact palindromes originated in a non-recombining context, they have evolved a strong recombinational activity in the form of abundant arm-to-arm gene conversion. Their independent appearance in different species suggests they can have a profound biological significance that has yet to be fully clarified. It has been theorized that natural selection may have favored palindromic organization of male-specific genes and that the establishment of intra-palindrome gene conversion has strong adaptive significance. Arm-to-arm gene conversion allows the efficient removal of deleterious mutations, increases the fixation rate of beneficial mutations and has played an important role in modulating the equilibrium between gene loss and acquisition during Y chromosome evolution. Additionally, a palindromic organization of duplicates could favor the formation of unusual chromatin structures and could optimize the use of gene conversion as a mechanism to maintain the structural integrity of male-specific genes. In this review, we describe the structural features of palindromes on mammalian sex chromosomes and summarize different hypotheses regarding palindrome evolution and the functional benefits of arm-to-arm gene conversion on the unique haploid portion of the nuclear genome.


Asunto(s)
Cromosomas Humanos Y/genética , Conversión Génica , Inestabilidad Cromosómica , Evolución Molecular , Genoma Humano , Humanos , Secuencias Invertidas Repetidas , Masculino , Mutación , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN
5.
Genome Res ; 24(3): 535-44, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24395829

RESUMEN

Sequence diversity and the ages of the deepest nodes of the MSY 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 2386 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 has survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our 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; and (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 that had been previously considered to be poorly accessible with paternally inherited markers.


Asunto(s)
Población Negra/genética , Cromosomas Humanos Y/genética , Polimorfismo de Nucleótido Simple/genética , Cromosomas Humanos Y/clasificación , Evolución Molecular , Variación Genética , Genoma Humano , Humanos , Tasa de Mutación , Mutación Missense , Filogenia , Selección Genética , Análisis de Secuencia de ADN
6.
Mol Biol Evol ; 31(8): 2108-23, 2014 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-24817545

RESUMEN

It has long been believed that the male-specific region of the human Y chromosome (MSY) is genetically independent from the X chromosome. This idea has been recently dismissed due to the discovery that X-Y gametologous gene conversion may occur. However, the pervasiveness of this molecular process in the evolution of sex chromosomes has yet to be exhaustively analyzed. In this study, we explored how pervasive X-Y gene conversion has been during the evolution of the youngest stratum of the human sex chromosomes. By comparing about 0.5 Mb of human-chimpanzee gametologous sequences, we identified 19 regions in which extensive gene conversion has occurred. From our analysis, two major features of these emerged: 1) Several of them are evolutionarily conserved between the two species and 2) almost all of the 19 hotspots overlap with regions where X-Y crossing-over has been previously reported to be involved in sex reversal. Furthermore, in order to explore the dynamics of X-Y gametologous conversion in recent human evolution, we resequenced these 19 hotspots in 68 widely divergent Y haplogroups and used publicly available single nucleotide polymorphism data for the X chromosome. We found that at least ten hotspots are still active in humans. Hence, the results of the interspecific analysis are consistent with the hypothesis of widespread reticulate evolution within gametologous sequences in the differentiation of hominini sex chromosomes. In turn, intraspecific analysis demonstrates that X-Y gene conversion may modulate human sex-chromosome-sequence evolution to a greater extent than previously thought.


Asunto(s)
Cromosomas Humanos X/genética , Cromosomas Humanos Y/genética , Conversión Génica , Pan troglodytes/genética , Animales , Evolución Molecular , Femenino , Haplotipos , Humanos , Masculino , Filogenia , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN , Cromosoma X/genética , Cromosoma Y/genética
7.
Am J Hum Genet ; 88(6): 814-818, 2011 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-21601174

RESUMEN

To shed light on the structure of the basal backbone of the human Y chromosome phylogeny, we sequenced about 200 kb of the male-specific region of the human Y chromosome (MSY) from each of seven Y chromosomes belonging to clades A1, A2, A3, and BT. We detected 146 biallelic variant sites through this analysis. We used these variants to construct a patrilineal tree, without taking into account any previously reported information regarding the phylogenetic relationships among the seven Y chromosomes here analyzed. There are several key changes at the basal nodes as compared with the most recent reference Y chromosome tree. A different position of the root was determined, with important implications for the origin of human Y chromosome diversity. An estimate of 142 KY was obtained for the coalescence time of the revised MSY tree, which is earlier than that obtained in previous studies and easier to reconcile with plausible scenarios of modern human origin. The number of deep branchings leading to African-specific clades has doubled, further strengthening the MSY-based evidence for a modern human origin in the African continent. An analysis of 2204 African DNA samples showed that the deepest clades of the revised MSY phylogeny are currently found in central and northwest Africa, opening new perspectives on early human presence in the continent.


Asunto(s)
Cromosomas Humanos Y/clasificación , Cromosomas Humanos Y/genética , Filogenia , África , Alelos , Variación Genética , Humanos , Masculino , Análisis de Secuencia de ADN
8.
Sci Rep ; 13(1): 11857, 2023 07 22.
Artículo en Inglés | MEDLINE | ID: mdl-37481605

RESUMEN

The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , Infertilidad Masculina , Humanos , Masculino , Cromosomas Humanos Y/genética , Incidencia , Infertilidad Masculina/genética , Irán , Azoospermia/genética
9.
Curr Biol ; 33(24): 5495-5504.e4, 2023 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-37995693

RESUMEN

The population history of the Sahara/Sahelian belt is understudied, despite previous work highlighting complex dynamics.1,2,3,4,5,6,7 The Sahelian Fulani, i.e., the largest nomadic pastoral population in the world,8 represent an interesting case because they show a non-negligible proportion of an Eurasian genetic component, usually explained by recent admixture with northern Africans.1,2,5,6,7,9,10,11,12 Nevertheless, their origins are largely unknown, although several hypotheses have been proposed, including a possible link to ancient peoples settled in the Sahara during its last humid phase (Green Sahara, 12,000-5,000 years before present [BP]).13,14,15 To shed light about the Fulani ancient genetic roots, we produced 23 high-coverage (30×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 from Europeans as controls, for a total of 43 new whole genomes. These data have been compared with 814 published modern whole genomes2,16,17,18 and with relevant published ancient sequences (> 1,800 samples).19 These analyses showed some evidence that the non-sub-Saharan genetic ancestry component of the Fulani might have also been shaped by older events,1,5,6 possibly tracing the Fulani origins to unsampled ancient Green Saharan population(s). The joint analysis of modern and ancient samples allowed us to shed light on the genetic ancestry composition of such ancient Saharans, suggesting a similarity with Late Neolithic Moroccans and possibly pointing to a link with the spread of cattle herding. We also identified two different Fulani clusters whose admixture pattern may be informative about the historical Fulani movements and their later involvement in the western African empires.


Asunto(s)
Población Negra , Genética de Población , Genómica , Humanos , África del Norte , Población Negra/genética
10.
Forensic Sci Int Genet ; 61: 102755, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-35985094

RESUMEN

Y chromosome short tandem repeats (Y-STRs) typing is becoming increasingly popular in forensic casework mainly because it allows the recovery of male-specific genetic information from severely unbalanced male-female DNA mixtures. The relatively low discrimination power of conventional Y-STR multiplexes, due to linkage disequilibrium among polymorphic loci, has been partially overcome by the introduction of rapidly mutating Y microsatellites (RM Y-STRs) with mutation rates exceeding 1 × 10-2/generation. In previous works, we reported an unexpectedly high level of haplotype sharing among African males using the Yfiler Plus PCR Amplification kit, the most powerful commercially available system, including 19 conventional Y-STRs and 6 RM Y-STRs. In particular, analyzing 1370 males from northern, eastern and central Africa, 240 subjects were found to share 100 Y-STR haplotypes. We attributed the relatively low discrimination capacity to several factors including patrilocality, endogamy, sampling bias and degree of urbanization. In the present study, using a blind search analysis based on 16 autosomal STRs, we first investigated the kinship between pairs of African males previously found to share the Yfiler Plus haplotype; then, we evaluated the improvement in identification capacity allowed by a PCR multiplex assay (RM-YPlex) based on 13 "first generation" RM Y-STR, seven of which are not included in the Yfiler Plus multiplex. Among 228 pairs of males sharing a Yfiler Plus haplotype, we detected 134 related (cousins or closer) and 94 unrelated (or distantly related) pairs of subjects. By using the RM-YPlex, we observed a full genotype concordance for the six loci shared with the Yfiler Plus, while the additional seven RM Y-STRs allowed the discrimination among 58.2 % related pairs and 84.0 % unrelated pairs. The discrimination capacity increased from 0.898 to 0.958, while the proportion of males sharing a haplotype decreased from 17.5 % to 8.0 %. These findings further highlight the capability of RM Y-STRs to distinguish males even in close kinship scenarios and in sub-structured populations as African ones, but at the same time call for the discovery and testing of additional RM Y-STRs to fully differentiate male relatives.


Asunto(s)
Cromosomas Humanos Y , Dermatoglifia del ADN , Humanos , Masculino , Femenino , Repeticiones de Microsatélite , Haplotipos , ADN/análisis , Genética de Población
11.
Mol Biol Evol ; 27(3): 714-25, 2010 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-19812029

RESUMEN

Different X-homologous regions of the male-specific portion of the human Y chromosome (MSY) are characterized by a different content of putative single nucleotide polymorphisms (SNPs), as reported in public databases. The possible role of X-to-Y nonallelic gene conversion in contributing to these differences remains poorly understood. We explored this issue by analyzing sequence variation in three regions of the MSY characterized by a different degree of X-Y similarity and a different density of putative SNPs: the PCDH11Y gene in the X-transposed (X-Y identity 99%, high putative SNP content); the TBL1Y gene in the X-degenerate (X-Y identity 86-88%, low putative SNP content); and VCY genes-containing region in the P8 palindrome (X-Y identity 95%, low putative SNP content). Present findings do not provide any evidence for gene conversion in the PCDH11Y and TBL1Y genes; they also strongly suggest that most putative SNPs of the PCDH11Y gene (and possibly the entire X-transposed region) are most likely X-Y paralogous sequence variants, which have been entered in the databases as SNPs. On the other hand, clear evidence for the VCY genes in the P8 palindrome having acted as an acceptor of X-to-Y gene conversion was obtained. A rate of 1.8 x 10(-7) X-to-Y conversions/bp/year was estimated for these genes. These findings indicate that in the VCY region of the MSY, X-to-Y gene conversion can be highly effective to increase the level of diversity among human Y chromosomes and suggest an additional explanation for the ability of the Y chromosome to retard degradation during evolution. Present data are expected to pave the way for future investigations on the role of nonallelic gene conversion in double-strand break repair and the maintenance of Y chromosome integrity.


Asunto(s)
Cromosomas Humanos X/genética , Cromosomas Humanos Y/genética , Análisis Mutacional de ADN/métodos , Evolución Molecular , Conversión Génica , Cadherinas/genética , Cromosomas Humanos X/química , Cromosomas Humanos Y/química , Humanos , Proteínas Nucleares/genética , Polimorfismo de Nucleótido Simple , Protocadherinas , Homología de Secuencia de Ácido Nucleico , Transducina/genética
12.
Proc Natl Acad Sci U S A ; 105(31): 10693-8, 2008 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-18678889

RESUMEN

Although geneticists have extensively debated the mode by which agriculture diffused from the Near East to Europe, they have not directly examined similar agropastoral diffusions in Africa. It is unclear, for example, whether early instances of sheep, cows, pottery, and other traits of the pastoralist package were transmitted to southern Africa by demic or cultural diffusion. Here, we report a newly discovered Y-chromosome-specific polymorphism that defines haplogroup E3b1f-M293. This polymorphism reveals the monophyletic relationship of the majority of haplotypes of a previously paraphyletic clade, E3b1-M35*, that is widespread in Africa and southern Europe. To elucidate the history of the E3b1f haplogroup, we analyzed this haplogroup in 13 populations from southern and eastern Africa. The geographic distribution of the E3b1f haplogroup, in association with the microsatellite diversity estimates for populations, is consistent with an expansion through Tanzania to southern-central Africa. The data suggest this dispersal was independent of the migration of Bantu-speaking peoples along a similar route. Instead, the phylogeography and microsatellite diversity of the E3b1f lineage correlate with the arrival of the pastoralist economy in southern Africa. Our Y-chromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa approximately 2,000 years ago.


Asunto(s)
Agricultura/historia , Cromosomas Humanos Y/genética , Demografía , Emigración e Inmigración/historia , Genética de Población , Cromatografía Líquida de Alta Presión , Genotipo , Haplotipos/genética , Historia Antigua , Humanos , Masculino , Repeticiones de Microsatélite/genética , Modelos Genéticos , Polimorfismo de Nucleótido Simple/genética , Tanzanía
13.
Front Genet ; 12: 669405, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33936180

RESUMEN

The azoospermia factor c region (AZFc), located in the long arm of the human Y chromosome, is frequently involved in chromosome rearrangements, mainly due to non-allelic homologous recombination events that occur between the nearly identical sequences (amplicon) that comprises it. These rearrangements may have major phenotypic effects like spermatogenic failure or other pathologies linked to male infertility. Moreover, they may also be relevant in forensic genetics, since some of the Y chromosome short tandem repeats (Y-STRs) commonly used in forensic analysis are located in amplicons or in inter-amplicon sequences of the AZFc. In a previous study, we identified four phylogenetically related samples with a null allele at DYS448 and a tetrallelic pattern at DYF387S1, two Y-STRs located in the AZFc. Through NGS read depth analysis, we found that the unusual Y-STR pattern may be due to a 1.6 Mb deletion arising concurrently or after a 3.5 Mb duplication event. The observed large genomic rearrangement results in copy number reduction for the RBMY gene family as well as duplication of other AZFc genes. Based on the diversity of 16 additional Y-STRs, we estimated that the duplication/deletion event occurred at least twenty generations ago, suggesting that it has not been affected by negative selection.

14.
Genome Biol Evol ; 12(9): 1579-1590, 2020 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-32835369

RESUMEN

The Dominican Republic is one of the two countries on the Hispaniola island, which is part of the Antilles. Hispaniola was affected by the European colonization and massive deportation of African slaves since the XVI century and these events heavily shaped the genetic composition of the present-day population. To shed light about the effect of the European rules, we analyzed 92 single nucleotide polymorphisms on the Y chromosome in 182 Dominican individuals from three different locations. The Dominican Y haplogroup composition was characterized by an excess of northern African/European lineages (59%), followed by the African clades (38%), whereas the Native-American lineages were rare (3%). The comparison with the mitochondrial DNA variability, dominated by African clades, revealed a sex-biased admixture pattern, in line with the colonial society dominated by European men. When other Caribbean and non-Caribbean former colonies were also considered, we noted a difference between territories under a Spanish rule (like the Dominican Republic) and British/French rule, with the former characterized by an excess of European Y lineages reflecting the more permissive Iberian legislation about mixed people and slavery. Finally, we analyzed the distribution in Africa of the Dominican lineages with a putative African origin, mainly focusing on central and western Africa, which were the main sources of African slaves. We found that most (83%) of the African lineages observed in Santo Domingo have a central African ancestry, suggesting that most of the slaves were deported from regions.


Asunto(s)
Cromosomas Humanos Y , Migración Humana , Grupos Raciales/genética , República Dominicana , Variación Genética , Haplotipos , Humanos , Masculino
15.
Forensic Sci Int Genet ; 49: 102374, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-32890883

RESUMEN

Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country (ΦST = 0.14) largely exceeded that found among countries (ΦST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches.


Asunto(s)
Cromosomas Humanos Y , Etnicidad/genética , Genética de Población , Haplotipos , Repeticiones de Microsatélite , Urbanización , Camerún , Chad , Dermatoglifia del ADN , Humanos , Masculino , Polimorfismo de Nucleótido Simple
16.
Forensic Sci Int Genet ; 45: 102209, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31812099

RESUMEN

DNA typing and genetic profile data interpretation are among the most relevant topics in forensic science; among other applications, genetic profile's capability to distinguish biogeographic information about population groups, subgroups and affiliations have been largely explored in the last decade. In fact, for investigative and intelligence purposes, it is extremely useful to identify subjects and estimate their biogeographic origins by examining the recovered DNA profiles from evidence on a crime scene. Current approaches for BiogeoGraphic Ancestry (BGA) estimation using STRs profiles are usually based on Bayesian methods, which quantify the evidence in terms of likelihood ratio, supporting or not the hypothesis that a certain profile belongs to a specific ethnic group. The present study provides an alternative approach to the likelihood ratio method that involves multivariate data analysis strategies for the estimation of multiple populations. Starting from the well-known NIST US autosomal STRs dataset involving African-American, Asian, and Caucasian individuals, and moving towards further and more geographically restricted populations (such as Northern Africans vs sub-Saharan Africans, Afghans vs Iraqis and Italians vs Romanians), powerful multivariate techniques such as Sparse and Logistic Principal Component Analysis (SL-PCA), Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) and Support Vector Machines (SVM) were employed and their discriminating power was also compared. Both sPLS-DA and SVM techniques provided robust classifications, yielding high sensitivity and specificity models capable of discriminating populations on ethnic basis. This application may represent a powerful and dynamic tool for law enforcement agencies whenever a standard autosomal STR profile is obtained from the biological evidence collected at a crime scene or recovered during mass-disaster and missing person investigations.


Asunto(s)
Dermatoglifia del ADN/métodos , Perfil Genético , Repeticiones de Microsatélite , Grupos Raciales/genética , Análisis Discriminante , Genética Forense/métodos , Marcadores Genéticos , Genética de Población , Genotipo , Humanos , Análisis de los Mínimos Cuadrados , Análisis de Componente Principal , Máquina de Vectores de Soporte
17.
Forensic Sci Int Genet ; 38: 185-194, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-30419518

RESUMEN

The male-specific northern African genetic pool is characterised by a high frequency of the E-M81 haplogroup, which expanded in very recent times (2-3 kiloyears ago). As a consequence of their recent coalescence, E-M81 chromosomes often cannot be completely distinguished on the basis of their Y-STR profiles, unless rapidly-mutating Y-STRs (RM Y-STRs) are analysed. In this study, we used the Yfiler® Plus kit, which includes 7 RM Y-STRs and 20 standard Y-STR, to analyse 477 unrelated males coming from 11 northern African populations sampled from Morocco, Algeria, Libya and Egypt. The Y chromosomes were assigned to monophyletic lineages after the analysis of 72 stable biallelic polymorphisms and, as expected, we found a high proportion of E-M81 subjects (about 46%), with frequencies decreasing from west to east. We found low intra-population diversity indexes, in particular in the populations that experienced long-term isolation. The AMOVA analysis showed significant differences between the countries and between most of the 11 populations, with a rough differentiation between northwestern Africa and northeastern Africa, where the Egyptians Berbers from Siwa represented an outlier population. The comparison between the Yfiler® and the Yfiler® Plus network of the E-M81 Y chromosomes confirmed the high power of discrimination of the latter kit, thanks to higher variability of the RM Y-STRs: indeed, the number of chromosomes sharing the same haplotype was drastically reduced from 201 to 81 and limited, in the latter case, to subjects from the same population.


Asunto(s)
Cromosomas Humanos Y , Genética de Población , Repeticiones de Microsatélite , Reacción en Cadena de la Polimerasa/instrumentación , Polimorfismo de Nucleótido Simple , África del Norte , Población Negra/genética , Dermatoglifia del ADN , Genotipo , Haplotipos , Humanos , Masculino
18.
Eur J Hum Genet ; 16(12): 1526-34, 2008 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-18575464

RESUMEN

Period 2 (PER2) is a key component of the mammalian circadian clock machinery. In humans, genetic variation of clock genes or chronic disturbance of circadian rhythmicity has been implied in the onset of several phenotypes, ranging from periodic insomnias to advanced or delayed sleep phases, to more severe disorders. Peculiar geographic diversity patterns in circadian genes might represent an adaptive response to different light/dark cycles or environmental changes to which different human populations are exposed. To investigate the degree and nature of PER2 gene variation in human populations of different geographic origin, and its possible correlation with different latitudes, we sequenced a 7.7 kb portion of the gene in 20 individuals worldwide. In total, 25 variable sites were identified. The geographic distribution of haplotypes defined by five polymorphic sites was analyzed in 499 individuals from 11 populations from four continents. No evidence for latitude-driven selective effects on PER2 genetic variability was found. However, a high and significant difference in the geographic distribution of PER2 polymorphisms was observed between Africans and non-Africans, suggesting a history of geographically restricted natural selection at this locus. In support of this notion, we found several signals for selection in the sequences. The putative selected haplotype showed a recent coalescent age (8.7 Kyr), and an unusually high frequency in non-African populations. Overall, these findings indicate that a human clock-relevant gene, PER2, might have been influenced by positive selection, and offer preliminary insights into the evolution of this functional class of genes.


Asunto(s)
Variación Genética/fisiología , Proteínas Nucleares/genética , Grupos de Población/genética , Selección Genética , Factores de Transcripción/genética , África , Américas , Asia , Relojes Biológicos/genética , Europa (Continente) , Frecuencia de los Genes , Genotipo , Humanos , Indígenas Norteamericanos/genética , Oceanía , Proteínas Circadianas Period , Filogenia
20.
Am J Hum Biol ; 20(5): 614-6, 2008.
Artículo en Inglés | MEDLINE | ID: mdl-18449920

RESUMEN

In a previous issue of AJHB, Fernandes et al. (2008. Am J Hum Biol 20:185-190.) describe instances of identity by state at multiple short tandem repeat loci between human Y chromosomes belonging to different E-M35 sub-haplogroups. They interpret these findings as evidence for multiple mutational events in at least two loci (M78 and M81). Here, we introduce a novel polymorphic marker (V68), potentially useful to investigate the issue. This marker and sequence data, reported here for the first time, reinforce our previous interpretations on the phylogenetic structure of the E3b haplogroup. We discuss these results in the frame of general approaches to attain robust phylogenetic inferences based on biallelic polymorphism data.


Asunto(s)
Cromosomas Humanos Y/genética , Mutación , Polimorfismo de Nucleótido Simple , Población Negra/genética , Marcadores Genéticos , Haplotipos , Humanos , Masculino , Repeticiones de Microsatélite , Filogenia
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