Journal articles: 'Selection pressures'

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Campbell, Robert L. "Selection pressures are mounting." Metascience 9, no. 2 (July 2000): 246–53. http://dx.doi.org/10.1007/bf02913608.

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Raven, John A. "Selection pressures on stomatal evolution." New Phytologist 153, no. 3 (March 2002): 371–86. http://dx.doi.org/10.1046/j.0028-646x.2001.00334.x.

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Salek Ardestani, Siavash, Mehdi Aminafshar, Mohammad Bagher Zandi Baghche Maryam, Mohammad Hossein Banabazi, Mehdi Sargolzaei, and Younes Miar. "Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes." Animals 10, no. 1 (December 26, 2019): 53. http://dx.doi.org/10.3390/ani10010053.

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Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima’s D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.

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Corus, Dogan, Andrei Lissovoi, Pietro S. Oliveto, and Carsten Witt. "On Steady-State Evolutionary Algorithms and Selective Pressure: Why Inverse Rank-Based Allocation of Reproductive Trials Is Best." ACM Transactions on Evolutionary Learning and Optimization 1, no. 1 (April 27, 2021): 1–38. http://dx.doi.org/10.1145/3427474.

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We analyse the impact of the selective pressure for the global optimisation capabilities of steady-state evolutionary algorithms (EAs). For the standard bimodal benchmark function TwoMax , we rigorously prove that using uniform parent selection leads to exponential runtimes with high probability to locate both optima for the standard ( +1) EA and ( +1) RLS with any polynomial population sizes. However, we prove that selecting the worst individual as parent leads to efficient global optimisation with overwhelming probability for reasonable population sizes. Since always selecting the worst individual may have detrimental effects for escaping from local optima, we consider the performance of stochastic parent selection operators with low selective pressure for a function class called TruncatedTwoMax, where one slope is shorter than the other. An experimental analysis shows that the EAs equipped with inverse tournament selection, where the loser is selected for reproduction and small tournament sizes, globally optimise TwoMax efficiently and effectively escape from local optima of TruncatedTwoMax with high probability. Thus, they identify both optima efficiently while uniform (or stronger) selection fails in theory and in practice. We then show the power of inverse selection on function classes from the literature where populations are essential by providing rigorous proofs or experimental evidence that it outperforms uniform selection equipped with or without a restart strategy. We conclude the article by confirming our theoretical insights with an empirical analysis of the different selective pressures on standard benchmarks of the classical MaxSat and multidimensional knapsack problems.

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Schneider, Kristan A., and Yuseob Kim. "Genetic Hitchhiking under Heterogeneous Spatial Selection Pressures." PLoS ONE 8, no. 4 (April 24, 2013): e61742. http://dx.doi.org/10.1371/journal.pone.0061742.

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Plotkin, Joshua B., Jonathan Dushoff, Michael M. Desai, and Hunter B. Fraser. "Estimating Selection Pressures from Limited Comparative Data." Molecular Biology and Evolution 23, no. 8 (June 5, 2006): 1457–59. http://dx.doi.org/10.1093/molbev/msl021.

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Dukes, Charles, Sharon M. Darling, and Kim Doan. "Selection Pressures on Special Education Teacher Preparation." Teacher Education and Special Education: The Journal of the Teacher Education Division of the Council for Exceptional Children 37, no. 1 (December 19, 2013): 9–20. http://dx.doi.org/10.1177/0888406413513273.

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Nowick, Katja, Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, and Peter F. Stadler. "Selection Pressures on RNA Sequences and Structures." Evolutionary Bioinformatics 15 (January 2019): 117693431987191. http://dx.doi.org/10.1177/1176934319871919.

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With the discovery of increasingly more functional noncoding RNAs (ncRNAs), it becomes eminent to more strongly consider them as important players during species evolution. Although tests for negative selection of ncRNAs already exist since the beginning of this century, the SSS-test is the first one for also investigating positive selection. When analyzing selection in ncRNAs, it should be taken into account that selection pressures can independently act on sequence and structure. We applied the SSS-test to explore the evolution of ncRNAs in primates and identified more than 100 long noncoding RNAs (lncRNAs) that might evolve under positive selection in humans. With this test, it is now possible to more thoroughly include ncRNAs into evolutionary studies.

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Reynolds, Austin W., Jaime Mata-Míguez, Aida Miró-Herrans, Marcus Briggs-Cloud, Ana Sylestine, Francisco Barajas-Olmos, Humberto Garcia-Ortiz, et al. "Comparing signals of natural selection between three Indigenous North American populations." Proceedings of the National Academy of Sciences 116, no. 19 (April 15, 2019): 9312–17. http://dx.doi.org/10.1073/pnas.1819467116.

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While many studies have highlighted human adaptations to diverse environments worldwide, genomic studies of natural selection in Indigenous populations in the Americas have been absent from this literature until very recently. Since humans first entered the Americas some 20,000 years ago, they have settled in many new environments across the continent. This diversity of environments has placed variable selective pressures on the populations living in each region, but the effects of these pressures have not been extensively studied to date. To help fill this gap, we collected genome-wide data from three Indigenous North American populations from different geographic regions of the continent (Alaska, southeastern United States, and central Mexico). We identified signals of natural selection in each population and compared signals across populations to explore the differences in selective pressures among the three regions sampled. We find evidence of adaptation to cold and high-latitude environments in Alaska, while in the southeastern United States and central Mexico, pathogenic environments seem to have created important selective pressures. This study lays the foundation for additional functional and phenotypic work on possible adaptations to varied environments during the history of population diversification in the Americas.

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Vicens, Alberto, and David Posada. "Selective Pressures on Human Cancer Genes along the Evolution of Mammals." Genes 9, no. 12 (November 28, 2018): 582. http://dx.doi.org/10.3390/genes9120582.

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Cancer is a disease driven by both somatic mutations that increase survival and proliferation of cell lineages and the evolution of genes associated with cancer risk in populations. Several genes associated with cancer in humans, hereafter cancer genes, show evidence of germline positive selection among species. Taking advantage of a large collection of mammalian genomes, we systematically looked for signatures of germline positive selection in 430 cancer genes available in COSMIC. We identified 40 cancer genes with a robust signal of positive selection in mammals. We found evidence for fewer selective constraints—higher number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site (dN/dS)—and higher incidence of positive selection—more positively selected sites—in cancer genes bearing germline and recessive mutations that predispose to cancer. This finding suggests a potential association between relaxed selection, positive selection, and risk of hereditary cancer. On the other hand, we did not find significant differences in terms of tissue or gene type. Human cancer genes under germline positive selection in mammals are significantly enriched in the processes of DNA repair, with high presence of Fanconi anaemia/Breast Cancer A (FA/BRCA) pathway components and T cell proliferation genes. We also show that the inferred positively selected sites in the two genes with the strongest signal of positive selection, i.e., BRCA2 and PTPRC, are in regions of functional relevance, which could be relevant to cancer susceptibility.

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Anderson, R. M., R. M. May, and S. Gupta. "Genetic heterogeneity in helminths — a reply." Parasitology 111, no. 4 (November 1995): 537–38. http://dx.doi.org/10.1017/s0031182000066051.

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The previous paper in this issue Computer model of the maintenance and selection of genetic heterogeneity in polygamous helminths by Saul uses an individual-based computer simulation to explore aspects of the transmission and maintenance of genetic heterogeneity among polygamous intestinal helminths, both in the absence and in the presence of external selection pressures resulting from chemotherapy. Saul finds that, in the absence of any selective effects, genetic heterogeneity persists, contradicting the results presented by Anderson, May & Gupta (1989) that mating probability functions create density-dependent and frequency-dependent selective pressures against a rare allele, which eventually leads to its elimination.

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Wang, Xiaohong, Zhipeng Chen, Duo Dong, Dongdong Zhu, Hongwei Wang, and Zunjie Wei. "Study on the Phase Selection and Debye Temperature of Hyper-Peritectic Al-Ni Alloy under High Pressure." Metals 11, no. 1 (January 4, 2021): 84. http://dx.doi.org/10.3390/met11010084.

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The phase selection of hyper-peritectic Al-47wt.%Ni alloy solidified under different pressures was investigated. The results show that Al3Ni2 and Al3Ni phases coexist at ambient pressure, while another new phase α-Al exists simultaneously when solidified at high pressure. Based on the competitive growth theory of dendrite, a kinetic stabilization of metastable peritectic phases with respect to stable ones is predicted for different solidification pressures. It demonstrates that Al3Ni2 phase nucleates and grows directly from the undercooled liquid. Meanwhile, the Debye temperatures of Al-47wt.%Ni alloy that fabricated at different pressures were also calculated using the low temperature heat capacity curve.

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Anisimova, Maria, Rasmus Nielsen, and Ziheng Yang. "Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites." Genetics 164, no. 3 (July 1, 2003): 1229–36. http://dx.doi.org/10.1093/genetics/164.3.1229.

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AbstractMaximum-likelihood methods based on models of codon substitution accounting for heterogeneous selective pressures across sites have proved to be powerful in detecting positive selection in protein-coding DNA sequences. Those methods are phylogeny based and do not account for the effects of recombination. When recombination occurs, such as in population data, no unique tree topology can describe the evolutionary history of the whole sequence. This violation of assumptions raises serious concerns about the likelihood method for detecting positive selection. Here we use computer simulation to evaluate the reliability of the likelihood-ratio test (LRT) for positive selection in the presence of recombination. We examine three tests based on different models of variable selective pressures among sites. Sequences are simulated using a coalescent model with recombination and analyzed using codon-based likelihood models ignoring recombination. We find that the LRT is robust to low levels of recombination (with fewer than three recombination events in the history of a sample of 10 sequences). However, at higher levels of recombination, the type I error rate can be as high as 90%, especially when the null model in the LRT is unrealistic, and the test often mistakes recombination as evidence for positive selection. The test that compares the more realistic models M7 (β) against M8 (β and ω) is more robust to recombination, where the null model M7 allows the positive selection pressure to vary between 0 and 1 (and so does not account for positive selection), and the alternative model M8 allows an additional discrete class with ω= dN/dS that could be estimated to be >1 (and thus accounts for positive selection). Identification of sites under positive selection by the empirical Bayes method appears to be less affected than the LRT by recombination.

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Travers, Simon A. A., Mary J. O'Connell, Grace P. McCormack, and James O. McInerney. "Evidence for Heterogeneous Selective Pressures in the Evolution of the env Gene in Different Human Immunodeficiency Virus Type 1 Subtypes." Journal of Virology 79, no. 3 (February 1, 2005): 1836–41. http://dx.doi.org/10.1128/jvi.79.3.1836-1841.2005.

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ABSTRACT Recent studies have demonstrated the emergence of human immunodeficiency virus type 1 (HIV-1) subtypes with various levels of fitness. Using heterogeneous maximum-likelihood models of adaptive evolution implemented in the PAML software package, with env sequences representing each HIV-1 group M subtype, we examined the various intersubtype selective pressures operating across the env gene. We found heterogeneity of evolutionary mechanisms between the different subtypes with a category of amino acid sites observed that had undergone positive selection for subtypes C, F1, and G, while these sites had undergone purifying selection in all other subtypes. Also, amino acid sites within subtypes A and K that had undergone purifying selection were observed, while these sites had undergone positive selection in all other subtypes. The presence of such sites indicates heterogeneity of selective pressures within HIV-1 group M subtype evolution that may account for the various levels of fitness of the subtypes.

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Cvijović, Ivana, Benjamin H. Good, Elizabeth R. Jerison, and Michael M. Desai. "Fate of a mutation in a fluctuating environment." Proceedings of the National Academy of Sciences 112, no. 36 (August 24, 2015): E5021—E5028. http://dx.doi.org/10.1073/pnas.1505406112.

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Natural environments are never truly constant, but the evolutionary implications of temporally varying selection pressures remain poorly understood. Here we investigate how the fate of a new mutation in a fluctuating environment depends on the dynamics of environmental variation and on the selective pressures in each condition. We find that even when a mutation experiences many environmental epochs before fixing or going extinct, its fate is not necessarily determined by its time-averaged selective effect. Instead, environmental variability reduces the efficiency of selection across a broad parameter regime, rendering selection unable to distinguish between mutations that are substantially beneficial and substantially deleterious on average. Temporal fluctuations can also dramatically increase fixation probabilities, often making the details of these fluctuations more important than the average selection pressures acting on each new mutation. For example, mutations that result in a trade-off between conditions but are strongly deleterious on average can nevertheless be more likely to fix than mutations that are always neutral or beneficial. These effects can have important implications for patterns of molecular evolution in variable environments, and they suggest that it may often be difficult for populations to maintain specialist traits, even when their loss leads to a decline in time-averaged fitness.

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Novembre, John, and Eunjung Han. "Human population structure and the adaptive response to pathogen-induced selection pressures." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1590 (March 19, 2012): 878–86. http://dx.doi.org/10.1098/rstb.2011.0305.

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The past few years of research in human evolutionary genetics have provided novel insights and questions regarding how human adaptations to recent selective pressures have taken place. Here, we review the advances most relevant to understanding human evolution in response to pathogen-induced selective pressures. Key insights come from theoretical models of adaptive evolution, particularly those that consider spatially structured populations, and from empirical population genomic studies of adaptive evolution in humans. We also review the CCR5 -Δ32 HIV resistance allele as a case study of pathogen resistance in humans. Taken together, the results make clear that the human response to pathogen-induced selection pressures depends on a complex interplay between the age of the pathogen, the genetic basis of potential resistance phenotypes, and how population structure impacts the adaptive process in humans.

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Chare, Elizabeth R., and Edward C. Holmes. "Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission." Journal of General Virology 85, no. 10 (October 1, 2004): 3149–57. http://dx.doi.org/10.1099/vir.0.80134-0.

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To determine the selection pressures faced by RNA viruses of plants, patterns of nonsynonymous (d N) and synonymous (d S) substitution in the capsid genes of 36 viruses with differing modes of transmission were analysed. This analysis provided strong evidence that the capsid proteins of vector-borne plant viruses are subject to greater purifying selection on amino acid change than those viruses transmitted by other routes and that virus–vector interactions impose greater selective constraints than those between virus and plant host. This could be explained by specific interactions between capsid proteins and cellular receptors in the insect vectors that are necessary for successful transmission. However, contrary to initial expectations based on phylogenetic relatedness, vector-borne plant viruses are subject to weaker selective constraints than vector-borne animal viruses. The results suggest that the greater complexity involved in the transmission of circulative animal viruses compared with non-circulative plant viruses results in more intense purifying selection.

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Simpson, Richard K., Allison F. Mistakidis, and Stéphanie M. Doucet. "Natural and sexual selection shape the evolution of colour and conspicuousness in North American wood-warblers (Parulidae)." Biological Journal of the Linnean Society 130, no. 1 (March 10, 2020): 89–100. http://dx.doi.org/10.1093/biolinnean/blaa015.

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Abstract Natural and sexual selection drive colour evolution in animals. However, these different selective forces are often studied independently or without considering environmental variation. We evaluated the roles of natural and sexual selection together on colour evolution in 15 sympatric wood-warbler species, while considering the influence of variation in the light environment and visual background. We tested the influence of each selective pressure on male and female coloration and contrast against the background using avian visual models in phylogenetically controlled analyses. We found natural and sexual selection simultaneously driving cryptic and conspicuous plumage in males by acting on different body regions. For example, we found that ground-nesting species had males with conspicuous under-body plumage and cryptic upper-body plumage, showing how natural and sexual selection can drive colour evolution concordantly. We also found interesting relationships with female plumage, such as nest predation positively covarying with female contrast against the background, suggesting a cost to female conspicuousness. Our findings here showcase the complexity of selection on coloration and illustrate the importance of: (1) accounting for environmental variation when assessing how natural and sexual selection drive colour evolution; and (2) testing how multiple selection pressures are shaping colour diversity among species.

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Xia, Tian, Lei Zhang, Guolei Sun, Xiufeng Yang, and Honghai Zhang. "Genomic evidence of adaptive evolution in the reptilian SOCS gene family." PeerJ 9 (June 24, 2021): e11677. http://dx.doi.org/10.7717/peerj.11677.

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The suppressor of the cytokine signaling (SOCS) family of proteins play an essential role in inhibiting cytokine receptor signaling by regulating immune signal pathways. Although SOCS gene functions have been examined extensively, no comprehensive study has been performed on this gene family’s molecular evolution in reptiles. In this study, we identified eight canonical SOCS genes using recently-published reptilian genomes. We used phylogenetic analysis to determine that the SOCS genes had highly conserved evolutionary dynamics that we classified into two types. We identified positive SOCS4 selection signals in whole reptile lineages and SOCS2 selection signals in the crocodilian lineage. Selective pressure analyses using the branch model and Z-test revealed that these genes were under different negative selection pressures compared to reptile lineages. We also concluded that the nature of selection pressure varies across different reptile lineages on SOCS3, and the crocodilian lineage has experienced rapid evolution. Our results may provide a theoretical foundation for further analyses of reptilian SOCS genes’ functional and molecular mechanisms, as well as their roles in reptile growth and development.

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Li, Dong, Rong Qi, Min Yang, Yu Zhang, and Tao Yu. "Bacterial community characteristics under long-term antibiotic selection pressures." Water Research 45, no. 18 (November 2011): 6063–73. http://dx.doi.org/10.1016/j.watres.2011.09.002.

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Coleman, M. L., and S. W. Chisholm. "Ecosystem-specific selection pressures revealed through comparative population genomics." Proceedings of the National Academy of Sciences 107, no. 43 (October 11, 2010): 18634–39. http://dx.doi.org/10.1073/pnas.1009480107.

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Grant, Alastair. "Selection pressures on vital rates in density–dependent populations." Proceedings of the Royal Society of London. Series B: Biological Sciences 264, no. 1380 (March 22, 1997): 303–6. http://dx.doi.org/10.1098/rspb.1997.0043.

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van Mölken, Tamara, and Josef F. Stuefer. "Virulence in clonal plants: conflicting selection pressures at work?" Evolutionary Ecology 22, no. 3 (September 1, 2007): 467–70. http://dx.doi.org/10.1007/s10682-007-9206-4.

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Moya, Cristina, and Robert Boyd. "Different Selection Pressures Give Rise to Distinct Ethnic Phenomena." Human Nature 26, no. 1 (March 2015): 1–27. http://dx.doi.org/10.1007/s12110-015-9224-9.

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Towner, K. J., and R. C. B. Slack. "Effect of changing selection pressures on trimethoprim resistance inEnterobacteriaceae." European Journal of Clinical Microbiology 5, no. 5 (October 1986): 502–6. http://dx.doi.org/10.1007/bf02017691.

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Wang, Xiaotong, Joseph A. Morton, Jaume Pellicer, Ilia J. Leitch, and Andrew R. Leitch. "Genome downsizing after polyploidy: mechanisms, rates and selection pressures." Plant Journal 107, no. 4 (July 5, 2021): 1003–15. http://dx.doi.org/10.1111/tpj.15363.

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Talbot, Benoit, Ondřej Balvín, Maarten J. Vonhof, Hugh G. Broders, Brock Fenton, and Nusha Keyghobadi. "Host association and selection on salivary protein genes in bed bugs and related blood-feeding ectoparasites." Royal Society Open Science 4, no. 6 (June 2017): 170446. http://dx.doi.org/10.1098/rsos.170446.

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Reciprocal selective pressures can drive coevolutionary changes in parasites and hosts, and result in parasites that are highly specialized to their hosts. Selection and host co-adaptation are better understood in endoparasites than in ectoparasites, whose life cycles may be more loosely linked to that of their hosts. Blood-feeding ectoparasites use salivary proteins to prevent haemostasis in the host, and maximize energy intake. Here we looked for signals of selection in salivary protein genes of ectoparasite species from a single genus ( Cimex ) that associate with a range of hosts including mammals (bats and humans) and birds (swallows). We analysed two genes that code for salivary proteins that inhibit platelet aggregation and vasoconstriction and may directly affect the efficiency of blood feeding in these species. Significant positive selection was detected at five codons in one gene in all bat-associated species groups. Our results suggest association with bats, versus humans or swallows, has posed a selective pressure on the salivary apyrase gene in species of Cimex .

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Fernàndez, Guerau, Anuska Llano, Miriam Esgleas, Bonaventura Clotet, José A. Esté, and Miguel Angel Martínez. "Purifying selection of CCR5-tropic human immunodeficiency virus type 1 variants in AIDS subjects that have developed syncytium-inducing, CXCR4-tropic viruses." Journal of General Virology 87, no. 5 (May 1, 2006): 1285–94. http://dx.doi.org/10.1099/vir.0.81722-0.

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Human immunodeficiency virus type 1 (HIV-1) infection is established by virus variants that use the CCR5 co-receptor for entry (CCR5-tropic or R5 variants), whereas viruses that use CXCR4 as co-receptor (CXCR4-tropic or X4 variants) emerge during disease progression in approximately 50 % of infected subjects. X4 variants may have a higher fitness ex vivo and their detection is usually accompanied by faster T-cell depletion and the onset of AIDS in HIV-1-positive individuals. Here, the relationship between the sequence variation of the HIV-1 env V3–V5 region and positive selective pressure on R5 and X4 variants from infected subjects with CD4 T cell counts below 200 cells μl−1 was studied. A correlation was found between genetic distance and CD4+ cell count at late stages of the disease. R5 variants that co-existed with X4 variants were significantly less heterogeneous than R5 variants from subjects without X4 variants (P<0·0001). Similarly, X4 variants had a significantly higher diversity than R5 variants (P<0·0001), although residues under positive selection had a similar distribution pattern in both variants. Therefore, both X4 and R5 variants were subjected to high selective pressures from the host. Furthermore, the interaction between X4 and R5 variants within the same subject resulted in a purifying selection on R5 variants, which only survived as a homogeneous virus population. These results indicate that R5 variants from X4 phenotype samples were highly homogeneous and under weakly positive selective pressures. In contrast, R5 variants from R5 phenotype samples were highly heterogeneous and subject to positive selective pressures.

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Solé, Ricard V., and Sergi Valverde. "Spontaneous emergence of modularity in cellular networks." Journal of The Royal Society Interface 5, no. 18 (July 11, 2007): 129–33. http://dx.doi.org/10.1098/rsif.2007.1108.

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Modularity is known to be one of the most relevant characteristics of biological systems and appears to be present at multiple scales. Given its adaptive potential, it is often assumed to be the target of selective pressures. Under such interpretation, selection would be actively favouring the formation of modular structures, which would specialize in different functions. Here we show that, within the context of cellular networks, no such selection pressure is needed to obtain modularity. Instead, the intrinsic dynamics of network growth by duplication and diversification is able to generate it for free and explain the statistical features exhibited by small subgraphs. The implications for the evolution and evolvability of both biological and technological systems are discussed.

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Bahi-Jaber, Narges, David Fouchet, and Dominique Pontier. "Stochastic extinction and the selection of the transmission mode in microparasites." Journal of The Royal Society Interface 5, no. 26 (January 30, 2008): 1031–39. http://dx.doi.org/10.1098/rsif.2007.1326.

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Stochastic fluctuations in the transmission process of microparasites generate a risk of parasite extinction that cannot be assessed by deterministic models, especially in host populations of small size. While this risk of extinction represents a strong selection pressure for microparasites, it is usually not clearly separated from the deterministic ones. We suggest here that this stochastic selection pressure can affect the selection of the transmission mode of microparasites. To avoid extinction, parasites should maximize their inter-population transmission to ensure frequent reintroductions. Since the types of contacts may differ if congeners belong to the same or distinct populations, strains that are mainly transmitted through inter-population contacts might be selected. To examine this assumption, we analyse the issue of the competition between two strains differing in their transmission mode using a stochastic metapopulation model in which hosts may display different behaviours inside and outside their populations. We show that stochastic selection pressures may drive parasite evolution towards a transmission mode that maximizes the persistence of the parasite. We study the conditions under which stochastic selection pressures may surpass the deterministic ones. Our results are illustrated by the cases of feline immunodeficiency virus in cats and of sexually transmitted diseases in mammals.

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Duan, Guohua, Jiandong Bao, Xiaomin Chen, Jiahui Xie, Yuchan Liu, Huiquan Chen, Huakun Zheng, Wei Tang, and Zonghua Wang. "Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex." Microorganisms 9, no. 3 (March 9, 2021): 562. http://dx.doi.org/10.3390/microorganisms9030562.

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Magnaporthe oryzae, one of the most notorious plant pathogens in the agronomic ecosystem, causes a destructive rice blast disease around the world. The blast fungus infects wide arrays of cultivated and non-cultivated plants within the Poaceae. Studies have shown that host speciation exerts selection pressure that drives the evolution and divergence of the M. oryzae population. Population genetic relationship deducted by genome-wide single nucleotide polymorphisms showed that M. oryzae differentiation is highly consistent with the host speciation process. In particular, the rice-infecting population of M. oryzae is distinct from populations from other hosts. However, how genome regions prone to host-mediated selection pressures associated with speciation in M. oryzae, especially at a large-scale population level, has not been extensively characterized. Here, we detected strong evidence of sweep selection throughout the genomes of rice and non-rice pathotypes of M. oryzae population using integrated haplotype score (iHS), cross population extended haplotype homozygosity (XPEHH), and cross population composite likelihood ratio (XPCLR) tests. Functional annotation analyses of the genes associated with host-mediated selection pressure showed that 14 pathogenicity-related genes are under positive selection pressure. Additionally, we showed that 17 candidate effector proteins are under positive and divergent selection among the blast fungus population through sweep selection analysis. Specifically, we find that a divergent selective gene, MGG_13871, is experiencing host-directed mutation in two amino acid residues in rice and non-rice infecting populations. These results provide a crucial insight into the impact of selective sweeping on the differentiation of M. oryzae populations and the dynamic influences of genomic regions in promoting host adaptation and speciation among M. oryzae species.

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Leese, Joseph, Jennifer Snekser, and Murray Itzkowitz. "Interactions of natural and sexual selection: damselfish prioritize brood defense with male–male competition or courtship." Behaviour 147, no. 1 (2010): 37–52. http://dx.doi.org/10.1163/000579509x12483520922089.

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AbstractNatural and sexual selection often act in opposing directions, forcing individuals to prioritize activities necessary for survival with those required for reproduction. We examined the interaction of natural and sexual selection pressures on the behaviour of beaugregory damselfish, Stegastes leucostictus, by presenting territorial males with an egg predator and either a male or female conspecific, requiring males to prioritize brood defense with either courtship or intra-sexual competition. By measuring the time spent near stimuli, we examined the influence of several factors, including stimuli type, variation in predator number, and the presence of eggs in a nest site. Generally, males spent more time with conspecific stimuli than egg predators, suggesting that the sexual selection pressures of deterring rivals and attracting mates outweigh the natural selection pressure to engage in brood defense. This decision was affected by the sex of the conspecific presented, the presence of eggs in a male's territory, and a number of interactions of these factors, indicating that male damselfish consider multiple factors before investing in certain types and intensities of behaviours. Furthermore, observations of behaviours associated with courtship and intrasexual aggression show that a natural selection pressure impacts intra- and inter-sexually selected behaviours differently in this system.

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Stoletzki, Nina. "Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures." BMC Evolutionary Biology 8, no. 1 (2008): 224. http://dx.doi.org/10.1186/1471-2148-8-224.

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Monro, Keyne, and Dustin J. Marshall. "Unravelling anisogamy: egg size and ejaculate size mediate selection on morphology in free-swimming sperm." Proceedings of the Royal Society B: Biological Sciences 283, no. 1834 (July 13, 2016): 20160671. http://dx.doi.org/10.1098/rspb.2016.0671.

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Gamete dimorphism (anisogamy) defines the sexes in most multicellular organisms. Theoretical explanations for its maintenance usually emphasize the size-related selection pressures of sperm competition and zygote survival, assuming that fertilization of all eggs precludes selection for phenotypes that enhance fertility. In external fertilizers, however, fertilization is often incomplete due to sperm limitation, and the risk of polyspermy weakens the advantage of high sperm numbers that is predicted to limit sperm size, allowing alternative selection pressures to target free-swimming sperm. We asked whether egg size and ejaculate size mediate selection on the free-swimming sperm of Galeolaria caespitosa , a marine tubeworm with external fertilization, by comparing relationships between sperm morphology and male fertility across manipulations of egg size and sperm density. Our results suggest that selection pressures exerted by these factors may aid the maintenance of anisogamy in external fertilizers by limiting the adaptive value of larger sperm in the absence of competition. In doing so, our study offers a more complete explanation for the stability of anisogamy across the range of sperm environments typical of this mating system and identifies new potential for the sexes to coevolve via mutual selection pressures exerted by gametes at fertilization.

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Gienapp, Phillip, Thomas E. Reed, and Marcel E. Visser. "Why climate change will invariably alter selection pressures on phenology." Proceedings of the Royal Society B: Biological Sciences 281, no. 1793 (October 22, 2014): 20141611. http://dx.doi.org/10.1098/rspb.2014.1611.

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The seasonal timing of lifecycle events is closely linked to individual fitness and hence, maladaptation in phenological traits may impact population dynamics. However, few studies have analysed whether and why climate change will alter selection pressures and hence possibly induce maladaptation in phenology. To fill this gap, we here use a theoretical modelling approach. In our models, the phenologies of consumer and resource are (potentially) environmentally sensitive and depend on two different but correlated environmental variables. Fitness of the consumer depends on the phenological match with the resource. Because we explicitly model the dependence of the phenologies on environmental variables, we can test how differential (heterogeneous) versus equal (homogeneous) rates of change in the environmental variables affect selection on consumer phenology. As expected, under heterogeneous change, phenotypic plasticity is insufficient and thus selection on consumer phenology arises. However, even homogeneous change leads to directional selection on consumer phenology. This is because the consumer reaction norm has historically evolved to be flatter than the resource reaction norm, owing to time lags and imperfect cue reliability. Climate change will therefore lead to increased selection on consumer phenology across a broad range of situations.

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Yang, Ziheng, Rasmus Nielsen, Nick Goldman, and Anne-Mette Krabbe Pedersen. "Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites." Genetics 155, no. 1 (May 1, 2000): 431–49. http://dx.doi.org/10.1093/genetics/155.1.431.

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AbstractComparison of relative fixation rates of synonymous (silent) and nonsynonymous (amino acid-altering) mutations provides a means for understanding the mechanisms of molecular sequence evolution. The nonsynonymous/synonymous rate ratio (ω = dN/dS) is an important indicator of selective pressure at the protein level, with ω = 1 meaning neutral mutations, ω < 1 purifying selection, and ω > 1 diversifying positive selection. Amino acid sites in a protein are expected to be under different selective pressures and have different underlying ω ratios. We develop models that account for heterogeneous ω ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences. These models are useful for testing for adaptive molecular evolution and identifying amino acid sites under diversifying selection. Ten data sets of genes from nuclear, mitochondrial, and viral genomes are analyzed to estimate the distributions of ω among sites. In all data sets analyzed, the selective pressure indicated by the ω ratio is found to be highly heterogeneous among sites. Previously unsuspected Darwinian selection is detected in several genes in which the average ω ratio across sites is <1, but in which some sites are clearly under diversifying selection with ω > 1. Genes undergoing positive selection include the β-globin gene from vertebrates, mitochondrial protein-coding genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to the specific distributional form assumed for ω and can be achieved using any of several models we implement. However, we encountered difficulties in estimating the precise distribution of ω among sites from real data sets.

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Reynolds, A. M. "Selection pressures give composite correlated random walks Lévy walk characteristics." Journal of Theoretical Biology 332 (September 2013): 117–22. http://dx.doi.org/10.1016/j.jtbi.2013.04.035.

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Huang, Huang-Chiao, Imran Rizvi, Joyce Liu, Sriram Anbil, Ashish Kalra, Helen Lee, Yan Baglo, et al. "Photodynamic Priming Mitigates Chemotherapeutic Selection Pressures and Improves Drug Delivery." Cancer Research 78, no. 2 (November 29, 2017): 558–71. http://dx.doi.org/10.1158/0008-5472.can-17-1700.

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Schreier, Tina B., and Julian M. Hibberd. "Variations in the Calvin–Benson cycle: selection pressures and optimization?" Journal of Experimental Botany 70, no. 6 (March 1, 2019): 1697–701. http://dx.doi.org/10.1093/jxb/erz078.

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Vishnoi, A., S. Kryazhimskiy, G. A. Bazykin, S. Hannenhalli, and J. B. Plotkin. "Young proteins experience more variable selection pressures than old proteins." Genome Research 20, no. 11 (October 4, 2010): 1574–81. http://dx.doi.org/10.1101/gr.109595.110.

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Templeton, C. N. "Multiple selection pressures influence Trinidadian guppy (Poecilia reticulata) antipredator behavior." Behavioral Ecology 15, no. 4 (July 1, 2004): 673–78. http://dx.doi.org/10.1093/beheco/arh065.

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Kosakovsky Pond, S. L., A. F. Y. Poon, S. Zárate, D. M. Smith, S. J. Little, S. K. Pillai, R. J. Ellis, et al. "Estimating selection pressures on HIV-1 using phylogenetic likelihood models." Statistics in Medicine 27, no. 23 (October 15, 2008): 4779–89. http://dx.doi.org/10.1002/sim.3192.

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Barbosa, Susana, William C. Black, and Ian Hastings. "Challenges in Estimating Insecticide Selection Pressures from Mosquito Field Data." PLoS Neglected Tropical Diseases 5, no. 11 (November 1, 2011): e1387. http://dx.doi.org/10.1371/journal.pntd.0001387.

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Blekhman, Ran, Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, and Yoav Gilad. "Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures." PLoS Genetics 4, no. 11 (November 21, 2008): e1000271. http://dx.doi.org/10.1371/journal.pgen.1000271.

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Osborne, Colin P., and Robert P. Freckleton. "Ecological selection pressures for C 4 photosynthesis in the grasses." Proceedings of the Royal Society B: Biological Sciences 276, no. 1663 (February 25, 2009): 1753–60. http://dx.doi.org/10.1098/rspb.2008.1762.

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Grasses using the C 4 photosynthetic pathway dominate grasslands and savannahs of warm regions, and account for half of the species in this ecologically and economically important plant family. The C 4 pathway increases the potential for high rates of photosynthesis, particularly at high irradiance, and raises water-use efficiency compared with the C 3 type. It is therefore classically viewed as an adaptation to open, arid conditions. Here, we test this adaptive hypothesis using the comparative method, analysing habitat data for 117 genera of grasses, representing 15 C 4 lineages. The evidence from our three complementary analyses is consistent with the hypothesis that evolutionary selection for C 4 photosynthesis requires open environments, but we find an equal likelihood of C 4 evolutionary origins in mesic, arid and saline habitats. However, once the pathway has arisen, evolutionary transitions into arid habitats occur at higher rates in C 4 than C 3 clades. Extant C 4 genera therefore occupy a wider range of drier habitats than their C 3 counterparts because the C 4 pathway represents a pre-adaptation to arid conditions. Our analyses warn against evolutionary inferences based solely upon the high occurrence of extant C 4 species in dry habitats, and provide a novel interpretation of this classic ecological association.

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Auer, Sonya K., Graeme J. Anderson, Simon McKelvey, Ronald D. Bassar, Darryl McLennan, John D. Armstrong, Keith H. Nislow, et al. "Nutrients from salmon parents alter selection pressures on their offspring." Ecology Letters 21, no. 2 (December 15, 2017): 287–95. http://dx.doi.org/10.1111/ele.12894.

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Chen, Yao, Wenju Jiang, David Tee Liang, and Joo Hwa Tay. "Aerobic granulation under the combined hydraulic and loading selection pressures." Bioresource Technology 99, no. 16 (November 2008): 7444–49. http://dx.doi.org/10.1016/j.biortech.2008.02.028.

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Kasumovic, Michael M., and Maydianne C. B. Andrade. "Male development tracks rapidly shifting sexual versus natural selection pressures." Current Biology 16, no. 7 (April 2006): R242—R243. http://dx.doi.org/10.1016/j.cub.2006.03.017.

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Lankinen, Åsa, and Mattias C. Larsson. "Conflicting selection pressures on reproductive functions and speciation in plants." Evolutionary Ecology 23, no. 1 (November 20, 2007): 147–57. http://dx.doi.org/10.1007/s10682-007-9227-z.

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Mochida, Koji. "Combination of local selection pressures drives diversity in aposematic signals." Evolutionary Ecology 25, no. 5 (March 27, 2011): 1017–28. http://dx.doi.org/10.1007/s10682-011-9471-0.

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Journal articles on the topic 'Selection pressures'

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