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Locomotion performance in reptiles is deeply associated with habitat use, escape from predators, prey capture, and territory defense. As ectotherms, this trait in lizards is extremely sensitive to body temperature (BT). However, most studies rarely look at locomotion patterns in an ontogenic perspective. The Moorish gecko, Tarentola mauritanica, was used to investigate the possible effects of distinct BTs on the locomotor performance within juveniles and adults. Not surprisingly, adult individuals significantly outperform the juveniles in speed at every BT. Moreover, except in the 30-day-old juveniles, there is a general trend for an increase of speed with BT. The comparison of these speed values with the ones obtained for diurnal lizard species, corroborates the premise that because nocturnal species are subject to low thermal heterogeneity, little selection for behavioral thermoregulation, but strong selection for high performance at relatively cool temperatures are expected. Furthermore, the higher locomotor performance in adults at 29°C, roughly coincides with previously obtained preferred BTs. However, further studies need to be conducted to build the full performance curve, and to validate the existence of coadaption between behavioral thermoregulation and thermal sensitivity of physiological performance. Finally, this study has found that adult males run significantly faster than females at the highest BTs, highlighting the importance in understanding sex differences, and its potential to drive sex-specific behaviors, ecology, and ultimately fitness.

Similar to other South American regions, Tierra del Fuego has an admixed population characterized by distinct ancestors: Native Americans who first occupied the continent, European settlers who arrived from the late 15th century onwards, and Sub-Saharan Africans who were brought to the Americas for slave labor. To disclose the paternal lineages in the current population from Tierra del Fuego, 196 unrelated males were genotyped for 23 Y-STRs and 52 Y-SNPs. Haplotype and haplogroup diversities were high, indicating the absence of strong founder or drift events. A high frequency of Eurasian haplogroups was detected (94.4%), followed by Native American (5.1%) and African (0.5%) ones. The haplogroup R was the most abundant (48.5%), with the sub-haplogroup R-S116* taking up a quarter of the total dataset. Comparative analyses with other Latin American populations showed similarities with other admixed populations from Argentina. Regarding Eurasian populations, Tierra del Fuego presented similarities with Italian and Iberian populations. In an in-depth analysis of the haplogroup R-M269 and its subtypes, Tierra del Fuego displayed a close proximity to the Iberian Peninsula. The results from this study are in line with the historical records and reflect the severe demographic change led mainly by male newcomers with paternal European origin.

San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise FST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions. We thank all sample donors for their contribution to this work and all the people who helped with sample collection, namely, Regina Miranda from the Community of San Basilio de Palenque, the personnel of the Benkos Biojó Rural school, and Miguel Obeso from the etnoeducación program. This work was supported by the University of Cartagena and FPIT—Fundación para la promoción de la investigación y la tecnología del Banco de la República, Colombia (FPIT-388) and partially financed by FEDER—Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT—Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Inovação in the framework of the projects “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274). FS was supported by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro—FAPERJ (E-26/202.275/2019). LG was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico—CNPq (ref. 306342/2019-7), and Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro—FAPERJ (CNE-2018). VG was supported by FCT, under the program contract provided in Decree-Law no.57/2016 of August 29. The IPATIMUP integrates the i3S research unit, which is partially supported by the Portuguese Foundation for Science and Technology.

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

COMPETE 2020. POCI-01-0145-FEDER-007274 to i3S. Submitted by Maria da Luz Antunes (mluz.antunes@estesl.ipl.pt) on 2019-08-27T10:17:35Z No. of bitstreams: 1 Unusual β-globin haplotype distribution in newborns from Bengo, Angola.pdf: 1300567 bytes, checksum: 707e68d119bc13ff44b0bde94b8ffabc (MD5) Made available in DSpace on 2019-08-27T10:17:35Z (GMT). No. of bitstreams: 1 Unusual β-globin haplotype distribution in newborns from Bengo, Angola.pdf: 1300567 bytes, checksum: 707e68d119bc13ff44b0bde94b8ffabc (MD5) Previous issue date: 2019-08 info:eu-repo/semantics/publishedVersion

To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures of Sub-Saharan (5.2%), European (3.45%) and Asiatic (1.33%) contributions. The remarkable frequency of T-M70 in Wesletia (17.4%) prompted to refine its phylogeographic analysis, allowing to confirm its Middle Eastern origin, though signs of local evolution in Northern Africa were also detected. Evidence was clear on the ancient introduction of T lineages into the region, probably since Neolithic times associated to spread of agriculture.

Made available in DSpace on 2020-12-12T00:58:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01 Anaesthetics Research Society The use of Y-chromosomal genetic markers in forensic investigations demands the establishment of reliable and representative DNA databases of different reference populations. The genetic characterization of the Y chromosome variation in human populations requires the analyses of haplotype frequencies allied to haplogroup determination. The present study aimed to contribute to the Brazilian database by providing 1,382 Yfiler Plus individual profiles, from 11 Brazilian states. The Yfiler Plus markers showed high haplotype diversities in all Brazilian populations (>0.9970), allowing high intra-population discrimination in forensic investigations. Pairwise genetic distances showed a homogeneity between Brazilian populations (FST ≤ 0.0043; non-differentiation p-values ≥ 0.0212), indicating that admixed populations from Brazil can be represented in a single Yfiler Plus haplotype database, for forensic purposes. The performance of Haplogroup Predictor and NevGen software in haplogroup prediction based on Yfiler Plus and Yfiler haplotypes was evaluated in a subset of 416 Brazilian samples that were also genotyped for 51 Y-SNPs. In 25% of the samples, no classification or errors were found for at least one of the prediction tools or marker sets. NevGen presented lower error rates (5.52% and 8.65% with Yfiler Plus and Yfiler, respectively) than Haplogroup Predictor (16.11% with Yfiler Plus and 13.70% with Yfiler). In conclusion, both haplogroup prediction tools can be useful to direct the SNP typing, but present large error rates to be used in forensic analysis, especially in predicting African haplogroups in admixed South American populations. DNA Diagnostic Laboratory (LDD) State University of Rio de Janeiro (UERJ) Laboratory of Human and Molecular Genetics Pontifícia Universidade Católica do Rio Grande do Sul Laboratório de Biologia e DNA Forense Superintendência de Polícia Técnico-Científica do Estado de Goiás UNESP-Universidade Estadual Paulista Faculdade de Ciências Farmacêuticas Laboratório de Investigação de Paternidade-NAC Coordenadoria de Perícias em Biologia Molecular POLITEC – Perícia Oficial e Identificação Técnica Faculdade Pitágoras Departamento de Medicina Legal Ética Médica e Medicina Social e do Trabalho da Faculdade de Medicina da USP Universidade de São Paulo (USP) IPATIMUP-Institute of Pathology and Molecular Immunology from the University of Porto I3S-Instituto de Investigação e Inovação em Saúde Universidade do Porto Postgraduate Program in Genetics and Molecular Biology Laboratory of Human and Medical Genetics Federal University of Pará Secretaria de Defesa Social Pernambuco Serviço de Endocrinologia e Metabologia do Hospital Universitário da Universidade Federal do Maranhão UNESP-Universidade Estadual Paulista Faculdade de Ciências Farmacêuticas Laboratório de Investigação de Paternidade-NAC Anaesthetics Research Society: 304413/2015-1

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample., Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.

Brazil has a large territory divided in five geographical regions harboring highly diverse populations that resulted from different degrees and modes of admixture between Native Americans, Europeans and Africans. In this study, a sample of 605 unrelated males was genotyped for 17 Y-STRs and 46 Y-SNPs aiming a deep characterization of the male gene pool of Rio de Janeiro and its comparison with other Brazilian populations. High values of Y-STR haplotype diversity (0.9999±0.0001) and Y-SNP haplogroup diversity (0.7589±0.0171) were observed. Population comparisons at both haplotype and haplogroup levels showed significant differences between Brazilian South Eastern and Northern populations that can be explained by differences in the proportion of African and Native American Y chromosomes. Statistical significant differences between admixed urban samples from the five regions of Brazil were not previously detected at haplotype level based on smaller size samples from South East, which emphasizes the importance of sample size to detected population stratification for an accurate interpretation of profile matches in kinship and forensic casework. Although not having an intra-population discrimination power as high as the Y-STRs, the Y-SNPs are more powerful to disclose differences in admixed populations. In this study, the combined analysis of these two types of markers proved to be a good strategy to predict population sub-structure, which should be taken into account when delineating forensic database strategies for Y chromosome haplotypes.

Y chromosome markers have been widely studied due to their various applications in the fields of forensic and evolutionary genetics. In this study, 35 Y-SNPs and 17 Y-STRs were genotyped in 253 males from the State of Espirito Santo, Brazil. A total of 18 haplogroups and 243 haplotypes were detected; the haplogroup and haplotype diversities were 0.7794 and 0.9997, respectively. Genetic distance analysis using the Y-STR data showed no statistically significant differences between Espirito Santo and other admixed populations from Brazil. The classification of paternal lineages based on haplogroups showed a predominant European contribution (85.88 %), followed by African (11.37 %) and Amerindian (2.75 %) contributions.

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material—including other animal species, plants, or microorganisms—is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities. MA, FP, MO, NP, AML and VG are supported by the Portuguese Foundation for Science and Technology (FCT), European RegionalDevelopment Fund (ERDF) and Programa Operacional Potencial Humano,through the grants IF/00955/2014, IF/01356/2012, SFRH/BPD/66071/2009, SFRH/BPD/97414/2013, IF/01262/2014 and SFRH/BPD/76207/2011, respectively. MA was also supported by the “Ramón y Cajal” grant RYC-2015-18241 from the Spanish Government. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT. The funders had no role in the preparation of the article.

The Y-STRs have high mutation rates, being useful to discriminate unrelated males. They are widely used in paternity and forensic investigations to study the recent history and migration movements of populations. Recently, the YfilerPlus was released to increase discrimination inside populations, by adding 9 Y-STRs to the previous Yfiler version. The genetic composition of Brazil is known to vary through 5 geopolitical regions: South, Southeast, North, Northeast and Central-west. Therefore, for this study, samples from Maranhao, Espirito Santo, Sao Paulo and Rio Grande do Sul were characterized for the Y-STR markers present in YfilerPlus kit, to evaluate if diversity increases with the enlargement of the Yfiler set, and if significant differences exists among populations. Genetic differentiation analysis did not reveal statistically significant differences in the YfilerPlus haplotype composition of the studied samples. High diversities were observed in all samples for both Yfiler and YfilerPlus marker sets. Inside populations, 20 haplotypes were shared by two individuals for the Yfiler-STRs. This number decreases to 14 when using the 25 Y-STRs from the YfilerPlus. The YfilerPlus demonstrated an increased discrimination power in comparison to the Yfiler kit, being suitable for forensic applications in the studied Brazilian populations, for which data were not yet available.

In this work 118 Nilote male samples were genotyped from Karamoja region, in Northeast Uganda, through 17 Y-chromosomal short tandem repeats (STRs)-DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. A total of 94 different haplotypes were found, where 19 were shared by at least two individuals, and haplotype diversity amounted to 0.9958+/-0.0017. When considering only the nine Y-STRs included in the minimal haplotype (YHRD) the haplotype diversity decreased to 0.9807+/-0.0048, a similar value to those found in other African populations such as Mozambique, Angola and Guinea-Bissau. Population comparisons were performed between our sample and nine other African populations. Significant R(st) genetic distances were obtained between the Nilote population from Karamoja and all African populations used for comparison, except Xhosa sample from South Africa. In the multidimensional scaling (MDS) plot, the Karamoja sample is well separated from all other populations, standing between the Ethiopia and the Bantu samples, although closer to this last group.

The most significant and widely studied remodeling of the African genetic landscape is the Bantu expansion, which led to an almost total replacement of the previous populations from the sub-Saharan region. However, a poor knowledge exists about other population movements, namely, the Nilotic migration, which is a pastoralist dispersal that, contrary to the Bantu expansion, impacted only East African populations. Here, samples from a Ugandan Nilotic-speaking population were studied for 37 Y chromosome-specific SNPs, and the obtained data were compared with those already available for other sub-Saharan population groups. Although Uganda lies on the fringe of both Bantu and Nilotic expansions, a low admixture with Bantu populations was detected, with haplogroups carrying M13, M182 and M75 mutations prevailing in Nilotes together with a low frequency of the main Bantu haplogroups from clade E1b1a-M2. The results of a comparative analysis with data from other population groups allowed a deeper characterization of some lineages in our sample, clarifying some doubts about the origin of some particular Y-SNPs in different ethnic groups, such as M150, M112 and M75. Moreover, it was also possible to identify a new Y-SNP apparently specific to Nilotic groups, as well as the presence of particular haplogroups that characterize Nilotic populations. The detection of a new haplogroup B2a1b defined by G1, could be, therefore, important to differentiate Nilotes from other groups, helping to trace migration and admixture events that occurred in eastern Africa.

In this study, 123 unrelated Portuguese Gypsies were analyzed for 15 highly polymorphic autosomal short tandem repeats (STRs). Average gene diversity across the 15 markers was 76.7%, which is lower than that observed in the non-Gypsy Portuguese population. Subsets of STRs were used to perform comparisons with other Gypsy and corresponding host populations. Interestingly, diversity reduction in Gypsy groups compared to their non-Gypsy surrounding populations apparently varied according to an East-West gradient, which parallels their dispersion in Europe as well as a decrease in complexity of their internal structure. Analysis of genetic distances revealed that the average level of genetic differentiation between Gypsy groups was much larger than that observed between the corresponding non-Gypsy populations. The high rate of heterogeneity among Gypsies can be explained by strong genetic drift and limited intergroup gene flow. However, when genetic relationships were addressed through principal component analysis, all Gypsy populations clustered together and was clearly distinguished from other populations, a pattern that suggests their common origin. Concerning the putative ancestral genetic component, admixture analysis did not reveal strong Indian ancestry in the current Gypsy gene pools, in contrast to the high admixture estimates for either Europeans or Western Asians.

Karamoja is a region located in the northeast edge of Uganda where it borders Kenya and Sudan. The majority of inhabitants of this region belong to Karimojong ethnic groups. In this work, we present allele frequencies for 15 STRs included in the AmpF/STR Identifiler kit (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) in 218 unrelated individuals from Karamoja region. Observed genotype distributions for each locus do not show deviations from Hardy-Weinberg equilibrium expectations. When comparing allele frequencies, for each locus, with other five African samples (Equatorial Guinea, Mozambique, Cabinda (Angola), Rwanda and Tanzania) the only population that did not show significant differences with Karamoja (Uganda) was Rwanda.

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago., This study was supported by Fundacao para a Ciencia e Tecnologia (FCT) and co-financed by the European Social Fund (Human Potential Thematic Operational Programme) through grants SFRH/BPD/76207/2011 (VG) and SFRH/BPD/81986/2011 (RP). PS is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme (IF/01641/2013) and acknowledges FCT/MEC for support to CBMA through Portuguese funds (PIDDAC)-PEst-OE/BIA/UI4050/2014. AS is supported by "Ministerio de Ciencia e Innovacion" (SAF2011-26983), the Plan Galego IDT (EM 2012/045) and the grant from the Sistema Universitario Gallego-Modalidad REDES (2012-PG226) from the Xunta de Galicia. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT, the Portuguese Foundation for Science and Technology. This work is funded by FEDER funds through the Operational Programme for Competitiveness Factors-COMPETE and National Funds through the FCT-Foundation for Science and Technology, under the project "PEst-C/SAU/LA0003/2013". NORTE-07-0162-FEDER-00018-Contributos para o reforco da capacidade do IPATIMUP enquanto actor do sistema regional de inovacao and NORTE-07-0162-FEDER-000067 Reforco e consolidacao da capacidade infraestrutural do IPATIMUP para o sistema regional de inovacao, both supported by Programa Operacional Regional do Norte (ON. 2-O Novo Norte), through FEDER funds under the Quadro de Referencia Estrategico Nacional (QREN). We would like to acknowledge the contribution of Magdalen Awor, Fr. Germano Serra and Iva Gomes for collecting the Karamoja samples. We thank Eric Bridgeland for collecting the Kabale samples, Dr Narcis Kabatereine (Vector Control Division, Uganda Ministry of Health) for the Piida samples, and Abigail Enaburekhan, Sadie Anderson- Mann, Rebecca Cole and Steven Groom for preliminary work on the Kabale and Piida sequences.

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.

Objectives We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172. Methods A total of 110 males of Portuguese descent were analyzed for 17 Y-chromosome bi-allelic markers and seven Y-chromosome short tandem repeats (Y-STR) loci. Results Among J1-M267 individuals (n = 36), five different sub-haplogroups were identified, with the most common being J1a2b2-L147.1 (∼72%), which encompassed the majority of representatives of the J1a2b-P58 subclade. One sample belonged to the rare J1a1-M365.1 lineage and presented a core Y-STR haplotype consistent with the Iberian settlement during the fifth century by the Alans, a people of Iranian heritage. The analysis of J2-M172 Portuguese males (n = 74) enabled the detection of the two main subclades at very dissimilar frequencies, J2a-M410 (∼80%) and J2b-M12 (∼20%), among which the most common branches were J2a1(xJ2a1b,h)-L26 (22.9%), J2a1b(xJ2a1b1)-M67 (20.3%), J2a1h-L24 (27%), and J2b2-M241 (20.3%). Conclusions While previous inferences based on modern haplogroup J Y-chromosomes implicated a main Neolithic dissemination, here we propose a later arrival of J lineages into Iberia using a combination of novel Portuguese Y-chromosomal data and recent evidence from ancient DNA. Our analysis suggests that a substantial tranche of J1-M267 lineages was likely carried into the Iberian Peninsula as a consequence of the trans-Mediterranean contacts during the first millennium BC, while most of the J2-M172 lineages may be associated with post-Neolithic population movements within Europe.

8 páginas Objectives: To determine the African, European and Native-American paternal contributions in genetic samples from the Department of Bolivar (Colombia) with the aims of establishing (1) possible population substructures, and (2) the proportion of biological African heritage in admixed populations of European, Amerindian, and African descent. Methods: Y-SNPs were typed in samples from six communities, including Palenque (renowned for its African linguistic and cultural heritage). Results: Findings reveal a high diversity of Y-haplogroups. With the exception of Palenque, the sum of European male lineages uniformly exceeded 57%. In Palenque, African lineages accounted for 57.7% of its chromosomes, with European male lineages constituting a mere 38.5%. In Pinillos, a significant proportion (23.8%) of the chromosomes belongs to the Native American haplogroup Q1a3a*-M3. Genetic differentiation analyses reveal significant divergences in most pairwise comparisons among the Bolivar municipalities, and the same holds between Bolivar and other South American populations. Conclusions: Heterogeneous patterns of admixture reveal a genetic substructure within the Department of Bolivar. On the paternal side, five out of the six communities studied exhibit a predominantly European gene pool. The exception is Palenque, where European input (38%) is more significant than we had expected.

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans., Author Summary In the largest population genetic study of South Americans to date, we analyzed the Y-chromosomal makeup of more than 1,000 male natives. We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships. This finding is consistent with a rapid initial peopling of South America, followed by long periods of isolation in small tribal groups. The observed continent-wide decoupling of geography, spoken language, and genetics contrasts strikingly with previous reports of such correlation from many parts of Europe and Asia. Moreover, we identified a cluster of Native American founding lineages of Y chromosomes, called C-M217 (C3*), within a restricted area of Ecuador in North-Western South America. The same haplogroup occurs at high frequency in Central, East, and North East Asia, but is virtually absent from North (except Alaska) and Central America. Possible scenarios for the introduction of C-M217 (C3*) into Ecuador may thus include a coastal or trans-Pacific route, an idea also supported by occasional archeological evidence and the recent coalescence of the C3* haplotypes, estimated from our data to have occurred some 6,000 years ago.

Human Y chromosomes belonging to the haplogroup R1b1-P25, although very common in Europe, are usually rare in Africa. However, recently published studies have reported high frequencies of this haplogroup in the central-western region of the African continent and proposed that this represents a 'back-to-Africa' migration during prehistoric times. To obtain a deeper insight into the history of these lineages, we characterised the paternal genetic background of a population in Equatorial Guinea, a Central-West African country located near the region in which the highest frequencies of the R1b1 haplogroup in Africa have been found to date. In our sample, the large majority (78.6%) of the sequences belong to subclades in haplogroup E, which are the most frequent in Bantu groups. However, the frequency of the R1b1 haplogroup in our sample (17.0%) was higher than that previously observed for the majority of the African continent. Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa. The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene.

With this study, we aimed to determine the different male ancestral components of two Native American communities from Argentina, namely Toba and Colla. The analysis of 27 Y-chromosome SNPs allowed us to identify seven different haplogroups in both samples. Chromosomes carrying the M3 mutation, which typically defines the Native American haplogroup Q1a3a, were seen most frequently in the Toba community (90%). Conversely, Q1a3a was represented in 34% of the Colla Y-chromosomes, whereas haplogroup R1b1, the main representative of western European populations, exhibited the highest frequency in this population (41%). Different M3 sublineages in the Toba community could be identified by observing point mutations at both DYS385 and M19 loci. A microvariant at DYS385, named 16.1, has been characterized, which helps to further subdivide Q1a3a. It is the first time the M19 mutated allele is described in a population from Argentina. This finding supports the old age of the lineages carrying the M19 mutation, but it contradicts the previous hypothesis that the M19 mutated allele is confined to only two Equatorial-Tucano population groups from the north region of South America. The detection of M19 further south than previously thought allows questioning of the hypothesis that this lineage serves as an example of isolation after colonization. This observation also affirms the strong genetic drift to which Native Americans have been subjected. Moreover, our study illustrates a heterogeneous contribution of Europeans to these populations and supports previous studies showing that most Native American groups were subjected to European admixture that primarily involved immigrant men.

Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent., Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies., Trabajo parcialmente financiado por la Fundación de Ciencia y Tecnología, a través del proyecto PTDC/ANT/70413/2006 y POCI 2010, Programa Operacional Ciencia e Inovación; Dirección General de Investigación, Ministerio de Educación y Ciencia, España (CGL2009-14944/BOS); Direcció General de Recerca, Generalitat de Catalunya (2009SGR1101) y la Austrian Science Fund (FWF): TR397.

Malaria endemicity in Southwest Iberia afforded conditions for an increase of sickle cell disease (SCD), which in the region follows a clinal pattern toward the south, where foci of high prevalence were found. SCD distribution is associated with specific geographical areas, and therefore, its introduction into Iberia may be related to the migration of different populations. We have analyzed the variation of uniparental markers in Portuguese populations with high frequency of SCD—Coruche, Pias, and Alcacer do Sal—to evaluate if their present-day pattern of neutral diversity could provide evidence about people inhabiting the area over different time periods. Two hundred and eighty-five individuals were sampled in Coruche, Pias, and Alcacer do Sal. All were analyzed for the control region of mitochondrial DNA (mtDNA); males were additionally examined for Y-chromosome markers. Results were then compared with data from other Portuguese and non-Portuguese populations. In Coruche, the genetic profile was similar to the profile usually found in Portugal. In Alcacer do Sal, the frequency of sub-Saharan mtDNA L lineages was the highest ever reported (22%) in Europe. In Pias, mtDNA diversity revealed higher frequencies of Mediterranean haplogroups I, J, and T than usually found in surrounding populations. The presence of Sub-Saharan maternal lineages in Alcacer do Sal is likely associated with the influx of African slaves between the 15th and 19th centuries, whereas in Pias, the Mediterranean influence might be traced to ancient contacts with Greeks, Phoenicians, and Carthaginians, who established important trading networks in southern Iberia. Am. J. Hum. Biol. 22:588–595, 2010. © 2010 Wiley-Liss, Inc.

The European Gypsies, commonly referred to as Roma, are represented by a vast number of groups spread across many countries. Although sharing a common origin, the Gypsy groups are highly heterogeneous as a consequence of genetic drift and different levels of admixture with surrounding populations. With this study we aimed at contributing to the knowledge of the Roma history by studying 17 Y-STR and 34 Y-SNP loci in a sample of 126 Portuguese Gypsies. Distinct genetic hallmarks of their past and migration route were detected, namely: an ancestral component, shared by all Roma groups, that reflects their origin in India (H1a-M82; approximately 17%); an influence from their long permanence in the Balkans/Middle-East region (J2a1b-M67, J2a1b1-M92, I-M170, Q-M242; approximately 31%); traces of contacts with European populations preceding the entrance in the Iberian Peninsula (R1b1c-M269, J2b1a-M241; approximately 10%); and a high proportion of admixture with the non-Gypsy population from Iberia (R1b1c-M269, R1-M173/del.M269, J2a-M410, I1b1b-M26, E3b1b-M81; approximately 37%). Among the Portuguese Gypsies the proportion of introgression from host populations is higher than observed in other groups, a fact which is somewhat unexpected since the arrival of the Roma to Portugal is documented to be more recent than in Central or East Europe.

The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFlSTR YFiler Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were typed in 250 samples from Portugal. A total of 231 different haplotypes were found, where 17 haplotypes were shared by two individuals and one haplotype by three. The overall haplotype diversity (HD) was 0.9994. DYS458 non-consensus alleles found in 5 samples (out of 85) are all associated with paragroup J*(xJ1,2). Population comparisons with available Yfiler loci data in European samples were undertaken, namely with Northern Portuguese data (N=174) where no significant differences were observed with our sample (Rst=0.0000; P=0.8649+/-0.0310). Since both Portuguese databases can be joined (N=424; HD=0.9997; 394 distinct haplotypes), a study on the best loci for HD increment in this sample was also undertaken: by fixing the haplotypes generated from the minimal haplotype and SWGDAM core set (www.yhrd.org) and adding the other Yfiler loci one by one, the order in which the loci contribute more is DYS458, DYS456, GATA H4.1, DYS437 or DYS635, and finally DYS448. Therefore, at least in this population sample, all Yfiler loci are contributing for haplotype discrimination.

The aim of the present work was to study the origin of paternal lineages in Angola population, namely in the three main ethnic groups, inferred by phylogeographic analyses of Y chromosome defined haplogroups. To determine the male lineages present in the Angola population studied, 112 unrelated males were typed using a PCR multiplex – minisequencing SnaPshot based method including 29Y-SNPs, which characterize the majority haplogroups in sub-Saharan Africa populations.

The Karimojong, an African group from the Karamoja region of Northeast Uganda, were genetically analysed using a decaplex system for X chromosome short tandem repeats (X-STRs). A total of 255 individuals (117 males and 138 females) were genotyped for the following loci: DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902 and DXS6789. Allele frequencies and parameters for forensic evaluation were calculated for each STR. No association was found between any pairs of loci studied. DXS6789 was the most polymorphic marker in this sample, followed by DXS6809, with gene diversities of 84.79% and 83.94%, respectively. The less discriminating locus observed was DXS7133, with a gene diversity of 39.79%. High overall values of power of discrimination were obtained for female (1 in 1.8 x 10(10)) and male samples (1 in 1.6 x 10(6)), as well as high power of exclusion in father/mother/daughter trios (99.9997%), in father daughter duos (99.9862%) and in half sisters with same father (99.0331%). These results confirm the potential of this 10-plex in parentage testing and in human identification.

Sickle cell anemia (HBB*S) and glucose-6-phosphatedehydrogenase (G6PD) deficiency, present a clinal distribution in Portugal, being more frequent in the South and showing foci of high prevalence in some places from Alentejo such as Coruche and Pias. Since the reconstruction of the evolutionary history of G6PD deficiency alleles and HBB*S lead to conclude that Sub-Saharan Africa was the place of origin of many of them, it is likely that at least some were introduced in Alentejo by Sub-Saharan individuals whose presence in the region is known to have had considerable demographic impact. To evaluate the male mediated Sub-Saharan influence in present-day populations from Coruche and Pias, we have performed a high resolution analysis of 16 Y-STRs and 23 Y-SNPs in 91 males from Coruche and 54 from Pias. The results showed the absence of haplogroups of Sub-Saharan origin and a Y-chromosome composition basically not differing from those previously reported for other Portuguese mainland regions. Therefore, from the forensic point of view the studied populations can be dealt without special concerns.

We analyzed 17 Y-chromosomal STR loci in a population sample of 126 unrelated Portuguese Gypsies. Fifty three different haplotypes were found, three represented with considerable high frequencies (≥8.7%). The percentage of unique haplotypes (71.2%) was rather low as well as haplotype diversity (94.37%). In the comparison with available Portuguese population data and with those from other Gypsy and general population samples from Bulgaria, Lithuania and Spain, our sample showed significant differences in comparison with the general population data from Portugal, Spain and Bulgaria. Significant differences were observed with Bulgarian Gypsies, but not with the Spanish or Lithuanian groups. The Gypsy populations from Portugal, Spain and Bulgaria were found to be more closely related to each other than with the general population from their own countries.