Julio Rozas
A5101768262- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Neurobiology and Insect Physiology Research
- Insect and Arachnid Ecology and Behavior
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Plant and animal studies
- Spider Taxonomy and Behavior Studies
- Insect-Plant Interactions and Control
- Insect Resistance and Genetics
- Genetic Mapping and Diversity in Plants and Animals
- Identification and Quantification in Food
- Bioinformatics and Genomic Networks
- Animal Behavior and Reproduction
- Evolution and Paleontology Studies
- RNA and protein synthesis mechanisms
- Insect symbiosis and bacterial influences
- Insect behavior and control techniques
- Marine Ecology and Invasive Species
- Invertebrate Immune Response Mechanisms
- Plant and Biological Electrophysiology Studies
- Horticultural and Viticultural Research
- Parasite Biology and Host Interactions
- Genetic and phenotypic traits in livestock
- Genetic and Environmental Crop Studies
Universitat de Barcelona
2015-2024
Institut de Recerca de la Biodiversitat de la Universitat de Barcelona
2019-2024
Institute for Biodiversity
2021
Universitat Autònoma de Barcelona
2011
Harvard University
1994
DnaSP is a software package for comprehensive analysis of DNA polymorphism data. Version 5 implements number new features and analytical methods allowing extensive analyses on large datasets. Among other features, the newly implemented allow for: (i) multiple data files; (ii) haplotype phasing; (iii) insertion/deletion data; (iv) visualizing sliding window results integrated with available genome annotations in UCSC browser.Freely to academic users from: (http://www.ub.edu/dnasp).
DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting large number coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses genetic differentiation gene flow populations; (4) analysing evolutionary pattern preferred unpreferred codons; (5) generating graphical outputs an easy...
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.
Abstract SUMMARY: DnaSP is a Windows integrated software package for the analysis of DNA polymorphism from nucleotide sequence data. version 3 incorporates several methods estimating amount and pattern divergence, conducting neutrality tests. AVAILABILITY: For academic uses, available free charge from: http://www.bio.ub.es/julio/DnaSP.html CONTACT: julio@porthos.bio.ub.es
A major challenge of biology is understanding the relationship between molecular genetic variation and in quantitative traits, including fitness. This determines our ability to predict phenotypes from genotypes understand how evolutionary forces shape within species. Previous efforts dissect genotype–phenotype map were based on incomplete genotypic information. Here, we describe Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis population genomics...
Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome identified a conserved gene order (see Perspective by Zamir). Although this species underwent fewer duplications than related relevant caffeine genes experienced tandem that expanded their numbers within species. Scientists have seen independent expansions in distantly of tea...
As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences its primary bacterial endosymbiont Candidatus Riesia pediculicola. The has smallest known insect genome, spanning 108 Mb. Despite status as obligate parasite, it retains a remarkably complete basal repertoire 10,773 protein-coding genes 57 microRNAs. Representing hemimetabolous...
Abstract Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of tick, Ixodes scapularis (Say), which vectors that cause Lyme disease, human granulocytic anaplasmosis, babesiosis diseases. The large reflects accumulation repetitive DNA, new lineages retro-transposons, gene architecture patterns resembling ancient metazoans rather pancrustaceans. Annotation scaffolds representing ∼57% genome, reveals 20,486 protein-coding genes...
Chemoreception is a biological process essential for the survival of animals, as it allows recognition important volatile cues detection food, egg-laying substrates, mates, or predators, among other purposes. Furthermore, its role in pheromone may contribute to evolutionary processes, such reproductive isolation and speciation. This key several vital processes makes chemoreception particularly interesting system studying natural selection molecular adaptation. Two major gene families are...
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,...
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently insects. Myriapoda is only arthropod not represented by sequenced genome. We present an analysis genome centipede Strigamia maritima. It retains compact that has undergone less gene loss shuffling than previously arthropods, many orthologues genes conserved from bilaterian ancestor have been...
The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade angiosperms, which has controversial phylogenetic position relative eudicots and monocots. We sequenced nuclear genomes avocado race, P. americana var. drymifolia, most commercially popular hybrid cultivar, Hass, anchored latter chromosomes using genetic map. Resequencing Guatemalan West Indian varieties...
DnaSP, DNA sequence polymorphism, is an interactive computer program for the analysis of polymorphism from nucleotide data. The program, addressed to molecular population geneticists, calculates several measures variation within and between populations, linkage disequilibrium parameters Tajima's D statistic. which written in Visual Basic v. 3.0 runs on IBM-compatible PC under Windows, can handle a large number sequences up thousands nucleotides each.
Abstract Odorant‐binding proteins (OBPs) and chemosensory (CSPs) are two families of small water‐soluble proteins, abundant in the aqueous fluid surrounding olfactory receptor neurons insect antennae. OBPs involved first step signal transduction, carrying airborne semiochemicals to odorant receptors can be classified into three groups: Classic OBPs, Plus‐C Atypical OBPs. Here, we identified annotated genes encoding putative CSPs pea aphid Acyrthosiphon pisum using bioinformatics. This 13...
Abstract Background Chemoreception is a widespread mechanism that involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the receptor (Or), gustatory (Gr), odorant-binding protein (OBP) families. Members of latter family establish first contact with odorants, thus constitute step chemosensory transduction pathway. Results Comparative analysis OBP 12 Drosophila genomes allowed...
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin evolution of carnivory-related traits. To investigate molecular bases carnivory, we sequenced genome heterophyllous pitcher plant Cephalotus follicularis, in which succeeded regulating developmental switch between carnivorous non-carnivorous leaves. Transcriptome comparison two leaf types gene repertoire analysis identified genetic changes associated with prey attraction,...
Abstract Motivation: The comparative analysis of gene gain and loss rates is critical for understanding the role natural selection adaptation in shaping family sizes. Studying complete genome data from closely related species allows accurate estimation turnover rates. Current methods software tools, however, are not well designed dealing with certain kinds functional elements, such as microRNAs or transcription factor binding sites. Results: Here, we describe BadiRate, a new tool to estimate...
Abstract The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture genomic changes that underlay this diversification. Mayflies, as one sister groups all other insects, are key understanding radiation. Here, describe genome mayfly Cloeon dipterum its gene expression throughout aquatic aerial life cycle specific organs. We discover expansion odorant-binding-protein genes, some expressed...
Abstract Gene annotation is a critical bottleneck in genomic research, especially for the comprehensive study of very large gene families genomes nonmodel organisms. Despite recent progress automatic methods, state‐of‐the‐art tools used this task often produce inaccurate annotations, such as fused, chimeric, partial or even completely absent models many family copies, errors that require considerable extra efforts to be corrected. Here we present bitacora , bioinformatics solution integrates...