A new paper I co-authored is online in Molecular Ecology.

  
Molecular Ecology just have published, as online early, the following paper I co-authored:

Allelic diversity for neutral markers retains a higher adaptive potential for quantitative traits than expected heterozygosity.

Ana Vilas, Andrés Pérez-Figueroa, Humberto Quesada and Armando Caballero

DOI: 10.1111/mec.13334  http://onlinelibrary.wiley.com/doi/10.1111/mec.13334/abstract

This paper is part of Ana Vilas' PhD Thesis which I have co-supervised and she successfully defended last November. 

Here we address, both through simulation analyses and experimental studies with Drosophila melanogaster, the question of whether allelic diversity for neutral markers is a better indicator of a high adaptive potential than expected heterozygosity. Briefly, our results show that maximizing the number of alleles of a low number of markers implies higher responses to selection than maximizing their heterozygosity. We conclude that, when the number of markers available is small, the optimization of the number of alleles is the best method to create synthetic populations with the largest adaptive potential. Our results also support the use of neutral markers to make optimization decisions in conservation. 

A lot of work in these pages so it is cool to see them finally published in a prestigious journal as Molecular Ecology.

I have moved to the Phylogenomics Lab at Uvigo

 

A slight change of scenery for me. I've recently been hired by David Posada's Phylogenomics Lab (University of Vigo) to work on NGS Phylogeography analyzing RNA-seq data to obtain a large number of homologous loci from a set of marine snail species, a recent radiation of the genus Trovaoconus endemic from the Cape Verde islands. Sounds good, isn't it?

A new research group, a new lab, a new building, new tasks and a new field, but merely 100 meters away from my past location at the Population Genetics and Cytogenetics Group. No change of institution or department but a change of status. Last year I held an extension of the postdoctoral fellowship from Xunta de Galicia that I've held from 2007 to 2010. Now I am hired for an specific project during all 2015, so the future still has a lot of uncertainty, as usual.

The paper on msap is in Early View status at Molecular Ecology Resources

The paper I wrote, describing msap and its utility, for Molecular Ecology Resources has been accepted a few weeks ago. It is avalailable now as online early view at Molecular Ecology Resources.


Pérez-Figueroa, A. (2013), msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data. Molecular Ecology Resources. doi: 10.1111/1755-0998.12064

Keywords: DNA methylation; MSAP ; epigenetic variation; epigenetic differentiation

ABSTRACT

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 cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user-friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user-defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments.

msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses.

New paper published: Effect of population fluctuations and variance in male reproductive success on variability in Yellowstone bison

There is a new paper online that I've coauthored. This paper is the result from the work I've done during my postdoc stays at CIBIO (Portugal) and University of Montana (USA) under supervision of Dr. Gordon Luikart.

In this study, we built an individual-based computer simulation model to examine how actual culling and hunting strategies influence the effective population size (Ne) and allelic diversity in Yellowstone bison over 200 years (∼28 generations). These simulations suggest that fluctuations in population census size do not necessarily accelerate the loss of genetic variation, at least for the relatively large census size and growing populations such as in Yellowstone bison. They also suggest that the conservation of high allelic diversity (>95%) at loci with many alleles (e.g., ⩾5) will require maintenance of a populations size greater than approximately 3250 and removal of mainly or only juveniles.

More information and paper available at: (http://www.sciencedirect.com/science/article/pii/S0006320712001395) 

Andrés Pérez-Figueroa, Rick L. Wallen, Tiago Antao, Jason A. Coombs, Michael K. Schwartz, P.J. White, Gordon Luikart. (2012) Conserving genomic variability in large mammals: Effect of population fluctuations and variance in male reproductive success on variability in Yellowstone bison.

Biological Conservation, 150 (1):159-166. doi:10.1016/j.biocon.2012.02.022. 

Keywords: Allelic diversity; Effective population size; Simulation modelling; Age structure; Population growth rate; Population viability; Genomic diversity; Conservation genetics; Yellowstone bison

Published a simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers

This week it has been published, at Journal of Evolutionary Biology, a new paper that I've coauthored:

VILAS, A., PÉREZ-FIGUEROA, A. and CABALLERO, A. (2012), A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers. Journal of Evolutionary Biology. doi: 10.1111/j.1420-9101.2012.02526.x

Abstract

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 loci (QTL) controlling a quantitative trait subject to divergent selection in two subpopulations connected by migration. The results are not particularly encouraging because for chromosome lengths above 0.5 morgan, at least 30% of outliers detected were positioned in chromosomes where QTL were absent, clearly denoting false positives. Outliers linked to QTL were on average closer to the nearest QTL than randomly chosen markers, but the methods showed a substantial uncertainty about the genetic association between markers and selected loci, as this association could be shown significantly only in a moderate number of replicates for most scenarios. At equal conditions, BAYESCAN seemed to perform somewhat more efficiently than DFDIST/FDIST, with little difference between results for dominant and codominant markers.

For more information or download the paper, visit this link to the publisher's site.

A new paper published: Methylation changes associated with early maturation stages in the Atlantic salmon

Recently, one of my papers was published online on publisher's website:
http://www.biomedcentral.com/1471-2156/12/86

Methylation changes associated with early maturation stages in the Atlantic salmon. 

Paloma Moran and Andres Perez-Figueroa 

BMC Genetics 2011, 12: 86                                              

 doi:10.1186/1471-2156-12-86 

Abstract

Background

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 this transitory stage is usually considered to be a threshold trait. Here, we compare methylation patterns between mature and immature salmon parr from two different rivers in order to infer if such methylation differences may be related to their maturation condition. First we analyzed genetic differences between rivers by means of AFLPs. Then, we compared the DNA methylation differences between mature and immature parrs, using a Methylation-Sensitive Amplified Polymorphism (MSAP), which is a modification of the AFLPs method by making use of the differential sensitivity of a pair of restriction enzymes isoschizomeres to cytosine methylation. The tissues essayed included brain, liver and gonads.

Results 

AFLPs statistical analysis showed that there was no significant differentiation between rivers or a significant differentiation between maturation states in each river. MSAP statistical analysis showed that among the three tissues sampled, the gonads had the highest number of significant single-locus variation among populations with 74 loci followed by brain with 70 and finally liver with only 12. Principal components analysis (PCA) of the MSAP profiles revealed different profiles among different tissues (liver, brain and testis) clearly separating maturation states in the testis tissue when compared to the liver.

Conclusions

Our results reveal that genetically-similar mature and immature salmon parr present high levels of DNA methylation variation in two of the three analyzed tissues. We hypothesize that early maturation may be mostly mediated by epigenetic processes rather than by genetic differences between parrs. To our knowledge this is the first study that attempt to link phenotypic plasticity in salmonids and epigenetic changes.

Updating my profile on ResearchGate

I'm updating my profile on ResearchGate, the scientific "social" network. I know that several scientist are not very confident with this kind of tools. However, scientific activities lie on the same principles as social web tools: collaboration, participation and spreading. Of course, not every social app in the web are suitable for scientific activities. But even widespread sites like Facebook could be useful with the right guidelines, although it could be easily misused.

I've joined ResearchGate long time ago, but it is now when it take my attention. I'm becoming more and more sharing aware. I think that our scientific activities should pass the "journals walls" and web 2.0 tools are helping me in change my mind and attitudes. ResearchGate is a good platform where you could find scientists looking for answers or even to share their knowledge. Yeah, maybe ResearchGate is not fully mature, but I think it has a big potential to be the basic platform where worldwide scientist make their relationships. Let's see.

New paper online: Comparing three different methods to detect selective loci using dominant markers

There is available a new paper online in the publisher's site: http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02093.x/abstract.

Comparing three different methods to detect selective loci using dominant markers.

A. PÉREZ-FIGUEROA, M. J. GARCÍA-PEREIRA,M. SAURA,E. ROLÁN-ALVAREZ, A. CABALLERO.

Keywords: amplified fragment length polymorphisms; candidate loci; F_ST; genome scan;neutral model; outliers.

Abstract

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 range of scenarios, we conclude that bayescan appears to be more efficient than the other methods, detecting a usually high percentage of true selective loci as well as less than 1% of outliers (false positives) under a fully neutral model. In addition, the percentage of outliers detected by this software is always correlated with the true percentage of selective loci in the genome. Our results show, nevertheless, that false positives are common even with a combination of methods and multitest correction, suggesting that conclusions obtained from this approach should be taken with extreme caution.

New paper online: Early detection of population declines: high power of genetic monitoring using effective population size estimators

It is free available online in the publisher's web: http://www3.interscience.wiley.com/journal/123601431/abstract

Early detection of population declines: high power of genetic monitoring using effective population size estimators

Tiago Antao, Andrés Pérez-Figueroa and Gordon Luikart

KEYWORDS

bottleneck • computational simulations • effective population size • endangered species • habitat fragmentation • population monitoring • statistical power

ABSTRACT
Early detection of population declines is essential to prevent extinctions and to ensure sustainable harvest. We evaluated the performance of two N_e 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 sizes, sample sizes and number of loci. Both methods usually detect a population decline only one generation after it occurs if N_e drops to less than approximately 100, and 40 microsatellite loci and 50 individuals are sampled. However, the LD method often out performed the temporal method by allowing earlier detection of less severe population declines (N_e approximately 200). Power for early detection increased more rapidly with the number of individuals sampled than with the number of loci genotyped, primarily for the LD method. The number of samples available is therefore an important criterion when choosing between the LD and temporal methods. We provide guidelines regarding design of studies targeted at monitoring for population declines. We also report that 40 single nucleotide polymorphism (SNP) markers give slightly lower precision than 10 microsatellite markers. Our results suggest that conservation management and monitoring strategies can reliably use genetic based methods for early detection of population declines.

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Received: 15 June 2010 Accepted: 25 June 2010

DIGITAL OBJECT IDENTIFIER (DOI)

10.1111/j.1752-4571.2010.00150.x

On vacation

I'm going to be away for a couple of weeks. I'll come back in September.