- Bustamante Lab
School of Medicine
Stanford University
450 Serra Mall 94305
California
United States - +1 650 440 8126
- IPATIMUP, Population Genetics, Graduate StudentUniversidad de La Laguna, Genetics, Graduate Student, and 2 moreadd
- Ancient DNA Research, Human Y Chromosome Variation, Human mtDNA variation, Population Genetics, Phylogenetics, Ancient DNA (Archaeology), and 13 moreHistory of Slavery, Human Migrations, Genetics, Ecology, Slavery, Threatened species and ecosystems, Canary Islands Archaeology, DNA Extraction, Pigeons, History of the Canary Islands, Post-glacial Expansion, Cantabrian Cornice, and Genome Wide Association Studiesedit
- My research interest has been centered on the use of paleogenetic techniques to deciphering the history of past popul... moreMy research interest has been centered on the use of paleogenetic techniques to deciphering the history of past populations and understanding how migration patters have shaped ancient and modern populations’ structure. Most of my projects have been related to European colonialism and how it impacted global demography, both on the Atlantic (Canary Islands) and the Indian Oceans (Mauritius).
My PhD project consisted of assessment of the temporal evolution of the human inhabitants of the Canary Islands using aDNA techniques. During the 13th century, Portuguese sailors discovered several archipelagos in the Atlantic Ocean, among which the Canary Islands was the only one inhabited. The European explorers were surprised to discover they did not have enough seafaring skills to have reached the islands from Africa. The Spanish kingdom of Castile conquered the islands during the 15th century, leading to the complete mixing of the indigenous people with the European colonizers. The results of my PhD project helped confirming the origin of the indigenous people of the Canary Islands based on uniparental and autosomal data, and provided a better understanding on the effects that the conquest and posterior European colonization had on the aboriginal people.
After finishing my PhD, I worked in a multidisciplinary team, together with La Universidad de Las Palmas de Gran Canaria and the Institute of Legal Medicine of Las Palmas (Spain), in a national project funded to allow the genetic identification of human remains in mass grave from the political repression that followed the Spanish Civil War (1936 - 1939). Using my experience with PCR amplification of severely degraded DNA, we were able to identify seven human remains excavated in the island of Gran Canaria.
In 2014, I moved to Stanford University (US) to gain expertise on whole genome techniques, such as next-generation sequencing (NGS) and genome-wide SNP analysis. I was also interested on applying and improving the new DNA capture technology developed at Stanford for enriching degraded ancient samples on endogenous DNA. At Stanford, in collaboration with the University of California at Santa Cruz (US), University of Rabat (Morocco) and University of La Laguna (Spain), we performed the first paleogenetic comparison of Neolithic populations at both sides of the Gibraltar Strait, including archaeological sites from both South Iberia and North Africa, to test the existence of prehistorical contact between the two areas.
Now, as an Assistant Professor at University of La Laguna , I'm leading two different projects:
a) In collaboration with the University of Las Palmas de Gran Canaria, and several local museums of the Canaries, we are performing the first aDNA analysis of ancient populations of the whole Canary Islands at a genomic level, to use nuclear admixture patterns for inferring the indigenous colonization process.
b) In collaboration with the Department of Anthropology at Stanford University, and the University of Mauritius (Mauritius), we are performing the first NGS and whole-genome SNP analysis of historical and current populations of Mauritius to obtain novel data on labor diaspora across the Indian Ocean during colonial times.edit
Research Interests:
Slavery, colonialism and emancipation are important aspects of archaeological research in the Atlantic region, but the lifeways of colonial populations remain understudied in the Indian Ocean World. Here, we help to redress this imbalance... more
Slavery, colonialism and emancipation are important aspects of archaeological research in the Atlantic region, but the lifeways of colonial populations remain understudied in the Indian Ocean World. Here, we help to redress this imbalance by undertaking stable isotope analysis (C, N and O) on human remains from Mauritius, a location which played an important role in the movement of people across the Indian Ocean and beyond. The results indicate that a wide range of diets was consumed in Mauritius during the nineteenth century, varying with location and circumstances of birth such that while a range of resources would have been available on the island, the proportions of the different resources consumed was different for different people. Most people consumed some C4 resources, likely maize, although the proportion of the diet that this represented varied widely. There is some evidence for the use of marine resources, with one individual consuming a very high proportion of marine foo...
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The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was... more
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and ...
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Objective We analyze the processing sequence involved in the manufacture of a skull‐cup and the manipulation of human bones from the Early Neolithic of Cueva de El Toro (Málaga, Spain). Materials and methods The Early Neolithic material... more
Objective We analyze the processing sequence involved in the manufacture of a skull‐cup and the manipulation of human bones from the Early Neolithic of Cueva de El Toro (Málaga, Spain). Materials and methods The Early Neolithic material studied includes human remains found in two separate assemblages. Assemblage A consists of one skull‐cup, a non‐manipulated adult human mandible, and four ceramic vessels. Assemblage B contains manipulated and non‐manipulated human remains that appeared mingled with domestic waste. Using a taphonomic approach, we evaluate the skull‐cup processing and the anthropogenic alteration of human bones. Results The skull‐cup was processed by careful paring away of skin, fragmentation of the facial skeleton and base of the skull, and controlled percussion of the edges of the calotte to achieve a regular shape. It was later boiled for some time in a container that caused pot polish in a specific area. The other human bones appeared scattered throughout the livi...
Research Interests: Evolutionary Biology, Archaeology, Prehistoric Archaeology, Anthropology, Bioarchaeology, and 11 moreMediterranean prehistory, Cannibalism, Neolithic Archaeology, Physical Anthropology, Taphonomy, Iberian Prehistory (Archaeology), Archaeology of the Iberian Peninsula, Neolithic Europe, American Journal of Physical Anthropology, Prehistoria, and Neolítico
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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... more
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 t...
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Research Interests:
The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the... more
The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route. MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, an...
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Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data... more
Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region.
In this study, we design: 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations. 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.
In this study, we design: 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations. 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.
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An analysis of the burial characteristics of the indi- viduals recovered from two Early Neolithic sites in Navarre (Los Cascajos and Paternanbidea), in the Spanish Basque Country, revealed a complex funerary ritual. The individuals... more
An analysis of the burial characteristics of the indi- viduals recovered from two Early Neolithic sites in Navarre (Los Cascajos and Paternanbidea), in the Spanish Basque Country, revealed a complex funerary ritual. The individuals recovered from the Paternanbidea site were distributed in three double graves and a multiple one, while the individuals from Los Cascajos were buried in individual pit-shaped tombs; furthermore, the tombs had a variety of cultural and funerary features. The aim of this study is to evaluate the burial ritual by means of mitochondrial DNA data and the funerary charac- teristics of 36 individuals recovered from these two sites. The results show that the diversity of these Early Neolithic burial practices from the northern Iberian Peninsula cannot be ex- plained by means of maternal kinship relationships.
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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... more
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.
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Background: Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return... more
Background: Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia.
Results: Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.
Conclusions: The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.
Results: Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.
Conclusions: The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.
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"Objectives: The aim of this study is to analyze mitochondrial DNA and Y-chromosome lineages in a range of Atlantic and Mediterranean populations of the Iberian Peninsula in search of genetic differences between both façades and to... more
"Objectives: The aim of this study is to analyze mitochondrial DNA and Y-chromosome lineages in a range of Atlantic and Mediterranean populations of the Iberian Peninsula in search of genetic differences between both façades and to uncover the most probable geographic origin and coalescence ages of lineages.
Methods: The control region of mitochondrial DNA and haplogroup diagnostic positions were analyzed in 575 subjects and Y-chromosome markers were typed in 260 unrelated males. Moreover, previously published data were compiled
and used in the analyses.
Results: The level of genetic structure deduced from uniparental markers for the Iberian Peninsula was weak, with stronger Atlantic versus Mediterranean than North to South differentiation and larger diversities in the South. In general, mitochondrial DNA haplogroups had mainly Paleolithic and Mesolithic coalescences in Europe, although some of them, ruling out drift effects, seem to have younger implantation in Central Europe and the Atlantic areas than in the Mediterranean (I, J, J2a, T1, and W) while others as N1 and X could have reached the Iberian Peninsula at the Neolithic transition. On the other hand, younger coalescence ages are being proposed for the arriving or spread of the bulk of Y-chromosome lineages in Europe.
Conclusions: The major haplotypic affinities found for all the Iberian Peninsula regions were always with North Africa and the Atlantic Islands. These results draw an Atlantic network that clearly resembles those of the Megalithic Copper and Bronze cultures at this part of Europe."
Methods: The control region of mitochondrial DNA and haplogroup diagnostic positions were analyzed in 575 subjects and Y-chromosome markers were typed in 260 unrelated males. Moreover, previously published data were compiled
and used in the analyses.
Results: The level of genetic structure deduced from uniparental markers for the Iberian Peninsula was weak, with stronger Atlantic versus Mediterranean than North to South differentiation and larger diversities in the South. In general, mitochondrial DNA haplogroups had mainly Paleolithic and Mesolithic coalescences in Europe, although some of them, ruling out drift effects, seem to have younger implantation in Central Europe and the Atlantic areas than in the Mediterranean (I, J, J2a, T1, and W) while others as N1 and X could have reached the Iberian Peninsula at the Neolithic transition. On the other hand, younger coalescence ages are being proposed for the arriving or spread of the bulk of Y-chromosome lineages in Europe.
Conclusions: The major haplotypic affinities found for all the Iberian Peninsula regions were always with North Africa and the Atlantic Islands. These results draw an Atlantic network that clearly resembles those of the Megalithic Copper and Bronze cultures at this part of Europe."
Research Interests:
A correct sex assignment of a given bone or bone fragment is of paramount importance for the archaeologist, anthropologist and in forensic medicine. Discriminant functions, combining several anthropometric measurements obtained from... more
A correct sex assignment of a given bone or bone fragment is of paramount importance for the archaeologist, anthropologist and in forensic medicine. Discriminant functions, combining several anthropometric measurements obtained from individuals with known sex are useful tools for this purpose, but it is essential to know exactly the sex from which the measures are obtained. This is an easy task in modern populations, but it is problematic in ancient ones, since even when the entire skeleton is available, diagnosis of sex is not 100% accurate. Sexing by genetic methods by amplifying the first intron of the amelogenin gene constitutes a much more accurate method for sexing bones and may be the gold standard for further elaboration of discriminant functions which may serve for sexing new bones dug up in future excavations. With this aim we have genetically sexed 52 (out of 59) tibiae belonging to the prehispanic population of El Hierro, in the Canary Islands (18 women), and then, performed discriminant functions combining several anthropometric variables. These functions show a high accuracy in sex diagnosis (94.2%, area under ROC curve=0.954 with the best of the functions), so that they allow correct sexing of tibiae or tibiae fragments (only proximal third, distal third or midshaft). Thus, genetic sexing obviates the problem of finding an accurate gold standard for the elaboration of discriminant functions for ancient bones. This method could be applied to other populations of different antiquity and different ethnicity.
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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... more
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.
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.
Research Interests:
Many studies presenting genetic analysis of dog breeds have been conducted without the inclusion of island dog breeds, although isolation can be one of the main factors in their origin. Here we report the genetic analysis at the nuclear... more
Many studies presenting genetic analysis of dog breeds have been conducted without the inclusion of island dog breeds, although isolation can be one of the main factors in their origin. Here we report the genetic analysis at the nuclear and mitochondrial DNA levels of five Canary Island dog breeds (Canarian Warren Hound, Canary Island Mastiff, Garafiano Shepherd, La Palma Rat-Hunter and El Hierro Wolfhound) to fill this gap and, at the same time, genetically characterize these breeds. We identified 168 alleles in autosomal microsatellites and 16 mitochondrial haplotypes. Observed and expected heterozygosities ranged from 0.556 to 0.783 and from 0.737 to 0.943 respectively. Furthermore, three
haplotypes were newly described and exclusive to a particular breed (A17+ in the Canary Island Mastiff; A33+ in the Canarian Warren Hound; Bi in the La Palma Rat-Hunter). The outcome of our analyses also revealed different breed histories consistent with historical documents and hypothetical origin designations. Although mtDNA haplotypes showed poor breed discriminating power, autosomal markers allowed a clear clustering of each single
population. We expect that our results, together with further analyses, will help to make the population histories of island dog breeds clearer.
haplotypes were newly described and exclusive to a particular breed (A17+ in the Canary Island Mastiff; A33+ in the Canarian Warren Hound; Bi in the La Palma Rat-Hunter). The outcome of our analyses also revealed different breed histories consistent with historical documents and hypothetical origin designations. Although mtDNA haplotypes showed poor breed discriminating power, autosomal markers allowed a clear clustering of each single
population. We expect that our results, together with further analyses, will help to make the population histories of island dog breeds clearer.
Research Interests:
Background: Caspase-12 (CASP12) modulates the susceptibility to sepsis. In humans, the ‘‘C’’ allele at CASP12 rs497116 has been associated with an increased risk of sepsis. Instead, the derived ‘‘T’’ allele encodes for an inactive... more
Background: Caspase-12 (CASP12) modulates the susceptibility to sepsis. In humans, the ‘‘C’’ allele at CASP12 rs497116 has been associated with an increased risk of sepsis. Instead, the derived ‘‘T’’ allele encodes for an inactive caspase-12. Interestingly, Eurasians are practically fixed for the inactive variant, whereas in Sub-Saharan Africa the active variant is still common (24%). This marked structure has been explained as a function of the selective advantage that the inactive caspase-12 confers by increasing resistance to infection. As regards to both when positive selection started acting and as to the speed with which fixation was achieved in Eurasia, estimates depend on the method and assumptions used, and can vary substantially. Using experimental evidence, we propose that, least in Eurasia, the increase in the frequency of the T allele might be related to the selective pressure exerted by the increase in zoonotic diseases transmission caused by the interplay between increased human population densities and a closer contact with animals during the Neolithic.
Methodolog/Principal Findings: We genotyped CASP12 rs497116 in prehistoric individuals from 6 archaeological sites from the North of the Iberian Peninsula that date from Late Upper Paleolithic to Late Neolithic. DNA extraction was done from teeth lacking cavities or breakages using standard anti-contamination procedures, including processing of the samples in a positive pressure, ancient DNA-only chamber, quantitation of DNAs by qPCR, duplication, replication, genotyping of associated animals, or cloning of PCR products. Out of 50, 24 prehistoric individuals could finally be genotyped for rs497116. Only the inactive form of CASP12 was found.
Conclusions/Significance: We demonstrate that the loss of caspase-12 in Europe predates animal domestication and that consequently CASP12 loss is unlikely to be related to the impact of zoonotic infections transmitted by livestock.
Methodolog/Principal Findings: We genotyped CASP12 rs497116 in prehistoric individuals from 6 archaeological sites from the North of the Iberian Peninsula that date from Late Upper Paleolithic to Late Neolithic. DNA extraction was done from teeth lacking cavities or breakages using standard anti-contamination procedures, including processing of the samples in a positive pressure, ancient DNA-only chamber, quantitation of DNAs by qPCR, duplication, replication, genotyping of associated animals, or cloning of PCR products. Out of 50, 24 prehistoric individuals could finally be genotyped for rs497116. Only the inactive form of CASP12 was found.
Conclusions/Significance: We demonstrate that the loss of caspase-12 in Europe predates animal domestication and that consequently CASP12 loss is unlikely to be related to the impact of zoonotic infections transmitted by livestock.
Research Interests:
El yacimiento de Paternanbidea (Ibero, Pamplona) resulta excepcional tanto por su antigüedad, Neolítico Antiguo (6.090-5.960 ± 40 años BP), como por las evidencias culturales que ha proporcionado. Los individuos recuperados se encuentran... more
El yacimiento de Paternanbidea (Ibero, Pamplona) resulta excepcional tanto por su antigüedad, Neolítico Antiguo (6.090-5.960 ± 40 años BP), como por las evidencias culturales que ha proporcionado. Los individuos recuperados se encuentran dispuestos en tres fosas dobles y una múltiple. El objetivo de este estudio es evaluar, mediante datos antropológicos y moleculares basados en la variabilidad del ADN mitocondrial (ADNmt), algunas interpretaciones tradicionales generadas a partir de las evidencias arqueológicas. Se han recuperado individuos de diferente sexo y edad lo que plantea la posibilidad de que existan relaciones familiares entre ellos. Sin embargo, los haplotipos mitocondriales resultantes no apoyan la existencia de relaciones familiares via materna entre los inhumados dentro de cada fosa. En cuanto a la variación genética entre fosas, la presencia del subhaplogrupo H3 en dos individuos de este yacimiento podría apoyar esta posibilidad. Del presente estudio podemos deducir que el patrón de enterramiento en este yacimiento, no se basa en relaciones familiares via materna, al menos para los individuos recuperados en la excavación arqueológica.
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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... more
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.
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.
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In this Short Communication, a shorter version of the standard DNA ethanol precipitacion and purification protocol is described. It uses a mixture of 70% ethanol, 75mM ammonium acetate and different concentrations of different carriers to... more
In this Short Communication, a shorter version of the standard DNA ethanol precipitacion and purification protocol is described. It uses a mixture of 70% ethanol, 75mM ammonium acetate and different concentrations of different carriers to perform DNA precipitation and washing in only one step.
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Comparison of available mitochondrial DNA data is some times hindered by the data presentation format. HaploSearch is a simple tool for transforming DNA sequences into haplotype data and vice versa, speeding up the manipulation of large... more
Comparison of available mitochondrial DNA data is some times hindered by the data presentation format. HaploSearch is a simple tool for transforming DNA sequences into haplotype data and vice versa, speeding up the manipulation of large datasets. Although designed for mitochondrial DNA, HaploSearch could be used with any kind of DNA type. HaploSearch program, detailed software instructions and example files are freely available on the web http://www.haplosite.com/haplosearch/.
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Mitochondrial DNA (mtDNA) and Y-chromosome variation has been studied in Bou Omrane and Bou Saad, two Tunisian Berber populations. In spite of their close geographic proximity, genetic distances between them were high and significant with... more
Mitochondrial DNA (mtDNA) and Y-chromosome variation has been studied in Bou Omrane and Bou Saad, two Tunisian Berber populations. In spite of their close geographic proximity, genetic distances between them were high and significant with both uniparental markers. A global analysis, including all previously studied Tunisian samples, confirmed the existence of a high female and male population structure in this country. Analyses of molecular variance analysis evidenced that this differentiation was not attributable to ethnic differences. Mantel test showed that, in all cases, Y-chromosome haplotypic distances correlated poorly with geography, whereas after excluding the more isolated samples of Bou Omrane and Bou Saad, the mtDNA pattern of variation is significantly correlated with geography. Congruently, the Nm ratio of males versus females pointed to a significant excess of female migration rate across localities, which could be explained by patrilocality, a common marriage system in rural Tunisia. In addition, it has been observed that cultural isolation in rural communities promotes, by the effect of genetic drift, stronger loss of diversity and larger genetic differentiation levels than those observed in urban areas as deduced from comparisons of their respective mean genetic diversity and their respective mean genetic distances among populations. It is likely that the permanent exodus from rural to urban areas will have important repercussions in the future genetic structure of this country.
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DNA quantification is a prerequisite for both low copy number (LCN) forensic analysis and ancient DNA (aDNA) studies. Moreover, if nuclear quantification is focused on the amelogenin locus, it also allows sex determination. Some of the... more
DNA quantification is a prerequisite for both low copy number (LCN) forensic analysis and ancient DNA (aDNA) studies. Moreover, if nuclear quantification is focused on the amelogenin locus, it also allows sex determination. Some of the problems of these techniques are allelic drop-out phenomenon in amelogenin locus and mitochondrial DNA (mtDNA) quantification biases, due to human intraspecific variation affecting the annealing of primers and/or probes. The method presented here combines two multiplex TaqMan1 real-time PCR (qPCR) for nuclear and mtDNA quantification in degraded or limited samples. Nuclear DNA detection is based on the independent amplification of X and Y chromosome specific fragments in the amelogenin locus and an internal PCR control (IPC) to recognize inhibition problems. The small length of the fragments (71 bp) favors the quantification of severely degraded DNA, whereas the use of two distinct primer sets for X and Y chromosome amplification is directed to reduce allelic drop-out in LCN analysis. MtDNA quantification is based on the amplification of three PCR fragments located in the mtDNA 16S region. Two of them are amplified with human specific conservative primers and probes, which allows a world-wide application of this technique. Moreover, their length difference (167 and 314 bp respectively), provides information about the DNA degradation level. In order to also recognize non-human DNA an interspecific mtDNA fragment (187 bp) was also designed.
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During the Spanish Civil War (1936–1939), the Canary Islands suffered one of the highest levels of repression by the insurgent side, even though there were no battles in the islands. More than 50 people were killed in the island of La... more
During the Spanish Civil War (1936–1939), the Canary Islands suffered one of the highest levels of repression by the insurgent side, even though there were no battles in the islands. More than 50 people were killed in the island of La Palma between July 1936 and June 1937. The Association for the Recovery of Historical Memory in La Palma, made up of relatives of people who went missing during the Civil War, located the Fuencaliente mass graves in 2004. The excavation process recovered eight skeletal remains. The aim of this work was the genetic identification of these reprisal victims. In general, obtaining nuclear DNA profiles from old skeletal samples is known to be difficult. Due to the age and conservation conditions, this was the case for the Fuencaliente remains. For these reasons, we firstly attempted to analyze the mitochondrial DNA (mtDNA). Although mtDNA control region sequences were obtained for the eight skeletal remains, the limited number of possible maternal relative donors complicated identification based only on mtDNA. Taking into account the problems in establishing identity by using mtDNA, a few years later we were presented with the possibility of analyzing nuclear DNA using the new PrepFiler Express BTATM Forensic DNA extraction methodology. This extraction protocol, in combination with the new AmpF‘STR1 NGMTM PCR Amplification Kit (Applied Biosystems), allowed us to obtain full nuclear DNA profiles for the eight victims. In conclusion, the use of specific protocols designed for old DNA samples, such as PrepFiler Express BTATM Forensic DNA extraction and AmpF‘STR1 NGMTM PCR amplification kit seems to be crucial for obtaining full nuclear profiles that allow statistically significant identification of the putative relatives.
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Hairs are common biological samples in crime scene investigation. However, most of this evidence is comprised of hair fragments without the root. As the major part of DNA is located in the root, hair shafts are usually problematic samples... more
Hairs are common biological samples in crime scene investigation. However, most of this evidence is comprised of hair fragments without the root. As the major part of DNA is located in the root, hair shafts are usually problematic samples in forensic analysis. For these reasons, hair DNA typing is directed at mitochondrial DNA (mtDNA), which is present in high copy number in each cell, instead of nuclear DNA analysis. In our laboratory, we have used the PrepFiler BTATM extraction method for routinely processing difficult samples such as old bones or cigarette butts, obtaining good quality DNA in all cases. As the use of automatic extraction methods has been progressively introduced in forensic laboratories, we have tested the applicability of the PrepFiler BTATM extraction method in combination with AutoMate ExpressTM equipment, to the analysis of hair shafts. In order to determine the efficiency of the method, DNA extractions were quantified using a real-time PCR approach, and mtDNA fragments of different lengths were amplified to determine DNA degradation. We also processed several types of hairs, with different characteristics (thickness, gender, antiquity and hair dyeing) and from diverse ethnical groups. In all cases, the PrepFiler BTA ExpressTM extraction method showed very reproducible results in obtaining DNA from hair shafts, its application being highly recommendable as a routine protocol in forensic laboratories.
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Macaronesia covers four Atlantic archipelagos: the Azores, Madeira, the Canary Islands, and the Cape Verde islands. When discovered by Europeans in the 15th century, only the Canaries were inhabited. Historical reports highlight the... more
Macaronesia covers four Atlantic archipelagos: the Azores, Madeira, the Canary Islands, and the Cape Verde islands. When discovered by Europeans in the 15th century, only the Canaries were inhabited. Historical reports highlight the impact of Iberians on settlement in Macaronesia. Although important differences in their settlement are documented, its influence on their genetic structures and relationships has yet to be ascertained. In this study, the hypervariable region I (HVRI) sequence and coding region polymorphisms of mitochondrial DNA (mtDNA) in 623 individuals from the Azores (120) and Canary Islands (503) were analyzed. Combined with published data, these give a total of 1,542 haplotypes from Macaronesia and 1,067 from the Iberian Peninsula. The results obtained indicate that Cape Verde is the most distinctive archipelago, with an mtDNA pool composed almost exclusively of African lineages. However, the other archipelagos present an mtDNA profile dominated by the presence of West-Eurasian mtDNA haplogroups with African lineages present in varying proportions. Moreover, no signs of integration of typical Canarian U6 lineages in the other archipelagos were detected. The four Macaronesia archipelagos currently have differentiated genetic profiles, and the Azores present the highest intra-archipelago differentiation and the lowest values of diversity. The analyses performed show that the present-day genetic profile of the Macaronesian archipelagos was mainly determined by the initial process of settlement and further microdifferentiation probably as a consequence of the small population size of some islands. Moreover, contacts between archipelagos seem to have had a low impact on the mtDNA genetic pool of each archipelago.
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It has been proposed that the distribution patterns and coalescence ages found in Europeans for mitochondrial DNA (mtDNA) haplogroups V, H1 and H3 are the result of a post-glacial expansion from a Franco-Cantabrian refuge that recolonized... more
It has been proposed that the distribution patterns and coalescence ages found in Europeans for mitochondrial DNA (mtDNA) haplogroups V, H1 and H3 are the result of a post-glacial expansion from a Franco-Cantabrian refuge that recolonized central and northern areas. In contrast, in this refined mtDNA study of the Cantabrian Cornice that contributes 413 partial and 9 complete new mtDNA sequences, including a large Basque sample and a sample of Asturians, no experimental evidence was found to support the human refuge-expansion theory. In fact, all measures of gene diversity point to the Cantabrian Cornice in general and the Basques in particular, as less polymorphic for V, H1 and H3 than other southern regions in Iberia or in Central Europe. Genetic distances show the Cantabrian Cornice is a very heterogeneous region with significant local differences. The analysis of several minor subhaplogroups, based on complete sequences, also suggests different focal expansions over a local and peninsular range that did not affect continental Europe. Furthermore, all detected clinal trends show stronger longitudinal than latitudinal profiles. In Northern Iberia, it seems that the highest diversity values for some haplogroups with Mesolithic coalescence ages are centred on the Mediterranean side, including Catalonia and South-eastern France.
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DNA extraction methods for genotyping non-invasive samples have led to great advances in molecular research for ecological studies, and have been particularly useful for analyzing threatened species. However, scarce amounts of fragmented... more
DNA extraction methods for genotyping non-invasive samples have led to great advances in molecular research for ecological studies, and have been particularly useful for analyzing threatened species. However, scarce amounts of fragmented DNA and the presence of Taq polymerase inhibitors in non-invasive samples are potential problems for subsequent PCR amplifications. In this study we describe a novel technique for extracting DNA from alimentary tract cells found on external surfaces of feces and regurgitated seeds. The presence of contaminants and inhibitors is minimized and samples are preserved intact for use in other ecological research (e.g. trophic studies). The amplification efficiency and purity of the extracted DNA from feces were significantly higher than in commonly used extraction procedures. Moreover, DNA of two bird species was identified from seeds expelled by regurgitation. Therefore, this method may be suitable for future ecological studies of birds, and other vertebrate groups.
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Teeth from 38 aboriginal remains of La Palma (Canary Islands) were analyzed for external and endogenous mitochondrial DNA control region sequences and for diagnostic coding positions. Informative sequences were obtained from 30... more
Teeth from 38 aboriginal remains of La Palma (Canary Islands) were analyzed for external and endogenous mitochondrial DNA control region sequences and for diagnostic coding positions. Informative sequences were obtained from 30 individuals (78.9%). The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription. The bulk of the aboriginal haplotypes had exact matches in North Africa (70%). However, the indigenous Canarian sub-type U6b1, also detected in La Palma, has not yet been found in North Africa, the cradle of the U6 expansion. The most abundant H1 clade in La Palma, defined by transition 16260, is also very rare in North Africa. This means that the exact region from which the ancestors of the Canarian aborigines came has not yet been sampled or that they have been replaced by later human migrations. The high gene diversity found in La Palma (95.2±2.3), which is one of the farthest islands from the African continent, is of the same level than the previously found in the central island of Tenerife (92.4±2.8). This is against the supposition that the islands were colonized from the continent by island hopping and posterior isolation. On the other hand, the great similarity found between the aboriginal populations of La Palma and Tenerife is against the idea of an island-by-island independent maritime colonization without secondary contacts. Our data better fit to an island model with frequent migrations between islands.
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Background: The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th–18th century remains,... more
Background: The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th–18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.
Results: Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th–18th centuries than today.
Conclusion: The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.
Results: Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th–18th centuries than today.
Conclusion: The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.
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The indigenous Canary Islands population suffered a strong cultural and genetic impact when they were colonized by Europeans in the fifteenth century. The molecular analysis of the ABO blood group gene on aboriginal and seventeenth to... more
The indigenous Canary Islands population suffered a strong cultural and genetic impact when they were colonized by Europeans in the fifteenth century. The molecular analysis of the ABO blood group gene on aboriginal and seventeenth to eighteenth century remains confirms the demographic history of the islands depicted by previous archaeological, anthropological, and genetic studies. ABO allele frequencies clearly related Canarian aborigines with North African Berber populations, its most probable source of origin, and is far related to Iberian and to the current population of the archipelago. The historical sample shows a congruent intermediate position testifying already a strong European influence that would go in augment since then to present times, affecting all the islands with the important exception of La Gomera.
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The dietary pattern of 10 adults interred in the Acceso al Pescante de Vallehermoso cave (La Gomera, Canary Islands), dated from 1600 to 1800 years BP, has been investigated using carbon and nitrogen stable isotope signatures, bone barium... more
The dietary pattern of 10 adults interred in the Acceso al Pescante de Vallehermoso cave (La Gomera, Canary Islands), dated from 1600 to 1800 years BP, has been investigated using carbon and nitrogen stable isotope signatures, bone barium and strontium levels, and dental and oral pathologies. In addition, trabecular bone mass – as a parameter useful to evaluate overall nutrition – was also determined. The majority of the studied individuals died before 35 years. Diet was mixed, mainly based on C3 plants and probably sea snails. The prevalence of carious lesions was low, but the intensity of dental attrition was high. They did not show osteopenia, but bone mass was lower among those who died at earlier ages. Based on anatomical characteristics it was inferred that the majority of individuals buried in this cave were women. This sex determination was confirmed by DNA molecular sexing using the amelogenin gene. There were no gender differences in dietary pattern or bone mass.
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Aims: The calcium chloride chemical transformation of Escherichia coli is still the most widley used cloning method in small laboratories. Therefore, any practicable improvement in its transformation efficiency seems to be of general... more
Aims: The calcium chloride chemical transformation of Escherichia coli is still the most widley used cloning method in small laboratories. Therefore, any practicable improvement in its transformation efficiency seems to be of general interest.
Methods and Results: We found that giving calcium chloride competent cells a 1 min microwave pulse at the lowest power setting (180 W), instead of the classic 1–2 min 42_C heat-shock step, increases the transformation efficiency around threefold (3.3 ± 0.5). Moreover, when both treatments were given in a 2-min 42_C ) 5 min on ice ) 1 min microwave pluse sequence, an additional improvement of 1.6 was obtained, resulting in an overall increase in efficiency of approximately 5.3-fold compared to classical heat shock.
Conclusions: This transformation method significantly improves the classical heat shock treatment.
Significance and Impact of the Study: This method might be useful to those laboratories that cannot afford an electroporation apparatus.
Methods and Results: We found that giving calcium chloride competent cells a 1 min microwave pulse at the lowest power setting (180 W), instead of the classic 1–2 min 42_C heat-shock step, increases the transformation efficiency around threefold (3.3 ± 0.5). Moreover, when both treatments were given in a 2-min 42_C ) 5 min on ice ) 1 min microwave pluse sequence, an additional improvement of 1.6 was obtained, resulting in an overall increase in efficiency of approximately 5.3-fold compared to classical heat shock.
Conclusions: This transformation method significantly improves the classical heat shock treatment.
Significance and Impact of the Study: This method might be useful to those laboratories that cannot afford an electroporation apparatus.
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Sex determination using mandible parameters is population dependent. In order to assess which measurements better characterize sex in prehispanic individuals from the Canary Islands, we blindly contrasted the results obtained by visual... more
Sex determination using mandible parameters is population dependent. In order to assess which measurements better characterize sex in prehispanic individuals from the Canary Islands, we blindly contrasted the results obtained by visual inspection and osteometric measurements with those obtained by molecular sexing using amelogenin ancient DNA analysis on teeth from the same material. Unambiguous sex classification was achieved by amplification of sex specific amelogenin alleles in 56 out of 76 mandibles (73.78% of the cases). Visual inspection led to a correct diagnosis in 66.04% of cases, with a greater proportion of errors for female (54.17%) than male (17.24%) mandibles. Osteometric measurements were able to assign sex correctly in 72.2% in the best of cases (mandibular height), a proportion similar to that obtained using a discriminant function (71.2%). By logistic regression analysis, ramus breadth, index ramus breadth/ramus height and mandibular length were the parameters independently related with a mistaken diagnosis of female sex, whereas bigonial width, ramus height and mandibular length were the parameters more closely and independently related to a mistaken diagnosis of male sex. In conclusion, diagnosis based on visual examination of the mandible or on its metric measurement only serves to roughly estimate sex with an accuracy of around 70% or less, at least among the prehispanic population from Gran Canaria. Amplification of amelogenin alleles leads to unambiguous identification of male and female alleles in 73.68% of cases, at least among the prehispanic population from Gran Canaria.
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Mitochondrial DNA sequences and restriction fragment polymorphisms were retrieved from three Islamic 12th–13th century samples of 71 bones and teeth (with >85% efficiency) from Madinat Baguh (today called Priego de Cordoba, Spain).... more
Mitochondrial DNA sequences and restriction fragment polymorphisms were retrieved from three Islamic 12th–13th century samples of 71 bones and teeth (with >85% efficiency) from Madinat Baguh (today called Priego de Cordoba, Spain). Compared with 108 saliva samples from the present population of the same area, the medieval samples show a higher proportion of sub-Saharan African lineages that can only partially be attributed to the historic Muslim occupation. In fact, the unique sharing of transition 16175, in L1b lineages, with Europeans, instead of Africans, suggests a more ancient arrival to Europe from Africa. The present day Priego sample is more similar to the current south Iberian population than to the medieval sample from the same area. The increased gene flow in modern times could be the main cause of this difference.
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Mitochondrial DNA sequences and restriction fragment length polymorphisms were retrieved (with >80% efficiency) from a 17th–18th century sample of 213 teeth from Tenerife. The genetic composition of this population reveals an important... more
Mitochondrial DNA sequences and restriction fragment length polymorphisms were retrieved (with >80% efficiency) from a 17th–18th century sample of 213 teeth from Tenerife. The genetic composition of this population reveals an important ethnic heterogeneity. Although the majority of detected haplotypes are of European origin, the high frequency of sub-Saharan African haplotypes (15.63%), compared to that of the present-day population (6.6%), confirms the importance of the Canary Islands in the black slave trade of that epoch. The aboriginal substrate, inferred from the U6b1 haplotypes (8.59%), has also decreased due to European input. Finally, the presence of Amerindian lineages (1.5%) reveals that the Canary Islands have also received genetic flow from America.
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A simple and affordable multiplex polymerase chain reaction–single-strand conformation polymorphism method is proposed for the molecular study of AB0 polymorphisms. Application of this method to the peopling of the Canary Islands,... more
A simple and affordable multiplex polymerase chain reaction–single-strand conformation polymorphism method is proposed for the molecular study of AB0 polymorphisms. Application of this method to the peopling of the Canary Islands, analyzing a total of 2,200 chromosomes, detected that in addition to Berbers and Basques, the rare alleles 0210 and O303 are also present in the Iberian Peninsula and in the Canary Islands. Allele B101, with the highest frequency in Northwest (NW) Africa, shows a negative correlation (R=−0.822, p=0.023) between geographic distances from this continent and insular frequencies, congruent with a main aborigine colonization from East to West still detectable today. Similar to previous autosomal studies, admixture estimations point to a major Iberian contribution (82±0.5%) to the Canary Islands, although, in some islands as La Gomera, the NW African component raised to 62±4.3%.
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During the archaeological study of infantile remains it is crucial to achieve sex determination through accurate methods. This enables the possibility to study the social component of various behaviors related with boys and girls. Sex... more
During the archaeological study of infantile remains it is crucial to achieve sex determination through accurate methods. This enables the possibility to study the social component of various behaviors related with boys and girls. Sex determination through molecular genetics - e.g. through the analysis of the amelogenin gene - entails many methodological difficulties, due to the infantile’s bones and teeth own consistency and characteristics. For adult populations this type of analysis has been made using well preserved teeth, achieving very good results. Infantile teeth are prone to be affected by DNA degradation and/or contamination, leading to the need of using alternative bones that diminish the risks. In this work a molar and a phalanx of a 7-years-old guanche individual, from Tenerife, were analyzed. The remains were found in an individual grave inside a cave, with signs of mummification. DNA extraction were carried out following the protocols presented by Maca-Meyer et al. 2004 and Casas et al. 2006, for teeth and bones respectively. Both mitochondrial and nuclear DNA was then quantified, following the methodology proposed in Fregel et al. 2011. As the nuclear amplicons are located in the amelogenin locus, this analysis allow both DNA quantification and sex determination. The quantification values for the mtDNA asses a good preservation state. A higher quantity of DNA was found in the phalanx (3,67E+0,4 copies/µl) than in the molar (1,75E+0,3 copias/ µl). Both samples showed a male profile, once again finding a higher concentration of DNA in the phalanx. The obtained results prove the applicability of well-preserved infantile phalanxes as a source of genetic material for DNA studies, and for the sex determination of infantile bone remains.
El género Gallotia (Arnold 1973) es endémico de las Islas Canarias, representado en las diferentes islas por 7 especies y 9 subespecies. Concretamente, el Lagarto Gigante de La Gomera (Gallotia bravoana) está restringido a una pequeña... more
El género Gallotia (Arnold 1973) es endémico de las Islas Canarias, representado en las diferentes islas por 7 especies y 9 subespecies. Concretamente, el Lagarto Gigante de La Gomera (Gallotia bravoana) está restringido a una pequeña área de poco más de una hectárea situada en el risco de La Mérica, al oeste de la isla. Esta especie es sin duda una de las especies más amenazadas del planeta, con una población natural de 120 individuos aproximadamente. El estado tan precario que presenta esta población y la necesidad de continuar con un plan de acción para evitar su extinción requieren de un conocimiento profundo de la diversidad genética que presenta tanto la población cautiva del Centro de Recuperación de Valle Gran Rey, como la población natural. Debido a su alta variabilidad y su amplia distribución por el genoma, los microsatélites son actualmente las herramientas moleculares de elección para determinar el grado de parentesco entre individuos de una misma especie. Además, éstos pueden ser amplificados a partir de pequeñas muestras que no implican el fallecimiento del animal, condición indispensable en el análisis de poblaciones amenazadas. Por todo ello, se realizó un aislamiento de microsatélites específicos para la especie Gallotia bravoana, a partir de una genoteca enriquecida para microsatélites tetranucleótidos (AAAG, AAGG, GATA y AAAT). De los 15 loci satisfactoriamente amplificados (n = 154; 121 cautivos y 33 de la población natural), 5 de ellos resultaron ser monomórficos, 9 fueron dimórficos y uno presentaba 3 alelos diferentes. Tanto el número de alelos detectados (max. 3 alelos / locus) como los valores de heterocigosidad obtenidos (0.189-0.664 para la población cautiva; 0.182-0.679 para la población natural) son relativamente bajos comparados con otras especies de Gallotia. Además, un locus se desvió significativamente de las condiciones de equilibrio de Hardy- Weinberg, y 9 parejas de loci presentaron valores significativos de desequilibrio de ligamiento. Con respecto al coeficiente de endogamia, ningún valor FIS fue significativo. Los valores estimados reflejan la baja variabilidad que presenta tanto la población cautiva como la natural del Lagarto Gigante de La Gomera. Sin embargo, los datos cosechados son de un valor incalculable para la conservación de esta especie, ya que conociendo el genotipado de los individuos cautivos, se puede establecer un plan de cría que permita, al menos, mantener el nivel de variabilidad existente.
During the Spanish Civil War (1936–1939), Canary Islands suffered the highest levels repression by the insurgent side, although there were no battles in the islands. More than 50 people were killed in La Palma Island between July 1936 and... more
During the Spanish Civil War (1936–1939), Canary Islands suffered the highest levels repression by the insurgent side, although there were no battles in the islands. More than 50 people were killed in La Palma Island between July 1936 and June 1937. The “Association for the Recovery of Historical Memory in La Palma”, made up of relatives of people who went missing during the Civil War, located “The Fuencaliente mass graves” in 2004. The excavation process recovered eight victims skeletal remains. The aim of this work was the genetic identification of the reprisal victims. In general, obtaining nuclear DNA profiles from old skeletal samples is assumed to be difficult, due to the age and conservation conditions of the remains. For these reasons, we firstly try to analyze the mithocondrial DNA (mtDNA). Although the mtDNA control region sequence was obtained for the eight skeletal remains, the limited number of suspected maternal relatives donors complicated the identification based on mtDNA. Taking into account the problems in stablishing the identity using mtDNA, a few years later we decided to analyze the nuclear DNA using the new forensic PrepFiler BTA DNA Automatic extraction methodology. This extraction method, in combination with the new AmpFℓSTR NGM PCR Amplification Kit (Applied Biosystems), allowed us to obtain the nuclear DNA full profile of eight skeletal bodies. In conclusion, the use of protocols designed for old DNA samples, such as PrepFiler BTA Extraction Kit and NGM PCR Amplification Kit was crucial for obtaining full profiles that allowed high significance results.
Hairs are common biological samples in crime scene investigation. However, most of hairs are fragments without root. As the majority of DNA is located in the root, hairs are usually problematic samples in forensic analysis. For these... more
Hairs are common biological samples in crime scene investigation. However, most of hairs are fragments without root. As the majority of DNA is located in the root, hairs are usually problematic samples in forensic analysis. For these reasons, hair DNA typing is directed to mitochondrial DNA (mtDNA), which is present in high copy numbers in each cell, instead of nuclear DNA profiles. There are some protocols for DNA isolation from hair shafts as phenol/chloroform, proteinase K, silica based methods, chelex, alkaline digestion. Some of these methods can involve a number of steps, each of which add time to the procedure and increase the risk of contamination. Other of these methods reduces the processing time, but leads to the DNA degradation. In our laboratory, we have used the PrepFiler BTA extraction method for routinely processing difficult samples as old bones or cigarette butts, obtaining in all cases clean DNA. The use of automatic extraction methods has been progressively introduced in forensic laboratories. For these reasons we decided to apply DNA extraction from hair shafts using the PrepFiler Express BTA extraction method in combination with AutoMate Express equipment. In order to determine the efficiency of the method, DNA extractions were quantified using a real-time PCR approach, and mtDNA fragments of different length were amplified to determine DNA degradation. Moreover, we have processed several types of hairs with different characteristics (gender, antiquity, hair dyeing) and from diverse ethical groups.
DNA quantification is a prerequisite for both low copy number (LCN) forensic analysis and ancient DNA studies. Moreover, if nuclear quantification is focused on the amelogenin locus, it also allows for sex determination. Some of the... more
DNA quantification is a prerequisite for both low copy number (LCN) forensic analysis and ancient DNA studies. Moreover, if nuclear quantification is focused on the amelogenin locus, it also allows for sex determination. Some of the problems of these techniques are allelic drop-out phenomenon in amelogenin locus and mitochondrial DNA (mtDNA) quantification biases, due to the occurrence of mutations affecting the annealing of primers and/or probes. The method presented here combines two multiplex TaqMan real-time PCR for nuclear and mtDNA quantification in degraded or limited samples. Nuclear DNA detection is based in the independent amplification of X and Y chromosome specific fragments in the amelogenin locus, and a internal PCR control to recognize inhibition problems. The small length of the fragments (71 bp) favors the quantification of severely degraded DNA, whereas the use of two distinct primer sets for X and Y chromosome amplification is directed to reduce allelic drop-out in LCN analysis. MtDNA quantification is based on the amplification of three PCR fragments located in the mtDNA 16S region. Two of them are amplified with conservative primers and probes, allowing a world-wide application for this technique. Moreover, their length difference (95 and 314 bp respectively), provides information about the DNA degradation level. As these conserved fragments could be amplified in other primate species (e.g. Pan troglodytes), a specific human mtDNA fragment (167 bp) was also designed to recognize non-specific amplification.
La Caspasa-12 (CASP12) es una proteasa que ejerce funciones apoptóticas, inhibe la inflamación celular y modula la susceptibilidad a sepsis. El SNP rs497116 determina dos estados funcionales para CASP12: un alelo funcional, supuestamente... more
La Caspasa-12 (CASP12) es una proteasa que ejerce funciones apoptóticas, inhibe la inflamación celular y modula la susceptibilidad a sepsis. El SNP rs497116 determina dos estados funcionales para CASP12: un alelo funcional, supuestamente el alelo ancestral, y que muestra una frecuencia sustancial en África Sub-Sahariana (24%) y un alelo inactivo, que está prácticamente fijado en Eurasia. La alta frecuencia de este alelo en Eurasia ha sido atribuida a una ventaja selectiva relacionada con la resistencia a la infección. Hemos investigado si la domesticación animal ocurrida a partir del Neolítico, asociada a un incremento significativo de infecciones zoonóticas, podría explicar la pérdida del alelo activo de CASP12 en Europa. Así, hemos genotipado el SNP de CASP12 rs497116 en 25 muestras seleccionadas de ADN humano Neolíticas y pre-Neolíticas del Norte de la Península Ibérica. Todas las muestras resultaron ser homocigotas para el alelo inactivo. Esto demuestra empíricamente que la pérdida de la función CASP12 en Europa fue un evento que precedió la domesticación animal, y que desestima que las infecciones zoonóticas hayan tenido un papel principal en la pérdida de CASP12 en humanos.
Catalunya, situada al NE de la Península Ibérica, ocupa un territorio de unos 32.000 km2. Orográficamente está condicionada por el litoral mediterráneo al E, con 580 kilómetros de costa y por los Pirineos al N. Hasta el momento, no se ha... more
Catalunya, situada al NE de la Península Ibérica, ocupa un territorio de unos 32.000 km2. Orográficamente está condicionada por el litoral mediterráneo al E, con 580 kilómetros de costa y por los Pirineos al N. Hasta el momento, no se ha realizado ningún estudio genético sistematizado de esta población dado que los estudios existentes se centran principalmente en la region de los Pirineos. El objetivo del presente trabajo es obtener el perfil genético, basado en el ADN mitocondrial (ADNmt) y hacer un análisis a nivel microgeográfico de dicha variación considerando las distintas provincias. Se han muestreado un total de 209 individuos autóctonos catalanes hasta 3 generaciones (71 de Barcelona, 31 de Girona, 38 de Lleida y 69 de Tarragona) y se han considerado a efectos de origen de la muestra el lugar de nacimiento de la abuela materna. Para cada uno de estos individuos se ha amplificado y secuenciado la región hipervariable del ADNmt. Los resultados muestran unas frecuencias de haplogrupos similares a las reportadas anteriormente para el conjunto de poblaciones del nordeste peninsular, aunque las frecuencias de los haplogrupos H y K son ligeramente más altas que la media obtenida para las mencionadas poblaciones. Considerando la distribución de haplogrupos por provincias, se pueden apreciar diferencias, destacando la heterogeneidad en la frecuencia de los haplogrupos H, K y J. Estos resultados muestran la importancia de realizar estudios genéticos a nivel microgeográfico que permiten poner de manufesto la verdadera heterogeneidad de un territorio.
La necrópolis de la Cueva de Montaña (S. Bartolomé) es prácticamente el único yacimiento de Lanzarote con restos humanos que puede atribuirse con seguridad de su población aborigen. Se trata de un depósito colectivo, organizado en dos... more
La necrópolis de la Cueva de Montaña (S. Bartolomé) es prácticamente el único yacimiento de Lanzarote con restos humanos que puede atribuirse con seguridad de su población aborigen. Se trata de un depósito colectivo, organizado en dos áreas sepulcrales. En una de ellas se registró un depósito de 7 cráneos acompañados de una selección de huesos largos. En el trabajo actual se pretende abordar por primera vez la caracterización genética de la población aborigen de Lanzarote a a partir del estudio del ADN mitocondrial (ADNmt). Para ello se han utilizado 11 dientes en buen estado de conservación, procedentes de 10 mandíbulas y 1 maxilar pertenecientes a 8 individuos del citado yacimiento. El estudio morfológico de las mandíbulas mostró un alto grado de robustez, tanto en hombres como mujeres, que las distingue de otras series insulares. La extracción de ADNmt fue efectiva en seis de los ocho individuos estudiados. Los resultados muestran que los haplogrupos encontrados tienen una distribución similar a los establecidos por Rando, Maca-Meyer y Fregel para las poblaciones aborígenes de otras islas del Archipiélago. Destaca la presencia del haplogrupo U6 de origen norteafricano, así como el haplogrupo H.
El uso de marcadores autosómicos es necesario para obtener una visión complementaria a la de los marcadores uniparentales. En general, las frecuencias observadas en la población actual de Canarias son similares a las de la Península... more
El uso de marcadores autosómicos es necesario para obtener una visión complementaria a la de los marcadores uniparentales.
En general, las frecuencias observadas en la población actual de Canarias son similares a las de la Península Ibérica para todos los marcadores autosómicos, pero con cierta influencia norteafricana, explicada por ejemplo por la presencia del haplotipo 110(-) del marcador CD4/Alu o la alta frecuencia de alelo cDe del grupo Rh.
Igualmente, el uso de estimadores de mezcla señala a una mayor aportación de la Península Ibérica (en torno al 70-89%), con unos valores intermedios entre los obtenidos mediante el uso de ambos marcadores uniparentales, ADNmt (≈ 67%) y cromosoma Y (≈ 90%).
Por otro lado, el estudio en poblaciones actuales de marcadores autosómicos también ha aportado cierta información sobre el poblamiento de Canarias. Concretamente, los haplotipos CD4/Alu y el locus ABO han mostrado una correlación negativa entre la distancia de las islas al continente africano, y la heterocigocidad insular y la frecuencia del alelo B101, respectivamente. Este resultado, podría deberse a una colonización aborigen dominante de este a oeste desde África.
Finalmente, al determinar el marcador autosómico ABO en poblaciones aborígenes se confirma el origen norteafricano de la población prehispánica. Por otro lado, la muestra histórica del S.XVIII, se sitúa en una posición intermedia entre la población aborigen y la actual, evidenciando el fuerte impacto de la conquista y posterior colonización de la islas sobre la población indígena.
En general, las frecuencias observadas en la población actual de Canarias son similares a las de la Península Ibérica para todos los marcadores autosómicos, pero con cierta influencia norteafricana, explicada por ejemplo por la presencia del haplotipo 110(-) del marcador CD4/Alu o la alta frecuencia de alelo cDe del grupo Rh.
Igualmente, el uso de estimadores de mezcla señala a una mayor aportación de la Península Ibérica (en torno al 70-89%), con unos valores intermedios entre los obtenidos mediante el uso de ambos marcadores uniparentales, ADNmt (≈ 67%) y cromosoma Y (≈ 90%).
Por otro lado, el estudio en poblaciones actuales de marcadores autosómicos también ha aportado cierta información sobre el poblamiento de Canarias. Concretamente, los haplotipos CD4/Alu y el locus ABO han mostrado una correlación negativa entre la distancia de las islas al continente africano, y la heterocigocidad insular y la frecuencia del alelo B101, respectivamente. Este resultado, podría deberse a una colonización aborigen dominante de este a oeste desde África.
Finalmente, al determinar el marcador autosómico ABO en poblaciones aborígenes se confirma el origen norteafricano de la población prehispánica. Por otro lado, la muestra histórica del S.XVIII, se sitúa en una posición intermedia entre la población aborigen y la actual, evidenciando el fuerte impacto de la conquista y posterior colonización de la islas sobre la población indígena.
The discovery of a new burial site on a farmland in Santa Maria de Guia (Gran Canaria), motivated archaeological works which revealed a burial ground holding skeletal remains of fourteen individuals. There are numerous pieces of evidence... more
The discovery of a new burial site on a farmland in Santa Maria de Guia (Gran Canaria), motivated archaeological works which revealed a burial ground holding skeletal remains of fourteen individuals.
There are numerous pieces of evidence that point towards the interpretation that the individuals could have been part of a slave burial ground. These evidences are given by the immediate surrounds directly relevant to the cemetery use, and also by the burial practices, which have not been recorded yet in Gran Canaria.
In order to determine the genetic origins of the human remains, mitochondrial DNA determinations were carried out from each individual skeleton.
There are numerous pieces of evidence that point towards the interpretation that the individuals could have been part of a slave burial ground. These evidences are given by the immediate surrounds directly relevant to the cemetery use, and also by the burial practices, which have not been recorded yet in Gran Canaria.
In order to determine the genetic origins of the human remains, mitochondrial DNA determinations were carried out from each individual skeleton.
En el presente estudio nos centramos en el análisis morfológico y genético de los restos esqueléticos de 11 individuos inhumados en cuatro fosas diferentes en el yacimiento neolítico de Paternanbidea (Ibero, Pamplona). El objetivo es... more
En el presente estudio nos centramos en el análisis morfológico y genético de los restos esqueléticos de 11 individuos inhumados en cuatro fosas diferentes en el yacimiento neolítico de Paternanbidea (Ibero, Pamplona). El objetivo es evaluar mediante los datos antropológicos y moleculares, las interpretaciones generadas a partir de las evidencias arqueológicas. Se ha llevado a cabo la estimacion de la edad y el sexo de los inhumados a nivel morfológico, así como el estudio de la variabilidad del ADN mitocondrial (ADNmt) mediante el análisis de la secuencia del segmento I de la región control y los motivos de la región codificante. Se han tenido en cuenta todas las precauciones para evitar la contaminación, realizándose los diferentes criterios de autentificación de los resultados. Los haplotipos mitocondriales no apoyan la existencia de relaciones via materna entre los inhumados en cada fosa. A pesar del pequeño tamaño de la muestra, la diversidad hallada es alta, lo que nos estaría indicando que no se trata de una población pequeña ni aislada. Este tipo de analisis indica la importancia de los estudios antropológicos para evaluar las interpretaciones tradicionales del ambito arqueológico.
In this work, we present the results of the genetic analyses done on human remains from seven prehistorical sites of the Basque Country. The chronology of the sites ranges from the Mesolithic to the Bronze Age: Erralla (Gipuzkoa), Aizpea... more
In this work, we present the results of the genetic analyses done on human remains from seven prehistorical sites of the Basque Country. The chronology of the sites ranges from the Mesolithic to the Bronze Age: Erralla (Gipuzkoa), Aizpea (Navarra), Los Cascajos (Navarra), Paternanbidea (Navarra), Fuente Hoz (Álava), Marizulo (Gipuzkoa), Urtiaga (Gipuzkoa). We have sequenced the segment I of the control region of the mitochondrial DNA (mtDNA) in the global prehistoric sample of 46 individuals, and in addition, we have typed the coding region motifs that allow us to determine the main European mitochondrial haplogroups. During this process, we have taken into account all the authentification criteria that are usually demanded.
The frequencies of the mtDNA haplogroups observed are compared to those already reported in the literature from a) other ancient populations from the Basque Country (the prehistoric sites of Longar, Pico Ramos and SJAPL), b) the historical site of Aldaieta and c) those corresponding to extant European populations compiled in different databases.
We observed that the variability of the mtDNA haplogroupd of the historical population of Aldaieta falls within the range of the present-day populations of the European Atlantic fringe, whereas the prehistorical populations of the Basque Country differentiate from the rest of the samples. Consequently, we suggst that between 6,000-1,500 YBP approximately, a certain amount of gene flow amongst the western European populations that homogenised their mtDNA lineages, may have taken place.
The frequencies of the mtDNA haplogroups observed are compared to those already reported in the literature from a) other ancient populations from the Basque Country (the prehistoric sites of Longar, Pico Ramos and SJAPL), b) the historical site of Aldaieta and c) those corresponding to extant European populations compiled in different databases.
We observed that the variability of the mtDNA haplogroupd of the historical population of Aldaieta falls within the range of the present-day populations of the European Atlantic fringe, whereas the prehistorical populations of the Basque Country differentiate from the rest of the samples. Consequently, we suggst that between 6,000-1,500 YBP approximately, a certain amount of gene flow amongst the western European populations that homogenised their mtDNA lineages, may have taken place.
DNA extraction methods for genotyping non-invasive samples have provided a great advance in molecular research for ecological studies, and have been particularly useful for analyzing threatened species. However, scarce amounts of... more
DNA extraction methods for genotyping non-invasive samples have provided a great advance in molecular research for ecological studies, and have been particularly useful for analyzing threatened species. However, scarce amounts of fragmented DNA and the presence of Taq polymeras einhibitors contained in non-invasive samples are potential problems for subsequent PCR amplifications. In this study we describe a novel technique for extracting avian DNA from the external surfaces of faeces and regurgitated seeds that minimizes the presence of contaminants and preserves intact samples that may be used for other ecological scientific studies (e.g. trophic studies). The amplification efficiency and the purity of the extracted DNA from faeces were significantly increased compared with commonly used direct extraction procedures. Entire faecal samples can be later used avoiding the loss of any important parts of the faeces. Moreover, this technique allowed two bird species to be identified from DNA recovered from regurgitated seeds. The identification of their ecological role, such as seed-dispersers or predators, will be crucial in the analysis of ecological networks. Therefore, this method may be suitable for future ecological studies of vertebrate groups.
The evolutionary relationships among Columbidae species from the Palearctic Region and Macaronesian archipelagos was examined using mitochondrial control region sequences. Morphological and behavioural studies have indicated the close... more
The evolutionary relationships among Columbidae species from the Palearctic Region and Macaronesian archipelagos was examined using mitochondrial control region sequences. Morphological and behavioural studies have indicated the close relationships between the Wood Pigeon (Columba palumbus) from European mainland and the insular endemic pigeons, Madeira Laurel Pigeon (C. trocaz) from Madeira and Bolle’s Laurel Pigeon (C. bollii) and White-tailed Laurel Pigeon (C. junoniae) from the Canary Islands. In the present molecular study, we also included the Stock Pigeon (C. oenas), the Rock Pigeon (C. livia) and the Azorean endemic subspecies of Wood Pigeon C. palumbus azorica, in the phylogenetic analysis. Preliminary results suggest that White-tailed Laurel Pigeon is basal, showing mitochondrial sequences divergent to the rest of pigeons studied. Madeira Laurel Pigeon and Bolle’s Laurel Pigeon cluster with widely distributed Palearctic species. This work constitutes a genetic approach to the origin of threatened endemic pigeons that inhabit in the relic laurel forests of these Atlantic islands.
Macaronesia encompasses four inhabited Atlantic archipelagos: Azores, Madeira, Canary and Cape Verde. Canary archipelago was inhabited when conquered by Spaniards in the 15th century. By contrast, the other archipelagos were uninhabited... more
Macaronesia encompasses four inhabited Atlantic archipelagos: Azores, Madeira, Canary and Cape Verde. Canary archipelago was inhabited when conquered by Spaniards in the 15th century. By contrast, the other archipelagos were uninhabited when discovered by Portuguese in the 15th century. Historical reports point out the impact of Iberians in the settlement of Macaronesia; however, important differences in the peopling process of the archipelagos are documented. To date, there are no integrative works that aim to infer the genetic relationship and the impact of evolutionary forces in Macaronesia islands. In this work, we compile published data mtDNA for 919 individuals from Macaronesia (172 Azores, 300 Canary, 155 Madeira and 292 Cape Verde). To obtain a representative sample for the nine Azorean islands, we analyzed the HVRI and coding region polymorphisms of mtDNA in 84 additional Azoreans. Results obtained allowed to conclude that Cape Verde is the most distinctive archipelago of Macaronesia, with six islands presenting exclusively mtDNA lineages of African origin, and only 3 islands presenting West-Eurasian lineages in frequencies lower than 4%. On the contrary, the remaining archipelagos present a mtDNA profile dominated by the presence of West-Eurasian mtDNA haplogrous with typically African lineages being absent in some of the islands of the Canary and Azores archipelagos. The MDS representation of genetic distances evidenced the homogeneity of the Canary islands since they set in a separate cluster. In contrast, the islands of the Azores archipelago appear in different quadrants evidencing the important genetic substructure of this archipelago.
The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of... more
The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (9,000 BCE) and Pre-Pottery Neolithic farmers (6,500 BCE). Late Neolithic (3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia 5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.