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La Revue du praticien 02/2013; 63(2):289-93.
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ABSTRACT: A mummified head was identified in 2010 as belonging to Henri IV, King of France. A putative blood sample from the King Louis XVI preserved into a pyrographically decorated gourd was analyzed in 2011. Both kings are in a direct male-line descent, separated by seven generations. We have retrieved the hypervariable region 1 of the mitochondrial DNA as well as a partial Y-chromosome profile from Henri IV. Five STR loci match the alleles found in Louis XVI, while another locus shows an allele that is just one mutation step apart. Taking into consideration that the partial Y-chromosome profile is extremely rare in modern human databases, we concluded that both males could be paternally related. The likelihood ratio of the two samples belonging to males separated by seven generations (as opposed to unrelated males) was estimated as 246.3, with a 95% confidence interval between 44.2 and 9729. Historically speaking, this forensic DNA data would confirm the identity of the previous Louis XVI sample, and give another positive argument for the authenticity of the head of Henri IV.
Forensic science international 12/2012; · 2.10 Impact Factor
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Tomislav Maricic,
Viola Günther,
Oleg Georgiev,
Sabine Gehre,
Marija Curlin,
Christiane Schreiweis,
Ronald Naumann,
Hernán A Burbano,
Matthias Meyer, Carles Lalueza-Fox,
Marco de la Rasilla,
Antonio Rosas,
Srecko Gajovic,
Janet Kelso,
Wolfgang Enard,
Walter Schaffner,
Svante Pääbo
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ABSTRACT: The FOXP2 gene is required for normal development of speech and language. By isolating and sequencing FOXP2 genomic DNA fragments from a 49,000-year-old Iberian Neandertal and 50 present-day humans we have identified substitutions in the gene shared by all or nearly all present-day humans, but absent or polymorphic in Neandertals. One such substitution is localized in intron 8 and affects a binding site for the transcription factor POU3F2, which is highly conserved among vertebrates. We find that the derived allele of this site is less efficient than the ancestral allele in activating transcription from a reporter construct. The derived allele also binds less POU3F2 dimers than POU3F2 monomers compared to the ancestral allele. Since the substitution in the POU3F2 binding site is likely to alter the regulation of FOXP2 expression, and since it is localized in a region of the gene associated with a previously described signal of positive selection, it is a plausible candidate for having caused a recent selective sweep in the FOXP2 gene.
Molecular Biology and Evolution 11/2012; · 5.55 Impact Factor
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Karen Hardy,
Stephen Buckley,
Matthew J Collins,
Almudena Estalrrich,
Don Brothwell,
Les Copeland,
Antonio García-Tabernero,
Samuel García-Vargas,
Marco de la Rasilla, Carles Lalueza-Fox,
Rosa Huguet,
Markus Bastir,
David Santamaría,
Marco Madella,
Julie Wilson,
Angel Fernández Cortés,
Antonio Rosas
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ABSTRACT: Neanderthals disappeared sometime between 30,000 and 24,000 years ago. Until recently, Neanderthals were understood to have been predominantly meat-eaters; however, a growing body of evidence suggests their diet also included plants. We present the results of a study, in which sequential thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) and pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) were combined with morphological analysis of plant microfossils, to identify material entrapped in dental calculus from five Neanderthal individuals from the north Spanish site of El Sidrón. Our results provide the first molecular evidence for inhalation of wood-fire smoke and bitumen or oil shale and ingestion of a range of cooked plant foods. We also offer the first evidence for the use of medicinal plants by a Neanderthal individual. The varied use of plants that we have identified suggests that the Neanderthal occupants of El Sidrón had a sophisticated knowledge of their natural surroundings which included the ability to select and use certain plants.
Naturwissenschaften 07/2012; 99(8):617-26. · 2.28 Impact Factor
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Federico Sánchez-Quinto,
Hannes Schroeder,
Oscar Ramirez,
María C Avila-Arcos,
Marc Pybus,
Iñigo Olalde,
Amhed M V Velazquez,
María Encina Prada Marcos,
Julio Manuel Vidal Encinas,
Jaume Bertranpetit,
Ludovic Orlando,
M Thomas P Gilbert, Carles Lalueza-Fox
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ABSTRACT: The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain). The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.
Current biology: CB 06/2012; 22(16):1494-9. · 10.99 Impact Factor
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ABSTRACT: Genetic changes in regulatory elements are likely to result in phenotypic effects that might explain population-specific as well as species-specific traits. MicroRNAs (miRNAs) are posttranscriptional repressors involved in the control of almost every biological process. These small noncoding RNAs are present in various phylogenetic groups, and a large number of them remain highly conserved at the sequence level. MicroRNA-mediated regulation depends on perfect matching between the seven nucleotides of its seed region and the target sequence usually located at the 3' untranslated region of the regulated gene. Hence, even single changes in seed regions are predicted to be deleterious as they may affect miRNA target specificity. In accordance to this, purifying selection has strongly acted on these regions. Comparison between the genomes of present-day humans from various populations, Neanderthal, and other nonhuman primates showed an miRNA, miR-1304, that carries a polymorphism on its seed region. The ancestral allele is found in Neanderthal, nonhuman primates, at low frequency (~5%) in modern Asian populations and rarely in Africans. Using miRNA target site prediction algorithms, we found that the derived allele increases the number of putative target genes for the derived miRNA more than ten-fold, indicating an important functional evolution for miR-1304. Analysis of the predicted targets for derived miR-1304 indicates an association with behavior and nervous system development and function. Two of the predicted target genes for the ancestral miR-1304 allele are important genes for teeth formation, enamelin, and amelotin. MicroRNA overexpression experiments using a luciferase-based assay showed that the ancestral version of miR-1304 reduces the enamelin- and amelotin-associated reporter gene expression by 50%, whereas the derived miR-1304 does not have any effect. Deletion of the corresponding target sites for miR-1304 in these dental genes avoided their repression, which further supports their regulation by the ancestral miR-1304. Morphological studies described several differences in the dentition of Neanderthals and present-day humans like slower dentition timing and thicker enamel for present-day humans. The observed miR-1304-mediated regulation of enamelin and amelotin could at least partially underlie these differences between the two Homo species as well as other still-unraveled phenotypic differences among modern human populations.
Molecular Biology and Evolution 01/2012; 29(7):1797-806. · 5.55 Impact Factor
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Marcello A Mannino,
Giulio Catalano,
Sahra Talamo,
Giovanni Mannino,
Rosaria Di Salvo,
Vittoria Schimmenti, Carles Lalueza-Fox,
Andrea Messina,
Daria Petruso,
David Caramelli,
Michael P Richards,
Luca Sineo
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ABSTRACT: Hunter-gatherers living in Europe during the transition from the late Pleistocene to the Holocene intensified food acquisition by broadening the range of resources exploited to include marine taxa. However, little is known on the nature of this dietary change in the Mediterranean Basin. A key area to investigate this issue is the archipelago of the Ègadi Islands, most of which were connected to Sicily until the early Holocene. The site of Grotta d'Oriente, on the present-day island of Favignana, was occupied by hunter-gatherers when Postglacial environmental changes were taking place (14,000-7,500 cal BP). Here we present the results of AMS radiocarbon dating, palaeogenetic and isotopic analyses undertaken on skeletal remains of the humans buried at Grotta d'Oriente. Analyses of the mitochondrial hypervariable first region of individual Oriente B, which belongs to the HV-1 haplogroup, suggest for the first time on genetic grounds that humans living in Sicily during the early Holocene could have originated from groups that migrated from the Italian Peninsula around the Last Glacial Maximum. Carbon and nitrogen isotope analyses show that the Upper Palaeolithic and Mesolithic hunter-gatherers of Favignana consumed almost exclusively protein from terrestrial game and that there was only a slight increase in marine food consumption from the late Pleistocene to the early Holocene. This dietary change was similar in scale to that at sites on mainland Sicily and in the rest of the Mediterranean, suggesting that the hunter-gatherers of Grotta d'Oriente did not modify their subsistence strategies specifically to adapt to the progressive isolation of Favignana. The limited development of technologies for intensively exploiting marine resources was probably a consequence both of Mediterranean oligotrophy and of the small effective population size of these increasingly isolated human groups, which made innovation less likely and prevented transmission of fitness-enhancing adaptations.
PLoS ONE 01/2012; 7(11):e49802. · 4.09 Impact Factor
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Antonio Rosas,
Almudena Estalrrich,
Antonio García-Tabernero,
Markus Bastir,
Samuel García-Vargas,
Andrea Sánchez-Meseguer,
Rosa Huguet, Carles Lalueza-Fox,
Ángel Peña-Melián,
Elena F. Kranioti,
David Santamaría,
Marco de la Rasilla,
Javier Fortea
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ABSTRACT: Résumé Ce travail synthétise et actualise les nouvelles données du gisement d’El Sidrón (Asturies, Nord de l’Espagne). Depuis 2000, le site d’El Sidrón, daté d’environ 49 000 ans, délivre systématiquement de nouveaux restes d’Homo neanderthalensis. L’assemblage osseux se trouve en position secondaire et provient certainement d’un lieu extérieur attenant. L’échantillon est composé presque exclusivement de restes humains. Un modeste outillage lithique (n ≈ 415) du Paléolithique moyen est présent tandis qu’il n’y a que très peu de restes de macro-faune. Tous les éléments squelettiques sont bien conservés, y compris un os rare comme l’os hyoïde. Les dents sont très nombreuses (n = 213), les restes crâniens bien représentés, mais fragmentaires, tout comme le postcrâne, pour lequel on note spécialement la présence des os des mains et des pieds. Un nombre minimum de 13 individus a été identifié, représentant plusieurs stades de développement des jeunes enfants jusqu’aux adultes. La paléobiologie des humains d’El Sidrón est conforme à celle trouvée dans d’autres échantillons néandertaliens : forte fréquence d’hypoplasies dentaires et de sillons interproximaux, bien qu’il n’y ait aucune lésion traumatique sérieuse. De plus, des traces de modifications anthropiques (cannibalisme) ont été identifiées clairement sur les restes humains : traces de découpes, marques de percussions, fractures conchoïdales et éclats de remontage. Il semble y avoir eu un traitement différencié des individus. Morphologiquement, les humains d’El Sidrón montrent un grand nombre de caractères dérivés néandertaliens même si certains traits placent l’échantillon à la limite de la variation néandertalienne. L’intégration des mandibules et des os occipitaux d’El Sidrón à un plus large échantillon néandertalien révèle une possible variation géographique, avec des Néandertaliens du Sud présentant des faces plus larges associées à des hauteurs faciales plus basses. Des analyses d’ADN ancien ont été menées en développant un protocole de fouille anti-contamination afin de minimiser les risques de contamination par l’ADN moderne. Ainsi, de l’ADN mitochondrial mais aussi nucléaire ont été extraits des restes dentaires et osseux. Curieusement, les analyses comparatives d’ADNm suggèrent une affinité des Néandertaliens de la Péninsule ibérique avec les Néandertaliens d’Europe centrale. Les analyses de l’ADN nucléaire ont permis l’identification de quelques gènes fonctionnels tels que le récepteur de la mélanocortine 1 (MC1R) qui régule la pigmentation des cheveux et de la peau ; le FOXP2, un gène impliqué dans le développement du langage ; et le gène impliqué dans le système des groupes sanguins ABO. Aujourd’hui l’échantillon humain d’El Sidrón est le plus important de la Péninsule ibérique et augmente le registre fossile de la lignée évolutive européenne, confirmant ainsi une variabilité écogéographique au sein des populations néandertaliennes. This paper synthesizes and updates the information coming from the El Sidrón (Asturias, Northern Spain) neandertal site. Since 2000, a new sample of Homo neanderthalensis dated to at least 49,000 years old is being systematically recovered at the El Sidrón cave site. The bone assemblage is located in a secondary position, and certainly derives from a close location. The sample is almost exclusively composed of human remains. There is a moderate number of Middle Paleolithic stone tools (n ≈ 415) and very few macro-faunal remains. All skeletal parts are preserved, including some rare bones such as the hyoid bone. Teeth are abundant (n = 213), cranial and postcranial remains are also well represented, but fragmentary, with a special presence of foot and hand bones. A minimum number of thirteen individuals has been identified, comprising different developmental stages from infancy to adulthood: one infant, two juveniles, three adolescents, and seven adults. Paleobiology of the El Sidrón humans fits the pattern found in other neandertal samples: a high incidence of dental hypoplasia and interproximal grooves, yet no serious traumatic lesions are present. Moreover, unambiguous evidence of human-induced modifications (cannibalism) was found on the human remains: cut marks, percussion pitting, conchoidal scars and adhering flakes. Individuals seem to have been treated differentially. Morphologically, the El Sidrón humans show a large number of neandertal lineage-derived features even though certain traits place the sample at the limits of neandertal variation. Integrating the El Sidrón human mandibles and occipital bones into the larger neandertal sample reveals a possible geographic patterning, with southern Neandertals showing broader faces with increased lower facial heights. Ancient DNA analyses have been carried out, developing an anti-contamination protocol of excavation for minimizing the risk of modern human DNA contamination. As a result both mitochondrial and nuclear DNA have been extracted from dental and osteological remains. Curiously, mtDNA comparative analyses suggest a population affinity of Iberian Peninsula Neandertals with Central European Neandertals. Nuclear DNA analyses have permitted the identification of some functional genes such as the melanocortin 1 receptor (MC1R), which regulates hair and skin pigmentation; the FOXP2, a gene involved in the development of language; and the gene involved in the ABO blood group system. Nowadays the large El Sidrón sample is the most significant neandertal sample from the Iberian Peninsula, and augments the European evolutionary lineage fossil record, supporting ecogeographical variability across neandertal populations.
L'Anthropologie. 01/2012; 116(1):57-76.
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ABSTRACT: Several previous comparisons of the human genome with other primate and vertebrate genomes identified genomic regions that are highly conserved in vertebrate evolution but fast-evolving on the human lineage. These human accelerated regions (HARs) may be regions of past adaptive evolution in humans. Alternatively, they may be the result of non-adaptive processes, such as biased gene conversion. We captured and sequenced DNA from a collection of previously published HARs using DNA from an Iberian Neandertal. Combining these new data with shotgun sequence from the Neandertal and Denisova draft genomes, we determine at least one archaic hominin allele for 84% of all positions within HARs. We find that 8% of HAR substitutions are not observed in the archaic hominins and are thus recent in the sense that the derived allele had not come to fixation in the common ancestor of modern humans and archaic hominins. Further, we find that recent substitutions in HARs tend to have come to fixation faster than substitutions elsewhere in the genome and that substitutions in HARs tend to cluster in time, consistent with an episodic rather than a clock-like process underlying HAR evolution. Our catalog of sequence changes in HARs will help prioritize them for functional studies of genomic elements potentially responsible for modern human adaptations.
PLoS ONE 01/2012; 7(3):e32877. · 4.09 Impact Factor
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ABSTRACT: One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.
PLoS ONE 01/2012; 7(10):e47765. · 4.09 Impact Factor
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ABSTRACT: In order to understand the genetic basis for the evolutionary success of modern humans, it is necessary to compare their genetic makeup to that of closely related species. Unfortunately, our closest living relatives, the chimpanzees, are evolutionarily quite distant. With the advent of ancient DNA study and more recently paleogenomics - the study of the genomes of ancient organisms - it has become possible to compare human genomes to those of much more closely related groups. Our closest known relatives are the Neanderthals, which evolved and lived in Europe and Western Asia, from about 600,000 years ago until their disappearance around 30,000 years ago following the expansion of anatomically modern humans into their range. The closely related Denisovans are only known by virtue of their DNA, which has been extracted from bone fragments dating around 30,000 to 50,000 years ago found in a single Siberian cave. Analyses of Neanderthal and Denisovan nuclear and mitochondrial genomes have revealed surprising insights into these archaic humans as well as our own species. The genomes provide a preliminary catalogue of derived amino acids that are specific to all extant modern humans, thus offering insights into the functional differences between the three lineages. In addition, the genomes provide evidence of gene flow between the three lineages after anatomically modern humans left Africa, drastically changing our view of human evolution.
Current biology: CB 12/2011; 21(24):R1002-9. · 10.99 Impact Factor
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Ricardo Rodríguez,
Oscar Ramírez,
Cristina E Valdiosera,
Nuria García,
Fernando Alda,
Joan Madurell-Malapeira,
Josep Marmi,
Ignacio Doadrio,
Eske Willerslev,
Anders Götherström,
Juan Luis Arsuaga,
Mark G Thomas, Carles Lalueza-Fox,
Love Dalén
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ABSTRACT: Low genetic diversity in the endangered Iberian lynx, including lack of mitochondrial control region variation, is thought to result from historical or Pleistocene/Holocene population bottlenecks, and to indicate poor long-term viability. We find no variability in control region sequences from 19 Iberian lynx remains from across the Iberian Peninsula and spanning the last 50,000 years. This is best explained by continuously small female effective population size through time. We conclude that low genetic variability in the Iberian lynx is not in itself a threat to long-term viability, and so should not preclude conservation efforts.
Molecular Ecology 08/2011; 20(18):3785-95. · 5.52 Impact Factor
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Proceedings of the National Academy of Sciences 05/2011; 108(18):E88-E88. · 9.68 Impact Factor
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ABSTRACT: Recent advances in ancient DNA technology have made it possible to recover DNA from paleontological remains allowing the scientist
to go back in time studying the genetic relationships between Humans and Neandertals. However, the field is fraught with technical
pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human and Neanderthal remains
are studied.
KeywordsPaleogenetics-Ancient DNA-Evolution
03/2011: pages 219-221;
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ABSTRACT: El Sidrón (Asturias, north of Spain) is a subterranean karstic system, where the remains of a contemporaneous social Neanderthal group dated to about 49,000 years ago have been being excavated since their accidental discovery in 1994. Due to the particular preservation conditions of this site, all individuals identified so far have preserved DNA, and the anticontamination measures implemented during the excavation have made palaeogenetic studies possible on all individuals. The El Sidrón samples provide unique information on the kinship relationships and on the internal genetic diversity of Neanderthal groups, thus yielding for first time empirical data for the generation of demographic models of these extinct humans. Moreover, the exceptional preservation of some bone samples has allowed the retrieval of nuclear genes associated with some phenotypic traits involved in pigmentation, blood group, language or taste perception, as well as a significant fraction (0.1%) of the nuclear genome. A future project on Neanderthal genomic diversity could be based on at least some of the El Sidrón specimens.
Annals of anatomy = Anatomischer Anzeiger: official organ of the Anatomische Gesellschaft 03/2011; 194(1):133-7. · 0.88 Impact Factor
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ABSTRACT: BACKGROUND: Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. CONCLUSIONS: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.
PLoS ONE 01/2011; 6(8):e24161. · 4.09 Impact Factor
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Carles Lalueza-Fox,
Antonio Rosas,
Almudena Estalrrich,
Elena Gigli,
Paula F Campos,
Antonio García-Tabernero,
Samuel García-Vargas,
Federico Sánchez-Quinto,
Oscar Ramírez,
Sergi Civit,
Markus Bastir,
Rosa Huguet,
David Santamaría,
M Thomas P Gilbert,
Eske Willerslev,
Marco de la Rasilla
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ABSTRACT: The remains of 12 Neandertal individuals have been found at the El Sidrón site (Asturias, Spain), consisting of six adults, three adolescents, two juveniles, and one infant. Archaeological, paleontological, and geological evidence indicates that these individuals represent all or part of a contemporaneous social group of Neandertals, who died at around the same time and later were buried together as a result of a collapse of an underground karst. We sequenced phylogenetically informative positions of mtDNA hypervariable regions 1 and 2 from each of the remains. Our results show that the 12 individuals stem from three different maternal lineages, accounting for seven, four, and one individual(s), respectively. Using a Y-chromosome assay to confirm the morphological determination of sex for each individual, we found that, although the three adult males carried the same mtDNA lineage, each of the three adult females carried different mtDNA lineages. These findings provide evidence to indicate that Neandertal groups not only were small and characterized by low genetic diversity but also were likely to have practiced patrilocal mating behavior.
Proceedings of the National Academy of Sciences 01/2011; 108(1):250-3. · 9.68 Impact Factor
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Antonio Rosas González,
Antonio García Tabernero,
Almudena Estalrrich,
Samuel García Vargas,
Markus Bastir, Carles Lalueza Fox,
Rosa Huguet,
Angel Luis Peña Melian,
David Santamaría Alvarez,
Marco de la Rasilla Vives,
Javier Fortea Pérez
Arqueología, Paleontología y Geomorfología del Cuaternario en España: X aniversario del Seminario Francisco Sousa (La Rinconada, Sevilla); 01/2011
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01/2011: pages 229-233;
