Antonio Barbadilla

Antonio Barbadilla
Autonomous University of Barcelona | UAB

Dr.

About

94
Publications
26,053
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Introduction
Antonio Barbadilla is Associate Professor of the Department of Genetics and Microbiology and the Institute of Biotechnology and Biomedicine at the University Autònoma of Barcelona. His research field is Population Genetics and Bioinformatics. At present, he is the research leader of the Bioinformatics of Genomic Diversity group. The representation, analysis and interpretation of DNA variation and its relationship with phenotypic variation is the focus of his research (SNPs and QTLs).
Additional affiliations
October 1994 - present
Autonomous University of Barcelona
Position
  • Professor (Associate)

Publications

Publications (94)
Article
Full-text available
Adaptive challenges that humans faced as they expanded across the globe left specific molecular footprints that can be decoded in our today's genomes. Different sets of metrics are used to identify ge-nomic regions that have undergone selection. However , there are fewer methods capable of pinpointing the allele ultimately responsible for this sele...
Article
Full-text available
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipeli...
Article
Full-text available
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipeline...
Preprint
Full-text available
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic...
Article
Full-text available
A main assumption of molecular population genetics is that genomic mutation rate does not depend on sequence function. Challenging this assumption, a recent study has found a reduction in the mutation rate in exons compared to introns in somatic cells, ascribed to an enhanced exonic mismatch repair system activity. If this reduction happens also in...
Preprint
Full-text available
A main assumption of molecular population genetics is that genomic mutation rate does not depend on sequence function. Challenging this assumption, a recent study has found a reduction in the mutation rate in exons compared to introns in somatic cells. This reduction was ascribed to an enhanced exonic mismatch repair system activity. If this reduct...
Article
Full-text available
The McDonald and Kreitman test (MKT) is one of the most powerful and widely used methods to detect and quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative McDonald and Kreitman test), a novel web-based service performing four distinct MKT types. It allows the detection and estimation of four d...
Article
Full-text available
Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from non-adaptive substitutions when using non-synonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and divergence data between D. m...
Article
La teoría neutralista, planteada por Motoo Kimura en 1968, propone que gran parte de la variación genética observada en las poblaciones se debe a la fluctuación aleatoria de variantes genéticas que son neutras, sobre las que apenas actúa la selección natural. La simplicidad, la robustez y la capacidad de predicción de la teoría la convierten en un...
Article
Full-text available
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today’s genomes. Here, we (i) perform an outlier approach on eight different population genetic statistics for 22 non-admixed human populations of...
Article
Full-text available
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 geno...
Article
We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns and development, with the aim of mapping adaptation over the entire embryo’s anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-b...
Article
The recent compilation of over 1100 worldwide wild-derived Drosophila melanogaster genome sequences reassembled using a standardized pipeline provides a unique resource for population genomic studies (Drosophila Genome Nexus, DGN). A visual display of the estimated metrics describing genome-wide variation and selection patterns would allow gaining...
Conference Paper
Full-text available
Introduction. The bacteria that causes tuberculosis, Mycobacterium tuberculosis, is known for the high rate of drug resistance, causes health problems and affects the economy to public health worldwide. In Mexico, the presence and persistence of tuberculosis remains a major problem. The annual number of identified cases increased by 15% every year....
Article
Full-text available
Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular po...
Article
Full-text available
Background The aim of the study was to evaluate the association of two SNPs of EVER1/2 genes’ region (rs2290907, rs16970849) and the FAS-670 polymorphism with the susceptibility to precancerous lesions and cervical cancer in a Greek population. Methods Among the 515 women who were included in the statistical analysis, 113 belong to the case group a...
Article
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Hill–Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adapt...
Preprint
It is known that rates of mutation and recombination vary across the genome in many species. Here we investigate whether these factors affect the rate at which genes undergo adaptive evolution both individually and in combination and quantify the degree to which Hill-Robertson interference (HRi) impedes the rate of adaptive evolution. To do this we...
Article
Full-text available
Cactophilic Drosophila species provide a valuable model to study gene-environment interactions and ecological adaptation. D. buzzatii and D. mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, w...
Article
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The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs)...
Article
Full-text available
The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant human polymorphic inversions. Due...
Article
Full-text available
Extreme personality traits in humans often have detrimental life consequences, so they have long been supposed to be diseases. However,many other species display personality variants that are maintained due to their fitness advantages; in this case, they are construed as strategies. To examine the fitness costs and benefits of pathological personal...
Article
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A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect th...
Article
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The completion of 168 genome sequences from a single population of Drosophila melanogaster provides a global view of genomic variation and an understanding of the evolutionary forces shaping the patterns of DNA polymorphism and divergence along the genome. We present the 'Population Drosophila Browser' (PopDrowser), a new genome browser specially d...
Article
Unlabelled: Grass seeds are complex organs composed by multiple tissues and cell types that develop coordinately to produce a viable embryo. The identification of genes involved in seed development is of great interest, but systematic spatial analyses of gene expression on maize seeds at the cell level have not yet been performed. MASISH is an onl...
Article
Full-text available
The nearly neutral theory of molecular evolution states that the efficiency of natural selection depends on the effective population size. By using a wide range of multispecies data on nucleotide polymorphism, we have tried to ascertain whether there are any differences in the level of selective constraints of metabolic process genes between Mammal...
Article
Full-text available
A corollary of the nearly neutral theory of molecular evolution is that the efficiency of natural selection depends on effective population size. In this study, we evaluated the differences in levels of synonymous polymorphism among Drosophila species and showed that these differences can be explained by differences in effective population size. Th...
Article
Full-text available
The McDonald and Kreitman test (MKT) is one of the most powerful and extensively used tests to detect the signature of natural selection at the molecular level. Here, we present the standard and generalized MKT website, a novel website that allows performing MKTs not only for synonymous and nonsynonymous changes, as the test was initially described...
Article
Full-text available
The majority of metazoan genomes consist of nonprotein-coding regions, although the functional significance of most noncoding DNA sequences remains unknown. Highly conserved noncoding sequences (CNSs) have proven to be reliable indicators of functionally constrained sequences such as cis-regulatory elements and noncoding RNA genes. However, CNSs ma...
Article
Full-text available
As a growing number of haplotypic sequences from resequencing studies are now accumulating for Drosophila in the main primary sequence databases, collectively they can now be used to describe the general pattern of nucleotide variation across species and genes of this genus. The Drosophila Polymorphism Database (DPDB) is a secondary database that p...
Article
Full-text available
We report a significant negative correlation between nonsynonymous polymorphism and intron length in Drosophila melanogaster. This correlation is similar to that between protein divergence and intron length previously reported in Drosophila. We show that the relationship can be explained by the content of conserved noncoding sequences (CNS) within...
Article
Full-text available
Multi-locus and multi-species nucleotide diversity studies would benefit enormously from a public database encompassing high-quality haplotypic sequences with their associated genetic diversity measures. MamPol, ‘Mammalia Polymorphism Database’, is a website containing all the well-annotated polymorphic sequences available in GenBank for the Mammal...
Data
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Structure and expression of non-Hox proteins.
Data
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Genes from D. buzzatii, D. melanogaster and D. pseudoobscura used in the analyses with their accession number in Genbank or Flybase and their location on the chromosome.
Data
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Set of tables of the main text, obtained according to three different annotation criteria to define repetitive sequences.
Data
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ANOVA and contrast analyses for all group comparisons.
Data
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Parameters of gene structure, base composition and nucleotide evolution for each gene.
Article
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Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (DPDB). A new version of the pipeline presented here...
Article
Full-text available
It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserv...
Article
Full-text available
Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures. We define a data model for the storage, representation and analysis of genotypic and haplotypic da...
Article
Full-text available
Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been rearranged differently in seve...
Article
Full-text available
Polymorphism studies are one of the main research areas of this genomic era. To date, however, no available web server or software package has been designed to automate the process of exploring and estimating nucleotide polymorphism in large DNA databases. Here, we introduce a novel software, PDA, Pipeline Diversity Analysis, that automatically can...
Article
Full-text available
Recombination is a main factor determining nucleotide variability in different regions of the genome. Chromosomal inversions, which are ubiquitous in the genus Drosophila, are known to reduce and redistribute recombination, and thus their specific effect on nucleotide variation may be of major importance as an explanatory factor for levels of DNA v...