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As a consequence of the process of domestication, wild and domestic individuals are adapted to very different environmental conditions. Although the phenotypic consequences of domestication are observable, the genetic causes are not evident in many cases. Artificial selection could be modifying the selection coefficients of new and standing variation in the population under domestication. Here, we aim to detect a genome-wide signal of domestication under a model of polygenic adaptation. We use forward simulations to investigate the 1D and 2D site frequency spectra (SFS) of mutations in two populations (Wild and Domestic) with divergent histories (demographic and selective) following a domestication split. We simulate ten different scenarios, varying the strength of selection upon beneficial mutations and the proportion of mutations whose selection coefficients change after domestication. First, we describe that in domesticated populations selection at linked sites needs to be invoked to explain the SFS of neutral mutations and that the mode of linked selection affecting the neutral SFS depends on the duration of the domestication bottleneck. Second, we find that some aspects of the full distribution of fitness effects (DFE), such as the shape and strength of the deleterious DFE, are accurately estimated in both populations when using only the 1D-SFS. However, the detection of significant differences in the beneficial DFE between populations remains challenging in most, but not all simulated scenarios when only the 1D-SFS is used. Third, when considering the 2D-SFS and a new joint DFE model, we are able to detect more subtle differences in the full DFE that are hidden in the 1D-SFS analysis. In conclusion, our work highlights the strengths and limitations of detecting a polygenic signal of domestication under a variety of domestication scenarios and genetic architectures.

Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population., This work was supported by Ministerio de Economia y Competividad grants AGL2013-41834-R (MEC, Spain), AGL2016-78709-R (MEC, Spain) and by the CERCA Programme/Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV-2015-0533). Genotyping of the CHCU samples was funded by the Animal Genetics Division of INRAE, as part of the CHACUBA project. Y. Rodriguez-Valera was funded by the French Embassy in Havana (Cuba) and INRAE. Y. Ramayo-Caldas was funded by the European Union H2020 Research and Innovation programme under Marie Skłodowska-Curie grant (P-Sphere) agreement No 6655919.

Animal domestication typically affected numerous polygenic quantitative traits, such as behaviour, development and reproduction. However, uncovering the genetic basis of quantitative trait variation is challenging, since it is probably caused by small allele-frequency changes. To date, only a few causative mutations related to domestication processes have been reported, strengthening the hypothesis that small effect variants have a prominent role. So far, the studies on domestication have been limited to the detection of the global effect of domestication on deleterious mutations and on strong beneficial variants, ignoring the importance of variants with small selective effects. In addition, very often, the study of the effects of selection are conducted on genome sequences that contain a non-negligible fraction of missing data, especially in non-model organisms. Hence, appropriate methods to account for these positions are needed. To overcome these difficulties, here we propose to estimate the proportion of beneficial variants using the asymptotic MacDonald-Kreitman (MK) method based on estimates of variability that summarizes the site frequency spectrum (SFS) while accounting for missing data and use them to perform an Approximate Bayesian Computation (ABC) analysis to infer the Distribution of Fitness Effects (DFE) of each population. We applied this approach to 46 genome sequences of pigs from three different populations, one wild and two domestics, with very different demographic histories and selective pressures. The obtained results showed that domestic and wild pig populations do not differ in nonsynonymous fixed mutations. Therefore, differences in α estimation among breeds are determined by their polymorphisms. The comparison of α for total and exclusive mutations suggests that the different domestic populations have suffered recent divergent changes in their functional versus neutral polymorphisms ratio, while the wild population is compatible with α=0. Besides, the DFE inferred with ABC indicates that both wild and domestic pigs display a large number of deleterious mutations at low frequency and a high number of neutral and/or nearly-neutral mutations that may have a significant effect on the evolution of domestic and wild populations. In addition, models not considering beneficial mutations have higher posterior probabilities, suggesting that beneficial mutations are difficult to detect or are scarce. Indeed, for all three populations, the median proportion of the strong favourable mutations are very low (≤ 0.1%) in those models that includes positive selection, with the average values of weak beneficial mutations around 0.6% for wild boar and 0.8-1.0% for the domestic pigs. Lastly, the analysis based on exclusive mutations showed that recent demographic changes may have severely affected the fitness of populations, especially that of the local Iberian breed.

The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution., This research was funded by the European Research Council (ERC) through the “AdaptoSCOPE” grant 648617 to JdM, by the German American Fulbright Commission to JdM, and by grant AGL2016-78709-R (MEC, Spain) to S.E.R.-O. S.E.R.-O also acknowledges the financial support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) and by the CERCA Programme/Generalitat de Catalunya. We further acknowledge grants R35 GM127131 and RO1 MH101244 from the National Institutes of Health (NIH) for S.S and E.M.K.

Newcastle disease virus (NDV) infections are well known to harbour quasispecies, due to the error-prone nature of the RNA polymerase. Quasispecies variants in the fusion cleavage site of the virus are known to significantly change its virulence. However, little is known about the genomic patterns of diversity and selection in NDV viral swarms. We analyse deep sequencing data from in vitro and in vivo NDV infections to uncover the genomic patterns of diversity and the signatures of selection within NDV swarms. Variants in viruses from in vitro samples are mostly localised in non-coding regions and 3&prime, and 5&prime, untranslated regions (3&prime, UTRs or 5&prime, UTRs), while in vivo samples contain an order of magnitude more variants. We find different patterns of genomic divergence and diversity among NDV genotypes, as well as differences in the genomic distribution of intra-host variants among in vitro and in vivo infections of the same strain. The frequency spectrum shows clear signatures of intra-host purifying selection in vivo on the matrix protein (M) coding gene and positive or diversifying selection on nucleocapsid (NP) and haemagglutinin-neuraminidase (HN). The comparison between within-host polymorphisms and phylogenetic divergence reveals complex patterns of selective pressure on the NDV genome at between- and within-host level. The M sequence is strongly constrained both between and within hosts, fusion protein (F) coding gene is under intra-host positive selection, and NP and HN show contrasting patterns: HN RNA sequence is positively selected between hosts while its protein sequence is positively selected within hosts, and NP is under intra-host positive selection at the RNA level and negative selection at the protein level.

Transposable elements (TEs) are a major driver of plant genome evolution. A part from being a rich source of new genes and regulatory sequences, TEs can also affect plant genome evolution by modifying genome size and shaping chromosome structure. TEs tend to concentrate in heterochromatic pericentromeric regions and their proliferation may expand these regions. Here, we show that after the split of melon and cucumber, TEs have expanded the pericentromeric regions of melon chromosomes that, probably as a consequence, show a very low recombination frequency. In contrast, TEs have not proliferated to a high extent in cucumber, which has small TE-dense pericentromeric regions and shows a relatively constant recombination rate along chromosomes. These differences in chromosome structure also translate in differences in gene nucleotide diversity. Although gene nucleotide diversity is essentially constant along cucumber chromosomes, melon chromosomes show a bimodal pattern of genetic variability, with a gene-poor region where variability is negatively correlated with gene density. Interestingly, genes are not homogeneously distributed in melon, and the high variable low-recombining pericentromeric regions show a higher concentration of melon-specific genes whereas genes shared with cucumber and other plants are essentially found in gene-rich chromosomal arms. The results presented here suggest that melon pericentromeric regions may allow gene sequences to evolve more freely than in other chromosomal compartments which may allow new ORFs to arise and eventually be selected. These results show that TEs can drastically change the structure of chromosomes creating different chromosomal compartments imposing different constraints for gene evolution., This work was supported by Ministerio de Economia y Competitividad grants AGL2013-43244-R and AGL2016-78992-R to J.C., Ministerio de Economia y Competitividad grant AGL2015-64625-C2-1-R to J.G.-M. and Centro de Excelencia Severo Ochoa 2016–2020, and the CERCA Programme/Generalitat de Catalunya to J.C., J.G.-M. and S.R.-O.

bioRxiv, We introduce the conditional Site Frequency Spectrum (SFS) for a genomic region linked to a focal mutation of known frequency. An exact expression for its expected value is provided for the neutral model without recombination. Its relation with the expected SFS for two sites, 2-SFS, is discussed. These spectra derive from the coalescent approach of Fu (1995) for finite samples, which is reviewed. Remarkably simple expressions are obtained for the linked SFS of a large population, which are also solutions of the multi-allelic Kolmogorov equations. These formulae are the immediate extensions of the well known single site θ/f neutral SFS. Besides the general interest in these spectra, they relate to relevant biological cases, such as structural variants and introgressions. As an application, a recipe to adapt Tajima’s and other SFS-based neutrality tests to a non-recombining region containing a neutral marker is presented., GA and LF were supported by grant ANR-12-JSV7-0007 TempoMut from Agence Nationale de la Recherche. GA was also supported by grant ANR-12-BSV7-0012 Demochips, AK and TW by grants of the German Science Foundation (DFG-SFB680 and DFG-SPP 1590).

We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the 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 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp., This work was supported by grants of the Ministerio de Economía y Competitividad, Spain (BFU2010-15484, CGL2013-45211, AGL2013-41834-R, AGL2016-78709-R, and CGL2016-75255), and by the Comissió Interdepartamental de Recerca I Innovació Tecnològica of Catalonia, Spain (2009SGR-1287 and 2014SGR-1055). J.R. was partially supported by ICREA Academia (Generalitat de Catalunya), and S.G.-R. by a Beatriu de Pinós Postdoctoral Fellowship (AGAUR; 2014 BP-B 00027).

Pig-like species (Suidae) are found in many different parts of the world. This superfamily consists of at least 15 different extant species found in Africa, South America, Europe, and Asia (Table 34.1). Suid species in Eurasia exhibit a striking dichotomy in their distribution. While there are at least seven recognized suid species on Island South East Asia (ISEA), only two are found on the Eurasian mainland (Table 34.1). Even in these two species on the Eurasian mainland, the dichotomy could not have been starker: one species, the pygmy hog (Porcula salvania) is confined to a relatively small region in the north of India and south of Nepal, where it relies on a rather special ecosystem, i.e. the grasslands near the southern foothills of the Himalayas. The pygmy hog was recently proposed to be reassigned to a separate genus relative to the genus Sus (Funk et al. 2007). On the other hand, Sus scrofa, the other Eurasian mainland species, can be found throughout this largest landmass on our planet, whenever woodlands or shrubs are present, and snow cover in winter is not too prolonged. Although wild boar certainly has a defined ecology, its wide range does exemplify the opportunistic nature of this species.

Trabajo presentado al 4th International Workshop on Parallelism in Bioinformatics (euro-Par), celebrado del 22 al 26 de agosto de 2016 en Grenoble, France., Next-generation sequencing (NGS) technologies initiated a revolution in genomics, producing massive amounts of biological data and the consequent need for adapting current computing infrastructures. Multiple alignment of genomes, analysis of variants or phylogenetic tree construction, with quadratic polynomial complexity in the best case are tools that can take days or weeks to complete in conventional computers. Most of these analysis, involving several tools integrated in workflows, present the possibility of dividing the computational load in independent tasks allowing parallel execution. Determining adequate load balancing, data partitioning, granularity and I/O tuning are key factors for achieving suitable speedups. In this paper we present a coarse-grain parallelization of GH caller (Genotype/Haplotype caller), a tool used in population genomics workflows that performs a probabilistic identification process to account for the frequency of variants present between population individuals. It implements a master-worker model, using the standard Message Passing Interface (MPI), and concurrently and iteratively distributes the data among the available worker processes by mapping subsets of data and leaving the orchestration to the master process. Our results show a performance gain factor of 260x using 64 processes and additional optimizations with regard to the initial non-parallelized version., This work was supported by Ministerio de Ciencia y Tecnología (Spain) under project number TIN2014-53234-C2-1-R, and Ministerio de Economía y Competitividad (grant AGL2013-41834-R) to S.E.R.-O.

[Background]: Taste receptors (TASRs) are essential for the body’s recognition of chemical compounds. In the tongue, TASRs sense the sweet and umami and the toxin-related bitter taste thus promoting a particular eating behaviour. Moreover, their relevance in other organs is now becoming evident. In the intestine, they regulate nutrient absorption and gut motility. Upon ligand binding, TASRs activate the appetite-reward circuitry to signal the nervous system and keep body homeostasis. With the aim to identify genetic variation in the swine TASRs and in the genes from the appetite and the reward pathways, we have sequenced the exons of 201 TASRs and appetite-reward genes from 304 pigs belonging to ten breeds, wild boars and to two phenotypically extreme groups from a F2 resource with data on growth and fat deposition., [Results]: We identified 2,766 coding variants 395 of which were predicted to have a strong impact on protein sequence and function. 334 variants were present in only one breed and at predicted alternative allele frequency (pAAF) ≥ 0.1. The Asian pigs and the wild boars showed the largest proportion of breed specific variants. We also compared the pAAF of the two F2 groups and found that variants in TAS2R39 and CD36 display significant differences suggesting that these genes could influence growth and fat deposition. We developed a 128-variant genotyping assay and confirmed 57 of these variants., [Conclusions]: We have identified thousands of variants affecting TASRs as well as genes involved in the appetite and the reward mechanisms. Some of these genes have been already associated to taste preferences, appetite or behaviour in humans and mouse. We have also detected indications of a potential relationship of some of these genes with growth and fat deposition, which could have been caused by changes in taste preferences, appetite or reward and ultimately impact on food intake. A genotyping array with 57 variants in 31 of these genes is now available for genotyping and start elucidating the impact of genetic variation in these genes on pig biology and breeding., This work was funded by grants from the Spanish Ministry of Science and Innovation (project AGL2010-22358-C02-01) and the Spanish Ministry of Economy and Competitiveness (AGL2013-44978-R; CSD2007-00036, IPT-2012-0378-060000). We would also like to thank the Danish Ministry of Science, Technology and Innovation for the grant to the “UNIK Project for Food Fitness and Pharma for Health” that funded the development of the F2 resource. Alex Clop acknowledges the Ramon y Cajal Fellowship program from the Spanish Ministry of Economy and Competitiveness (RYC-2011-07763). Sophia Derdak is supported by the Parc Científic de Barcelona through the Torres Quevedo subprogram (MICINN) under grant agreement PTQ-12-05391.

Missing data are common in DNA sequences obtained through high-throughput sequencing. Furthermore, samples of low quality or problems in the experimental protocol often cause a loss of data even with traditional sequencing technologies. Here we propose modified estimators of variability and neutrality tests that can be naturally applied to sequences with missing data, without the need to remove bases or individuals from the analysis. Modified statistics include the Watterson estimator θW, Tajima’s D, Fay and Wu’s H, and HKA. We develop a general framework to take missing data into account in frequency spectrum-based neutrality tests and we derive the exact expression for the variance of these statistics under the neutral model. The neutrality tests proposed here can also be used as summary statistics to describe the information contained in other classes of data like DNA microarrays., Work funded by grant CGL2009-09346 to S.R.O., grant AG2010-14822 to Miguel Pérez-Enciso, and Consolider grant CSD2007-00036 “Centre for Research in Agrigenomics” (Ministerio de Ciencia e Innovación, Spain). S.R.O. is recipient of a Ramón y Cajal position (Ministerio de Ciencia e Innovación, Spain). L.F. acknowledges support from Consejo Superior de Investigaciones Científicas (Spain) under the JAE-doc program.

The ascertainment of the demographic and selective history of populations has been a major research goal in genetics for decades. To that end, numerous statistical tests have been developed to detect deviations between expected and observed frequency spectra, e.g., Tajima's D, Fu and Li's F and D tests, and Fay and Wu's H. Recently, Achaz developed a general framework to generate tests that detect deviations in the frequency spectrum. In a further development, we argue that the results of these tests should be as independent on the sample size as possible and propose a scale-free form for them. Furthermore, using the same framework as that of Achaz, we develop a new family of neutrality tests based on the frequency spectrum that are optimal against a chosen alternative evolutionary scenario. These tests maximize the power to reject the standard neutral model and are scalable with the sample size. Optimal tests are derived for several alternative evolutionary scenarios, including demographic processes (population bottleneck, expansion, contraction) and selective sweeps. Within the same framework, we also derive an optimal general test given a generic evolutionary scenario as a null model. All formulas are relatively simple and can be computed very fast, making it feasible to apply them to genome-wide sequence data. A simulation study showed that, generally, the tests proposed are more consistently powerful than standard tests like Tajima's D. We further illustrate the method with real data from a QTL candidate region in pigs.

A. halleri is a psuedometallophyte with a patchy distribution in Europe and is often spread by human activity. To determine the population history and whether this history is consistent with potential human effects, we surveyed nucleotide variation using 24 loci from 12 individuals in a large A. halleri population. The means of total and silent nucleotide variation (theta(W)) are within the range expected for the species. The population genetic neutrality tests Tajima's D and Wall's B had significant composite results rejecting panmixia, and Approximate Bayesian Computation analysis revealed that a subdivision model better explained the variation than the standard neutral model, refugia (or admixture), bottleneck or change of population size models. A categorical regression analysis further supports the subdivision model, and under the subdivision model, the neutrality tests are no longer significant. The best support was for two source populations, a situation consistent with the mixing of two populations possibly mediated by human activity. This scenario might limit the genetic diversity and adaptive potential of the population. The non-neutral population variation described here should be considered in bioinformatic searches for adaptation.

Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in ∼10 kb or less. For tightly linked SNPs separated by, This work was supported by the National Science Foundation (award EF-0723447), the National Institutes of Health (award R01 GM086496-01), Duke University, and the Max-Planck Society.

The msParSm application is an evolution of msPar, the parallel version of the coalescent simulation program ms, which removes the limitation for simulating long stretches of DNA sequences with large recombination rates, without compromising the accuracy of the standard coalescence. This work introduces msParSm, describes its significant performance improvements over msPar and its shared memory parallelization details, and shows how it can get better, if not similar, execution times than MaCS. Two case studies with different mutation rates were analyzed, one approximating the human average and the other approximating the Drosophila melanogaster average. Source code is available at https://github.com/cmontemuino/msparsm., This work has been supported by projects (number: AGL2013-41834-R and TIN2014-53234-C2-1-R) of Spanish Ministerio de Ciencia y Tecnologia.

bioRxiv preprint, We investigate the dependence of the site frequency spectrum on the topological structure of genealogical trees. We show that basic population genetic statistics, for instance, estimators of θ or neutrality tests such as Tajima’s D, can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima’s D and Fay and Wu’s H depend in a direct way on a peculiar measure of tree balance, which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu’s H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulas for these extreme values as a function of sample size and number of segregating sites., A.L. is funded by the United Kingdom National Institute for Health Research, Health Protection Research Unit on Modelling Methodology (grant HPRU-2012-10080). L.F. and G.A. acknowledge support from the grant ANR-12-JSV7-0007 from Agence Nationale de Recherche (France). G.A. acknowledges support from the grant ANR-12-BSV7-0012-04 from Agence Nationale de Recherche (France). T.W. acknowledges support from DFG-SPP1590 by the German Science Foundation. S.E.R.O. is supported by grants CGL2009-09346 (MICINN, Spain), AGL2013-41834-R (MEC, Spain), by the CERCA Programme/Generalitat de Catalunya and acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the Severo Ochoa Programme for Centres of Excellence in R&D 2016-2019 (SEV‐2015‐0533).

Coalescent simulations were used to investigate the possible role of population subdivision and history in shaping nucleotide variation in a recombining 88-kb genomic fragment of Drosophila simulans displaying an unusual large-scale haplotype structure. The multilocus analysis, based on summary statistics using specific demographic null models under recombination, indicates that the observed levels of linkage disequilibrium differed significantly from the values expected under different bottleneck and population admixture scenarios. These results indicate that demography alone may not account for the observed pattern of variation and support the previous claim that the data are better described by a model in which an adaptive mutation has not yet gone to fixation.

A comprehensive catalog of variability in a given species is useful for many important purposes, e.g., designing high density arrays or pinpointing potential mutations of economic or physiological interest. Here we provide a genomewide, worldwide catalog of single nucleotide variants by simultaneously analyzing the shotgun sequence of 128 pigs and five suid outgroups. Despite the high SNP missing rate of some individuals (up to 88%), we retrieved over 48 million high quality variants. Of them, we were able to assess the ancestral allele of more than 39M biallelic SNPs. We found SNPs in 21,455 out of the 25,322 annotated genes in pig assembly 10.2. The annotation showed that more than 40% of the variants were novel variants, not present in dbSNP. Surprisingly, we found a large variability in transition / transversion rate along the genome, which is very well explained (R2=0.79) primarily by genome differences in in CpG content and recombination rate. The number of SNPs per window also varied but was less dependent of known factors such as gene density, missing rate or recombination (R2=0.48). When we divided the samples in four groups, Asian wild boar (ASWB), Asian domestics (ASDM), European wild boar (EUWB) and European domestics (EUDM), we found a marked correlation in allele frequencies between domestics and wild boars within Asia and within Europe, but not across continents, due to the large evolutive distance between pigs of both continents (~1.2 MYA). In general, the porcine species showed a small percentage of SNPs exclusive of each population group. EUWB and EUDM were predicted to harbor a larger fraction of potentially deleterious mutations, according to the SIFT algorithm, than Asian samples, perhaps a result of background selection being less effective due to a lower effective population size in Europe., This work was funded by AGL2010-14822 and AGL2013-41834-R (Ministry of Economy and Science, Spain) to MPE and SERO.

The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution., This work was supported by Ministerio de Ciencia e Innovación (grant BFU2009-11932 to J.M.C. and grant AGL2012-40130-C02-01 to J.G.-M.); Ministerio de Economía y Competitividad (grant AGL2013-43244-R to J.M.C., grant AGL2013-41834-R to S.E.R.-O., and grant AGL2009-12698-C02-01 to J.G.-M.); and Fundación Genoma España to J.G.-M.

There is an increasing interest in direct screening of polymorphisms at candidate loci to associate them with adaptations in natural situations. We report primers that amplify regions at 22 putatively orthologous functional loci in the family Brassicaceae: Arabidopsis thaliana, its two wild outcrossing relatives, and Brassica oleracea. Four groups of genes were known to have specific functions in the model species A. thaliana in ecologically important traits: timing of reproduction; metabolism of secondary compounds; defence against pathogens or light perception. In addition, genes of a fifth group were selected with no consideration of their function, as reference loci. [KEYWORDS: Arabidopsis; candidate genes; defence-genes; flowering time; molecular adaptation; phenylpropanoid pathway; phytochromes]

Decreasing costs of next-generation sequencing (NGS) experiments have made a wide range of genomic questions open for study with nonmodel organisms. However, experimental designs and analysis of NGS data from less well-known species are challenging because of the lack of genomic resources. In this work, we investigate the performance of alternative experimental designs and bioinformatics approaches in estimating variability and neutrality tests based on the site-frequency-spectrum (SFS) from individual resequencing data. We pay particular attention to challenges faced in the study of nonmodel organisms, in particular the absence of a species-specific reference genome, although phylogenetically close genomes are assumed to be available. We compare the performance of three alternative bioinformatics approaches – genotype calling, genotype–haplotype calling and direct estimation without calling genotypes. We find that relying on genotype calls provides biased estimates of population genetic statistics at low to moderate read depth (2–8×). Genotype–haplotype calling returns more accurate estimates irrespective of the divergence to the reference genome, but requires moderate depth (8–20×). Direct estimation without calling genotypes returns the most accurate estimates of variability and of most SFS tests investigated, including at low read depth (2–4×). Studies without species-specific reference genome should thus aim for low read depth and avoid genotype calling whenever individual genotypes are not essential. Otherwise, aiming for moderate to high depth at the expense of number of individuals, and using genotype–haplotype calling, is recommended., Work funded by Consolider CSD2007-00036 ‘Centre for Research in Agrigenomics’ and AGL2010-14822 grants (Spain) to MPE and CGL2009-09346 grant (Spain) to SRO.

Human DNA sequence variation data are useful for studying the origin, evolution, and demographic history of modern humans and the mechanisms of maintenance of genetic variability in human populations, and for detecting linkage association of disease. Here, we report worldwide variation data from a ≈10-kilobase noncoding autosomal region. We identified 75 variant sites in 64 humans (128 sequences) and 463 variant sites among the human, chimpanzee, and orangutan sequences. Statistical tests suggested that the region is selectively neutral. The average nucleotide diversity (π) across the region was 0.088% among all of the human sequences obtained, 0.085% among African sequences, and 0.082% among non-African sequences, supporting the view of a low nucleotide diversity (≈0.1%) in humans. The comparable π value in non-Africans to that in Africans indicates no severe bottleneck during the evolution of modern non-Africans; however, the possibility of a mild bottleneck cannot be excluded because non-Africans showed considerably fewer variants than Africans. The present and two previous large data sets all show a strong excess of low frequency variants in comparison to that expected from an equilibrium population, indicating a relatively recent population expansion. The mutation rate was estimated to be 1.15 × 10 −9 per nucleotide per year. Estimates of the long-term effective population size N e by various statistical methods were similar to those in other studies. The age of the most recent common ancestor was estimated to be ≈1.29 million years ago among all of the sequences obtained and ≈634,000 years ago among the non-African sequences, providing the first evidence from a noncoding autosomal region for ancient human histories, even among non-Africans.

We implemented a parallel version (hereafter referred as “msPar”) of the coalescent simulation program ms, providing the same functionality and output, parallelized using a Master-Worker scheme with on-demand scheduling and MPI to run on an HPC cluster. To our knowledge this is the first time such parallelization has been applied to ms, and shown to be effective in using all computational resources of an HPC cluster, performing up to 42 times faster than original ms when using 72 logical processors. We propose msPar as an alternative to ms and other simulators using approximations to the standard coalescent approach. Source code is available at https://github.com/cmontemuino/mspar

Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches. Here, we present PopGenome, a population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual loci. It reads DNA alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects. PopGenome also reads associated annotation files in GFF format, enabling users to easily define regions or classify SNPs based on their annotation; all analyses can also be applied to sliding windows. PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. PopGenome is linked to Hudson’s MS and Ewing’s MSMS programs to assess statistical significance based on coalescent simulations. PopGenome’s integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics. Developers can easily incorporate new analyses methods into the PopGenome framework. PopGenome and R are freely available from CRAN (http://cran.r-project.org/) for all major operating systems under the GNU General Public License., This work was supported by the Spanish Ministerio de Ciencia e Innovación Grant CGL2009-09346 to S.E.R.O. and by the German Research Foundation DFG grants EXC 1028 and CRC 680 to M.J.L.

Altres ajuts: CERCA Programme/Generalitat de Catalunya The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. The most popular single-nucleotide polymorphism (SNP) callers are designed to obtain a high SNP recovery and low false discovery rate but are not designed to account appropriately the frequency of the variants. Instead, algorithms designed to account for the frequency of SNPs give precise results for estimating the levels and the patterns of variability. These algorithms are focused on the unbiased estimation of the variability and not on the high recovery of SNPs. Here, we implemented a fast and optimized parallel algorithm that includes the method developed by Roesti et al and Lynch, which estimates the genotype of each individual at each site, considering the possibility to call both bases from the genotype, a single one or none. This algorithm does not consider the reference and therefore is independent of biases related to the reference nucleotide specified. The pipeline starts from a BAM file converted to pileup or mpileup format and the software outputs a FASTA file. The new program not only reduces the running times but also, given the improved use of resources, it allows its usage with smaller computers and large parallel computers, expanding its benefits to a wider range of researchers. The output file can be analyzed using software for population genetics analysis, such as the R library PopGenome, the software VariScan, and the program mstatspop for analysis considering positions with missing data.

[Background]: In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data., [Results]: A total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism., [Conclusions]: This work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of structural variation in the species, including Iberian pigs, and allowed us to identify new paralogs for known gene families., AE is funded by the Spanish Ministry of Research PhD studentship program (FPI). Work funded by grants AGL2010-14822 to MPE, CGL2009-09346 (MICINN, Spain) to SERO , by a Consolider grant from Spanish Ministry of Research, CSD2007-00036 “Centre for Research in Agrigenomics”, and by the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013) / ERC Grant agreement n° 249894 (SelSweep project) to MAMG.

The phylogeography of the porcine X chromosome has not been studied despite the unique characteristics of this chromosome. Here, we genotyped 59 single nucleotide polymorphisms (SNPs) in 312 pigs from around the world, representing 39 domestic breeds and wild boars in 30 countries. Overall, widespread commercial breeds showed the highest heterozygosity values, followed by African and American populations. Structuring, as inferred from FST and analysis of molecular variance, was consistently larger in the non-pseudoautosomal (NPAR) than in the pseudoautosomal regions (PAR). Our results show that genetic relationships between populations can vary widely between the NPAR and the PAR, underscoring the fact that their genetic trajectories can be quite different. NPAR showed an increased commercial-like genetic component relative to the PAR, probably because human selection processes to obtain individuals with high productive parameters were mediated by introgressing boars rather than sows., WBP is funded by COLCIENCIAS (Departamento Administrativo de Ciencia, Tecnología e Innovación, Francisco José de Caldas fellowship 497/2009, Colombia). CAS was funded by a PhD grant from CAPES (Coordenaçao de Aperfeiçoamento de Pessoal de Nível Superior, Brazil) and Universidade Catolica de Brasilia, Brazil. This work is funded by grants AGL2010-14822 (MICINN, Spain) to MPE, CGL2009-09346 (MICINN, Spain) to SERO, and Consolider project (MICINN, Spain) to Centre of Research in Agricultural Genomics.

[Background]: Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity., [Methodology/Main Findings]: Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar., [Conclusions/Significance]: These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection., This work was conducted as part of the SABRETRAIN Project funded by the Marie Curie Host Fellowships for Early Stage Research Training and as part of the 6th Framework Programme of the European Commission. This work was supported by USDA AG 2008-34480-19328, USDA-ARS 538 AG58-5438-7-3171, USDA AG 2007-04315, EU SABRE project FOOD-CT-2006-01625 and Consolider-Ingenio Programme CSD2007-00036 “Centre for Research in Agrigenomics”. MP-E is funded by a MICINN grant AGC2007-65563-C02-01/GAN (Spain). SER-O is recipient of a Ramon y Cajal position and is funded by a MICINN grant CGL2009-09346/BOS (Spain). LF holds a JAEdoc post doc fellowship from CSIC (Spain).

Domestication, modern breeding and artificial selection have shaped dramatically the genomic variability of domestic animals. In livestock, the so-called FAT1 quantitative trait locus (QTL) in porcine chromosome 4 was the first QTL uncovered although, to date, its precise molecular nature has remained elusive. Here, we characterize the nucleotide variability of 13 fragments of ∼500 bp equally spaced in a 2 Mb region in the vicinity of the FAT1 region in a wide-diversity panel of 32 pigs. Asian and European animals, including local Mediterranean and international pig breeds, were sequenced. Patterns of genetic variability were very complex and varied largely across loci and populations; they did not reveal overall a clear signal of a selective sweep in any breed, although FABP4 fragment showed a significantly higher diversity. We used an approximate Bayesian computation approach to infer the evolutionary history of this SSC4 region. Notably, we found that European pig populations have a much lower effective size than their Asian counterparts: in the order of hundreds vs hundreds of thousands. We show also an important part of extant European variability is actually due to introgression of Asian germplasm into Europe. This study shows how a potential loss in diversity caused by bottlenecks and possible selective sweeps associated with domestication and artificial selection can be counterbalanced by migration, making it much more difficult the identification of selection footprints based on naive demographic assumptions. Given the small fragment analyzed here, it remains to be studied how these conclusions apply to the rest of the genome., AO is recipient of FPI PhD fellowships from Ministerio de Ciencia e Innovación (MICINN), Spain; SERO is recipient of a Ramón y Cajal position (MICINN). This work was funded by Grants AGL2007-65563-C02-01/GAN and Consolider project (MICINN, Spain) to MPE, the China National 973 Project 2006CB102100 to LSH and CGL2009-0934 (MICINN, Spain) to SERO.

The orientation of flanking genes may influence the evolution of intergenic regions in which cis-regulatory elements are likely to be located: divergently transcribed genes share their 5′ regions, resulting either in smaller “private” spaces or in overlapping regulatory elements. Thus, upstream sequences of divergently transcribed genes (bi-directional upstream regions, or URs) may be more constrained than those of uni-directional gene pairs. We investigated this effect by analyzing nucleotide variation segregating within and between Arabidopsis species. Compared to uni-directional URs, bi-directional URs indeed display lower population mutation rate, as well as more low-frequency polymorphisms. Furthermore, we find that bi-directional regions undergo selection for the maintenance of intergenic distance. Altogether, however, we observe considerable variation in evolutionary rates, with putative signatures of selection on two uni-directional upstream regions., This research was funded by the German Funding Agency (SFB680).

Coalescent theory is a powerful tool for population geneticists as well as molecular biologists interested in understanding the patterns and levels of DNA variation. Using coalescent Monte Carlo simulations it is possible to obtain the empirical distributions for a number of statistics across a wide range of evolutionary models; these distributions can be used to test evolutionary hypotheses using experimental data. The mlcoalsim application presented here (based on a version of the ms program, Hudson, 2002) adds important new features to improve methodology (uncertainty and conditional methods for mutation and recombination), models (including strong positive selection, finite sites and heterogeneity in mutation and recombination rates) and analyses (calculating a number of statistics used in population genetics and P-values for observed data). One of the most important features of mlcoalsim is the analysis of multilocus data in linked and independent regions. In summary, mlcoalsim is an integrated software application aimed at researchers interested in molecular evolution. mlcoalsim is written in ANSI C and is available at: http://www.ub.es/softevol/mlcoalsim.

Detecting the signature of adaptation on nucleotide variation is often difficult in species that like Arabidopsis thaliana might have a complex demographic history. Recent re-sequencing surveys in this species provided genome-wide information that would mainly reflect its demographic history. We have used a large empirical data set (LED) as well as multilocus coalescent simulations to analyse sequence variation at loci involved in the phenylpropanoid pathway of this species. We surveyed and examined DNA sequence variation at nine of these loci (about 19.7 kb) in 23 accessions of A. thaliana and one accession of its closely related species Arabidopsis lyrata. Nucleotide variation was lower at nonsynonymous sites than at silent sites in all loci, indicating generalized functional constraint at the protein level. No association between variation and position in the metabolic pathway was detected. When the data were contrasted against the standard neutral model, significant deviations for silent variation were detected with Tajima's D, Fu's F(S) and Fay and Wu's H multilocus test statistics. These deviations were in the same direction than in previous large-scale multilocus analyses, suggesting a genome-wide effect. When the nine-locus data set was contrasted against the large empirical data set, the level (Watterson's theta) and pattern of variation (Tajima's D) detected in these loci did not deviate either at the single-locus or multilocus level from the corresponding empirical distributions. These results would support an important role of the demographic history of A. thaliana in shaping nucleotide variation at the nine studied phenylpropanoid loci. The potential and limitations of the empirical distribution approach are discussed.

SummaryCoalescent theory is commonly used to perform population genetic inference at the nucleotide level. Here, we examine the procedure that fixes the number of segregating sites (henceforth theFSprocedure). In this approach a fixed number of segregating sites (S) are placed on a coalescent tree (independently of the total and internode lengths of the tree). Thus, although widely used, theFSprocedure does not strictly follow the assumptions of coalescent theory and must be considered an approximation of (i) the standard procedure that uses a fixed population mutation parameter θ, and (ii) procedures that condition on the number of segregating sites. We study the differences in the false positive rate for nine statistics by comparing theFSprocedure with the procedures (i) and (ii), using several evolutionary models with single-locus and multilocus data. Our results indicate that for single-locus data theFSprocedure is accurate for the equilibrium neutral model, but problems arise under the alternative models studied; furthermore, for multilocus data, theFSprocedure becomes inaccurate even for the standard neutral model. Therefore, we recommend a procedure that fixes the θ value (or alternatively, procedures that condition onSand take into account the uncertainty of θ) for analysing evolutionary models with multilocus data. With single-locus data, theFSprocedure should not be employed for models other than the standard neutral model.

Nucleotide variation at the FAH1 and DFR gene regions was surveyed in four populations of Arabidopsis lyrata (two European A. l. petraea and two North American A. l. lyrata populations). In contrast to previous results, levels of variation were not consistently lower in A. l. lyrata than in A. l. petraea, and similar degrees of genetic differentiation were detected between and within subspecies. These observations and the significant genetic differentiation detected among populations suggest population substructure and no real subdivision between subspecies. For each gene studied, genotypic data were obtained, which allowed comparing nucleotide diversity within individuals (between sequences from the same individual) and within populations (between sequences from the same population). The generally lower level of variation within than among individuals detected in each population yielded a significant deviation from panmixia within populations. In three of the four populations studied, two highly divergent alleles were detected within populations at the highly variable DFR locus. This pattern and the significant excess of derived variants detected in most populations suggest that most variation segregating within populations results from rare migration events between relatively small and isolated populations exhibiting reduced panmixia.

The simultaneous analysis of multiple genomic loci is a powerful approach to studying the effects of population history and natural selection on patterns of genetic variation of a species. By surveying nucleotide sequence polymorphism at 334 randomly distributed genomic regions in 12 accessions of Arabidopsis thaliana, we examined whether a standard neutral model of nucleotide sequence polymorphism is consistent with observed data. The average nucleotide diversity was 0.0071 for total sites and 0.0083 for silent sites. Although levels of diversity are variable among loci, no correlation with local recombination rate was observed, but polymorphism levels were correlated for physically linked loci (

Cecropins are insect antibacterial peptides that are part of the insect humoral immune response and could, therefore, be potential targets of natural selection. In Drosophila, the Cec genes constitute a multigene family whose members are arranged in tandem. The complete Cec family was isolated in two obscura group species: D. subobscura and D. pseudoobscura. The chromosomal regions encompassing the Cec genes were subsequently sequenced and mapped by in situ hybridization. In D. pseudoobscura, as in species of the D. melanogaster complex and in D. virilis, the Cec genes constitute a single cluster with five genes. In D. subobscura, unlike in the rest of the species, the eight members of the family are split into two clusters located in different parts of the same chromosome. Remarkable differences in levels of divergence were observed between copies in both species. The genomic organization and the phylogenetic relationships among members of this family in the genus Drosophila indicate (i) that the presence of two clusters is the derived state of the family, (ii) repeated gene duplication within species, (iii) nonfunctionalization and loss of some Cec copies, and (iv) the presence of both highly divergent and highly similar copies within species. These features are better explained by the birth-and-death model of molecular evolution, which posits that the high instability of the Cec multigene family in Drosophila is simply determined by the duplication rate and the subsequent loss of duplicated loci.

Nucleotide variation in eight effectively unlinked genes was surveyed in species-wide samples of the closely related outbreeding species Arabidopsis halleri and A. lyrata ssp. petraea and in three of these genes in A. lyrata ssp. lyrata and A. thaliana. Significant genetic differentiation was observed more frequently in A. l. petraea than in A. halleri. Average estimates of nucleotide variation were highest in A. l. petraea and lowest in A. l. lyrata, reflecting differences among species in effective population size. The low level of variation in A. l. lyrata is concordant with a bottleneck effect associated with its origin. The A. halleri/A. l. petraea speciation process was studied, considering the orthologous sequences of an outgroup species (A. thaliana). The high number of ancestral mutations relative to exclusive polymorphisms detected in A. halleri and A. l. petraea, the significant results of the multilocus Fay and Wu H tests, and haplotype sharing between the species indicate introgression subsequent to speciation. Average among-population variation in A. halleri and A. l. petraea was ∼1.5- and 3-fold higher than that in the inbreeder A. thaliana. The detected reduction of variation in A. thaliana is less than that expected from differences in mating system alone, and therefore from selective processes related to differences in the effective recombination rate, but could be explained by differences in population structure.

A region of approximately 1.6 kb encompassing the ribosomal protein 49 gene ( rp49 ) has been sequenced and compared in nine species of the obscura group of Drosophila: four species belonging to the obscura subgroup, three to the pseudoobscura subgroup, and two to the affinis subgroup. Our data provide strong support that the Nearctic species ( pseudoobscura and affinis subgroups) are monophyletic and place D. bifasciata with the other species of the obscura subgroup. Nucleotide sequence information at the rp49 gene region (located very close to one of the breakpoints of inversion O 3 ) has also been used to infer the phylogeny of the O chromosome in the subobscura species cluster. Analysis based both on parsimony-informative sites and on genetic distances confirms that the O 3 gene arrangement, present in D. guanche (together with inversion g ) and in D. madeirensis, is ancestral to gene arrangements O 3+4 and O st present in extant populations of D. subobscura.

Approximately 4 kb of the Cecropin cluster region have been sequenced in nine lines of Drosophila melanogaster and one line of the sibling species D. simulans, D. mauritiana, and D. sechellia. This region includes three functional genes (CecA1, CecA2, and CecB), which are involved in the insect immune response, and two pseudogenes (CecΨ1 and CecΨ2). The level of silent polymorphism in the three Cec genes is rather high (0.028), and there is no excess of nonsynonymous polymorphism. There is no evidence of gene conversion in the history of these genes. The interspecific comparison has revealed that in the three species of the simulans cluster the CecA2 gene is partially deleted and has therefore lost its function and become a pseudogene; in each of the species, subsequent deletions have accumulated. Divergence estimates indicate that the CecΨ1 and CecΨ2 pseudogenes are highly diverged, both between themselves and relative to the other three Cec genes. However, both CecΨ1 and CecΨ2 have conserved transcriptional signals and splice sites, and they present an open reading frame; also, correctly spliced transcripts have been detected for both CecΨ1 and CecΨ2. The data support that these genes are either active genes with some null alleles or young pseudogenes.

Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for the maintenance of genetic diversity. Therefore, an appreciation of how this variation is created and maintained is of critical importance to our understanding of biodiversity and evolutionary change. Here, we analysed the recombination features from species representing the major eutherian taxonomic groups Afrotheria, Rodentia, Primates and Carnivora to better understand the dynamics of mammalian recombination. Our results suggest a phylogenetic component in recombination rates (RRs), which appears to be directional, strongly punctuated and subject to selection. Species that diversified earlier in the evolutionary tree have lower RRs than those from more derived phylogenetic branches. Furthermore, chromosome-specific recombination maps in distantly related taxa show that crossover interference is especially weak in the species with highest RRs detected thus far, the tiger. This is the first example of a mammalian species exhibiting such low levels of crossover interference, highlighting the uniqueness of this species and its relevance for the study of the mechanisms controlling crossover formation, distribution and resolution., A.R-H.'s laboratory is funded by Ministerio de Ciencia e Innovacion (MICINN-Spain, CGL2010 20170) and the Barcelona Zoological Gardens (BSM, Zoo Barcelona). T.J.R.'s research is supported by a grant from the South African National Research Foundation. M.O.-B. is funded by Instituto de Salud Carlos III (CP07/0258 and PI08/1185).