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Selective Sweep (selective + sweep)
Selected AbstractsThe structure of a local population of phytopathogenic Pseudomonas brassicacearum from agricultural soil indicates development under purifying selection pressureENVIRONMENTAL MICROBIOLOGY, Issue 3 2001Johannes Sikorski Among the isolates of a bacterial community from a soil sample taken from an agricultural plot in northern Germany, a population consisting of 119 strains was obtained that was identified by 16S rDNA sequencing and genomic fingerprinting as belonging to the recently described species Pseudomonas brassicacearum. Analysis of the population structure by allozyme electrophoresis (11 loci) and random amplified polymorphic DNA,polymerase chain reaction (RAPD,PCR; four primers) showed higher resolution with the latter method. Both methods indicated the presence of three lineages, one of which dominated strongly. Stochastic tests derived from the neutral theory of evolution (including Slatkin's exact test, Watterson's homozygosity test and the Tajima test) indicated that the population had developed under strong purifying selection pressure. The presence of strains clearly divergent from the majority of the population can be explained by in situ evolution or by influx of strains as a result of migration or both. Phytopathogenicity of a P. brassicacearum strain determined with tomato plants reached the level obtained with the type strain of the known pathogen Pseudomonas corrugata. The results show that a selective sweep was identified in a local population. Previously, a local selective sweep had not been seen in several populations of different bacterial species from a variety of environmental habitats. [source] ASSORTATIVE MATING FOR FITNESS AND THE EVOLUTION OF RECOMBINATIONEVOLUTION, Issue 7 2006Alistair Blachford Abstract To understand selection on recombination, we need to consider how linkage disequilibria develop and how recombination alters these disequilibria. Any factors that development of disequilbria, including nonrandom mating, can potentially change selectio on recombination. Assortative mating is known to affect linkage disequilbria but its effect on the evolution of recombination have not been previously studied. Given that assortative arise indirectly via a number of biologically realistic scenarios, it is plausible that weak assortative mating occurs across a diverse set of taxa. Using a modifier model, we examine how assortative mating for fitness affects the evolution of recombination under two evolutionary scenarios: selective sweeps and mutation-selection balance. We find there is no net effect of assortative mating during a selective sweep. In contrast, assortative mating could have a large effect on recombination when deleterious alleles are maintained at mutation-selection balance but only if assortative mating is sufficiently strong. Upon considering reasonable values for the number of loci affecting fitness components, the strength of selection, and the mutation rate, we conclude that the correlation in fitness between mates is unlikely to be sufficiently high for assortative mating to affect the evolution of recombination in most species. [source] High population differentiation and unusual haplotype structure in a shade-intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear lociMOLECULAR ECOLOGY, Issue 10 2008K. KAMIYA Abstract Differences in demographic history, life-history traits, and breeding systems affect nucleotide variation patterns. It is expected that shade-intolerant pioneer tree species have different patterns of genetic polymorphism and population structure than climax species. We studied patterns of nucleotide polymorphism at four putative starch pathway loci (agpSA, agpSB, agpL, and GBSSI) in Zanthoxylum ailanthoides, a shade-intolerant pioneer tree species that occupies forest gaps in warm-temperate forests of East Asia. Genetic diversity was lower within each population than among populations, and differentiation among populations was high across the loci (FST = 0.32,0.64), as expected from the insect-pollinated breeding system and the metapopulation structure of this pioneer species. Numbers of haplotypes were smaller than those expected from the observed numbers of segregating sites. Single haplotypes accounted for more than 47% of all the sampled genes at the respective loci. These variation patterns were incompatible with neutral predictions for populations of a finite island model. Complex population dynamics, such as bottleneck and/or admixture, in the history of this pioneer tree species might have resulted in the observed patterns of genetic variation and population structure, which are different from those of climax wind-pollinated tree species, such as conifers. In contrast to the other loci investigated in this study, agpL showed nearly no variation in Z. ailanthoides (one singleton only), but there was some extent of variation in a closely related species, Zanthoxylum schinifolium. This suggests possibly a recent selective sweep at or near the locus in Z. ailanthoides. [source] Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomicsMOLECULAR ECOLOGY, Issue 8 2008NATASJA G. DE GROOT Abstract Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep. [source] World-wide survey of an Accord insertion and its association with DDT resistance in Drosophila melanogasterMOLECULAR ECOLOGY, Issue 8 2004F. CATANIA Abstract Previous work showed that insecticide resistance in Drosophila melanogaster is correlated with the insertion of an Accord -like element into the 5, region of the cytochrome P450 gene, Cyp6g1. Here, we study the distribution of the Accord -like element in 673 recently collected D. melanogaster lines from 34 world-wide populations. We also examine the extent of microsatellite variability along a 180-kilobase (kb) genomic region of chromosome II encompassing the resistance gene. We confirm a 100% correlation of the Accord insertion with insecticide resistance and a significant reduction in variability extending at least 20 kb downstream of the Cyp6g1 gene. The frequency of the Accord insertion differs significantly between East African (32,55%) and nonAfrican (85,100%) populations. This pattern is consistent with a selective sweep driving the Accord insertion close to fixation in nonAfrican populations as a result of the insecticide resistance phenotype it confers. This study confirms that hitchhiking mapping can be used to identify beneficial mutations in natural populations. [source] Genetic heterogeneity at the bovine KIT gene in cattle breeds carrying different putative alleles at the spotting locusANIMAL GENETICS, Issue 3 2010L. Fontanesi Summary According to classical genetic studies, piebaldism in cattle is largely influenced by the allelic series at the spotting locus (S), which includes the SH (Hereford pattern), S+ (non-spotted) and s (spotted) alleles. The S locus was mapped on bovine chromosome 6 in the region containing the KIT gene. We investigated the KIT gene, analysing its variability and haplotype distribution in cattle of three breeds (Angus, Hereford and Holstein) with different putative alleles (S+, SH and s respectively) at the S locus. Resequencing of a whole of 0.485 Mb revealed 111 polymorphisms. The global nucleotide diversity was 0.087%. Tajima's D- values were negative for all breeds, indicating putative directional selection. Of the 28 inferred haplotypes, only five were observed in the Hereford breed, in which one was the most frequent. Coalescent simulation showed that it is highly unlikely (P < 10E-6) to obtain this low number of haplotypes conditionally on the observed number of segregating SNPs. Therefore, the neutral model could be rejected for the Hereford breed, suggesting that a selection sweep occurred at the KIT locus. Twelve haplotypes were inferred in Holstein and Angus. For these two breeds, the neutral model could not be rejected. High heterogeneity of the KIT gene was confirmed from a phylogenetic analysis. Our results suggest a role of the KIT gene in determining the SH allele(s) in the Hereford, but no evidence of selective sweep was obtained in Holstein, suggesting that complex mechanisms (or other genes) might be the cause of the spotted phenotype in this breed. [source] Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009MARC OREMUS Pilot whales (Globicephala spp.) provide an interesting example of recently diverged oceanic species with a complex evolutionary history. The two species have wide but largely non-overlapping ranges. Globicephala melas (long-finned pilot whale; LFPW) has an antitropical distribution and is found in the cold-temperate waters of the North Atlantic and Southern Hemisphere, whereas Globicephala macrorhynchus (short-finned pilot whale; SFPW) has a circumglobal distribution and is found mainly in the tropics and subtropics. To investigate pilot whale evolution and biogeography, we analysed worldwide population structure using mitochondrial DNA (mtDNA) control region sequences (up to 620 bp) from a variety of sources (LFPW = 643; SFPW = 150), including strandings in New Zealand and Tasmania, and whale-meat products purchased on the markets of Japan and Korea. Phylogenetic reconstructions failed to support a reciprocal monophyly of the two species, despite six diagnostic substitutions, possibly because of incomplete lineage sorting or inadequate phylogenetic information. Both species had low haplotype and nucleotide diversity compared to other abundant widespread cetaceans (LFPW, , = 0.35%; SFPW, , = 0.87%) but showed strong mtDNA differentiation between oceanic basins. Strong levels of structuring were also found at the regional level. In LFPW, phylogeographic patterns were suggestive either of a recent demographic expansion or selective sweep acting on the mtDNA. For SFPW, the waters around Japan appear to represent a centre of diversity, with two genetically-distinct forms, as well as a third population of unknown origin. The presence of multiple unique haplotypes among SFPW from South Japan, together with previously documented morphological and ecological differences, suggests that the southern form represents a distinct subspecies and/or evolutionary significant unit. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 729,744. [source] ASSORTATIVE MATING FOR FITNESS AND THE EVOLUTION OF RECOMBINATIONEVOLUTION, Issue 7 2006Alistair Blachford Abstract To understand selection on recombination, we need to consider how linkage disequilibria develop and how recombination alters these disequilibria. Any factors that development of disequilbria, including nonrandom mating, can potentially change selectio on recombination. Assortative mating is known to affect linkage disequilbria but its effect on the evolution of recombination have not been previously studied. Given that assortative arise indirectly via a number of biologically realistic scenarios, it is plausible that weak assortative mating occurs across a diverse set of taxa. Using a modifier model, we examine how assortative mating for fitness affects the evolution of recombination under two evolutionary scenarios: selective sweeps and mutation-selection balance. We find there is no net effect of assortative mating during a selective sweep. In contrast, assortative mating could have a large effect on recombination when deleterious alleles are maintained at mutation-selection balance but only if assortative mating is sufficiently strong. Upon considering reasonable values for the number of loci affecting fitness components, the strength of selection, and the mutation rate, we conclude that the correlation in fitness between mates is unlikely to be sufficiently high for assortative mating to affect the evolution of recombination in most species. [source] A METAPOPULATION PERSPECTIVE ON GENETIC DIVERSITY AND DIFFERENTIATION IN PARTIALLY SELF-FERTILIZING PLANTSEVOLUTION, Issue 12 2002Pärk. Ingvarsson Abstract., Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable out crossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration. [source] Nuclear and mitochondrial markers reveal distinctiveness of a small population of bottlenose whales (Hyperoodon ampullatus) in the western North AtlanticMOLECULAR ECOLOGY, Issue 11 2006MEREL L. DALEBOUT Abstract Small populations at the edge of a species' distribution can represent evolutionary relics left behind after range contractions due to climate change or human exploitation. The distinctiveness and genetic diversity of a small population of bottlenose whales in the Gully, a submarine canyon off Nova Scotia, was quantified by comparison to other North Atlantic populations using 10 microsatellites and mitrochondrial DNA (mtDNA) control region sequences (434 bp). Both markers confirmed the distinctiveness of the Gully (n = 34) from the next nearest population, off Labrador (n = 127; microsatellites ,FST= 0.0243, P < 0.0001; mtDNA ,,ST = 0.0456, P < 0.05). Maximum likelihood microsatellite estimates suggest that less than two individuals per generation move between these areas, refuting the hypothesis of population links through seasonal migration. Both males and females appear to be philopatric, based on significant differentiation at both genomes and similar levels of structuring among the sexes for microsatellites. mtDNA diversity was very low in all populations (h = 0.51, , = 0.14%), a pattern which may be due to selective sweeps associated with this species' extreme deep-diving ecology. Whaling had a substantial impact on bottlenose whale abundance, with over 65 000 animals killed before the hunt ceased in the early 1970s. Genetic diversity was similar among all populations, however, and no signal for bottlenecks was detected, suggesting that the Gully is not a relic of a historically wider distribution. Instead, this unique ecosystem appears to have long provided a stable year-round habitat for a distinct population of bottlenose whales. [source] Variability patterns and positively selected sites at the gametophytic self-incompatibility pollen SFB gene in a wild self-incompatible Prunus spinosa (Rosaceae) populationNEW PHYTOLOGIST, Issue 3 2006Maria D. S. Nunes Summary ,,Current models for the generation of new gametophytic self-incompatibility specificities require that neutral variability segregates within specificity classes. Furthermore, one of the models predicts greater ratios of nonsynonymous to synonymous substitutions in pollen than in pistil specificity genes. All models assume that new specificities arise by mutation only. ,,To test these models, 21 SFB (the pollen S -locus) alleles from a wild Prunus spinosa (Rosaceae) population were obtained. For seven of these, the corresponding S -haplotype was also characterized. The SFB data set was also used to identify positively selected sites. Those sites are likely to be the ones responsible for defining pollen specificities. ,,Of the 23 sites identified as being positively selected, 21 are located in the variable (including a new region described here) and hypervariable regions. Little variability is found within specificity classes. There is no evidence for selective sweeps being more frequent in pollen than in pistil specificity genes. The S-RNase and the SFB genes have only partially correlated evolutionary histories. ,,None of the models is compatible with the variability patterns found in the SFB and the S -haplotype data. [source] Admixture facilitates adaptation from standing variation in the European aspen (Populus tremula L.), a widespread forest treeMOLECULAR ECOLOGY, Issue 8 2010DULCINEIA DE CARVALHO Abstract Adaptation to new environments can start from new mutations or from standing variation already present in natural populations. Whether admixture constrains or facilitates adaptation from standing variation is largely unknown, especially in ecological keystone or foundation species. We examined patterns of neutral and adaptive population divergence in Populus tremula L., a widespread forest tree, using mapped molecular genetic markers. We detected the genetic signature of postglacial admixture between a Western and an Eastern lineage of P. tremula in Scandinavia, an area suspected to represent a zone of postglacial contact for many species of animals and plants. Stringent divergence-based neutrality tests provided clear indications for locally varying selection at the European scale. Six of 12 polymorphisms under selection were located less than 1 kb away from the nearest gene predicted by the Populus trichocarpa genome sequence. Few of these loci exhibited a signature of ,selective sweeps' in diversity-based tests, which is to be expected if adaptation occurs primarily from standing variation. In Scandinavia, admixture explained genomic patterns of ancestry and the nature of clinal variation and strength of selection for bud set, a phenological trait of great adaptive significance in temperate trees, measured in a common garden trial. Our data provide a hitherto missing direct link between past range shifts because of climatic oscillations, and levels of standing variation currently available for selection and adaptation in a terrestrial foundation species. [source] | ||||||||||