Filters








206 Hits in 1.3 sec

Further confirmation for unknown archaic ancestry in Andaman and South Asia [article]

Mayukh Mondal, Ferran Casals, Partha P Majumder, Jaume Bertranpetit
2016 bioRxiv   pre-print
In a recent paper, we have derived three main conclusions: i) that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves; ii) that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, different from the Neanderthal and the Denisovan, which is absent in Europeans; and, iii) that the characteristic distinctive phenotypes (including very short
more » ... ) of Andamanese do not reflect an ancient African origin, but have resulted from strong natural selection on genes related to human body size. Although the single wave out of Africa and single origin for Asian and Pacific populations have been confirmed, the existence of admixture with an extinct hominin has been challenged by Skoglund et al., as they were unable to replicate our results in their data sets. While we had used a wide variety of statistical methods and data sets from diverse populations to draw our inference, Skoglund et al. have used only one method (Dstats, for the whole genome, not specifically for the relevant genomic regions) and compared only with the Asians, not even with the Europeans. Skoglund et al. have alleged that our statistical treatment of the data was faulty and have pointed out some possible sources of error. We have reexamined our data focusing on possible sources of error flagged by Skoglund et al. We have also performed new analyses. The reexamination and new analyses have bolstered our confidence that our earlier inferences were correct and have resulted in an improved model of introgression of modern humans with a hitherto unknown archaic ancestry. We also propose a possible reason for the inability of Skoglund et al. to validate our inference.
doi:10.1101/071175 fatcat:yn7nremvrjfo3ke7yjc6jkg3am

Minimizing recombinations in consensus networks for phylogeographic studies

Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell, Jaume Bertranpetit
2009 BMC Bioinformatics  
We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation and recombination events, defined on overlapping sets of extant units the objective is to compute a consensus network G3 with minimum number of additional recombinations. We describe a polynomial time algorithm with a guarantee that the number of computed new recombination events is
more » ... in = sz(G1, G2) (function sz is a well-behaved function of the sizes and topologies of G1 and G2) of the optimal number of recombinations. To date, this is the best known result for a network consensus problem. Results: Although the network consensus problem can be applied to a variety of domains, here we focus on structure of human populations. With our preliminary analysis on a segment of the human Chromosome X data we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. These results have been verified independently using traditional manual procedures. To the best of our knowledge, this is the first recombinations-based characterization of human populations. Conclusion: We show that our mathematical model identifies recombination spots in the individual haplotypes; the aggregate of these spots over a set of haplotypes defines a recombinational landscape that has enough signal to detect continental as well as population divide based on a short segment of Chromosome X. In particular, we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. The agreement with mutation-based analysis can be viewed as an indirect validation of our results and the model. Since the model in principle gives us more information embedded in the networks, in our future work, we plan to investigate more non-traditional questions via these structures computed by our methodology. Abstract Background: We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G 1 and G 2 , with both mutation and recombination events, defined on overlapping sets of extant units the objective is to compute a consensus network G 3 with minimum number of additional recombinations. We describe a polynomial time algorithm with a guarantee that the number of computed new recombination events is within = sz(G 1 , G 2 ) (function sz is a well-behaved function of the sizes and topologies of G 1 and G 2 ) of the optimal number of recombinations. To date, this is the best known result for a network consensus problem. Results: Although the network consensus problem can be applied to a variety of domains, here we focus on structure of human populations. With our preliminary analysis on a segment of the human Chromosome X data we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. These results have been verified independently using traditional manual procedures. To the best of our knowledge, this is the first recombinations-based characterization of human populations. Conclusion: We show that our mathematical model identifies recombination spots in the individual haplotypes; the aggregate of these spots over a set of haplotypes defines a recombinational landscape that has enough signal to detect continental as well as population divide based on a short segment of Chromosome X. In particular, we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. The agreement with mutation-based analysis can be viewed as an indirect validation of our results and the model. Since the model in principle gives us more information embedded in the networks, in our future work, we plan to investigate more non-traditional questions via these structures computed by our methodology.
doi:10.1186/1471-2105-10-s1-s72 pmid:19208177 pmcid:PMC2648726 fatcat:7wv4zszxhzhajfl5yaqxap4zmq

Parental age in schizophrenia in a case-controlled study

Jaume Bertranpetit, Lourdes Fañanás
1993 British Journal of Psychiatry  
subjective distress, burden on the family, and finance) and shortened hospital stay justifies its use. Maintenance neuroleptics are employed to sustain the improvement gained. The average number of ECTs required are greater than the amount employed for depression. We also use it as an early
doi:10.1192/bjp.162.4.574 pmid:8481765 fatcat:cnridmkisffxtjmbucegfm6dr4

Sequence Variability of a Human Pseudogene

Rosa Martínez-Arias, Francesc Calafell, Eva Mateu, David Comas, Aida Andrés, Jaume Bertranpetit
2001 Genome Research  
Bertranpetit, unpubl.) to the haplotypic data for psGBA.  ...  We can estimate as an average number of differences from the ancestral sequence in haplogroup 3 (Bertranpetit and Calafell 1996) .  ... 
doi:10.1101/gr.167701 fatcat:iz55sblqundvthnosmqpwajvce

Positive selection in admixed populations from Ethiopia

Sandra Walsh, Luca Pagani, Yali Xue, Hafid Laayouni, Chris Tyler-Smith, Jaume Bertranpetit
2020 BMC Genetics  
Background In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history. Results Here, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world.
more » ... The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens. Conclusions Signals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.
doi:10.1186/s12863-020-00908-5 pmid:33092534 fatcat:5lxi4znzozge3p6ah6r3tafhde

Gene connectivity and enzyme evolution in the human metabolic network

Begoña Dobon, Ludovica Montanucci, Juli Peretó, Jaume Bertranpetit, Hafid Laayouni
2019 Biology Direct  
Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic genes to explore the associations between network structure and the presence and strength of natural selection in the genes whose products are involved in metabolism. Purifying and positive selection are estimated at interspecific (among mammals) and intraspecific (among human
more » ... levels, and the connections between enzymatic reactions are differentiated between incoming (in-degree) and outgoing (out-degree) links.
doi:10.1186/s13062-019-0248-7 pmid:31481097 pmcid:PMC6724310 fatcat:d7s44ksjwzg4fk6fykj2lqpfu4

A system-level, molecular evolutionary analysis of mammalian phototransduction

Brandon M Invergo, Ludovica Montanucci, Hafid Laayouni, Jaume Bertranpetit
2013 BMC Evolutionary Biology  
doi:10.1186/1471-2148-13-52 pmid:23433342 pmcid:PMC3616935 fatcat:ch4rqx7vv5bwpmtpiljdydmhta

A genome-wide survey does not show the genetic distinctiveness of Basques

Hafid Laayouni, Francesc Calafell, Jaume Bertranpetit
2010 Human Genetics  
When analyzing a large set of classical genetic markers (Bertranpetit and Cavalli-Sforza 1991; Calafell and Bertranpetit 1994a, b) their distinctiveness with surrounding populations was reported and  ...  Calafell and Bertranpetit (1994a, b) compiled and analyzed the data available on allele frequencies in the Iberian Peninsula and France.  ... 
doi:10.1007/s00439-010-0798-3 pmid:20157828 fatcat:z6pmjwr5eja37l5ys7bezs2wru

Geographic Patterns of mtDNA Diversity in Europe

Lucia Simoni, Francesc Calafell, Davide Pettener, Jaume Bertranpetit, Guido Barbujani
2000 American Journal of Human Genetics  
Olaisen (1996) Portugal (54) 38Њ39 N 9 Њ09 W Corte-Real et al. (1996) Saami (240) 68Њ54 N 2 7 Њ00 E Sajantila et al. (1995), Dupuy and Olaisen (1996) Spain: Basques (106) 43Њ24 N 2 Њ00 W Bertranpetit  ... 
doi:10.1086/302706 pmid:10631156 pmcid:PMC1288355 fatcat:q4cadjwagzcnthj4acq5zuhnyq

VCF2Networks: applying Genotype Networks to Single Nucleotide Variants data [article]

Giovanni Marco Dall'Olio, Ali R. Vahdati, Bertranpetit Jaume, Wagner Andreas, Laayouni Hafid
2014 arXiv   pre-print
Summary: Genotype networks are a method used in systems biology to study the innovability of a given phenotype, determining whether the phenotype is robust to mutations, and how do the genotypes associated to it are distributed in the genotype space. Here we developed VCF2Networks, a tool to apply this method to population genetics data, and in particular to single Nucleotide Variants data encoded in the Variant Call file Format (VCF). A complete summary of the properties of the genotype
more » ... that can be calculated by VCF2Networks is given in the Supplementary Materials 1. Availability and Implementation: The home page of the project is https://bitbucket.org/dalloliogm/vcf2networks . VCF2Networks is also available directly from the Python Package Index (PyPI), under the name vcf2networks.
arXiv:1401.2016v2 fatcat:4pmm5u7ipnfq7n3g37dgeugvle

PopHuman: the human population genomics browser

Sònia Casillas, Roger Mulet, Pablo Villegas-Mirón, Sergi Hervas, Esteve Sanz, Daniel Velasco, Jaume Bertranpetit, Hafid Laayouni, Antonio Barbadilla
2017 Nucleic Acids Research  
The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of
more » ... c variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat.
doi:10.1093/nar/gkx943 pmid:29059408 pmcid:PMC5753332 fatcat:of2owioxfbf2vicjeaogos2oky

Nuclear Gene Indicates Coat-Color Polymorphism in Mammoths

Holger Römpler, Nadin Rohland, Carles Lalueza-Fox, Eske Willerslev, Tatyana Kuznetsova, Gernot Rabeder, Jaume Bertranpetit, Torsten Schöneberg, Michael Hofreiter
2006 Science  
doi:10.1126/science.1128994 pmid:16825562 fatcat:7yzd3injzza7lk6ai3db5srwg4

Influence of pathway topology and functional class on the molecular evolution of human metabolic genes [article]

Ludovica Montanucci, Hafid Laayouni, Begoña Dobón, Kevin L. Keys, Jaume Bertranpetit, Juli Peretó
2018 bioRxiv   pre-print
Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular
more » ... ionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways during the divergence of primates and rodents. Then, we related those selective pressures to the functional and topological characteristics of the pathways. We have used DNA sequences of all enzymes (956) of the metabolic pathways comprised in the HumanCyc database, using genome data for humans and five other mammalian species. We have found that the evolution of metabolic genes is primarily constrained by the layer of the metabolism in which the genes participate: while genes encoding enzymes of the inner core of metabolism are much conserved, those encoding enzymes participating in the outer layer, mediating the interaction with the environment, are evolutionarily less constrained and more plastic, having experienced faster functional evolution. Genes that have been targeted by adaptive selection are endowed by higher out-degree centralities than non-adaptive genes, while genes with high in-degree centralities are under stronger purifying selection. When the position along the pathway is considered, a funnel-like distribution of the strength of the purifying selection is found. Genes at bottom positions are highly preserved by purifying selection, whereas genes at top positions, catalyzing the first steps, are open to evolutionary changes. These results show how functional and topological characteristics of metabolic pathways contribute to shape the patterns of evolutionary pressures driven by natural selection and how pathway network structure matters in the evolutionary process that shapes the evolution of the system.
doi:10.1101/292714 fatcat:gq4rytvkvrczbmj4nmb5udlw64

Selection in the Introgressed Regions of the Chimpanzee Genome

Jessica Nye, Hafid Laayouni, Martin Kuhlwilm, Mayukh Mondal, Tomas Marques-Bonet, Jaume Bertranpetit
2018 Genome Biology and Evolution  
During the demographic history of the Pan clade, there has been gene-flow between species, likely >200,000 years ago. Bonobo haplotypes in three subspecies of chimpanzee have been identified to be segregating in modern-day chimpanzee populations, suggesting that these haplotypes, with increased differentiation, may be a target of natural selection. Here, we investigate signatures of adaptive introgression within the bonobo-like haplotypes in chimpanzees using site frequency spectrum-based
more » ... We find evidence for subspecies-specific adaptations in introgressed regions involved with male reproduction in central chimpanzees, the immune system in eastern chimpanzees, female reproduction and the nervous system in Nigeria-Cameroon chimpanzees. Furthermore, our results indicate signatures of balancing selection in some of the putatively introgressed regions. This might be the product of long-term balancing selection resulting in a similar genomic signature as introgression, or possibly balancing selection acting on alleles reintroduced through gene flow.
doi:10.1093/gbe/evy077 pmid:29635458 pmcid:PMC5905441 fatcat:mfpivtmairhvjk7bnyfwouwmfm

Intronic enhancers regulate the expression of genes involved in tissue-specific functions and homeostasis [article]

Beatrice Borsari, Pablo Villegas-Miron, Hafid Laayouni, Alba Segarra-Casas, Jaume Bertranpetit, Roderic Guigo, Sandra Acosta
2020 bioRxiv   pre-print
Tissue function and homeostasis reflects the gene expression signature by which the combination of ubiquitous and tissue-specific genes contribute to the tissue maintenance and stimuli-responsive function. Enhancers are central to control this tissue-specific gene expression pattern. Here, we explore the correlation between the genomic distribution of enhancers and their role in tissue-specific gene expression. We found that enhancers showing tissue-specific activity are highly enriched in
more » ... nic regions and regulate the expression of genes involved in tissue-specific functions, while housekeeping genes are more often controlled by intergenic enhancers. Notably, an intergenic-to-intronic active enhancers continuum is observed in the transition from developmental to adult stages: the most differentiated tissues present higher rates of intronic enhancers, while the lowest rates are observed in embryonic stem cells. Altogether, our results suggest that the genomic distribution of active enhancers is key for the tissue-specific control of gene expression.
doi:10.1101/2020.08.21.260836 fatcat:24d7bmlfprgyjakm3c63vc3foq
« Previous Showing results 1 — 15 out of 206 results