Andrés Pérez-Figueroa

Industry

We carried out a simulation study to compare the efficiency of three alternative programs (DFDIST, DETSELD and BAYESCAN) to detect loci under directional selection from genome-wide scans using dominant markers. We also evaluated the efficiency of correcting for multiple testing those methods that use a classical probability approach. Under a wide r...

We investigated the performance of two of the most popular differentiation-based methods to detect loci under selection (dfdist/fdist and bayescan) in order to ascertain the average chromosome map distance between the detected outlier markers and the nearest loci under selection. We used a model of neutral markers genetically linked to selected loc...

The adaptive potential of a population depends on the amount of additive genetic variance for quantitative traits of evolutionary importance. This variance is a direct function of the expected frequency of heterozygotes for the loci which affect the trait (QTL). It has been argued, but not demonstrated experimentally, that long-term response to sel...

In this study msap, an R package which analyses methylation-sensitive amplified polymorphism (MSAP or MS-AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cy...

We introduce a computer program for the dynamic and flexible management of conserved subdivided populations. Using molecular marker data or pedigree information, the software determines the optimal contributions (i.e., number of offspring) of each individual, the number of migrants, and the particular subpopulations involved in the exchange of indi...

Human mitochondria can be genetically distinct within the same individual, a phenomenon known as heteroplasmy. In cancer, this phenomenon seems exacerbated, and most mitochondrial mutations seem to be heteroplasmic. How this genetic variation is arranged within and among normal and tumor cells is not well understood. To address this question, here...

The standard relationship between the dN/dS statistic and the selection coefficient is contingent upon the computation of the rate of fixation of non-synonymous and synonymous mutations among divergent lineages (substitutions). In cancer genomics, however, dN/dS is typically calculated by including mutations that are still segregating in the cell p...

Human mitochondria can be genetically distinct within the same individual, a phenomenon known as heteroplasmy. In cancer, this phenomenon seems exacerbated, and most mitochondrial mutations seem to be heteroplasmic. How this genetic variation is arranged within and among normal and tumor cells is not well understood. To address this question, here...

The morphological and biological characteristics of ectothermic vertebrates are known to be strongly influenced by environmental conditions, particularly temperature. Epigenetic mechanisms such as DNA methylation have been reported to contribute to the phenotypic plasticity observed in vertebrates in response to environmental changes. Additionally,...

One of the main objectives of conservation programs is the maintenance of genetic diversity because this provides the adaptive potential of populations to face new environmental challenges. Genetic diversity is generally assessed by means of neutral molecular markers, and it is usually quantified by the expected heterozygosity under Hardy-Weinberg...

Non-muscle invasive bladder cancer (NMIBC) represents a crucial problem for the national health care systems due to its high rates of recurrence and the consequent need of frequent follow-ups. Here, gene expression analyses in patients diagnosed as NMIBC were performed to determine those molecular pathways involved in tumor initiation, finding that...

Management programs often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity,...

Abstract Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of p...

The mussels Mytilus edulis and Mytilus galloprovincialis are marine organisms with external fertilization able to hybridize where their distributions overlap allowing the study of reproductive isolation mechanisms in nature. We provide raw data of a transcriptomic analysis of mature male gonads from these two Mytilus spp. using NGS (Illumina) techn...

Speciation mechanisms in marine organisms have attracted great interest because of the apparent lack of substantial barriers to genetic exchange in marine ecosystems. Marine mussels of the Mytilus edulis species complex provide a good model to study mechanisms underlying species formation. They hybridise extensively at many localities and both pre-...

The impact of contrasting environments on organisms can result in the establishment of distinct phenotypic traits. Environmentally induced epigenetic mechanisms directly regulate gene expression and potentially lead to long-lasting effects. How phenotypic, epigenetic, and genetic components of wild populations relate to each other is, however, stil...

Using computer simulation we explore the consequences of linkage on the inbreeding load of an equilibrium population, and on the efficiency of purging and the loss of genetic diversity after a reduction in population size. We find that linkage tends to cause increased inbreeding load due to the built up of coupling groups of (partially) recessive d...

The induction of triploidization in fish is a very common practice in aquaculture. Although triploidization has been applied successfully in many salmonid species, little is known about the epigenetic mechanisms implicated in the maintenance of the normal functions of the new polyploid genome. By means of methylation-sensitive amplified polymorphis...

Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N e) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar le...

A major goal of conservation genetics is to determine which specific populations are most crucial for in situ or ex situ conservation. Genetic divergence and diversity are the two foundations by which priorities for conservation are typically determined. However, these measures may be confounded when past bottlenecks reduce genetic diversity of pop...

For a quantitative trait under stabilizing selection, the effect of epistasis on its genetic architecture and on the changes of genetic variance caused by bottlenecking were investigated using theory and simulation. Assuming empirical estimates of the rate and effects of mutations and the intensity of selection, we assessed the impact of two-locus...

METAPOP (http://webs.uvigo.es/anpefi/metapop/) is a desktop application that provides an analysis of gene and allelic diversity in subdivided populations from molecular genotype or coancestry data as well as a tool for the management of genetic diversity in conservation programs. A partition of gene and allelic diversity is made within and between...

Loss of genetic variation through genetic drift can reduce population viability. However, relatively little is known about loss of variation caused by the combination of fluctuating population size and variance in reproductive success in age structured populations. We built an individual-based computer simulation model to examine how actual culling...

Early maturation in the Atlantic salmon is an interesting subject for numerous research lines. Prior to sea migration, parr can reach sexual maturation and successfully fertilize adult female eggs during the reproductive season. These individuals are known as precocious parr, mature parr or "sneakers". Reasons for early maturation are unknown and t...

Early detection of population declines is essential to prevent extinctions and to ensure sustainable harvest. We evaluated the performance of two Ne estimators to detect population declines: the two-sample temporal method and a one-sample method based on linkage disequilibrium (LD). We used simulated data representing a wide range of population siz...

Loss of genetic variation through genetic drift in isolated populations can reduce population viability. However, relatively little is known about loss of variation caused by fluctuating population size and realistic variance in reproductive success in age structured populations. We built an individual-based simulation model to examine how actual m...

For different fitness mutational models, with epistasis introduced, we simulated the consequences of drift (D scenario) or mutation, selection, and drift (MSD scenario) in populations at the MSD balance subsequently subjected to bottlenecks of size N = 2, 10, 50 during 100 generations. No "conversion" of nonadditive into additive variance was obser...

Question: How can we establish the biological factors that contribute to variation in assortative mating (based on a quantitative or qualitative trait)? Key assumptions: Assortative (or disassortative) mating for a particular trait can produce sexual isolation between ecotypes or incipient species. The individual contribution to population assortat...

Optimization of contributions of parents to progeny by minimizing the average coancestry of the progeny is an effective strategy for maintaining genetic diversity in ex situ conservation programs, but its application on the basis of molecular markers has the negative collateral effect of homogenizing the allelic frequencies at each locus. Because o...

We investigated the putative conversion of non-additive genetic variance into additive variance for fitness in bottlenecked populations under a model of partially recessive deleterious mutations with pair-wise epistatic interactions. Three different sets of mutational parameters were used to model genetic variability at the mutation-selection-drift...

The genetic architecture of fitness-related traits in Drosophila is usually studied using populations that have been maintained in the laboratory for some period of time, sometimes years. A population in captivity may suffer from the joint action of random drift and adaptation to captivity, with variable outcomes, depending on particular circumstan...

On exposed rocky shores in Galicia (northwest Spain), a striking polymorphism exists between two ecotypes (RB and SU) of Littorina saxatilis that occupy different levels of the intertidal zone and exhibit an incomplete reproductive isolation. The setting has been suggested to represent ongoing sympatric speciation by ecological adaptation of the tw...

Sexual isolation is a key component of reproductive isolation, involving mate choice among mature adults. While there are various statistics for estimating sexual isolation from mating frequencies, their ability to produce unbiased estimates varies considerably, depending on the particular situation. We investigated, under different biological scen...

Two rocky shore ecotypes of Littorina saxatilis from north-west Spain live at different shore levels and habitats and have developed an incomplete reproductive isolation through size assortative mating. The system is regarded as an example of sympatric ecological speciation. Several experiments have indicated that different evolutionary forces (mig...

We carried out an experiment of inbreeding and upward artificial selection for egg-to-adult viability in a recently captured population of Drosophila melanogaster, as well as computer simulations of the experimental design, in order to obtain information on the nature of genetic variation for this important fitness component. The inbreeding depress...

Fecundity is usually considered as a trait closely connected to fitness and is expected to exhibit substantial nonadditive genetic variation and inbreeding depression. However, two independent experiments, using populations of different geographical origin, indicate that early fecundity in Drosophila melanogaster behaves as a typical additive trait...

The genetic properties of life-history traits have been investigated for a long time. On the one hand, a number of estimates of heritability and inbreeding depression are available for reproductive traits in a variety of species. On the other, estimates of mutational parameters, such as mutational variances and rates and effects of deleterious muta...