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374 results for “Selection: natural”
Data from: Assessing the alignment of sexual and natural selection using radio-mutagenized seed beetles
A major unsolved question in evolutionary biology concerns the relationship between natural and sexual selection. Sexual selection might augment natural selection, e.g. if mutations that harm female fecundity also reduce male mating success. Conversely, sexual selection might favor traits that impair naturally-selected fitness components. We induced detrimental mutations in Callosobruchus maculatus beetles using X-ray irradiation, and then experimentally measured the effect of pre-copulatory sexual selection on offspring number and survival rate. Sexual selection treatment had a negative effect on egg-to-adult survivorship, though the number of progeny reaching adulthood was unaffected, perhaps because eggs and juveniles that failed to develop lessened competition on the survivors. We hypothesize that the negative effect of sexual selection arose because sexually competitive males transmitted a smaller nuptial gift, or carried alleles that conferred reduced survival. Although we found no evidence that sexual selection on males can purge alleles that are detrimental to naturally-selected fitness components, such benefits might exist in other environmental or genetic contexts.
Data from: Sexual and natural selection in the evolution of extended phenotypes: the use of green nesting material in starlings
Although sexual selection is typically considered the predominant force driving the evolution of ritualized sexual behaviors, natural selection may also play an important and often underappreciated role. The use of green aromatic plants among nesting birds has been interpreted as a component of extended phenotype that evolved either via natural selection due to potential sanitary functions, or via sexual selection as a signal of male attractiveness. Here we compared both hypotheses using comparative methods in starlings, a group where this behavior is widespread. We found that the use of green plants was positively related to male-biased size dimorphism, and that it was most likely to occur among cavity-nesting species. These results suggest that this behavior is likely favored by sexual selection, but also related to its sanitary use in response to higher parasite loads in cavities. We speculate that the use of green plants in starlings may be facilitated by cavity nesting, and was subsequently co-opted as a sexual signal by males. Our results represent an example of how an extended phenotypic component of males becomes sexually selected by females. Thus, both natural and sexual selection are necessary to fully understand the evolution of ritualized behaviors involved in courtship.
Data from: The incidental response to uniform natural selection
When populations are exposed to novel conditions of growth they often become adapted to a similar extent, and at the same time evolve some degree of impairment in their original environment. They may also come to vary widely with respect to characters which are uncorrelated with fitness, as the result of chance genetic associations among the founders, when these are a small sample from a large and variable ancestral population. I report an experiment in which 240 replicate lines of the unicellular chlorophyte Chlamydomonas were derived from primarily photoautotrophic ancestors and cultured as heterotrophs in the dark. All adapted to the dark and were impaired in the light after several hundred generations of culture. They also displayed a wide range of colony morphologies that were uncorrelated with fitness. This incidental response to selection probably arose through random variation in the initial composition of the lines. The differences between closely related species or varieties may likewise arise, in similar circumstances, by sampling error rather than natural selection.
Data from: Gain-of-function experiments in bacteriophage lambda uncover residues under diversifying selection in nature
Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here we demonstrate that two residues of λ's J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative of ecological diversification. Our results show that viral evolution in the laboratory mirrors that in nature and that laboratory experiments can be coupled with protein sequence analyses to identify the causes of viral evolution in the real world. Furthermore, our results provide evidence for widespread host-shift evolution in lambdoid viruses.
Data from: Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution
Background. The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. Results. Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. Conclusions. To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.
Data from: Population demography and heterozygosity-fitness correlations in natural guppy populations: an examination using sexually selected fitness traits
Heterozygosity-fitness correlations (HFCs) have been examined in a wide diversity of contexts, and the results are often used to infer the role of inbreeding in natural populations. Although population demography, reflected in population-level genetic parameters such as allelic diversity or identity disequilibrium, is expected to play a role in the emergence and detectability of HFCs, direct comparisons of variation in HFCs across many populations of the same species, with different genetic histories, are rare. Here, we examined the relationship between individual microsatellite heterozygosity and a range of sexually selected traits in 660 male guppies from 22 natural populations in Trinidad. Similar to previous studies, observed HFCs were weak overall. However, variation in HFCs among populations was high for some traits (although these variances were not statistically different from zero). Population-level genetic parameters, specifically genetic diversity levels (number of alleles, observed/expected heterozygosity) and measures of identity disequilibrium (g2 and heterozygosity-heterozygosity correlations) were not associated with variation in population-level HFCs. This latter result indicates that these metrics do not necessarily provide a reliable predictor of HFC effect sizes across populations. Importantly, diversity and identity disequilibrium statistics were not correlated, providing empirical evidence that these metrics capture different essential characteristics of populations. A complex genetic architecture likely underpins multiple fitness traits, including those associated with male fitness, which may have reduced our ability to detect HFCs in guppy populations. Further advances in this field would benefit from additional research to determine the demographic contexts in which HFCs are most likely to occur.
Data from: Genomic signatures of divergent selection and speciation patterns in a 'natural experiment', the young parallel radiations of Nicaraguan crater lake cichlid fishes
Divergent selection is the main driving force in sympatric ecological speciation and may also play a strong role in divergence between allopatric populations. Characterizing the genome-wide impact of divergent selection constitutes often a first step in the process of unraveling the genetic bases underlying adaptation and ecological speciation. The Midas cichlid fish (Amphilophus citrinellus) species complex in Nicaragua is a powerful system for studying evolutionary processes. Independent colonizations of isolated young crater lakes by Midas cichlid populations from the older and great lakes of Nicaragua resulted in the repeated evolution of adaptive radiations by intralacustrine sympatric speciation. In this study we performed genome scans on two repeated radiations of crater lake species and their great lake source populations (1030 polymorphic AFLPs, n ≈ 30 individuals per species). We detected regions under divergent selection (0.3 % in the crater lake Xiloá flock and 1.7 % in the older crater lake Apoyo radiation) that might be responsible for the sympatric diversification. We find no evidence that the same genomic regions have been involved across crater lake flocks. The data provide evidence, however, for some genetic parallelism (seven out of 51 crater lake to great lake outlier loci are shared; 13.7%) associated with the allopatric divergence of both crater lake flocks. Furthermore, our results suggest that the number of outlier loci involved in sympatric and allopatric divergence increases with time. A phylogeny based on our data clearly supports the monophyly of both crater lake species flocks and provides evidence for a parallel branching order with a primary divergence along the limnetic-benthic axis in both radiations.
Data from: Testis asymmetry in birds: the influences of sexual and natural selection
Gonad size and shape asymmetries are particularly common in birds. Although some obvious size and shape differences between the left and right testes in birds were first documented more than a century ago, little is known about what influences the variation across species in either the degree or the direction of these asymmetries. Here we show that a left bias in size is the most likely ancestral state in most orders and families, and that there is a weak but significant negative relation between the degree of size and shape asymmetries. In extant species, testis size and shape symmetries increase with the degree of sperm competition (relative testes mass), but those relations are significant only in those species with left bias in each of these traits. When space is particularly constrained on the left side of the body cavity due to a large gizzard (e.g. in granivores), the left testis is more elongated and the degree of size symmetry is larger. Despite significant patterns, relative testes mass and gizzard complexity together explain < 10% of the variation in testis asymmetry in species with left biases. Thus our analyses suggest that some other factor is largely responsible for the evolution of gonad asymmetry in birds: 1) that a left bias in testis size might be a correlated response to selection for a left bias in the development of a single (left) ovary in females of most bird species, and/or 2) that physiological efficiency due to the dramatic and rapid increase in testis size of most species during the breeding season might favour enlargement of one testis. Our conclusions highlight the need to rethink and improve our understanding of the physiological processes underlying the investment in gonads by male birds.
Data from: Genetic drift outweighs natural selection at toll-like receptor (TLR) immunity loci in a reintroduced population of a threatened species
During population establishment, genetic drift can be the key driver of changes in genetic diversity, particularly while the population is small. However, natural selection can also play a role in shaping diversity at functionally important loci. We used a well-studied, re-introduced population of the threatened Stewart Island robin (N = 722 pedigreed individuals) to determine whether selection shaped genetic diversity at innate immunity toll-like receptor (TLR) genes, over a 9-year period of population growth following establishment with 12 genetic founders. We found no evidence for selection operating with respect to TLR diversity on first-year overwinter survival for the majority of loci, genotypes and alleles studied. However, survival of individuals with TLR4BE genotype was significantly improved: these birds were less than half as likely to die prior to maturity compared with all other TLR4 genotypes. Furthermore, the population frequency of this genotype, at a two-fold excess over Hardy–Weinberg expectation, was increased by nonrandom mating. Near-complete sampling and full pedigree and reproductive data enabled us to eliminate other potential causes of these patterns including inbreeding, year effects, density dependence, selection on animals at earlier life history stages or genome-level association of the TLR4E allele with 'good genes'. However, comparison of observed levels of gene diversity to predictions under simulated genetic drift revealed results consistent with neutral expectations for all loci, including TLR4. Although selection favoured TLR4BE heterozygotes in this population, these effects were insufficient to outweigh genetic drift. This is the first empirical study to show that genetic drift can overwhelm natural selection in a wild population immediately following establishment.
A meta-analysis of natural selection on plant functional traits
<p>A common assumption in plant physiological ecology is that variation in functional traits reflects the adaptation of organisms to their abiotic environment. This assumption can be tested by estimating natural selection as the relationship between a functional trait and a fitness component (i.e. survival or reproduction) within a population. To understand how natural selection operates on plant functional traits, we compiled directional selection gradients (<i>β</i><span><span></span></span>), which estimate direct selection, and differentials (<i>S</i><span><span></span></span>), which estimate both direct and indirect selection, from studies conducted in manipulated and unmanipulated environments. We found that relative to manipulating biotic factors, manipulating abiotic factors had a ~5.7´ larger effect on <i>β </i><span><span></span></span>and a ~16´ larger effect on <i>S</i><span><span></span></span>, suggesting that functional traits primarily evolve in response to the abiotic environment. We found that the strength of selection on functional traits <i>(</i><span></span><i>β</i><i>)</i><span><span></span></span> did not vary with trait type, performance/fitness component, or measurement context (i.e. common garden vs. natural population). However, the direction of selection did differ between some trait types: <i>β</i><span><span></span></span> was positive for plant size traits, but negative for phenology traits. Lastly, we found that the absolute value of selection differentials (<span></span><i>S</i><span><span></span></span>) was ~2´ larger than the absolute value of selection gradients (<span></span><i>β</i><span><span></span></span>), indicating that there was indirect selection on functional traits. Overall, our meta-analysis illustrates that natural selection on plant functional traits is common, and that estimates of selection on these traits in experimentally manipulated environments can be used effectively to test hypotheses about the causes of adaptation.</p>
Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.
In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognised as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study the sequence of eIF4E was analysed in 1090 barley landraces and non-current cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eIF4E haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 out of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest eIF4E may play a role in barley adaptation to local habitats.
Data from: Are heritability and selection related to population size in nature? Meta-analysis and conservation implications
It is widely thought that small populations should have less additive genetic variance and respond less efficiently to natural selection than large populations. Across taxa, we meta-analytically quantified the relationship between adult census population size (N) and additive genetic variance (proxy: h2) and found no reduction in h2 with decreasing N; surveyed populations ranged from four to one million individuals (1735 h2estimates, 146 populations, 83 species). In terms of adaptation, ecological conditions may systematically differ between populations of varying N; the magnitude of selection these populations experience may therefore also differ. We thus also meta-analytically tested whether selection changes with N, and found little evidence for systematic differences in the strength, direction, or form of selection with N across different trait types and taxa (7344 selection estimates, 172 populations, 80 species). Collectively, our results (i) indirectly suggest that genetic drift neither overwhelms selection more in small than in large natural populations, nor weakens adaptive potential/h2 in small populations, and (ii) imply that natural populations of varying sizes experience a variety of environmental conditions, without consistently differing habitat quality at small N. However, we caution that the data are currently insufficient to determine whether some small populations may retain adaptive potential definitively. Further study is required into (i) selection and genetic variation in completely isolated populations of known N, underrepresented taxonomic groups, and non-generalist species, (ii) adaptive potential using multidimensional approaches, and (iii) the nature of selective pressures for specific traits.
Data from: Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes
The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response, and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of opposing evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta-analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is approximately 15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency-dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre-bottlenecked populations.
Context-dependent selectivity to natural scenes in the retina
<p>Here a sample dataset to replicate the study published in https://www.biorxiv.org/content/10.1101/2021.10.01.462157v1</p>
Data from: The strength of phenotypic selection in natural populations
How strong is phenotypic selection on quantitative traits in the wild? We reviewed the literature from 1984 through 1997 for studies that estimated the strength of linear and quadratic selection in terms of standardized selection gradients or differentials on natural variation in quantitative traits for field populations. We tabulated 63 published studies of 62 species that reported over 2,500 estimates of linear or quadratic selection. More than 80% of the estimates were for morphological traits; there is very little data for behavioral or physiological traits. Most published selection studies were unreplicated and had sample sizes below 135 individuals, resulting in low statistical power to detect selection of the magnitude typically reported for natural populations. The absolute values of linear selection gradients |β| were exponentially distributed with an overall median of 0.16, suggesting that strong directional selection was uncommon. The values of |β| for selection on morphological and on life-history/phenological traits were significantly different: on average, selection on morphology was stronger than selection on phenology/life history. Similarly, the values of |β| for selection via aspects of survival, fecundity, and mating success were significantly different: on average, selection on mating success was stronger than on survival. Comparisons of estimated linear selection gradients and differentials suggest that indirect components of phenotypic selection were usually modest relative to direct components. The absolute values of quadratic selection gradients |γ| were exponentially distributed with an overall median of only 0.10, suggesting that quadratic selection is typically quite weak. The distribution of γ values was symmetric about 0, providing no evidence that stabilizing selection is stronger or more common than disruptive selection in nature.
Data from: Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana
Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.
Assessing the Nature of Chiral-Induced Spin Selectivity by Magnetic Resonance. Open data set
<p>Data supporting the original figures 2,3,4 of the related publication.</p>
Reproducibility package for: Assessing natural selection during range expansions: Insights from a spatially explicit ABC study
<p>Study-reproducibility set with complete source code plus simulation results for the manuscript entitled "Assessing natural selection during range expansions: Insights from a spatially explicit ABC study".</p>
CD3/CD19 Depleted or CD3 Depleted/CD56 Selected Haploidentical Donor Natural Killer (NK) Cell Based Therapy for AML Patients Not in CR
ClinicalTrials.gov study NCT03152526. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: The incidental response to uniform natural selection
Open the record for dataset details and reuse information.
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