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5. Europe

Author

Bertranpetit, Jaume, Barbujani, Guido, and Saitou, Naruya, Series Editor

Published
2021
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7. Cosmic phylogeny: reconstructing the chemical history of the solar neighbourhood with an evolutionary tree

Author

Jofre, Paula, Das, Payel, Bertranpetit, Jaume, and Foley, Robert

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics
Abstract

Using 17 chemical elements as a proxy for stellar DNA, we present a full phylogenetic study of stars in the solar neighbourhood. This entails applying a clustering technique that is widely used in molecular biology to construct an evolutionary tree from which three branches emerge. These are interpreted as stellar populations which separate in age and kinematics and can be thus attributed to the thin disk, the thick disk, and an intermediate population of probable distinct origin. We further find six lone stars of intermediate age that could not be assigned to any population with enough statistical significance. Combining the ages of the stars with their position on the tree, we are able to quantify the mean rate of chemical enrichment of each of the populations, and thus show in a purely empirical way that the star formation rate in the thick disk is much higher than in the thin disk. We are also able to estimate the relative contribution of dynamical processes such as radial migration and disk heating to the distribution of chemical elements in the solar neighbourhood. Our method offers an alternative approach to chemical tagging methods with the advantage of visualising the behaviour of chemical elements in evolutionary trees. This offers a new way to search for `common ancestors' that can reveal the origin of solar neighbourhood stars., Comment: MNRAS in press

Published
2016
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9. The making of the oral microbiome in Agta hunter–gatherers

Author

Leverhulme Trust, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), Universidad Pompeu Fabra, Dobon, Begoña [0000-0002-5608-6021], Bertranpetit, Jaume [0000-0003-0100-0590], Dobon, Begoña, Musciotto, Federico, Mira, Alex, Greenacre, Michael, Schlaepfer, Rodolph, Aguileta, Gabriela, Astete, Leonora H., Ngales, Marilyn, Latora, Vito, Battiston, Federico, Vinicius, Lucio, Migliano, Andrea B., Bertranpetit, Jaume, Leverhulme Trust, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), Universidad Pompeu Fabra, Dobon, Begoña [0000-0002-5608-6021], Bertranpetit, Jaume [0000-0003-0100-0590], Dobon, Begoña, Musciotto, Federico, Mira, Alex, Greenacre, Michael, Schlaepfer, Rodolph, Aguileta, Gabriela, Astete, Leonora H., Ngales, Marilyn, Latora, Vito, Battiston, Federico, Vinicius, Lucio, Migliano, Andrea B., and Bertranpetit, Jaume

Abstract

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analysed the oral microbiota of the Agta, a hunter–gatherer population where some members have adopted an agricultural diet. We show that age is the strongest factor modulating the microbiome, probably through immunosenescence since we identified an increase in the number of species classified as pathogens with age. We also characterised biological and cultural processes generating sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggest that shifting from a fish/meat diet to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All of these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial and shaped by various ecological and social factors that modify the oral environment.

Published
2023

10. Agta hunter–gatherer oral microbiomes are shaped by contact network structure

Author

Leverhulme Trust, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Dobon, Begoña [0000-0002-5608-6021], Bertranpetit, Jaume [0000-0003-0100-0590], Musciotto, Federico, Dobon, Begoña, Greenacre, Michael, Mira, Alex, Chaudhary, Nikhil, Salali, Gul Deniz, Gerbault, Pascale, Schlaepfer, Rodolph, Astete, Leonora H., Ngales, Marilyn, Gomez-Gardenes, Jesus, Latora, Vito, Battiston, Federico, Bertranpetit, Jaume, Vinicius, Lucio, Migliano, Andrea B., Leverhulme Trust, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Dobon, Begoña [0000-0002-5608-6021], Bertranpetit, Jaume [0000-0003-0100-0590], Musciotto, Federico, Dobon, Begoña, Greenacre, Michael, Mira, Alex, Chaudhary, Nikhil, Salali, Gul Deniz, Gerbault, Pascale, Schlaepfer, Rodolph, Astete, Leonora H., Ngales, Marilyn, Gomez-Gardenes, Jesus, Latora, Vito, Battiston, Federico, Bertranpetit, Jaume, Vinicius, Lucio, and Migliano, Andrea B.

Abstract

Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter–gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African BaYaka hunter–gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses and even unrelated friends can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter–gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

Published
2023

11. Extreme selective sweeps independently targeted the X chromosomes of the great apes

Author

Nam, Kiwoong, Munch, Kasper, Hobolth, Asger, Dutheil, Julien Yann, Veeramah, Krishna R, Woerner, August E, Hammer, Michael F, Mailund, Thomas, Schierup, Mikkel Heide, Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, O’Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Eichler, Evan E, and Marques-Bonet, Tomas

Subjects
Human Genome, Genetics, Animals, Computational Biology, Databases, Genetic, Genetic Variation, Genetics, Population, Hominidae, Models, Genetic, Polymorphism, Genetic, Selection, Genetic, Species Specificity, X Chromosome, Great Ape Genome Diversity Project, X-chromosome evolution, ampliconic genes, great apes, meiotic drive, selective sweeps
Abstract

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis.

Published
2015

12. Human Genome Variation and the concept of Genotype Networks

Author

Dall'Olio, Giovanni Marco, Bertranpetit, Jaume, Wagner, Andreas, and Laayouni, Hafid

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of systems such as metabolic networks and RNA folds. Recently, they have been the base for re-conciliating the two neutralist and selectionist schools on evolution. Here, we adapted the concept of genotype networks to the study of population genetics data, applying them to the 1000 Genomes dataset. We used networks composed of short haplotypes of Single Nucleotide Variants (SNV), and defined phenotypes as the presence or absence of a haplotype in a human population. We used coalescent simulations to determine if the number of samples in the 1000 Genomes dataset is large enough to represent the genetic variation of real populations. The result is a scan of how properties related to the genetic heterogeneity and stability to mutations are distributed along the human genome. We found that genes involved in acquired immunity, such as some HLA and MHC genes, tend to have the most heterogeneous and connected networks; and we have also found that there is a small, but significant difference between networks of coding regions and those of non-coding regions, suggesting that coding regions are both richer in genotype diversity, and more stable to mutations. Together, the work presented here may constitute a starting point for applying genotype networks to study genome variation, as larger datasets of next-generation data will become availa, Comment: 31 pages, 8 figures, 2 tables

Published
2013
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13. HLA-G genetic diversity and evolutive aspects in worldwide populations

Author

Castelli, Erick C., de Almeida, Bibiana S., Muniz, Yara C. N., Silva, Nayane S. B., Passos, Marília R. S., Souza, Andreia S., Page, Abigail E., Dyble, Mark, Smith, Daniel, Aguileta, Gabriela, Bertranpetit, Jaume, Migliano, Andrea B., Duarte, Yeda A. O., Scliar, Marília O., Wang, Jaqueline, Passos-Bueno, Maria Rita, Naslavsky, Michel S., Zatz, Mayana, Mendes-Junior, Celso Teixeira, and Donadi, Eduardo A.

Published
2021
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15. Europe

Author

Bertranpetit, Jaume, primary and Barbujani, Guido, additional

Published
2021
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17. Correction to: Origins, admixture and founder lineages in European Roma

Author

Martínez-Cruz, Begoña, Mendizabal, Isabel, Harmant, Christine, de Pablo, Rosario, Ioana, Mihai, Angelicheva, Dora, Kouvatsi, Anastasia, Makukh, Halyna, Netea, Mihai G., Pamjav, Horolma, Zalán, Andrea, Tournev, Ivailo, Marushiakova, Elena, Popov, Vesselin, Bertranpetit, Jaume, Kalaydjieva, Luba, Quintana-Murci, Lluis, and Comas, David

Published
2022
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18. Great ape genetic diversity and population history.

Author

Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, Veeramah, Krishna R, Woerner, August E, O'Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Munch, Kasper, Hobolth, Asger, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Mailund, Thomas, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Hammer, Michael F, Eichler, Evan E, and Marques-Bonet, Tomas

Subjects
Animals, Animals, Wild, Animals, Zoo, Hominidae, Gorilla gorilla, Humans, Pan paniscus, Pan troglodytes, Inbreeding, Genetics, Population, Population Density, Evolution, Molecular, Phylogeny, Polymorphism, Single Nucleotide, Genome, Africa, Asia, Southeastern, Gene Flow, Genetic Variation, General Science & Technology
Abstract

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Published
2013

19. Genome-wide diversity in the levant reveals recent structuring by culture.

Author

Haber, Marc, Gauguier, Dominique, Youhanna, Sonia, Patterson, Nick, Moorjani, Priya, Botigué, Laura, Platt, Daniel, Matisoo-Smith, Elizabeth, Soria-Hernanz, David, Wells, R, Bertranpetit, Jaume, Tyler-Smith, Chris, Comas, David, and Zalloua, Pierre

Subjects
African Continental Ancestry Group, Archaeology, Chromosomes, Human, Y, Cultural Evolution, DNA, Mitochondrial, Ethnic Groups, European Continental Ancestry Group, Genetic Variation, Genetics, Population, Genome, Human, Haplotypes, Humans, Middle East, Phylogeny
Abstract

The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ∼23,700-15,500 years ago during the last glacial period, and diverged from Europeans ∼15,900-9,100 years ago between the last glacial warming and the start of the Neolithic.

Published
2013

20. Genomic ancestry of North Africans supports back-to-Africa migrations.

Author

Henn, Brenna M, Botigué, Laura R, Gravel, Simon, Wang, Wei, Brisbin, Abra, Byrnes, Jake K, Fadhlaoui-Zid, Karima, Zalloua, Pierre A, Moreno-Estrada, Andres, Bertranpetit, Jaume, Bustamante, Carlos D, and Comas, David

Subjects
Humans, DNA, Mitochondrial, Genomics, Population Dynamics, Emigration and Immigration, Gene Pool, Genotype, Haplotypes, Polymorphism, Single Nucleotide, History, Ancient, African Continental Ancestry Group, European Continental Ancestry Group, Population, Africa, Northern, Morocco, Africa South of the Sahara, Middle East, Europe, Gene Flow, Genetic Variation, Egypt, Ancient, Genetics, Human Genome, Clinical Research, Developmental Biology
Abstract

North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from "back-to-Africa" gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.

Published
2012

21. Population interconnectivity shapes the distribution and complexity of chimpanzee cumulative culture

Author

Gunasekaram, Cassandra, primary, Kuhlwilm, Martin, additional, Battiston, Federico, additional, Fontsere, Claudia, additional, Padilla-Iglesias, Cecilia, additional, Kalan, Ammie K., additional, van Noordwiijk, Maria A., additional, Manica, Andrea, additional, Carvalho, Susana, additional, Bertranpetit, Jaume, additional, Marques-Bonet, Tomas, additional, Whiten, Andrew, additional, van Schaik, Carel, additional, Vinicius, Lucio, additional, and Migliano, Andrea Bamberg, additional

Published
2023
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26. Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G.

Author

Sinigaglia, Barbara, Escudero, Jorge, Biagini, Simone A, Garcia-Calleja, Jorge, Moreno, Josep, Dobon, Begoña, Acosta, Sandra, Mondal, Mayukh, Walsh, Sandra, Aguileta, Gabriela, Vallès, Mònica, Forrow, Stephen, Martin-Caballero, Juan, Migliano, Andrea Bamberg, Bertranpetit, Jaume, Muñoz, Francisco J, and Bosch, Elena

Subjects
CALCIUM-sensing receptors, HUMAN phenotype, HIGH-fat diet, NATURAL selection, RAIN forests, SHORT stature
Abstract

Rainforest hunter–gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)—fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter–gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter–gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests. [ABSTRACT FROM AUTHOR]

Published
2024
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28. Neandertal Genetics

Author

Cooper, Alan, Poinar, Hendrik N., Pääbo, Svante, Radovc̆ić, J., Debénath, A., Caparros, Miguel, Barroso-Ruiz, Cecilio, Bertranpetit, Jaume, Nielsen-Marsh, Christina, Sykes, Bryan, and Clark, G. A.

Published
1997

29. The making of the oral microbiome in Agta hunter–gatherers

Author

Dobon, Begoña; https://orcid.org/0000-0002-5608-6021, Musciotto, Federico, Mira, Alex, Greenacre, Michael, Schlaepfer, Rodolph, Aguileta, Gabriela, Astete, Leonora H, Ngales, Marilyn, Latora, Vito; https://orcid.org/0000-0002-0984-8038, Battiston, Federico; https://orcid.org/0000-0001-9646-6232, Vinicius, Lucio; https://orcid.org/0000-0002-9396-3249, Migliano, Andrea B; https://orcid.org/0000-0003-4364-2735, Bertranpetit, Jaume, Dobon, Begoña; https://orcid.org/0000-0002-5608-6021, Musciotto, Federico, Mira, Alex, Greenacre, Michael, Schlaepfer, Rodolph, Aguileta, Gabriela, Astete, Leonora H, Ngales, Marilyn, Latora, Vito; https://orcid.org/0000-0002-0984-8038, Battiston, Federico; https://orcid.org/0000-0001-9646-6232, Vinicius, Lucio; https://orcid.org/0000-0002-9396-3249, Migliano, Andrea B; https://orcid.org/0000-0003-4364-2735, and Bertranpetit, Jaume

Abstract

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analysed the oral microbiota of the Agta, a hunter–gatherer population where some members have adopted an agricultural diet. We show that age is the strongest factor modulating the microbiome, probably through immunosenescence since we identified an increase in the number of species classified as pathogens with age. We also characterised biological and cultural processes generating sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggest that shifting from a fish/meat diet to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All of these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial and shaped by various ecological and social factors that modify the oral environment.

Published
2023

30. Agta hunter–gatherer oral microbiomes are shaped by contact network structure

Author

Musciotto, Federico, Dobon, Begoña; https://orcid.org/0000-0002-5608-6021, Greenacre, Michael, Mira, Alex, Chaudhary, Nikhil; https://orcid.org/0000-0001-7528-8529, Salali, Gul Deniz; https://orcid.org/0000-0001-9538-3064, Gerbault, Pascale, Schlaepfer, Rodolph, Astete, Leonora H, Ngales, Marilyn, Gomez-Gardenes, Jesus, Latora, Vito; https://orcid.org/0000-0002-0984-8038, Battiston, Federico; https://orcid.org/0000-0001-9646-6232, Bertranpetit, Jaume, Vinicius, Lucio; https://orcid.org/0000-0002-9396-3249, Bamberg Migliano, Andrea; https://orcid.org/0000-0003-4364-2735, Musciotto, Federico, Dobon, Begoña; https://orcid.org/0000-0002-5608-6021, Greenacre, Michael, Mira, Alex, Chaudhary, Nikhil; https://orcid.org/0000-0001-7528-8529, Salali, Gul Deniz; https://orcid.org/0000-0001-9538-3064, Gerbault, Pascale, Schlaepfer, Rodolph, Astete, Leonora H, Ngales, Marilyn, Gomez-Gardenes, Jesus, Latora, Vito; https://orcid.org/0000-0002-0984-8038, Battiston, Federico; https://orcid.org/0000-0001-9646-6232, Bertranpetit, Jaume, Vinicius, Lucio; https://orcid.org/0000-0002-9396-3249, and Bamberg Migliano, Andrea; https://orcid.org/0000-0003-4364-2735

Abstract

Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter–gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African BaYaka hunter–gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses and even unrelated friends can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter–gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

Published
2023

31. Genome-Wide Pathway Analysis Identifies Genetic Pathways Associated with Psoriasis

Author

Aterido, Adrià, Julià, Antonio, Ferrándiz, Carlos, Puig, Lluís, Fonseca, Eduardo, Fernández-López, Emilia, Dauden, Esteban, Sánchez-Carazo, José Luís, López-Estebaranz, José Luís, Moreno-Ramírez, David, Vanaclocha, Francisco, Herrera, Enrique, de la Cueva, Pablo, Dand, Nick, Palau, Núria, Alonso, Arnald, López-Lasanta, María, Tortosa, Raül, García-Montero, Andrés, Codó, Laia, Gelpí, Josep Lluís, Bertranpetit, Jaume, Absher, Devin, Capon, Francesca, Myers, Richard M., Barker, Jonathan N., and Marsal, Sara

Published
2016
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35. The making of the oral microbiome in Agta hunter–gatherers

Author

Dobon, Begoña, primary, Musciotto, Federico, additional, Mira, Alex, additional, Greenacre, Michael, additional, Schlaepfer, Rodolph, additional, Aguileta, Gabriela, additional, Astete, Leonora H., additional, Ngales, Marilyn, additional, Latora, Vito, additional, Battiston, Federico, additional, Vinicius, Lucio, additional, Migliano, Andrea B., additional, and Bertranpetit, Jaume, additional

Published
2023
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36. Agta hunter–gatherer oral microbiomes are shaped by contact network structure

Author

Musciotto, Federico, primary, Dobon, Begoña, additional, Greenacre, Michael, additional, Mira, Alex, additional, Chaudhary, Nikhil, additional, Salali, Gul Deniz, additional, Gerbault, Pascale, additional, Schlaepfer, Rodolph, additional, Astete, Leonora H., additional, Ngales, Marilyn, additional, Gomez-Gardenes, Jesus, additional, Latora, Vito, additional, Battiston, Federico, additional, Bertranpetit, Jaume, additional, Vinicius, Lucio, additional, and Migliano, Andrea Bamberg, additional

Published
2023
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37. Identification of Risk Loci for Crohn’s Disease Phenotypes Using a Genome-Wide Association Study

Author

Alonso, Arnald, Domènech, Eugeni, Julià, Antonio, Panés, Julián, García-Sánchez, Valle, Mateu, Pilar Nos, Gutiérrez, Ana, Gomollón, Fernando, Mendoza, Juan L., Garcia-Planella, Esther, Barreiro-de Acosta, Manuel, Muñoz, Fernando, Vera, Maribel, Saro, Cristina, Esteve, Maria, Andreu, Montserrat, Chaparro, Maria, Manyé, Josep, Cabré, Eduard, López-Lasanta, María, Tortosa, Raül, Gelpí, Josep Lluís, García-Montero, Andrés C., Bertranpetit, Jaume, Absher, Devin, Myers, Richard M., Marsal, Sara, and Gisbert, Javier P.

Published
2015
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47. Origins, admixture and founder lineages in European Roma

Author

Martínez-Cruz, Begoña, Mendizabal, Isabel, Harmant, Christine, de Pablo, Rosario, Ioana, Mihai, Angelicheva, Dora, Kouvatsi, Anastasia, Makukh, Halyna, Netea, Mihai G, Pamjav, Horolma, Zalán, Andrea, Tournev, Ivailo, Marushiakova, Elena, Popov, Vesselin, Bertranpetit, Jaume, Kalaydjieva, Luba, Quintana-Murci, Lluis, and Comas, David

Published
2016
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50. Image1_Evolutionary Trajectories of Complex Traits in European Populations of Modern Humans.JPEG

Author

Kuijpers, Yunus, Domínguez-Andrés, Jorge, Bakker, Olivier B., Gupta, Manoj Kumar, Grasshoff, Martin, Xu, Cheng-Jian, Joosten, Leo A. B., Bertranpetit, Jaume, Netea, Mihai G., Li, Yang, Kuijpers, Yunus, Domínguez-Andrés, Jorge, Bakker, Olivier B., Gupta, Manoj Kumar, Grasshoff, Martin, Xu, Cheng-Jian, Joosten, Leo A. B., Bertranpetit, Jaume, Netea, Mihai G., and Li, Yang

Abstract

Humans have a great diversity in phenotypes, influenced by genetic, environmental, nutritional, cultural, and social factors. Understanding the historical trends of physiological traits can shed light on human physiology, as well as elucidate the factors that influence human diseases. Here we built genome-wide polygenic scores for heritable traits, including height, body mass index, lipoprotein concentrations, cardiovascular disease, and intelligence, using summary statistics of genome-wide association studies in Europeans. Subsequently, we applied these scores to the genomes of ancient European populations. Our results revealed that after the Neolithic, European populations experienced an increase in height and intelligence scores, decreased their skin pigmentation, while the risk for coronary artery disease increased through a genetic trajectory favoring low HDL concentrations. These results are a reflection of the continuous evolutionary processes in humans and highlight the impact that the Neolithic revolution had on our lifestyle and health.

Published
2022

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