Demographic history of Canary Islands male gene-pool: replacement of native lineages by European

El Hierro Genome Study: A Genomic and Health Study in an Isolated Canary Island Population

El Hierro is the smallest and westernmost island of the Canary Islands, whose population derives from an admixture of different ancestral components and that has been subjected to genetic isolation. We established the "El Hierro Genome Study" to characterize the health status and the genetic composition of ~10% of the current population of the island, accounting for a total of 1054 participants. Detailed demographic and clinical data and a blood sample for DNA extraction were obtained from each participant. Genomic genotyping was performed with the Global Screening Array (Illumina). The genetic composition of El Hierro was analyzed in a subset of 416 unrelated individuals by characterizing the mitochondrial DNA (mtDNA) and Y-chromosome haplogroups and performing principal component analyses (PCAs). In order to explore signatures of isolation, runs of homozygosity (ROHs) were also estimated. Among the participants, high blood pressure, hypercholesterolemia, and diabetes were the most prevalent conditions. The most common mtDNA haplogroups observed were of North African indigenous origin, while the Y-chromosome ones were mainly European. The PCA showed that the El Hierro population clusters near 1000 Genomes' European population but with a shift toward African populations. Moreover, the ROH analysis revealed some individuals with an important portion of their genomes with ROHs exceeding 400 Mb. Overall, these results confirmed that the "El Hierro Genome" cohort offers an opportunity to study the genetic basis of several diseases in an unexplored isolated population.

New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages

Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.

The genomic history of the indigenous people of the Canary Islands

The indigenous population of the Canary Islands, which colonized the archipelago around the 3rd century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3rd-16rd centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.

Digging into the admixture strata of current-day Canary Islanders based on mitogenomes

The conquest of the Canary Islands by Europeans began at the beginning of the 15th century and culminated in 1496 with the surrender of the aborigines. The collapse of the aboriginal population during the conquest and the arrival of settlers caused a drastic change in the demographic composition of the archipelago. To shed light on this historical process, we analyzed 896 mitogenomes of current inhabitants from the seven main islands. Our findings confirm the continuity of aboriginal maternal contributions and the persistence of their genetic footprints in the current population, even at higher levels (>60% on average) than previously evidenced. Moreover, the age estimates for most autochthonous founder lineages support a first aboriginal arrival to the islands at the beginning of the first millennium. We also revealed for the first time that the main recognizable genetic influences from Europe are from Portuguese and Galicians.

Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders

The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.

The incidence of skin melanoma in Gran Canaria (Canary Islands, Spain) is lower than expected in Southern Europe despite high-risk environmental conditions: an island-wide cross-sectional study

BACKGROUND

The Canary Islands are a leading European touristic destination. The ultraviolet index (UVI) in the region is the highest in Spain, and similar to indexes registered in Australia and New Zealand, which hold the highest incidence of skin melanoma worldwide. Yet according to cancer registry data, the incidence in the Canary Islands in the late 1990s was the lowest in Spain (among the lowest in Europe) and about six times lower than in New Zealand.

PURPOSE

To analyze the incidence rates of skin melanoma in Gran Canaria island between 2007 and 2018.

METHODS

The study was based in the two centres of the Canary Islands' Healthcare Service centralizing melanoma care in Gran Canaria. We analyzed crude and age-standardized (ASR) incidence rates of invasive cutaneous melanoma for the period 2007-2018 following the inclusion criteria of the International Agency for Research on Cancer (IARC). Clinical and histological characteristics of melanoma patients were assessed.

RESULTS

A total of 1058 patients were included. The incidence rates obtained matched the latest available Canary Islands' cancer registry data, confirming its reliability (ASR, Segi-Doll world standard population: 6.4 cases per 100,000 habitants for 2008-2012). The incidence was also below the latest IARC predictions for Southern Europe (GLOBOCAN 2018). Histological characteristics of patients were similar to other Southern European series.

CONCLUSIONS

The incidence of skin melanoma in Gran Canaria is unexpectedly low for a Southern European population exposed to such a high UVI. Further research in the Canary Islands could provide insight into a better understanding of melanoma pathogenesis.

The demography of the Canary Islands from a genetic perspective

The establishment of European colonies across the world had important demographic consequences because it brought together diverse and distant civilizations for the first time. One clear example of this phenomenon is observed in the Canary Islands. The modern Canarian population is mainly the result of the admixture of natives of North African origin and European colonizers. However, additional migratory flows reached the islands due to the importation of enslaved Africans to cultivate sugarcane and the intense commercial contact with the American continent. In this review, we evaluate how the genetic analysis of indigenous, historical and current populations has provided a glimpse into the Canary Islands' complex genetic composition. We show that each island subpopulation's characterization is needed to fully disentangle the demographic history of the Canarian archipelago. Finally, we discuss what research avenues remain to be explored to improve our knowledge of the impact that the European colonization had on its native population.

Population history of North Africa based on modern and ancient genomes

Compared with the rest of the African continent, North Africa has provided limited genomic data. Nonetheless, the genetic data available show a complex demographic scenario characterized by extensive admixture and drift. Despite the continuous gene flow from the Middle East, Europe and sub-Saharan Africa, an autochthonous genetic component that dates back to pre-Holocene times is still present in North African groups. The comparison of ancient and modern genomes has evidenced a genetic continuity in the region since Epipaleolithic times. Later population movements, especially the gene flow from the Middle East associated with the Neolithic, have diluted the genetic autochthonous component, creating an east to west gradient. Recent historical movements, such as the Arabization, have also contributed to the genetic landscape observed currently in North Africa and have culturally transformed the region. Genome analyses have not shown evidence of a clear correlation between cultural and genetic diversity in North Africa, as there is no genetic pattern of differentiation between Tamazight (i.e. Berber) and Arab speakers as a whole. Besides the gene flow received from neighboring areas, the analysis of North African genomes has shown that the region has also acted as a source of gene flow since ancient times. As a result of the genetic uniqueness of North African groups and the lack of available data, there is an urgent need for the study of genetic variation in the region and its implications in health and disease.

An Evolutionary Approach to the History of Barley (Hordeum vulgare) Cultivation in the Canary Islands

The Canary Islands are an archipelago that lies about 100 km west of North Africa. Barley (Hordeum vulgare) has been continuously cultivated since the colonization of the islands. To investigate the agricultural history of the islands, the DNA from multiple individuals of six extant landraces of barley was sequenced, and the resulting data were analyzed with ABC modeling. Estimates of separation times of barley populations on the different islands and the mainland were congruent with archaeological dating of the earliest settlements on the islands. The results of the genetic analyses were consistent with the continuous cultivation of barley on Lanzarote island since it was first colonized, but suggested cultivation was carried out at a smaller scale than on Gran Canaria and Tenerife. Contrary to archaeological evidence and early written historical sources, the genetic analyses suggest that barley was cultivated on a larger scale on Tenerife than on Gran Canaria. The genetic analysis of contemporary barley added support to the dating of the colonization of the islands and pointed to the need for more archaeological data concerning barley cultivation on Tenerife.

Dissecting human North African gene-flow into its western coastal surroundings

North African history and populations have exerted a pivotal influence on surrounding geographical regions, although scant genetic studies have addressed this issue. Our aim is to understand human historical migrations in the coastal surroundings of North Africa. We built a refined genome-wide dataset of North African populations to unearth the fine-scale genetic structure of the region, using haplotype information. The results suggest that the gene-flow from North Africa into the European Mediterranean coast (Tuscany and the Iberian Peninsula) arrived mainly from the Mediterranean coast of North Africa. In Tuscany, this North African admixture date estimate suggests the movement of peoples during the fall of the Roman Empire around the fourth century. In the Iberian Peninsula, the North African component probably reflects the impact of the Arab expansion since the seventh century and the subsequent expansion of the Christian Kingdoms. By contrast, the North African component in the Canary Islands has a source genetically related to present-day people from the Atlantic North African coast. We also find sub-Saharan gene-flow from the Senegambia region in the Canary Islands. Specifically, we detect a complex signal of admixture involving Atlantic, Senegambian and European sources intermixing around the fifteenth century, soon after the Castilian conquest. Our results highlight the differential genetic influence of North Africa into the surrounding coast and show that specific historical events have not only had a socio-cultural impact but additionally modified the gene pool of the populations.

Genomic Analyses of Human European Diversity at the Southwestern Edge: Isolation, African Influence and Disease Associations in the Canary Islands

Despite the genetic resemblance of Canary Islanders to other southern European populations, their geographical isolation and the historical admixture of aborigines (from North Africa) with sub-Saharan Africans and Europeans have shaped a distinctive genetic makeup that likely affects disease susceptibility and health disparities. Based on single nucleotide polymorphism array data and whole genome sequencing (30×), we inferred that the last African admixture took place ∼14 generations ago and estimated that up to 34% of the Canary Islander genome is of recent African descent. The length of regions in homozygosis and the ancestry-related mosaic organization of the Canary Islander genome support the view that isolation has been strongest on the two smallest islands. Furthermore, several genomic regions showed significant and large deviations in African or European ancestry and were significantly enriched in genes involved in prevalent diseases in this community, such as diabetes, asthma, and allergy. The most prominent of these regions were located near LCT and the HLA, two well-known targets of selection, at which 40‒50% of the Canarian genome is of recent African descent according to our estimates. Putative selective signals were also identified in these regions near the SLC6A11-SLC6A1, KCNMB2, and PCDH20-PCDH9 genes. Taken together, our findings provide solid evidence of a significant recent African admixture, population isolation, and adaptation in this part of Europe, with the favoring of African alleles in some chromosome regions. These findings may have medical implications for populations of recent African ancestry.

Paternal portrait of populations of the middle Magdalena River region (Tolima and Huila, Colombia): New insights on the peopling of Central America and northernmost South America

The valley of the Magdalena River is one of the main population pathways in Colombia. The gene pool and spatial configuration of human groups in this territory have been outlined throughout three historical stages: the Native pre-Hispanic world, Spanish colonization, and XIX century migrations. This research was designed with the goal of characterizing the diversity and distribution pattern of Y-chromosome lineages that are currently present in the Tolima and Huila departments (middle Magdalena River region). Historic cartography was used to identify the main geographic sites where the paternal lineages belonging to this area have gathered. Twelve municipalities were chosen, and a survey that included genealogical information was administered. Samples collected from 83 male volunteers were analyzed for 48 Y-SNPs and 17 Y-STRs. The results showed a highly diverse region characterized by the presence of 16 sublineages within the major clades R, Q, J, G, T and E and revealed that 93% (n = 77) of haplotypes were different. Among these haplogroups, European-specific R1b-M269 lineages were the most representative (57.83%), with six different subhaplogroups and 43 unique haplotypes. Native American paternal ancestry was also detected based on the presence of the Q1a2-M3*(xM19, M194, M199) and Q1a2-M346*(xM3) lineages. Interestingly, all Q1a2-M346*(xM3) samples (n = 7, with five different haplotypes) carried allele six at the DYS391 locus. This allele has a worldwide frequency of 0.169% and was recently associated with a new Native subhaplogroup. An in-depth phylogenetic analysis of these samples suggests the Tolima and Huila region to be the principal area in all Central and South America where this particular Native lineage is found. This lineage has been present in the region for at least 1,809 (+/- 0,5345) years.

The female ancestor's tale: Long-term matrilineal continuity in a nonisolated region of Tuscany

OBJECTIVES

With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.

MATERIALS AND METHODS

We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups.

RESULTS

Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes.

CONCLUSIONS

The observed signals of long-term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors-arriving from far-had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long-term genealogical continuity is not necessarily linked to geographical isolation.

North African-Mediterranean HLA genetic contribution in a population of the kidney transplant waiting list patients of Canary origin (Gran Canaria)

The peopling of the Canary Islands has been widely debated. The mitochondrial DNA and Y-chromosome data support the idea of a Berber genetic origin coming from the North of Africa (maternal) and a later contribution of the Spanish invaders (paternal). The frequencies of the HLA class II alleles from the Tenerife Island (another Canary Island) have previously been published, postulating a Berber and Atlantic/Iberian contributions to the current population. The HLA class I and class II allele frequencies, haplotype frequencies and phylogenetic comparisons were performed in 215 unrelated individuals from Gran Canaria Island (belonging to the kidney transplant waiting list), with at least three generations of ancestors from Canary Islands, in order to study the different ethnical HLA contributions to the genetic background of the Canary Islanders. Results showed the presence of a compound HLA haplotype of putative Phoenician-Berber origin, A*33:01-C*08:02-B*14:02-DRB1*03:01-DQB1*02:01, likely coming from the combination of haplotypes A*30:02-C*05:01-B*18:01-DRB1*03:01-DQB1*02:01 and A*33:01-C*08:02-B*14:02-DRB1*01:02-DQB1*05:01 of North African (probably Berber) and West Asian Mediterranean (probably Phoenician) origins, respectively. The latter haplotypes and others from the same origin (Berber/Phoenician) are also present in the population studied. Besides, other contributions from the North of Europe, North England-Iberian (Atlantic contribution), and Western Europe/Mediterraneans (Spanish colonization) are also discussed. These data conclude that the current genetic background of the Canary Islands inhabitants has been generated over the years by different ways with an original Phoenician-Berber substrate and several genetic contributions generated in different invasions.

Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81)

E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000-3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.

Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans

The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5^th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7^th-11^th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.

Sonographic evaluation of atherosclerosis burden in carotid arteries of ischemic stroke patients and its relation to paraoxonase 1 and 2, MTHFR and AT1R genetic variants

OBJECTIVE

Common variants of the Paraoxonase (PON), 5-Methyl-Tetrahydrofolate-Reductase (MTHFR) and Angiotensin-II receptor 1 (AT1R) genes have been associated with ischemic stroke (IS) risk. Moreover, carotid atherosclerosis is a common cause of IS. The aim of this study is to explore whether variants in these genes associate with the severity of ultrasonographic determined atherosclerosis assessed in carotid arteries.

PATIENTS AND METHODS

Etiologic subtype of cerebral ischemia was determined according to the TOAST classification. Genotypes were detected by PCR and restriction analysis. An ultrasonographic supra-aortic trunks study was performed to all patients to assess their atherosclerotic involvement based on predefined criteria.

RESULTS

In IS patients, none of the analyzed gene distributions differed concerning the stenosis degree. Nevertheless, a trend was observed for the rs662 and rs7493 variants of the PON1 and PON2 genes respectively. When evaluated the results based on different inheritance models, a significant contribution of rs7493 variant according to a dominant (OR=2.397, 95% CI (1.001-5.376); p=0.045) and log-additive inheritance forms (OR=1.85, 95% CI (1.07-3.2); p=0.03) was observed. Only rs7493 reached statistical significance (p=0.013), when genotype distribution was analyzed according to carotid intima-media thickness (cIMT) and remain significant in multivariate logistic regression analysis (OR=2.66, 95% CI (1.1 to 6.4); p=0.03).

CONCLUSION

In IS patients of the north area of the Gran Canaria island the PON2 (rs7493) gene variant associates with a worse ultrasonographic profile. Conversely, the Cys311Cys homozygosis of the rs7493 variant was also related to a better ultrasonographic profile in our study.

Paraoxonase 1 and 2 gene variants and the ischemic stroke risk in Gran Canaria population: an association study and meta-analysis

PURPOSE OF THE STUDY

The present study aims to evaluate the relationship between rs662 (Gln(Q)192Arg(R)) and rs854560 (L55M) and the rs7493 (S311C) in the paraoxonase genes and ischemic stroke (IS) in the population of Gran Canaria (Canary Islands). The association with stroke was also evaluated using systematic review and meta-analysis.

METHODS

A total of 129 IS patients and 176 age and gender matched controls were enrolled. For meta-analysis, eligible studies were identified through search in public databases.

RESULTS

In multivariate regression analysis only the PON2 S311C variant showed to be an independent predictor of IS (OR = 0.093, 95% CI: 0.014-0.627). Overall, no significant association was found between L55M and IS when all studies were pooled nor by subgroup analysis by ethnicity. Gln192Arg showed a modest risk for IS in the global and in Asian population but with high heterogeneity among studies. A modest risk under a dominant inheritance model was found for the S311C variant with an overall random effect OR of 1.004 (95% CI: 1.00-1.35). There was strong evidence of heterogeneity among studies (  p = 0.0097, I² = 25.35%) which did not disappear after stratification by ethnicity.

CONCLUSIONS

The overall analysis shows a significant contribution of the rs662 variant to IS risk. We found that the CC genotype of the PON2 S311C polymorphism is a risk factor for IS. Results of the meta-analysis partially support this conclusion.

Role of HIF1A, VEGFA and VEGFR2 SNPs in the Susceptibility and Progression of COPD in a Spanish Population

Hypoxia is involved in the development of chronic inflammatory processes. Under hypoxic conditions HIF1A, VEGF and VEGFR2 are expressed and mediate the course of the resultant disease. The aim of the present study was to define the associations between tSNPs in these genes and COPD susceptibility and progression in a Spanish cohort. The T alleles in rs3025020 and rs833070 SNPs (VEGFA gene) were less frequent in the group of COPD cases and were associated with a lower risk of developing the disease (OR = 0.60; 95% CI = 0. 39–0.93; p = 0.023 and OR = 0.60; 95% CI = 0.38–0.96; p = 0.034, respectively) under a dominant model of inheritance. The haplotype in which both SNPs presented the T allele confirmed the association found (OR = 0.02; 95% CI = 0.00 to 0.66; p = 0.03). Moreover, patients with COPD carrying the T allele in homozygosis in rs3025020 SNP showed higher lung function values and this association remained constant during 3 years of follow-up. In conclusion, T allele in rs833070 and rs3025020 may confer a protective effect to COPD susceptibility in a Spanish population and the association of the SNP rs3025020 with lung function may be suggesting a role for VEGF in the progression of the disease.

Isolation and prominent aboriginal maternal legacy in the present-day population of La Gomera (Canary Islands)

The present-day population structure of La Gomera is outstanding in its high aboriginal heritage, the greatest in the Canary Islands. This was earlier confirmed by both mitochondrial DNA and autosomal analyses, although genetic drift due to the fifteenth century European colonization could not be excluded as the main factor responsible. The present mtDNA study of aboriginal remains and extant samples from the six municipal districts of the island indeed demonstrates that the pre-Hispanic colonization of La Gomera by North African people involved a strong founder event, shown by the high frequency of the indigenous Canarian U6b1a lineage in the aboriginal samples (65%). This value is even greater than that observed in the extant population (44%), which in turn is the highest of all the seven Canary Islands. In contrast to previous results obtained for the aboriginal populations of Tenerife and La Palma, haplogroups related to secondary waves of migration were not detected in La Gomera aborigines, indicating that isolation also had an important role in shaping the current population. The rugged relief of La Gomera divided into several distinct valleys probably promoted subsequent aboriginal intra-insular differentiation that has continued after the European colonization, as seen in the present-day population structure observed on the island.

Technical note: Advantages and limitations of authenticating Palmera goat dairy products by pyrosequencing the melanocortin 1 receptor (MC1R) gene

Inferring the breed of origin of dairy products can be achieved through molecular analysis of genetic markers with a population-specific pattern of segregation. The goal of the current work was to generate such markers in goats by resequencing several pigmentation genes [melanocortin 1 receptor (MC1R), v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT), tyrosinase (TYR), and tyrosinase-related protein 2 (TYRP2)]. This experiment revealed 10 single nucleotide polymorphisms (SNP), including 5 missense mutations and 1 nonsense mutation. These markers were genotyped in 560 goats from 18 breeds originally from Italy, the Iberian Peninsula, the Canary Islands, and North Africa. Although the majority of SNP segregated at moderate frequencies in all populations (including 2 additional markers that were used as a source of information), we identified a c.764G>A SNP in MC1R that displayed highly divergent allelic frequencies in the Palmera breed compared with the Majorera and Tinerfeña breeds from the Canary Islands. Thus, we optimized a pyrosequencing-based technique that allowed us to estimate, very accurately, the allele frequencies of this marker in complex DNA mixtures from different individuals. Once validated, we applied this method to generating breed-specific DNA profiles that made it possible to detect fraudulent cheeses in which Palmero cheese was manufactured with milk from Majorera goats. One limitation of this approach, however, is that it cannot be used to detect illegal manufacturing where Palmero dairy products are produced by mixing milk from Palmera and Majorera goats, because the c.764G>A SNP segregates in both breeds.

Multiple ethnic origins of mitochondrial DNA lineages for the population of Mauritius

This article reports on the first genetic assessment of the contemporary Mauritian population. Small island nodes such as Mauritius played a critical role in historic globalization processes and revealing high-resolution details of labour sourcing is crucial in order to better understand early-modern diaspora events. Mauritius is a particularly interesting case given detailed historic accounts attesting to European (Dutch, French and British), African and Asian points of origin. Ninety-seven samples were analysed for mitochondrial DNA to begin unravelling the complex dynamics of the island's modern population. In corroboration with general demographic information, the majority of maternal lineages were derived from South Asia (58.76%), with Malagasy (16.60%), East/Southeast Asian (11.34%) and Sub-Saharan African (10.21%) also making significant contributions. This study pinpoints specific regional origins for the South Asian genetic contribution, showing a greater influence on the contemporary population from northern and southeast India. Moreover, the analysis of lineages related to the slave trade demonstrated that Madagascar and East Asia were the main centres of origin, with less influence from West Africa.

Reconstruction of major maternal and paternal lineages of the Cape Muslim population

The earliest Cape Muslims were brought to the Cape (Cape Town - South Africa) from Africa and Asia from 1652 to 1834. They were part of an involuntary migration of slaves, political prisoners and convicts, and they contributed to the ethnic diversity of the present Cape Muslim population of South Africa. The history of the Cape Muslims has been well documented and researched however no in-depth genetic studies have been undertaken. The aim of the present study was to determine the respective African, Asian and European contributions to the mtDNA (maternal) and Y-chromosomal (paternal) gene pool of the Cape Muslim population, by analyzing DNA samples of 100 unrelated Muslim males born in the Cape Metropolitan area. A panel of six mtDNA and eight Y-chromosome SNP markers were screened using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Overall admixture estimates for the maternal line indicated Asian (0.4168) and African mtDNA (0.4005) as the main contributors. The admixture estimates for the paternal line, however, showed a predominance of the Asian contribution (0.7852). The findings are in accordance with historical data on the origins of the early Cape Muslims.

Introducing the Algerian mitochondrial DNA and Y-chromosome profiles into the North African landscape

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

No association between genetic ancestry and susceptibility to asthma or atopy in Canary Islanders

Asthma is a complex respiratory disease characterized by chronic inflammation of airways and frequently associated with atopic symptoms. The population from the Canary Islands, which has resulted from a recent admixture of North African and Iberian populations, shows the highest prevalence of asthma and atopic symptoms among the Spanish populations. Although environmental particularities would account for the majority of such disparity, genetic ancestry might play a role in increasing the susceptibility of asthma or atopy, as have been demonstrated in other recently African-admixed populations. Here, we aimed to explore whether genetic ancestry was associated with asthma or related traits in the Canary Islanders. For that, a total of 734 DNA samples from unrelated individuals of the GOA study, self-reporting at least two generations of ancestors from the Canary Islands (391 asthmatics and 343 controls), were successfully genotyped for 83 ancestry informative markers (AIMs), which allowed to precisely distinguishing between North African and Iberian ancestries. No association was found between genetic ancestry and asthma or related traits after adjusting by demographic variables differing among compared groups. Similarly, none of the individual AIMs was associated with asthma when results were considered in the context of the multiple comparisons performed (0.005 ≤ p value ≤ 0.042; 0.221 ≤ q value ≤ 0.443). Our results suggest that if genetic ancestry were involved in the susceptibility to asthma or related traits among Canary Islanders, its effects would be modest. Larger studies, examining more genetic variants, would be needed to explore such possibility.

Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe

Background/Principal Findings

The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe.

Methodology/Significance

Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe.

Conclusion

The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation.

Genetics, environment, and diabetes-related end-stage renal disease in the Canary Islands

AIMS

Type 1 and type 2 diabetes, complicated with renal disease, have a significantly higher incidence in the Canary Islands than in mainland Spain and other European countries. Present-day Canarian inhabitants consist of a mixed population with North African indigenous and European colonizer ancestors who have rapidly evolved from a rural to an urban life style. The aim of this work was to assess the possible role of genetic and environmental factors on diabetes-related end-stage renal disease incidence in the Canary Islands.

RESULTS

For both types of diabetes there is an ethnic susceptibility increased by diabetes family history. Whereas the Y-chromosome does not play a significant role, mitochondrial DNA (mtDNA) haplogroup differences point to a maternal origin for this ethnic predisposition, confirming susceptible and protective effects for haplogroups J and T, respectively. In addition, urban life style seems to be an additional risk factor for type 1 diabetes.

CONCLUSIONS

The maternal ethnic predisposition to diabetes complicated with kidney disease detected in the Canary Islands signals mtDNA and X-chromosome markers as the best candidates to uncover the genetic predisposition to this disease.

Partial recessive IFN-γR1 deficiency: genetic, immunological and clinical features of 14 patients from 11 kindreds

We report a series of 14 patients from 11 kindreds with recessive partial (RP)-interferon (IFN)-γR1 deficiency. The I87T mutation was found in nine homozygous patients from Chile, Portugal and Poland, and the V63G mutation was found in five homozygous patients from the Canary Islands. Founder effects accounted for the recurrence of both mutations. The most recent common ancestors of the patients with the I87T and V63G mutations probably lived 1600 (875-2950) and 500 (200-1275) years ago, respectively. The two alleles confer phenotypes that are similar but differ in terms of IFN-γR1 levels and residual response to IFN-γ. The patients suffered from bacillus Calmette-Guérin-osis (n= 6), environmental mycobacteriosis (n= 6) or tuberculosis (n= 1). One patient did not suffer from mycobacterial infections but had disseminated salmonellosis, which was also present in two other patients. Age at onset of the first environmental mycobacterial disease differed widely between patients, with a mean value of 11.25 ± 9.13 years. Thirteen patients survived until the age of 14.82 ± 11.2 years, and one patient died at the age of 7 years, 9 days after the diagnosis of long-term Mycobacterium avium infection and the initiation of antimycobacterial treatment. Up to 10 patients are currently free of infection with no prophylaxis. The clinical heterogeneity of the 14 patients was not clearly related to either IFNGR1 genotype or the resulting cellular phenotype. RP-IFN-γR1 deficiency is, thus, more common than initially thought and should be considered in both children and adults with mild or severe mycobacterial diseases.

North African influences and potential bias in case-control association studies in the Spanish population

Background

Despite the limited genetic heterogeneity of Spanish populations, substantial evidences support that historical African influences have not affected them uniformly. Accounting for such population differences might be essential to reduce spurious results in association studies of genetic factors with disease. Using ancestry informative markers (AIMs), we aimed to measure the African influences in Spanish populations and to explore whether these might introduce statistical bias in population-based association studies.

Methodology/Principal Findings

We genotyped 93 AIMs in Spanish (from the Canary Islands and the Iberian Peninsula) and Northwest Africans, and conducted population and individual-based clustering analyses along with reference data from the HapMap, HGDP-CEPH, and other sources. We found significant differences for the Northwest African influence among Spanish populations from as low as ≈5% in Spanish from the Iberian Peninsula to as much as ≈17% in Canary Islanders, whereas the sub-Saharan African influence was negligible. Strikingly, the Northwest African ancestry showed a wide inter-individual variation in Canary Islanders ranging from 0% to 96%, reflecting the violent way the Islands were conquered and colonized by the Spanish in the XV century. As a consequence, a comparison of allele frequencies between Spanish samples from the Iberian Peninsula and the Canary Islands evidenced an excess of markers with significant differences. However, the inflation of p-values for the differences was adequately controlled by correcting for genetic ancestry estimates derived from a reduced number of AIMs.

Conclusions/Significance

Although the African influences estimated might be biased due to marker ascertainment, these results confirm that Northwest African genetic footprints are recognizable nowadays in the Spanish populations, particularly in Canary Islanders, and that the uneven African influences existing in these populations might increase the risk for false positives in association studies. Adjusting for population stratification assessed with a few dozen AIMs would be sufficient to control this effect.

The Celtic fringe of Britain: insights from small mammal phylogeography

Recent genetic studies have challenged the traditional view that the ancestors of British Celtic people spread from central Europe during the Iron Age and have suggested a much earlier origin for them as part of the human recolonization of Britain at the end of the last glaciation. Here we propose that small mammals provide an analogue to help resolve this controversy. Previous studies have shown that common shrews (Sorex araneus) with particular chromosomal characteristics and water voles (Arvicola terrestris) of a specific mitochondrial (mt) DNA lineage have peripheral western/northern distributions with striking similarities to that of Celtic people. We show that mtDNA lineages of three other small mammal species (bank vole Myodes glareolus, field vole Microtus agrestis and pygmy shrew Sorex minutus) also form a 'Celtic fringe'. We argue that these small mammals most reasonably colonized Britain in a two-phase process following the last glacial maximum (LGM), with climatically driven partial replacement of the first colonists by the second colonists, leaving a peripheral geographical distribution for the first colonists. We suggest that these natural Celtic fringes provide insight into the same phenomenon in humans and support its origin in processes following the end of the LGM.