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PubMed2005

Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes.

The roles of positive directional selection (selective sweeps) and negative selection (background selection) in shaping the genome-wide distribution of genetic variation in humans remain largely unknown. Here, we optimize the parameter values of a model of the removal of deleterious mutations (background selection) to observed levels of human polymorphism, controlling for mutation rate heterogeneity by using interspecific divergence. A point of "best fit" was found between background-selection predictions and estimates of human effective population sizes, with reasonable parameter estimates whose uncertainty was assessed by bootstrapping. The results suggest that the purging of deleterious alleles has had some influence on shaping levels of human variation, although the effects may be subtle over the majority of the human genome. A significant relationship was found between background-selection predictions and measures of skew in the allele frequency distribution. The genome-wide action of selection (positive and/or negative) is required to explain this observation.

Alleles↗

PubMed2004

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.

The genetic study of diverging, closely related populations is required for basic questions on demography and speciation, as well as for biodiversity and conservation research. However, it is often unclear whether divergence is due simply to separation or whether populations have also experienced gene flow. These questions can be addressed with a full model of population separation with gene flow, by applying a Markov chain Monte Carlo method for estimating the posterior probability distribution of model parameters. We have generalized this method and made it applicable to data from multiple unlinked loci. These loci can vary in their modes of inheritance, and inheritance scalars can be implemented either as constants or as parameters to be estimated. By treating inheritance scalars as parameters it is also possible to address variation among loci in the impact via linkage of recurrent selective sweeps or background selection. These methods are applied to a large multilocus data set from Drosophila pseudoobscura and D. persimilis. The species are estimated to have diverged approximately 500,000 years ago. Several loci have nonzero estimates of gene flow since the initial separation of the species, with considerable variation in gene flow estimates among loci, in both directions between the species.

Animals↗

PubMed2004

Analysis of ephedra-alkaloids using sweeping and cation-selective exhaustive injection and sweeping micellar electrokinetic chromatography methods.

Two stacking methods of capillary electrophoresis (CE) were developed for the separation of very dilute solutions of ephedra-alkaloids, namely ephedrine, pseudoephedrine, methylephedrine, methylpseudoephedrine, norephedrine, and norpseudoephedrine. A sweeping method which uses a carrier comprised of phosphoric acid, sodium dodecyl sulfate (SDS), diethylamine and acetonitrile permits the detection of the alkaloids down to the 10(-1) microg/mL level, and the cation-selective exhaustive injection and sweeping micellar electrokinetic chromatography (CSEI-Sweep-MEKC) method using phosphoric acid, SDS, and acetronitrile as electrolytes can detect down to the 10(-3) microg/mL level. The former requires the conductance of the sample solution to be adjusted beforehand, and only five peaks were observed, two of which were overlapped. The latter is capable of separating the six alkaloids but has a somewhat poorer reproducibility. Using an optimized injection time, it was found that the more diluted a solution is, the greater the sweeping effect will be. The CSEI-Sweep-MEKC method with a 600 s injection time and a 10(-1) microg/mL solution concentration provides an amplification effect of approximately 10(4). The method is suitable for analyses of dilute herb drug extracts and mouse sera. The effect of buffers on the separation and validation of the methods in this study are also discussed.

Acetonitriles↗

PubMed2006

A genome-wide survey of R gene polymorphisms in Arabidopsis.

We used polymorphism analysis to study the evolutionary dynamics of 27 disease resistance (R) genes by resequencing the leucine-rich repeat (LRR) region in 96 Arabidopsis thaliana accessions. We compared single nucleotide polymorphisms (SNPs) in these R genes to an empirical distribution of SNP in the same sample based on 876 fragments selected to sample the entire genome. LRR regions are highly polymorphic for protein variants but not for synonymous changes, suggesting that they generate many alleles maintained for short time periods. Recombination is also relatively common and important for generating protein variants. Although none of the genes is nearly as polymorphic as RPP13, a locus previously shown to have strong signatures of balancing selection, seven genes show weaker indications of balancing selection. Five R genes are relatively invariant, indicating young alleles, but all contain segregating protein variants. Polymorphism analysis in neighboring fragments yielded inconclusive evidence for recent selective sweeps at these loci. In addition, few alleles are candidates for rapid increases in frequency expected under directional selection. Haplotype sharing analysis revealed significant underrepresentation of R gene alleles with extended haplotypes compared with 1102 random genomic fragments. Lack of convincing evidence for directional selection or selective sweeps argues against an arms race driving R gene evolution. Instead, the data support transient or frequency-dependent selection maintaining protein variants at a locus for variable time periods.

Arabidopsis↗

PubMed2002

Patterns of genetic variation at a chromosome 4 locus of Drosophila melanogaster and D. simulans.

DNA sequence surveys of Drosophila melanogaster populations show a strong positive correlation between the recombination rate experienced by a locus and its level of nucleotide polymorphism. In particular, surveys of the fourth chromosome gene ci(D) show greatly reduced levels of nucleotide variation; this observation was originally interpreted in terms of selective sweeps occurring on the nonrecombining fourth chromosome. Subsequent theoretical work has, however, uncovered several other selective processes that can reduce variation. In this study, we revisit the Drosophila fourth chromosome, investigating variation in 5-6 kb of the gene ankyrin in D. melanogaster and D. simulans. Silent nucleotide site diversity is approximately 5 x 10(-4) for both species, consistent with the previous observations of low variation at ci(D). Given the observed frequency spectra at ankyrin, coalescent simulations indicate that reduced diversity in the region is unlikely to be due to a selective sweep alone. We find evidence for recombinational exchange at this locus, and both species appear to be fixed for an insertion of the transposable element HB in an intron of ankyrin.

Animals↗

PubMed2019

Identifying loci under positive selection in complex population histories.

Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.

Animals↗

PubMed2005

Genetic consequences of selection during the evolution of cultivated sunflower.

We mapped quantitative trait loci (QTL) controlling differences in seed oil content and composition between cultivated and wild sunflower and used the results, along with those of a previous study of domestication-related QTL, to guide a genome-wide analysis of genetic variation for evidence of past selection. The effects of the seed oil QTL were almost exclusively in the expected direction with respect to the parental phenotypes. A major, oil-related QTL cluster mapped near a cluster of domestication-related QTL on linkage group six (LG06), the majority of which have previously been shown to have effects that are inconsistent with the parental phenotypes. To test the hypothesis that this region was the target of a past selective sweep, perhaps resulting in the fixation of the antagonistic domestication-related QTL, we analyzed simple sequence repeat (SSR) diversity from 102 markers dispersed throughout the sunflower genome. Our results indicate that LG06 was most likely the target of multiple selective sweeps during the postdomestication era. Strong directional selection in concert with genetic hitchhiking therefore offers a possible explanation for the occurrence of numerous domestication-related QTL with apparently maladaptive phenotypic effects.

Biological Evolution↗

PubMed2001

Genes in sweeping competition.

Analysis of DNA variation is a powerful tool for detecting adaptation at the genomic level. The contribution of adaptive evolution is evident from examples of rapidly evolving genes, which represent the likely targets for strong selection. More subtle adaptation is also an integral component of routine maintenance of gene performance, continuously applied to every gene. Adaptive changes in the population are accomplished through selective sweeps, i.e. complete or partial fixation of beneficial alleles. The evidence is accumulating that selective sweeps are quite frequent events which, together with associated genetic hitchhiking, represent dominant forces that influence molecular evolution by shaping the variability pattern in the genome.

Animals↗

PubMed2026

Multidimensional GWAS analyses on longitudinal phenotypes reveal candidate genes regulating multi-stage egg production traits in Wannan yellow chicken.

Egg production performance directly determines the economic viability of indigenous chicken breeding. However, the genetic regulation of multi-stage egg production traits remains difficult to characterize due to their complex and dynamic nature. Here, we integrated a multidimensional GWAS framework, including single-trait GWAS, multi-trait GWAS (MTAG), and longitudinal trajectory-based GWAS (TrajGWAS), to identify stage-specific and shared genetic effects underlying egg production traits in Wannan yellow chickens (WNY). Whole-genome sequencing of 354 WNY hens (10× depth) and quality control yielded 14,253,816 SNPs for analysis. Selective sweep analyses comparing red jungle fowl, commercial layers, and WNY identified a genomic region containing IGF1 under significant selection pressure. Single-trait GWAS identified SNPs 4_57990480 (BMPR1B) and 17_370912 (LOC112531479) associated with egg production across three laying stages (21-30, 31-40, and 21-40 weeks). MTAG further identified loci 8_4336468 (FASLG) and 21_654726 (CHD5) with shared effects across the laying period, whereas TrajGWAS revealed longitudinal associations involving PRKG1 and identified dynamic loci associated with clutch traits, including GRID1. For clutch traits, stage-specific loci were detected for average clutch size (ACS) and maximum clutch size (MCS), including SNP 8_8542036 at 21-30 weeks, PROK1 at 31-40 weeks, and CUL5, ALKBH8 across the entire laying period. These results demonstrate that integrating complementary GWAS strategies improves the resolution of genetic architecture underlying egg production traits by capturing trait-specific, shared, and stage-dependent genetic effects. The identified GWAS loci and selective-sweep candidate regions provide insights into the genetic architecture of egg production traits and breed differentiation.

Egg production↗

PubMed2000

Low variability in a Y-linked plant gene and its implications for Y-chromosome evolution.

Sex chromosomes have evolved independently in several different groups of organisms, but they share common features, including genetic degeneration of the Y chromosome. Suppression of recombination between ancestral proto-X and proto-Y chromosomes is thought to have led to their gradual divergence, and to degeneration of the Y chromosome, but the evolutionary forces responsible are unknown. In non-recombining Y chromosomes, deleterious mutations may be carried to fixation by linked advantageous mutations ("selective sweeps"). Occurrence of deleterious mutations may drive "Muller's ratchet" (stochastic loss of chromosomes with the fewest mutations). Selective elimination of deleterious mutations, causing "background selection" may accelerate stochastic fixation of mildly detrimental mutations. All these processes lower effective population sizes, and therefore reduce variability of genes in evolving Y chromosomes. We have studied DNA diversity and divergence in a recently described X- and Y-linked gene pair (SLX-1 and SLY-1) of the plant Silene latifolia to obtain evidence about the early stages of Y degeneration. Here we show that DNA polymorphism in SLY-1 is 20-fold lower than in SLX-1, but the pattern of polymorphism does not suggest a selective sweep.

Animals↗

PubMed1995

Properties of statistical tests of neutrality for DNA polymorphism data.

A class of statistical tests based on molecular polymorphism data is studied to determine size and power properties. The class includes Tajima's D statistic as well as the D* and F* tests proposed by Fu and Li. A new method of constructing critical values for these tests is described. Simulations indicate that Tajima's test is generally most powerful against the alternative hypotheses of selective sweep, population bottleneck, and population subdivision, among tests within this class. However, even Tajima's test can detect a selective sweep or bottleneck only if it has occurred within a specific interval of time in the recent past or population subdivision only when it has persisted for a very long time. For greatest power against the particular alternatives studied here, it is better to sequence more alleles than more sites.

Computer Simulation↗

PubMed1991

Lack of polymorphism on the Drosophila fourth chromosome resulting from selection.

Evolutionary processes can be inferred from comparisons of intraspecific polymorphism and interspecific divergence. We sequenced a 1.1-kb fragment of the cubitus interruptus Dominant (ciD) locus located on the nonrecombining fourth chromosome for ten natural lines of Drosophila melanogaster and nine of Drosophila simulans. We found no polymorphism within D. melanogaster and a single polymorphism within D. simulans; divergence between the species was about 5%. Comparison with the alcohol dehydrogenase gene and its two flanking regions in D. melanogaster, for which comparable data are available, revealed a statistically significant departure from neutrality in all three tests. This lack of polymorphism in the ciD locus may reflect recent positive selective sweeps on the fourth chromosome with extreme hitchhiking generated by the lack of recombination. By simulation, we estimate there to be a 50% chance that the selective sweeps occurred within the past 30,000 years in D. melanogaster and 75,000 in D. simulans.

Alcohol Dehydrogenase↗

PubMed2005

Genomic regions exhibiting positive selection identified from dense genotype data.

The allele frequency spectrum of polymorphisms in DNA sequences can be used to test for signatures of natural selection that depart from the expected frequency spectrum under the neutral theory. We observed a significant (P = 0.001) correlation between the Tajima's D test statistic in full resequencing data and Tajima's D in a dense, genome-wide data set of genotyped polymorphisms for a set of 179 genes. Based on this, we used a sliding window analysis of Tajima's D across the human genome to identify regions putatively subject to strong, recent, selective sweeps. This survey identified seven Contiguous Regions of Tajima's D Reduction (CRTRs) in an African-descent population (AD), 23 in a European-descent population (ED), and 29 in a Chinese-descent population (XD). Only four CRTRs overlapped between populations: three between ED and XD and one between AD and ED. Full resequencing of eight genes within six CRTRs demonstrated frequency spectra inconsistent with neutral expectations for at least one gene within each CRTR. Identification of the functional polymorphism (and/or haplotype) responsible for the selective sweeps within each CRTR may provide interesting insights into the strongest selective pressures experienced by the human genome over recent evolutionary history.

Black or African American↗

PubMed2007

The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence.

Recent studies have made great strides towards identifying putative genetic events underlying the evolution of the human brain and its emergent cognitive capacities. One of the most intriguing findings is the recurrent identification of adaptive evolution in genes associated with primary microcephaly, a developmental disorder characterized by severe reduction in brain size and intelligence, reminiscent of the early hominid condition. This has led to the hypothesis that the adaptive evolution of these genes has contributed to the emergence of modern human cognition. As with other candidate loci, however, this hypothesis remains speculative due to the current lack of methodologies for characterizing the evolutionary function of these genes in humans. Two primary microcephaly genes, ASPM and Microcephalin, have been implicated not only in the adaptive evolution of the lineage leading to humans, but in ongoing selective sweeps in modern humans as well. The presence of both the putatively adaptive and neutral alleles at these loci provides a unique opportunity for using normal trait variation within humans to test the hypothesis that the recent selective sweeps are driven by an advantage in cognitive abilities. Here, we report a large-scale association study between the adaptive alleles of these genes and normal variation in several measures of IQ. Five independent samples were used, totaling 2393 subjects, including both family-based and population-based datasets. Our overall findings do not support a detectable association between the recent adaptive evolution of either ASPM or Microcephalin and changes in IQ. As we enter the post-genomic era, with the number of candidate loci underlying human evolution growing rapidly, our findings highlight the importance of direct experimental validation in elucidating their evolutionary role in shaping the human phenotype.

Adolescent↗

PubMed2005

Multiple mutations and gene duplications conferring organophosphorus insecticide resistance have been selected at the Rop-1 locus of the sheep blowfly, Lucilia cuprina.

Sequences of the esterase gene alpha E7 were compared across 41 isogenic (IV) strains of the sheep blowfly, Lucilia cuprina, and one strain of the sibling species, L. sericata. The 1.2-kb region sequenced includes sites of two insecticide resistance mutations. Gly137Asp confers resistance to organophosphorus insecticides (OPs), particularly preferring diethyl OPs such as diazinon, while Trp251Leu prefers dimethyl OPs, and particularly malathion, with the additional presence of carboxylester moieties. We found that there are just eight haplotypes among the 41 chromosomes studied: two Gly137Asp containing haplotypes, two Trp251Leu containing haplotypes, and four susceptible haplotypes, including the L. sericata sequence. While phylogenetic analysis of these haplotypes suggests that the Asp137 and Leu251 mutations each arose at least twice, evidence for recombination was detected across the region, therefore single origins for these resistance mutations cannot be ruled out. Levels of linkage disequilibrium in the data are high and significant hitchhiking is indicated by Fay and Wu' s H test but not the Tajima test. A test of haplotype diversity indicates a paucity of diversity compared with neutral expectations. Both these results are consistent with a very recent selective sweep at the Lc alphaE7 locus. Interestingly, gene duplications of three different combinations of OP resistant haplotypes were identified in seven of the isogenic (IV) strains. All three types of duplication involve an Asp137 and a Trp251 haplotype. To examine whether more haplotypes existed before the hypothesised selective sweep, fragments of alpha E7 surrounding the resistance mutations were amplified from pinned material dating back to before OPs were used. Four new sequence haplotypes, not sampled in the survey of extant haplotypes, were obtained that are all associated with susceptibility. This is suggestive of a higher historical level of susceptible allelic diversity at this locus.

Animals↗

PubMed2026

Wheat breeding during and after the "green revolution" contributed to the reduced use of elite nitrogen metabolism alleles linked to nitrogen use efficiency.

The wheat "Green Revolution (GR)" that occurred from the 1960s to the 1970s significantly enhanced the harvest index and resistance to lodging, thereby increasing grain production, but at the cost of reduced nitrogen (N) use efficiency (NUE) in wheat. The NUE of wheat is mainly regulated by N metabolism genes (NMGs). However, the evolutionary process of NMGs during GR and post-GR wheat breeding, as well as which of them affect NUE, remains unclear. Here, we collected 265 wheat varieties that were released before, during, and after the GR and investigated grain yield per plant and 24 other traits under different N supply conditions. Next, we identified the genotypes of these wheat varieties using a 100 K targeted sequencing array. Then, we systematically analyzed the signatures in the genomes of GR and post-GR released varieties compared with pre-GR released varieties through population divergence (Fst) and nucleotide diversity (π) ratio analyses, and found that 41 NMGs were located within the selective sweep regions during the GR and post-GR breeding. We further identified 118 quantitative trait loci (QTLs) involved in regulating NUE through genome-wide association studies (GWAS). Four NMGs-NRT1 AND PEPTIDE TRANSPORTER FAMILY 2.7-D (TaNPF2.7-D), TaNPF2.3-D, TaNPF2.7 L-D, and QUASIMODO2-B (TaQUA2-B)-were located within overlapping regions of selective sweeps and NUE-related QTLs. Notably, the elite haplotypes of these genes for NUE are less utilized in GR and post-GR released cultivars. Furthermore, we found that TaNPF2.7-D positively regulates nitrate exudation as well as the wheat development. Collectively, our findings uncover an important reason for the reduction in NUE in modern cultivars and provide a valuable resource for improving wheat NUE.

Triticum↗

PubMed2026

Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.

UNLABELLED: Predator-mediated selection is an important ecological force shaping bacterial evolution, but its effects on genomic adaptation and virulence in opportunistic pathogens are not fully understood. Here, we used experimental evolution to study how exposure to the ciliate predator Tetrahymena thermophila affects Pseudomonas aeruginosa. Replicate populations were evolved for 60 days with or without the predator, followed by whole-genome shotgun metagenomic sequencing and phenotypic analyses. Both treatments showed strong selection and evidence of parallel evolution at gene and nucleotide levels, indicating constrained adaptation. However, predator exposure altered evolutionary dynamics. Predator-evolved populations showed a wider distribution of mutation frequencies, with many mutations persisting at intermediate frequencies, consistent with increased clonal interference and ongoing competition among lineages. In contrast, populations evolved without predators showed more high-frequency mutations, consistent with selective sweeps, although some low-frequency variants remained. Despite substantial genomic change, phenotypic outcomes were variable. Virulence in an invertebrate host model did not consistently increase. Instead, evolved isolates showed context-dependent changes, including modest decreases or occasional increases. Competition assays also showed no consistent fitness advantage for predator-evolved isolates, suggesting trade-offs between predator resistance and growth in other environments. Overall, predator-mediated selection reshaped evolutionary dynamics by maintaining diversity and altering the balance of lineages rather than producing uniform increases in virulence. These results highlight how ecological complexity influences adaptive evolution and the context-dependent nature of pathogen traits. IMPORTANCE: Opportunistic pathogens such as Pseudomonas aeruginosa often evolve in environmental settings before infecting hosts, raising questions about how ecological interactions influence virulence. Predator-mediated selection has been suggested to increase virulence via coincidental evolution, but evidence is inconsistent. Here, we show that exposure to a eukaryotic predator does not consistently elevate virulence but does reshape evolutionary dynamics by altering how mutations spread in populations. Predator-exposed populations retained more intermediate-frequency mutations, consistent with increased clonal interference and ongoing competition among lineages, whereas non-predator populations were dominated by selective sweeps. These differences were also reflected in functional targets of adaptation, with predator exposure favoring mutations in genes involved in environmental sensing and interaction. Together, these findings suggest that ecological complexity shapes the dynamics of adaptation rather than driving a single evolutionary outcome, highlighting that virulence is an emergent property influenced by underlying evolutionary processes.

Pseudomonas aeruginosa↗

PubMed2026

Identification of Candidate Genes Associated with Growth Traits in Procambarus clarkii Using Whole-Genome Resequencing.

Growth is a critical economic trait in all aquaculture industries. To address issues such as germplasm degradation, a comprehensive understanding of the growth and development mechanisms, along with genetic improvement strategies, for Procambarus clarkii (P. clarkii) is urgently required. In this study, we performed whole-genome resequencing on 89 individuals from five cultured stocks to investigate growth traits (body length) and identified a total of 46,919,297 high-quality single nucleotide polymorphisms (SNPs). Based on these SNPs, we conducted principal component analysis (PCA), phylogenetic analysis, and population genetic structure analysis. Furthermore, we performed selective sweep analysis (using FST, Pi, and XP-CLR) and a genome-wide association study (GWAS) to identify genetic variants associated with growth traits. The results revealed significant genetic differentiation among the five cultured stocks, with the Ma'anshan cultured stock exhibiting the fastest linkage disequilibrium (LD) decay. Additionally, long-term aquaculture in different geographical regions resulted in distinct genetic differences among cultured stocks. Through selective sweep analysis, the intersection of FST, Pi, and XP-CLR across the five populations yielded several growth-related candidate genes: Nephrin, Somatostatin, zinc finger protein 154, and yeti. Subsequent the GWAS identified two candidate genes associated with growth traits: Cullin-associated and neddylation-dissociated protein 1 (CAND1) and Baculoviral IAP repeat-containing protein 8 (BIRC8). These genes are presumed to play pivotal roles in the growth and development of P. clarkii. Overall, our findings provide new insights into the genetic mechanisms underlying growth and development in P. clarkii, and these identified genes serve as promising candidates for further functional studies and genetic improvement of this species.

Polymorphism, Single Nucleotide↗