A5055336012- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Biochemical Analysis and Sensing Techniques
- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Plant Virus Research Studies
- Gene expression and cancer classification
- Insect Resistance and Genetics
- Fractal and DNA sequence analysis
- Advances in Cucurbitaceae Research
- Plant Reproductive Biology
- Cancer Genomics and Diagnostics
- Genetics and Plant Breeding
- Gut microbiota and health
- Wheat and Barley Genetics and Pathology
- Drug Transport and Resistance Mechanisms
- Animal Genetics and Reproduction
- Silkworms and Sericulture Research
- Animal Behavior and Welfare Studies
- Plant and animal studies
- Antimicrobial Peptides and Activities
Center for Research in Agricultural Genomics
2015-2025
Universitat Autònoma de Barcelona
2008-2023
Consejo Superior de Investigaciones Científicas
2014-2023
Institute of Agrifood Research and Technology
2023
Universitat de Barcelona
1998-2015
Health First
2010
Max Planck Institute for Chemical Ecology
2005-2007
Max Planck Society
2007
Hungarian Academy of Sciences
2000
Institute of Molecular Life Sciences
2000
We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP implements: 1) modules reading and analyzing from genomic partitioning methods, RADseq or hybrid enrichment approaches, 2) faster methods...
A number of statistical tests for detecting population growth are described. We compared the power these with that others available in literature. The evaluated fall into three categories: those based on distribution mutation frequencies, haplotype distribution, and mismatch distribution. found that, an extensive variety cases, most powerful Fu's FS test newly developed R2 test. behavior is superior small sample sizes, whereas better large sizes. also show some popular statistics very conservative.
Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats offer; few applications process large sets produced by wholegenome resequencing projects.Furthermore, there is no coherent framework for easy integration of new statistics into existing pipelines, hindering development application genomics approaches.Here, we present PopGenome, a package R software environment (a de facto standard statistical...
Several tests have been proposed to detect departures of nucleotide variability patterns from neutral expectations. However, very different kinds evolutionary processes, such as selective events or demographic changes, can produce similar deviations these tests, thus making interpretation difficult when a significant departure neutrality is detected. Here we study the effects demography and recombination upon by analyzing their power under sudden population expansions, contractions,...
Abstract The simultaneous analysis of multiple genomic loci is a powerful approach to studying the effects population history and natural selection on patterns genetic variation species. By surveying nucleotide sequence polymorphism at 334 randomly distributed regions in 12 accessions Arabidopsis thaliana, we examined whether standard neutral model consistent with observed data. average diversity was 0.0071 for total sites 0.0083 silent sites. Although levels are variable among loci, no...
Abstract Next generation sequencing of pooled samples is an effective approach for studies variability and differentiation in populations. In this paper we provide a comprehensive set estimators the most common statistics population genetics based on frequency spectrum, namely Watterson estimator , nucleotide pairwise diversity Π, Tajima's D Fu Li's F Fay Wu's H McDonald‐Kreitman HKA tests corrected errors ascertainment bias. simulation study, show that pool individual θ estimates are highly...
Background Artificial selection has caused rapid evolution in domesticated species. The identification of footprints across genomes can contribute to uncover the genetic basis phenotypic diversity. Methodology/Main Findings Genome wide pig domestication and were identified using massive parallel sequencing pooled reduced representation libraries (RRL) representing ∼2% genome from wild boar four domestic breeds (Large White, Landrace, Duroc Pietrain) which have been under strong for muscle...
Human DNA sequence variation data are useful for studying the origin, evolution, and demographic history of modern humans mechanisms maintenance genetic variability in human populations, detecting linkage association disease. Here, we report worldwide from a ≈10-kilobase noncoding autosomal region. We identified 75 variant sites 64 (128 sequences) 463 among human, chimpanzee, orangutan sequences. Statistical tests suggested that region is selectively neutral. The average nucleotide diversity...
Abstract Nucleotide variation in eight effectively unlinked genes was surveyed species-wide samples of the closely related outbreeding species Arabidopsis halleri and A. lyrata ssp. petraea three these thaliana. Significant genetic differentiation observed more frequently l. than halleri. Average estimates nucleotide were highest lowest lyrata, reflecting differences among effective population size. The low level is concordant with a bottleneck effect associated its origin. halleri/A....
Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for maintenance genetic diversity. Therefore, an appreciation how this variation is created maintained critical importance our understanding biodiversity evolutionary change. Here, we analysed recombination features from species representing major eutherian taxonomic groups Afrotheria, Rodentia, Primates Carnivora better understand...
The availability of extensive databases crop genome sequences should allow analysis variability at an unprecedented scale, which have important impact in plant breeding. However, up to now the genetic whole-genome scale has been mainly restricted single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion are frequent species had mutational role domestication Here, we present first comprehensive melon diversity, includes detailed...
The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% scaffold assembly anchored oriented to 12 linkage groups, respectively. However, insufficient marker coverage a lack recombination left several large, gene rich scaffolds unanchored, some unoriented. To improve anchoring orientation assembly, we used resequencing data between parental lines develop new set SNP markers from unanchored scaffolds.A high-resolution genetic map composed...
Olive tree (Olea europaea L. subsp. var. europaea) is one of the most important species Mediterranean region and ancient domesticated. The availability whole genome assemblies annotations olive cultivars oleaster (O. sylvestris) has contributed to a better understanding genetic genomic differences between cultivars. However, compared other plant there still lack resources for populations that span entire region. In present study we developed complete variation map comprehensive...
Decreasing costs of next-generation sequencing (NGS) experiments have made a wide range genomic questions open for study with nonmodel organisms. However, experimental designs and analysis NGS data from less well-known species are challenging because the lack resources. In this work, we investigate performance alternative bioinformatics approaches in estimating variability neutrality tests based on site-frequency-spectrum (SFS) individual resequencing data. We pay particular attention to...
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP by resequencing 81 accessions. For the validation of array, a set 210 accessions were genotyped and 82.8% SNPs classified best recommended SNPs. The rate missing data was between 0.4% 2.7% less than 15.5% few peach wild accessions, suggesting that can be used interspecific × genetic studies....
Abstract Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide have focused on model systems, with very few analyses undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci a sample 46 genotypes Boechera stricta two individuals B. holboellii, both wild relatives Arabidopsis. Isolation by distance was significant across the species range stricta, three...
In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model study both domestication and relevance of genes in pig. Besides, pigs exhibit high meat quality as well appetite propensity obesity. Here we provide a genome wide analysis nucleotide structural diversity reduced representation library from pool (n=9 sows) shotgun genomic sequence single sow highly inbred Guadyerbas strain. pool, applied newly developed tools...
Missing data are common in DNA sequences obtained through high-throughput sequencing. Furthermore, samples of low quality or problems the experimental protocol often cause a loss even with traditional sequencing technologies. Here we propose modified estimators variability and neutrality tests that can be naturally applied to missing data, without need remove bases individuals from analysis. Modified statistics include Watterson estimator θW, Tajima's D, Fay Wu's H, HKA. We develop general...
The rate at which plants grow is a major functional trait in plant ecology. However, little known about its evolution natural populations. Here, we investigate evolutionary and environmental factors shaping variation the growth of Arabidopsis thaliana . We used diameter as proxy to monitor over time environments that mimicked latitudinal differences intensity light radiation, across set 278 genotypes sampled within four broad regions, including an outgroup from China. A field experiment...
Transposon insertion polymorphisms can improve prediction of complex agronomic traits in rice compared to using SNPs only, especially when accessions be predicted are less related the training set. (TIPs) significant sources genetic variation. Previous work has shown that TIPs detection causative loci on rice. Here, we quantify fraction variance explained by single nucleotide (SNPs) TIPs, and explore whether only SNPs. We used eleven relevance from five different population groups (Aus,...
Abstract Approximately 4 kb of the Cecropin cluster region have been sequenced in nine lines Drosophila melanogaster and one line sibling species D. simulans, mauritiana, sechellia. This includes three functional genes (CecA1, CecA2, CecB), which are involved insect immune response, two pseudogenes (CecΨ1 CecΨ2). The level silent polymorphism Cec is rather high (0.028), there no excess nonsynonymous polymorphism. There evidence gene conversion history these genes. interspecific comparison...
Abstract We investigate the dependence of site frequency spectrum on topological structure genealogical trees. show that basic population genetic statistics, for instance, estimators θ or neutrality tests such as Tajima’s D, can be decomposed into components waiting times between coalescent events and tree topology. Our results clarify relative impact two these statistics. provide a rigorous interpretation positive negative values an important class in terms underlying shape. In particular,...
Domestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication are well documented, its basis-particularly dynamics selection-remain less understood. To investigate these dynamics, we performed simulations designed to approximate history large domestic mammals. These used selection coefficients as modeling tool represent in recognizing that such abstractions...