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Phoretic insects utilize other animals to disperse to new environments. We recently discovered how egg parasitoids use an exciting phoretic strategy to reach egg-laying sites of their butterfly hosts. In the laboratory, female Trichogramma wasps detect and mount mated female cabbage white butterflies that emit an anti-aphrodisiac pheromone. Hardly any information exists about the natural occurrence of phoresy in wasps of this genus. Therefore, we monitored the presence of phoretic Trichogramma wasps on lepidopteran hosts in the field. Only female wasps were found at low prevalence on six lepidopteran species. Wasps were mostly found on female hosts and mainly on abundant solitary host species. This is the first report of phoretic Trichogramma wasps on butterflies in nature. We suggest that phoresy is only one of several strategies used by these polyphagous egg parasitoids. The evolution of phoresy is discussed in relation to the nutritional ecology of egg parasitoids. [ABSTRACT FROM AUTHOR]

Mutators have been shown to hitchhike in asexual populations when the anticipated beneficial mutation supply rate of the mutator subpopulation, NUb (for subpopulation of size N and beneficial mutation rate Ub) exceeds that of the wild-type subpopulation. Here, we examine the effect of total population size on mutator dynamics in asexual experimental populations of Saccharomyces cerevisiae. Although mutators quickly hitchhike to fixation in smaller populations, mutator fixation requires more and more time as population size increases; this observed delay in mutator hitchhiking is consistent with the expected effect of clonal interference. Interestingly, despite their higher beneficial mutation supply rate, mutators are supplanted by the wild type in very large populations. We postulate that this striking reversal in mutator dynamics is caused by an interaction between clonal interference, the fitness cost of the mutator allele, and infrequent large-effect beneficial mutations in our experimental populations. Our work thus identifies a potential set of circumstances under which mutator hitchhiking can be inhibited in natural asexual populations, despite recent theoretical predictions that such populations should have a net tendency to evolve ever-higher genomic mutation rates. [ABSTRACT FROM AUTHOR]

In a recent work on the wave of advance of a beneficial technology and associated hitchhiking of cultural and biological traits, we simulated the advance of neolithic agriculture into Europe. That model embraced geographical variation of land fertility and human mobility, conversion of indigenous mesolithic hunter-gatherers to agriculture, and competition between invading farmers and indigenous converts. A key result is a sharp cultural boundary across which the agriculturalists' heritage changes from that of the invading population to that of the converts. Here we present an analytical study of the cultural boundary for some simple cases. We show that the width of the boundary is determined by human mobility and the strength of competition. Simulations for the full model give essentially the same result. The finite width facilitates irreversible gene flow between the populations, so over time genetic differences appear as gradients while e.g. linguistic barriers may remain sharp. We also examine the various assumptions of the model relating to purposeful versus. random movement of peoples and the competition between cultures, demonstrating its richness and flexibility. [ABSTRACT FROM AUTHOR]

Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor species O. rufipogon, we observe a significant negative association between levels of polymorphism and both gene and coding site density, but either no association, or a negative correlation, between nucleotide variability and recombination rate. We establish that these patterns are unlikely to be explained by neutral mutation rate biases and demonstrate that a model of background selection with variable rates of deleterious mutation is sufficient to account for the gene density effect in O. rufipogon. In O. sativa ssp. japonica, we report a strong negative correlation between polymorphism and recombination rate and greater losses of variation during domestication in the euchromatic chromosome arms than heterochromatin. This is consistent with Hill–Robertson interference in low-recombination regions, which may limit the efficacy of selection for domestication traits. Our results suggest that the physical distribution of selected mutations is a primary factor that determines the genomic pattern of polymorphism in wild and domesticated rice species. [ABSTRACT FROM PUBLISHER]

Background: With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP) discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular. Methods and Results: On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a low minor allele frequency are included in the analysis. The reason is that these 'uninformative' polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans. Bias associated with uninformative polymorphisms is not eliminated by just avoiding technical artifacts in the data (PCR and sequencing errors), as a high proportion of SNPs with a low minor allele frequency is a general biological feature of natural populations. Conclusions: We suggest that uninformative markers should be excluded from genome scans based on empirical criteria derived from careful inspection of the data, and that these criteria should be reported explicitly. Together, this should increase the quality and comparability of genome scans, and hence promote our understanding of the processes driving genomic differentiation. [ABSTRACT FROM AUTHOR]

We investigated structurally polymorphic Alu insertions (POALINs) at five loci in the major histocompatibility complex (MHC) class I genomic region to determine their allele and haplotype frequencies and associations with the human leukocyte antigen (HLA)-A, -B, and -C genes in three populations, the Australian Caucasians, Japanese, and African Americans. The POALINs varied in allelic frequency between 0% and 42.3% with significant differences between populations at three of the five loci. The linkage disequilibrium (LD) between Alu insertions and the HLA-A, -B, or -C alleles and previously published polymorphic retroelements (four SVA and human endogenous retrovirus type 9 (HERVK9) loci) within the class I region of the MHC were calculated in pairwise analyses of haplotypes to show strong allelic associations and possible crossing-over events between some loci. Each POALIN was in significant LD with a variety of HLA-A, -B, or -C two-digit alleles probably as a result of hitchhiking. The POALINs helped to further stratify the HLA-A:B:C haplotypes into different POALIN:HLA-A:B:C haplotype frequencies. Of the multilocus haplotype analyses, the seven- and eight-locus haplotypes showed the largest number of differences between the populations, and fewer matched haplotypes between populations that ranged, for example, from 49% for HLA-B:HLA-A haplotypes to 7% for AluMICB:HLA-B:HLA-C:AluTF:AluHJ:HLA-A:AluHG:AluTF haplotypes in the Japanese. This comparative study of multilocus POALINs in the HLA class I region of three ethnic populations shows that POALINs alone or together with the HLA class I alleles and other retroelements are informative ancestral markers for assessing the interrelationship of HLA class I haplotype lineages, LD, and genetic diversity within the same and/or different populations. [ABSTRACT FROM AUTHOR]

Information about several topics discussed at the annual meeting of the Junior Members of the Royal Society for Asian Affairs, which was held at the East India Club in London, England on April 8, 2011, is presented. Featured discussions within the meeting included Steve Dew-Jones on his book "The Rule of Thumb," Susanna Hudson on her experiences driving through the country of Iran, and Arjit Sen on conflict in north-eastern India.

Goose barnacles (Lepas australis) were found attached to satellite-tracking and time-depth recording (TDR) instruments carried by two lactating Subantarctic fur seals (Arctocephalus tropical is) from Marion Island. We report on the movements of these seals, both of which crossed the Subantarctic Front. Barnacles surrounding the temperature probe of one TDR device did not appear to directly influence temperature recordings, although disturbances to recording accuracies by other high precision devices carrying goose barnacles are considered likely. [ABSTRACT FROM AUTHOR]

When new advantageous alleles arise and spread within a population, deleterious alleles at neighboring loci can hitchhike alongside them and spread to fixation in areas of low recombination, introducing a fixed mutation load. We use branching processes and diffusion equations to calculate the probability that a deleterious allele hitchhikes and fixes alongside an advantageous mutant. As expected, the probability of fixation of a deleterious hitchhiker rises with the selective advantage of the sweeping allele and declines with the selective disadvantage of the deleterious hitchhiker. We then use computer simulations of a genome with an infinite number of loci to investigate the increase in load after an advantageous mutant is introduced. We show that the appearance of advantageous alleles on genetic backgrounds loaded with deleterious alleles has two potential effects: it can fix deleterious alleles, and it can facilitate the persistence of recombinant lineages that happen to occur. The latter is expected to reduce the signals of selection in the surrounding region. We consider these results in light of human genetic data to infer how likely it is that such deleterious hitchhikers have occurred in our recent evolutionary past. [ABSTRACT FROM AUTHOR]

Religious people nowadays have more children on average than their secular counterparts. This paper uses a simple model to explore the evolutionary implications of this difference. It assumes that fertility is determined entirely by culture, whereas subjective predisposition towards religion is influenced by genetic endowment. People who carry a certain 'religiosity' gene are more likely than average to become or remain religious. The paper considers the effect of religious defections and exogamy on the religious and genetic composition of society. Defections reduce the ultimate share of the population with religious allegiance and slow down the spread of the religiosity gene. However, provided the fertility differential persists, and people with a religious allegiance mate mainly with people like themselves, the religiosity gene will eventually predominate despite a high rate of defection. This is an example of 'cultural hitchhiking', whereby a gene spreads because it is able to hitch a ride with a high-fitness cultural practice. The theoretical arguments are supported by numerical simulations. [ABSTRACT FROM AUTHOR]

Deleterious mutations present a significant obstacle to adaptive evolution. Deleterious mutations can inhibit the spread of linked adaptive mutations through a population; conversely, adaptive substitutions can increase the frequency of linked deleterious mutations and even result in their fixation. To assess the impact of adaptive mutations on linked deleterious mutations, we examined the distribution of deleterious and neutral amino acid polymorphism in the human genome. Within genomic regions that show evidence of recent hitchhiking, we find fewer neutral but a similar number of deleterious SNPs compared to other genomic regions. The higher ratio of deleterious to neutral SNPs is consistent with simulated hitchhiking events and implies that positive selection eliminates some deleterious alleles and increases the frequency of others. The distribution of disease-associated alleles is also altered in hitchhiking regions. Disease alleles within hitchhiking regions have been associated with auto-immune disorders, metabolic diseases, cancers, and mental disorders. Our results suggest that positive selection has had a significant impact on deleterious polymorphism and may be partly responsible for the high frequency of certain human disease alleles. [ABSTRACT FROM AUTHOR]

n analytically feasible, deterministic model for the spread of drug resistance among human malaria parasites, which incorporates all characteristics of the complex malaria-transmission cycle was introduced by Schneider and Kim (Theor. Popul Biol, 2010). The model accounts for the fact that only a fraction of infected hosts receive drug treatment and that hosts can be co-infected by differently many parasites. Furthermore, the model also incorporates host heterogeneity. Antimalarial-drug resistance is assumed to be caused by a single locus with two alleles-a sensitive one and a resistance one. The most important result for this model is that an analytical solution for the frequencies of a linked neutral biallelic locus exists. However, the exact solution does not admit an explicit form, and cannot straightforwardly be interpreted in terms of the model parameters. Here, we establish simple approximations for the equilibrium frequency at the neutral locus. Under the assumption that the resistant allele is initially rare-the biologically most relevant assumption in this context-and that recombination is weak, the approximations become similar to the approximations in the standard hitchhiking model. However, there are crucial differences. In particular, because of the high degree of selfing among malaria parasites in their sexual phase, a genome-wide reduction of relative heterozygosity occurs if selection is sufficiently strong. It turns out that the approximations are accurate even if the recombination rates are not small and the resistant allele is initially not very rare. The main advantage of our approximations is that they are easy to interpret in terms of model parameters. Moreover, they allow to make predictions of the size of the valley of reduced heterozygosity around the selected locus for given model parameters. Reversely, for a given reduction of heterozygosity, it is possible to identify the corresponding parameters. Moreover, we will show that incorporating host heterogeneity leads to an increased hitchhiking effect. [ABSTRACT FROM AUTHOR]

Selection mapping applies the population genetics theory of hitchhiking to the localization of genomic regions containing genes under selection. This approach predicts that neutral loci linked to genes under positive selection will have reduced diversity due to their shared history with a selected locus, and thus, genome scans of diversity levels can be used to identify regions containing selected loci. Most previous approaches to this problem ignore the spatial genomic pattern of diversity expected under selection. The regression-based approach advocated in this paper takes into account the expected pattern of decreasing genetic diversity with increased proximity to a selected locus. Simulated data are used to examine the patterns of diversity under different scenarios, in order to assess the power of a regression-based approach to the identification of regions under selection. Application of this method to both simulated and empirical data demonstrates its potential to detect selection. In contrast to some other methods, the regression approach described in this paper can be applied to any marker type. Results also suggest that this approach may give more precise estimates of the location of the selected locus than alternative methods, although the power is slightly lower in some cases. [ABSTRACT FROM PUBLISHER]

HIV adaptation to a host in chronic infection is simulated by means of a Monte-Carlo algorithm that includes the evolutionary factors of mutation, positive selection with varying strength among sites, random genetic drift, linkage, and recombination. By comparing two sensitive measures of linkage disequilibrium (LD) and the number of diverse sites measured in simulation to patient data from one-time samples of pol gene obtained by single-genome sëquencing from representative untreated patients, we estimate the effective recombination rate and the average selection coefficient to be on the order of 1% per genome per generation (1% per base per generation) and 0.5%, respectively. The adaptation rate is twofold higher and fourfold lower than predicted in the absence of recombination and in the limit of very frequent recombination, respectively. The level of ID and the number of diverse sites observed in data also range between the values predicted in simulation for these two limiting cases. These results demonstrate the critical importance of finite population size, linkage, and recombination in HIV evolution. [ABSTRACT FROM AUTHOR]

In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species. [ABSTRACT FROM AUTHOR]

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed 'recombinational neighborhoods,' where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5-7 Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation. [ABSTRACT FROM AUTHOR]

We consider the genome of a sample of n individuals taken at the end of a selective sweep, which is the fixation of an advantageous allele in the population. When the selective advantage is high, the genealogy at a locus under selective sweep can be approximated by a comb with n teeth. However, because of recombinations during the selective sweep, the hitchhiking effect decreases as the distance from the selected site increases, so that far from this locus, the tree can be approximated by a Kingman coalescent tree, as in the neutral case. We first give the distribution of the tree at a given locus. Then we focus on the evolution of this tree along the genome. Since this tree-valued process is not Markovian, we study the evolution of the Ancestral Recombination Graph along the genome in case of selective sweep. [ABSTRACT FROM AUTHOR]

Loci with higher levels of population differentiation than the neutral expectation are traditionally interpreted as evidence of ongoing selection that varies in space. This article emphasizes an alternative explanation that has been largely overlooked to date: in species subdivided into large subpopulations, enhanced differentiation can also be the signature left by the fixation of an unconditionally favorable mutation on its chromosomal neighborhood. This is because the hitchhiking effect is expected to diminish as the favorable mutation spreads from the deme in which it originated to other demes. To discriminate among the two alternative scenarios one needs to investigate how genetic structure varies along the chromosomal region of the locus. Local hitchhiking is shown to generate a single sharp peak of differentiation centered on the adaptive polymorphism and the standard signature of a selective sweep only in those subpopulations in which the allele is favored. Global hitchhiking produces two domes of differentiation on either side of the fixed advantageous mutation and signatures of a selective sweep in every subpopulation, albeit of different magnitude. Investigating population differentiation around a locus that strongly differentiates two otherwise genetically similar populations of the marine mussel Mytilus edulis, plausible evidence for the global hitchhiking hypothesis has been obtained. Global hitchhiking is a neglected phenomenon that might prove to be important in species with large population sizes such as many marine invertebrates. [ABSTRACT FROM AUTHOR]

Abstract: We analytically study a deterministic model for the spread of drug resistance among human malaria parasites. The model incorporates all major characteristics of the complex malaria transmission cycle and accounts for the fact that only a fraction of infected hosts receive drug treatment. Furthermore, the model incorporates that hosts can be co-infected. The number of parasites co-infecting a host is either a constant or, more generally, follows a given frequency distribution. Although the model is formulated in a multilocus setup, for our results we assume that drug resistance is caused by a single locus with two alleles — a sensitive one and a resistant one. We assume that the resistant allele has a selective advantage only in treated hosts and pays metabolic costs, which causes this allele to be deleterious in untreated hosts. We provide necessary and sufficient conditions for the fixation of the resistant allele. Moreover, provided the resistant allele will sweep through the population, we derive a formula for the time until it reaches a given frequency and in particular for the time until quasi-fixation. Furthermore, we establish an analytical solution for allele frequency changes at a linked neutral biallelic locus due to the rapid increase in frequency of the resistant allele. Our solution describes a local reduction in heterozygosity among parasite chromosomes around the resistant allele, the effect commonly referred to as the hitchhiking effect, as a function of and . The result therefore allows the investigation of selective sweep patterns under specific demographic settings. We find that the hitchhiking effect is similar but different from the standard model of genetic hitchhiking that assumes random mating and homogeneous selection. In particular, the process of recombination and selection cannot be decoupled. We further explain why standard hitchhiking theory cannot be applied to drug resistance in malaria. Furthermore, we will show that a genome-wide reduction in relative heterozygosity can occur provided a fraction of hosts is infected by a single parasite haplotype. Finally, we show how to incorporate host heterogeneity, and generalize our results to this biologically more realistic case. [Copyright &y& Elsevier]

1. The ecologically dominant leaf-cutting ants exhibit one of the most complex forms of morphological caste-based division of labour in order to efficiently conduct tasks, ranging from harvesting fresh leaf material to caring for the vulnerable fungal crop they farm as food. While much of their division of labour is well known, the role of the smallest workers on foraging trails is puzzling. Frequently these minim workers hitchhike on leaf fragments and it has been suggested that they may act to reduce the microbial contamination of leaf material before they enter the nest. Here we investigated this potentially important role of minims with field colonies of Atta colombica. 2. We experimentally increased the microbial load of leaf fragments and found that this resulted in minims hitchhiking on leaf fragments for longer. Furthermore, we show that leaves naturally have a significant microbial load and that the presence of hitchhikers reduces the microbial load of both experimentally manipulated and natural leaf fragments. 3. Intriguingly, the microbial load of leaves high in the canopy where ants were foraging was much lower than closer to the ground where the ants avoided cutting leaves. This suggests that the often perplexing foraging patterns of leaf-cutting ants may in part be explained by the ants avoiding leaves that are more heavily contaminated with microbes. 4. The removal of microbial contaminants is therefore an important role of hitchhiking minim workers in natural colonies of Atta leaf-cutting ants, although other tasks such as trail maintenance and defence also explain their occurrence on trails. [ABSTRACT FROM AUTHOR]

Abstract: Many threatened species are being maintained in captivity to save them from extinction, often with the eventual aim of reintroduction. The objective of genetic management in captivity is to ‘freeze’ evolution i.e. to avoid genetic adaptation to captivity and to retain genetic diversity. Most current genetic management of threatened species addresses the latter, but does not explicitly address the former. The theory underlying current genetic management and its practical implementation assumes neutrality of loci. However, genetic adaptation in captive populations may cause non-neutral behavior at neutral loci due to selective sweeps (hitchhiking) caused by rapid allele frequency changes at linked fitness loci. We compared changes in microsatellite genetic diversity at eight non-coding loci with neutral predictions in 23 pedigreed captive populations of Drosophila melanogaster maintained with effective sizes of 25 (eight replicates), 50 (6), 100 (4), 250 (3) and 500 (2) for 48 generations. Loss of microsatellite heterozygosity was significantly faster (by 12%) than predicted by neutral theory, as assessed by regressing proportion of heterozygosity retained on pedigree inbreeding coefficients. Further, greater than neutral changes were observed for both variances in allele frequencies across replicates (by 25%), and for temporal changes in allele frequencies (by 33%). All eight microsatellite loci showed signals of selectively-driven changes. Rather than having their evolution ‘frozen’, captive populations are undergoing major genome-wide selective sweeps that affect not only fitness loci but linked neutral loci. Captive genetic management for threatened species destined for reintroduction requires modification to explicitly minimize genetic adaptation to captivity. [Copyright &y& Elsevier]

The most remarkable outcome of a gene duplication event is the evolution of a novel function. Little information exists on how the rise of a novel function affects the evolution of its paralogous sister gene copy, however. We studied the evolution of the feminizer (fern) gene from which the gene complementary sex determiner (csd) recently derived by tandem duplication within the honey bee (Apis) lineage. Previous studies showed that fern retained its sex determination function, whereas the rise of csd established a new primary signal of sex determination. We observed a specific reduction of nonsynonymous to synonymous substitution ratios in Apis to non-Apis fern. We found a contrasting pattern at two other genetically linked genes, suggesting that hitchhiking effects to csd, the locus under balancing selection, is not the cause of this evolutionary pattern. We also excluded higher synonymous substitution rates by relative rate testing. These results imply that stronger purifying selection is operating at the fern gene in the presence of csd. We propose that csd's new function interferes with the function of Fern protein, resulting in molecular constraints and limited evolvability of fern in the Apis lineage. Elevated silent nucleotide polymorphism in fern relative to the genome-wide average suggests that genetic linkage to the csd gene maintained more nucleotide variation in today's population. Our findings provide evidence that csd functionally and genetically interferes with fern, suggesting that a newly evolved gene and its functions can limit the evolutionary capability of other genes in the genome. [ABSTRACT FROM AUTHOR]

Genes under divergent selection flow less readily between populations than other loci. This observation has led to verbal “divergence hitchhiking” models of speciation in which decreased interpopulation gene flow surrounding loci under divergent selection can generate large regions of differentiation within the genome (genomic islands). The efficacy of this model in promoting speciation depends on the size of the region affected by divergence hitchhiking. Empirical evidence is mixed, with examples of both large and small genomic islands. To address these empirical discrepancies and to formalize the theory, we present mathematical models of divergence hitchhiking, which examine neutral differentiation around selected sites. For a single locus under selection, regions of differentiation do not extend far along a chromosome away from a selected site unless both effective population sizes and migration rates are low. When multiple loci are considered, regions of differentiation can be larger. However, with many loci under selection, genome-wide divergence occurs and genomic islands are erased. The results show that divergence hitchhiking can generate large regions of differentiation, but that the conditions under which this occurs are limited. Thus, speciation may often require multifarious selection acting on many, isolated and physically unlinked genes. How hitchhiking promotes further adaptive divergence warrants consideration. [ABSTRACT FROM AUTHOR]

We used computer simulations to investigate to what extent true inbreeding, i.e. identity-by-descent, is affected by the use of marker-assisted selection (MAS) relative to traditional best linear unbiased predictions (BLUP) selection. The effect was studied by varying the heritability ( h 2 = 0.04 vs. 0.25), the marker distance (MAS vs. selection on the gene, GAS), the favourable QTL allele effect ( α = 0.118 vs. 0.236) and the initial frequency of the favourable QTL allele ( p = 0.01 vs. 0.1) in a population resembling the breeding nucleus of a dairy cattle population. The simulated genome consisted of two chromosomes of 100 cM each in addition to a polygenic component. On chromosome 1, a biallelic QTL as well as 4 markers were simulated in linkage disequilibrium. Chromosome 2 was selectively neutral. The results showed that, while reducing pedigree estimated inbreeding, MAS and GAS did not always reduce true inbreeding at the QTL relative to BLUP. MAS and GAS differs from BLUP by increasing the weight on Mendelian sampling terms and thereby lowering inbreeding, while increasing the fixation rate of the favourable QTL allele and thereby increasing inbreeding. The total outcome in terms of inbreeding at the QTL depends on the balance between these two effects. In addition, as a result of hitchhiking, MAS results in extra inbreeding in the region surrounding QTL, which could affect the overall genomic inbreeding. [ABSTRACT FROM AUTHOR]

Previous studies have revealed a major difference in the phylogenetic structure, extent of genetic diversity, and selection pressure between the surface glycoproteins and internal gene segments of avian influenza viruses (AIV) sampled from wild birds. However, what evolutionary processes are responsible for these strikingly different evolutionary patterns is unclear. To address this issue, we estimated the rate of evolutionary change and time of origin of each segment of AIV sampled globally. Strikingly, the internal segments of the sampled AIV strains possess common ancestors that existed less than 200 years ago. Similarly recent times of origin were observed for each of the individual subtypes within the HA, NA, and NS gene segments. Such a shallow history of genetic diversity suggests an evolutionary model in which the genetic structure of AIV is shaped by a combination of occasional selective sweeps in the HA and NA (and possibly NS) segments, coupled with transient genetic linkage to the internal gene segments. [ABSTRACT FROM AUTHOR]

In fewer than two decades after invading the Americas, the fly Drosophila subobscura evolved latitudinal clines for chromosomal inversion frequencies and wing size that are parallel to the long-standing ones in native Palearctic populations. By sharp contrast, wing shape clines also evolved in the New World, but the relationship with latitude was opposite to that in the Old World. Previous work has suggested that wing trait differences among individuals are partially due to the association between chromosomal inversions and particular alleles which influence the trait under consideration. Furthermore, it is well documented that a few number of effective individuals founded the New World populations, which might have modified the biometrical effect of inversions on quantitative traits. Here we evaluate the relative contribution of chromosomal inversion clines in shaping the parallel clines in wing size and contrasting clines in wing shape in native and colonizing populations of the species. Our results reveal that inversion-size and inversion-shape associations in native and colonizing (South America) populations are generally different, probably due to the bottleneck effect. Contingent, unpredictable evolution was suggested as an explanation for the different details involved in the otherwise parallel wing size clines between Old and New World populations of D. subobscura. We challenge this assertion and conclude that contrasting wing shape clines came out as a correlated response of inversion clines that might have been predicted considering the genetic background of colonizers. [ABSTRACT FROM AUTHOR]

To test the effect of women's hair color on the frequency of offering help, male (n=1,508) and female (n=892) French motorists were tested in a hitch- hiking situation. Five 20- to 22-yr-old female confederates wore a wig with blonde, brown, or black hair. Each confederate was instructed to stand by the side of a road frequented by hitchhikers and hold out her thumb to catch a ride. Blonde hair, compared with brown hair or black hair, was associated with a small but significantly larger number of male drivers who stopped to offer a ride (18 vs 14%). No difference was found for those with brown and black hair (14 and 13%, respectively). No effect of hair color was found for female drivers who stopped. The greater attractiveness associated with blonde hair for women appears to explain these data. [ABSTRACT FROM AUTHOR]

Domestic species provide a unique opportunity to examine the effects of selection on the genome. The myostatin gene ( GDF-8) has been under strong selection in a number of cattle breeds because of its influence on muscle conformation and association with the ‘double-muscling’ phenotype. This study examined genetic diversity near this gene in a set of breeds including some nearly fixed for the allele associated with double-muscling (MH), some where the allele is segregating at intermediate frequency and some where the allele is absent. A set of microsatellites and SNPs were used to examine patterns of diversity at the centromeric end of bovine chromosome 2, the region where GDF-8 is located, using various statistical methods. The putative position of a selected gene was moved across the genomic region to determine, by regression, a best position of reduced heterozygosity. Additional analyses examined extended homozygous regions and linkage disequilibrium patterns. While the SNP data was not found to be very informative for selection mapping in this dataset, analyses of the microsatellite data provided evidence of selection on GDF-8 in several breeds. These results suggested that, of the breeds examined, the allele was most recently introduced into the South Devon. Limitations to the selection-mapping approach were highlighted from the analysis of the SNP data and the situation where the MH allele was at intermediate frequency. [ABSTRACT FROM AUTHOR]

Over the past five or six decades, contamination and pollution of the world’s enclosed seas, coastal waters and the wider open oceans by plastics and other synthetic, non-biodegradable materials (generally known as ‘marine debris’) has been an ever-increasing phenomenon. The sources of these polluting materials are both land- and marine-based, their origins may be local or distant, and the environmental consequences are many and varied. The more widely recognized problems are typically associated with entanglement, ingestion, suffocation and general debilitation, and are often related to stranding events and public perception. Among the less frequently recognized and recorded problems are global hazards to shipping, fisheries and other maritime activities. Today, there are rapidly developing research interests in the biota attracted to freely floating (i.e. pelagic) marine debris, commonly known as ‘hangers-on and hitch-hikers’ as well as material sinking to the sea floor despite being buoyant. Dispersal of aggressive alien and invasive species by these mechanisms leads one to reflect on the possibilities that ensuing invasions could endanger sensitive, or at-risk coastal environments (both marine and terrestrial) far from their native habitats. [ABSTRACT FROM AUTHOR]

Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based on the capability of phage-carrying non-host bacteria to move along mycelia out of soil and form colonies in plaques of their co-transported phages. The approach was tested using two model phages of differing surface hydrophobicity, i.e., hydrophobic Escherichia virus T4 (T4) and hydrophilic Pseudoalteromonas phage HS2 (HS2). The phages were mixed into soil and allowed to be transported by soil bacteria along the mycelia of Pythium ultimum. Five phage-carrying bacterial species were isolated (Viridibacillus sp., Enterobacter sp., Serratia sp., Bacillus sp., Janthinobacterium sp.). These bacteria exhibited phage adsorption efficiencies of ≈90–95% for hydrophobic T4 and 30–95% for hydrophilic HS2. The phage adsorption efficiency of Viridibacillus sp. was ≈95% for both phages and twofold higher than T4-or HS2-adsorption to their respective hosts, qualifying Viridibacillus sp. as a potential super carrier for phages. Our approach offers an effective and target-specific way to identify and isolate phage-carrying bacteria in natural and man-made environments. [ABSTRACT FROM AUTHOR]

Understanding how speciation can take place in the presence of homogenizing gene flow remains a major challenge in evolutionary biology. In the early stages of ecological speciation, reproductive isolation between populations occupying different habitats is expected to be concentrated around genes for local adaptation. These genomic regions will show high divergence while gene exchange in other regions of the genome should continue relatively unimpaired, resulting in low levels of differentiation. The problem is to explain how speciation progresses from this point towards complete reproductive isolation, allowing genome-wide divergence. A new study by Via and West (2008) on speciation between host races of the pea aphid, Acyrthosiphon pisum, introduces the mechanism of ‘divergence hitchhiking’ which can generate large ‘islands of differentiation’ and facilitate the build-up of linkage disequilibrium, favouring increased reproductive isolation. This idea potentially removes a major stumbling block to speciation under continuous gene flow. [ABSTRACT FROM AUTHOR]

The neutral polymorphism pattern in the vicinity of a selective sweep can be altered by both stochastic and deterministic factors. Here, we focus on the impact of another selective sweep in the region of influence of a first one. We study the signature left on neutral polymorphism by positive selection at two closely linked loci, when both beneficial mutations reach fixation. We show that, depending on the timing of selective sweeps and on their selection coefficients, the two hitchhiking effects can interfere with each other, leading to less reduction in heterozygosity than a single selective sweep of the same magnitude and more importantly to an excess of intermediate-frequency variants relative to neutrality under some parameter values. This pattern can l)C sustained and potentially alter the detection of positive selection, including by provoking spurious detection of balancing selection. In situations where positive selection is suspected apriori at several closely linked loci, the polymorphism pattern in the region may also be informative about their selective histories. [ABSTRACT FROM AUTHOR]

Natural selection is expected to leave an imprint on the neutral polymorphisms at the adjacent genomic regions of a selected gene. While directional selection tends to reduce within-population genetic diversity and increase among-population differentiation, the reverse is expected under balancing selection. To identify targets of natural selection in the three-spined stickleback ( Gasterosteus aculeatus) genome, 103 microsatellite and two indel markers including expressed sequence tags (EST) and quantitative trait loci (QTL)-associated loci, were genotyped in four freshwater and three marine populations. The results indicated that a high proportion of loci (14.7%) might be affected by balancing selection and a lower proportion (2.8%) by directional selection. The strongest signatures of directional selection were detected in a microsatellite locus and two indel markers located in the intronic regions of the Eda-gene coding for the number of lateral plates. Yet, other microsatellite loci previously found to be informative in QTL-mapping studies revealed no signatures of selection. Two novel microsatellite loci ( Stn12 and Stn90) located in chromosomes I and VIII, respectively, showed signals of directional selection and might be linked to genomic regions containing gene(s) important for adaptive divergence. Although the coverage of the total genomic content was relatively low, the predominance of balancing selection signals is in agreement with the contention that balancing, rather than directional selection is the predominant mode of selection in the wild. [ABSTRACT FROM AUTHOR]

Automobiles—particularly convertibles—serve in films noir as symbols of social mobility and expanded identity, as surrogate homes and amoral spaces. The recurrent figure of the hitchhiker, however, challenges the ideology of automobility, and in certain late films noir, automobiles are linked with explosive technologies that threaten to turn humans into atomized automatons. [ABSTRACT FROM AUTHOR]

We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes. [ABSTRACT FROM AUTHOR]

Phylogenetic trees based upon major histocompatibility complex (MHC) gene sequences, particularly those encompassing sites encoding the antigen recognition site, are often discordant with the species tree. It has been argued that the principal cause of such discordance is the presence of ancestrally derived polymorphisms persisting through speciation events as a consequence of selection. In the present study, we examine the evolution of the MHC class II DQα1 gene in an unusual family of hystricomorph rodents, the African mole-rats (Family: Bathyergidae). We show that there is a high level of trans-species polymorphism and that this is a result of positive selection. Furthermore, the major lineages of the gene tree are characterized by allelic motifs occurring in regions that coincide with the pocket domains of the putative antigen recognition site, a region that has been shown to be under positive selection in a number of MHC genes from a range of species. Finally, these alleles may have been retained for at least 48 million years. This is significantly older than the estimate for the equivalent primate locus and appears to be one of the oldest documented sets of MHC alleles. We suggest that these allelic motifs possess polymorphisms that have been immunologically important to African mole-rats over long periods of evolutionary history. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 493–503. [ABSTRACT FROM AUTHOR]

One of the central goals of evolutionary biology is to understand the genetic basis of adaptive evolution. The availability of nearly complete genome sequences from a variety of organisms has facilitated the collection of data on naturally occurring genetic variation on the scale of hundreds of loci to whole genomes. Such data have changed the focus of molecular population genetics from making inferences about adaptive evolution at single loci to identifying which loci, out of hundreds to thousands, have been recent targets of natural selection. A major challenge in this effort is distinguishing the effects of selection from those of the demographic history of populations. Here we review some current progress and remaining challenges in the field.Heredity (2007) 98, 340–348. doi:10.1038/sj.hdy.6800967; published online 2 May 2007 [ABSTRACT FROM AUTHOR]

In this study, we estimate the amount of human leukocyte antigen (HLA) genetic diversity in the global human population at three levels of population hierarchy: within populations; among populations within continents and among continents on large sets of HLA population data gathered during the last international histocompatibility and immunogenetics workshops and conferences. The results indicate that loci HLA-A, B, C, DRB1, DQA1 and DQB1 exhibit a higher amount of diversity among individuals of the same population than observed for neutral polymorphisms (average diversity of 90.3% compared with 84.4%–87.6% for neutral DNA markers). On the other hand, the value (84%) obtained for HLA-DPB1 is very similar to those observed for non-HLA nuclear markers, in agreement with other results suggesting the neutrality of this locus. In addition to the results of the hierarchical analysis of variance, selective neutrality tests indicate that loci B, C and DRB1 are the most affected by balancing selection. However, one cannot discriminate between a direct selective effect acting on those loci or a general effect of associative overdominance acting over the large HLA region (in linkage disequilibrium) encompassing those loci. [ABSTRACT FROM AUTHOR]

Abstract: This study analyzes the age and gender related risk-taking behaviors of Turkish adolescents in an urban sample. A self-report risk taking scale was administered to 280 adolescents between the ages of 12–21. Results revealed that both the type and the frequency of risk-taking behaviors were changed according to age and gender. All risky behaviors except hitchhiking increased until the college level and than decreased. Boys outperformed the girls in most of the risk-taking behaviors. [Copyright &y& Elsevier]

Neutral mutations may hitchhike to high frequency when they are situated close to sites under positive selection, generating local reductions in genetic diversity. This process is thought to be an important determinant of levels of genomic variation in natural populations. The size of genome regions affected by genetic hitchhiking is expected to be dependent on the strength of selection, but there is little empirical data supporting this prediction. Here, we compare microsatellite variation around two drug resistance genes (chloroquine resistance transporter (pfcrt), chromosome 7, and dihydrofolate reductase (dhfr), chromosome 4) in malaria parasite populations exposed to strong (Thailand) or weak selection (Laos) by anti-malarial drugs. In each population, we examined the point mutations underlying resistance and length variation at 22 (chromosome 4) or 25 (chromosome 7) microsatellite markers across these chromosomes. All parasites from Thailand carried the K76T mutation in pfcrt conferring resistance to chloroquine (CQ) and 2–4 mutations in dhfr conferring resistance to pyrimethamine. By contrast, we found both wild-type and resistant alleles at both genes in Laos. There were dramatic differences in the extent of hitchhiking in the two countries. The size of genome regions affected was smaller in Laos than in Thailand. We observed significant reduction in variation relative to sensitive parasites for 34–64kb (2–4cM) in Laos on chromosome 4, compared with 98–137kb (6–8cM) in Thailand. Similarly, on chromosome 7, we observed reduced variation for 34–69kb (2–4cM) around pfcrt in Laos, but for 195–268kb (11–16cM) in Thailand. Reduction in genetic variation was also less extreme in Laos than in Thailand. Most loci were monomorphic in a 12kb region surrounding both genes on resistant chromosomes from Thailand, whereas in Laos, even loci immediately proximal to selective sites showed some variation on resistant chromosomes. Finally, linkage disequilibrium (LD) decayed more rapidly around resistant pfcrt and dhfr alleles from Laos than from Thailand. These results demonstrate that different realizations of the same selective sweeps may vary considerably in size and shape, in a manner broadly consistent with selection history. From a practical perspective, genomic regions containing resistance genes may be most effectively located by genome-wide association in populations exposed to strong drug selection. However, the lower levels of LD surrounding resistance alleles in populations under weak selection may simplify identification of functional mutations. [ABSTRACT FROM AUTHOR]

We present here a stochastic two-locus, two-habitat model for the evolution of migration with local adaptation and kin selection. One locus determines the migration rate while the other causes local adaptation. We show that the opposing forces of kin competition and local adaptation can lead to the existence of one or two convergence stable migration rates, notably depending on the recombination rate between the two loci. We show that linkage between migration and local adaptation loci has two antagonist effects: when linkage is tight, cost of local adaptation increases, leading to smaller equilibrium migration rates. However, when linkage is tighter, the population structure at the migration locus tends to be very high because of the indirect selection, and thus equilibrium migration rates increases. This result, qualitatively different from results obtained with other models of migration evolution, indicates that ignoring drift or the detail of the genetic architecture may lead to incorrect conclusions. [ABSTRACT FROM AUTHOR]