Reductions in genetic variation inDrosophila andE. coli caused by selection at linked sites

Selection at linked sites has important consequences for the properties of neutral variation and for tests of the predictions of the neutral theory of molecular evolution. We review the theory of the effect of adaptive gene substitutions on neutral variability at linked sites (hitchhiking or selective sweeps) and discuss theoretical results on the effect of selection against deleterious alleles on variation at linked sites (background selection). InDrosophila melanogaster there is a clear relation between the frequency of recombination in a given region of the chromosome and the amount of natural variability in that region. Attempts to predict this relation have given rise to models of selective sweeps and background selection. We describe possible methods of discriminating between these models, and also discuss the probable strong influence of selective sweeps on variation in largely nonrecombining genomes, with particular reference toEscherichia coll. Finally we present some unresolved questions and possible directions for future research.     

Assessment of selection mapping near the myostatin gene (GDF-8) in cattle

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.     

Behaviour and dispersal in adult Taeniopteryx nebulosa (Linnaeus, 1758) and Perlodes microcephalus (Pictet, 1833) (Plecoptera) in Denmark

Adult Taeniopteryx nebulosa (Linnaeus, 1758 Linnaeus, C. (1758), Systema Naturae (10th ed.), Tom 1, Holmiae. [Google Scholar]) and Perlodes microcephalus (Pictet, 1833 Pictet, J., (1833), ‘Memoire sur la Metamorphoses des Perles’, Annales des Sciences Naturelles, XXVII, 44–55. [Google Scholar]) emerge late winter to early spring in Danish streams. Based on 13 years of study, we have provided new data and discussed little-known aspects of biology of these two species. Taeniopteryx nebulosa male deposits a spermatophore on the female gonopore. Both species are poor fliers and seek high posts for take-off, where they thermoregulate by basking in a pre-flight sun posture for heating flight muscles. Oviposition flight is erratic and short. The females skim back to land. Taeniopteryx nebulosa eggs drift a long distance as single eggs before adhering to vegetation. Perlodes microcephalus eggs drift a short distance as intact eggpackets before they fasten and disintegrate on the bottom. Perlodes microcephalus females select oviposition sites on or close to upstream a riffle. This is critical in ensuring that eggs fasten on stable gravel and stone bottoms. The fast recolonisation of P. microcephalus in Danish streams following restoration measures indicates efficient dispersal ability despite poor flight performance. Adults of both species adhere to clothes, feather and fur. Taeniopteryx nebulosa tarsomeres have many hooked setae, P. microcephalus tarsomeres have some hooked setae and a dense cover of microtrichia. They may disperse by hitchhiking on birds and mammals.     

Revisiting the notion of deleterious sweeps

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites—both in the presence and absence of interference amongst deleterious mutations—and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of F_ST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.     

Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa

The last 50,000-150,000 years of human history have been characterized by rapid demographic expansions and the colonization of novel environments outside of sub-Saharan Africa. Mass migrations outside the ancestral species range likely entailed many new selection pressures, suggesting that genetic adaptation to local environmental conditions may have been more prevalent in colonizing populations outside of sub-Saharan Africa. Here we report a test of this hypothesis using genome-wide patterns of DNA polymorphism. We conducted a multilocus scan of microsatellite variability to identify regions of the human genome that may have been subject to continent-specific hitchhiking events. Using published polymorphism data for a total of 624 autosomal loci in multiple populations of humans, we used coalescent simulations to identify candidate loci for geographically restricted selective sweeps. We identified a total of 13 loci that appeared as outliers in replicated population comparisons involving different reference samples for Africa. A disproportionate number of these loci exhibited reduced levels of relative variability in non-African populations alone, suggesting that recent episodes of positive selection have been more prevalent outside of sub-Saharan Africa.     

Selection at linked sites in the partial selfer Caenorhabditis elegans

Natural selection can produce a correlation between local recombination rates and levels of neutral DNA polymorphism as a consequence of genetic hitchhiking and background selection. Theory suggests that selection at linked sites should affect patterns of neutral variation in partially selfing populations more dramatically than in outcrossing populations. However, empirical investigations of selection at linked sites have focused primarily on outcrossing species. To assess the potential role of selection as a determinant of neutral polymorphism in the context of partial self-fertilization, we conducted a multivariate analysis of single-nucleotide polymorphism (SNP) density throughout the genome of the nematode Caenorhabditis elegans. We based the analysis on a published SNP data set and partitioned the genome into windows to calculate SNP densities, recombination rates, and gene densities across all six chromosomes. Our analyses identify a strong, positive correlation between recombination rate and neutral polymorphism (as estimated by noncoding SNP density) across the genome of C. elegans. Furthermore, we find that levels of neutral polymorphism are lower in gene-dense regions than in gene-poor regions in some analyses. Analyses incorporating local estimates of divergence between C. elegans and C. briggsae indicate that a mutational explanation alone is unlikely to explain the observed patterns. Consequently, we interpret these findings as evidence that natural selection shapes genome-wide patterns of neutral polymorphism in C. elegans. Our study provides the first demonstration of such an effect in a partially selfing animal. Explicit models of genetic hitchhiking and background selection can each adequately describe the relationship between recombination rate and SNP density, but only when they incorporate selfing rate. Clarification of the relative roles of genetic hitchhiking and background selection in C. elegans awaits the development of specific theoretical predictions that account for partial self-fertilization and biased sex ratios.     

The Function of Hitchhiking Behavior in the Leaf‐cutting Ant Atta cephalotes1

In some leaf‐cutting ant species, minim workers ride on the fragments of leaves as they are carried back to the nest from the cutting site. There is convincing evidence that these “hitchhikers” can protect the leaf carriers from attack by phorid (Diptera: Phoridae) parasitoids, but we consider the possibility of other functions for the hitchhiking behavior. It has been hypothesized that the hitchhikers (1) feed on leaf sap from the edges of the cut leaves; (2) ride back to the nest to save energy; (3) get caught on the fragments as they are cut, and hitchhike because they cannot (or will not) get off; and (4) begin the process of preparing the leaf to enter the fungal gardens in the nest, perhaps by removing microbial contaminants. We observed hitchhikers of Atta cephalotes in 14 nests at the La Selva Biological Station in Costa Rica. There was no difference in the proportion of leaf carriers with hitchhikers between day and night. Because the nests we observed were largely nocturnal, more than 90 percent of the hitchhiking occurred at night. The phorid parasitoids are usually considered to be diurnal, so the preponderance of nocturnal hitchhiking suggests other functions in addition to parasitoid defense. Hitchhikers spent more time in the defensive head‐up posture during the day, but spent more time in the head‐down posture at night. The head‐down posture may indicate cleaning or other leaf preparation. The hitchhikers were never observed feeding on sap. Hitchhikers frequently got onto and off of the fragments, and so they were not “marooned.” Few hitchhikers rode all the way back to the nest and were often moving on the leaf fragment; these observations make the energy conservation hypothesis less likely, although we cannot reject it. We conclude that parasitoid defense is an important function of hitchhiking but also that there are probably other functions when parasitoids are absent. Based on available data, the most likely possibility is preparation of the leaf fragment before it enters the nest.     

Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites

When selection is strong and beneficial alleles have a single origin, local reductions in genetic diversity are expected. However, when beneficial alleles have multiple origins or were segregating in the population prior to a change in selection regime, the impact on genetic diversity may be less clear. We describe an example of such a "soft" selective sweep in the malaria parasite Plasmodium falciparum that involves adaptive genome rearrangements. Amplification in copy number of genome regions containing the pfmdr1 gene on chromosome 5 confer resistance to mefloquine and spread rapidly in the 1990s. Using flanking microsatellite data and real-time polymerase chain reaction determination of copy number, we show that 5-15 independent amplification events have occurred in parasites on the Thailand/Burma border. The amplified genome regions (amplicons) range in size from 14.7 to 49 kb and contain 2-11 genes, with 2-4 copies arranged in tandem. To examine the impact of drug selection on flanking variation, we genotyped 48 microsatellites on chromosome 5 in 326 parasites from a single Thai location. Diversity was reduced in a 170- to 250-kb (10-15 cM) region of chromosomes containing multiple copies of pfmdr1, consistent with hitchhiking resulting from the rapid recent spread of selected chromosomes. However, diversity immediately flanking pfmdr1 is reduced by only 42% on chromosomes bearing multiple amplicons relative to chromosomes carrying a single copy. We highlight 2 features of these results: 1) All amplicon break points occur in monomeric A/T tracts (9-45 bp). Given the abundance of these tracts in P. falciparum, we expect that duplications will occur frequently at multiple genomic locations and have been underestimated as drivers of phenotypic evolution in this pathogen. 2) The signature left by the spread of amplified genome segments is broad, but results in only limited reduction in diversity. If such "soft" sweeps are common in nature, statistical methods based on diversity reduction may be inefficient at detecting evidence for selection in genome-wide marker screens. This may be particularly likely when mutation rate is high, as appears to be the case for gene duplications, and in pathogen populations where effective population sizes are typically very large.     

Impacts of climate warming on hybrid zone movement: Geographically diffuse and biologically porous “species borders”

Abstract The ecology and evolutionary biology of insect–plant associations has realized extensive attention, especially during the past 60 years. The classifications (categorical designations) of continuous variation in biodiversity, ranging from global patterns (e.g., latitudinal gradients in species richness/diversity and degree of herbivore feeding specialization) to localized insect–plant associations that span the biospectrum from polyphenisms, polymorphisms, biotypes, demes, host races, to cryptic species, remain academically contentious. Semantic and biosystematic (taxonomical) disagreements sometimes detract from more important ecological and evolutionary processes that drive diversification, the dynamics of gene flow and local extinctions. This review addresses several aspects of insect specialization, host‐associated divergence and ecological (including “hybrid”) speciation, with special reference to the climate warming impacts on species borders of hybridizing swallowtail butterflies (Papilionidae). Interspecific hybrid introgression may result in collapse of multi‐species communities or increase species numbers via homoploid hybrid speciation. We may see diverging, merging, or emerging genotypes across hybrid zones, all part of the ongoing processes of evolution. Molecular analyses of genetic mosaics and genomic dynamics with “divergence hitchhiking”, combined with ecological, ethological and physiological studies of “species porosity”, have already begun to unveil some answers for some important ecological/evolutionary questions. (i) How rapidly can host‐associated divergence lead to new species (and why doesn't it always do so, e.g., resulting in “incomplete” speciation)? (ii) How might “speciation genes” function, and how/where would we find them? (iii) Can oscillations from specialists to generalists and back to specialists help explain global diversity in herbivorous insects? (iv) How could recombinant interspecific hybridization lead to divergence and speciation? From ancient phytochemically defined angiosperm affiliations to recent and very local geographical mosaics, the Papilionidae (swallowtail butterflies) have provided a model for enhanced understanding of ecological patterns and evolutionary processes, including host‐associated genetic divergence, genomic mosaics, genetic hitchhiking and sex‐linked speciation genes. Apparent homoploid hybrid speciation in Papilio appears to have been catalyzed by climate warming‐induced interspecific introgression of some, but not all, species diagnostic traits, reflecting strong divergent selection (discordant), especially on the Z (= X) chromosome. Reproductive isolation of these novel recombinant hybrid genotypes appears to be accomplished via a delayed post‐diapause emergence or temporal isolation, and is perhaps aided by the thermal landscape. Changing thermal landscapes appear to have created (and may destroy) novel recombinant hybrid genotypes and hybrid species.