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This study aimed to assess the genetic diversity and molecular evolution of tomato (Solanum lycopersicum) populations from various countries, which hold significant potential for future breeding strategies and germplasm conservation. To achieve this, a total of 15 sequences deposited in GenBank were analyzed using the complete internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA). The spacer sequence lengths ranged from 156 base pairs (bp) in the Swedish tomato to 713 bp in the Palestinian tomato. A notable variation in GC content was observed, with the Thai tomato exhibiting the highest value (67.48%) and the South Korean tomato the lowest (49.56%). Phylogenetic trees were constructed using both the distance-based Neighbor-Joining (NJ) and Maximum Parsimony (MP) methods. Sequence analysis revealed 38 monomorphic (invariable) sites and 15 polymorphic sites, of which 14 were singleton variable sites and one was parsimony-informative. Alignment of the 15 sequences enabled the identification of five haplotypes. The estimated transition/transversion bias (R) was 17.339, indicating a greater frequency of transitions over transversions in this region. Neutrality tests, including Tajima’s D and Fu and Li’s statistics, produced statistically significant results. The highest levels of genetic diversity were observed in South Korean, Iraqi, and Indian tomato samples. هدفت هذه الدراسة إلى تقييم التنوع الوراثي والتطور الجزيئي لمجتمعات الطماطم (Solanum lycopersicum) من دول مختلفة، لما لها من أهمية كبيرة في تطوير استراتيجيات التربية المستقبلية وحفظ الموارد الوراثية, و لذلك، قد تم تحليل 15 تسلسلاً وراثيًا مودعًا في قاعدة بيانات GenBank باستخدام منطقة فاصل النسخ الداخلي (ITS) بالكامل من الحمض النووي الريبوسومي (nrDNA), تراوح طول تسلسلات الفاصل بين 156 زوجًا قاعديًا في الطماطم السويدية و713 زوجًا قاعديًا في الطماطم الفلسطينية, كما لوحظ تباين واضح في محتوى GC، حيث سجلت الطماطم التايلاندية أعلى نسبة (67.48%)، بينما سجلت الطماطم الكورية الجنوبية أدنى نسبة (49.56%)وقد تم بناء الأشجار الوراثية باستخدام طريقتي ربط الجوار الأقرب (Neighbor-Joining) والحد الأدنى للتغير (Maximum Parsimony), وكشف تحليل التسلسلات عن وجود 38 موقعًا ثابتًا (أحادِي الشكل) و15 موقعًا متغيرًا، منها 14 موقعًا متغيرًا منفردًا وموقع واحد معلوماتياً (parsimony-informative), وقد أتاحت محاذاة التسلسلات التعرف على خمسة أنماط فردية (haplotypes), وبلغ معدل انحياز التحولات/التبدالات (R) نحو 17.339، مما يشير إلى أن التحولات تحدث بمعدل أكبر من التبدالات في هذه المنطقة, كما أظهرت اختبارات الحيادية، بما في ذلك اختبار تاجما (Tajima’s D) واختبار فو ولي (Fu and Li)، نتائج ذات دلالة إحصائية. 

One of the principal goals of population genetics is to understand the processes by which genetic variation within species (polymorphism) becomes converted into genetic differences between species (divergence). In this transformation, selective neutrality, near neutrality, and positive selection may each play a role, differing from one gene to the next. Synonymous nucleotide sites are often used as a uniform standard of comparison across genes on the grounds that synonymous sites are subject to relatively weak selective constraints and so may, to a first approximation, be regarded as neutral. Synonymous sites are also interdigitated with nonsynonymous sites and so are affected equally by genomic context and demographic factors. Hence a comparison of levels of polymorphism and divergence between synonymous sites and amino acid replacement sites in a gene is potentially informative about the magnitude of selective forces associated with amino acid replacements. We have analyzed 56 genes in which polymorphism data from D. simulans are compared with divergence from a reference strain of D. melanogaster. The framework of the analysis is Bayesian and assumes that the distribution of selective effects (Malthusian fitnesses) is Gaussian with a mean that differs for each gene. In such a model, the average scaled selection intensity (gamma = N(e)s) of amino acid replacements eligible to become polymorphic or fixed is -7.31, and the standard deviation of selective effects within each locus is 6.79 (assuming homoscedasticity across loci). For newly arising mutations of this type that occur in autosomal or X-linked genes, the average proportion of beneficial mutations is 19.7%. Among the amino acid polymorphisms in the sample, the expected average proportion of beneficial mutations is 47.7%, and among amino acid replacements that become fixed the average proportion of beneficial mutations is 94.3%. The average scaled selection intensity of fixed mutations is +5.1. The presence of positive selection is pervasive with the single exception of kl-5, a Y-linked fertility gene. We find no evidence that a significant fraction of fixed amino acid replacements is neutral or nearly neutral or that positive selection drives amino acid replacements at only a subset of the loci. These results are model dependent and we discuss possible modifications of the model that might allow more neutral and nearly neutral amino acid replacements to be fixed.

I examined mitochondrial ND2 sequences in species of tits (genus Parus) to determine whether substitutions were neutral or under selection. Haplotype trees in these species are shallow and geographically unstructured, which could be a signature of recent demographic expansion or purifying selection. McDonald-Kreitman tests revealed a pattern of excess replacement polymorphisms for closely related taxa. Replacement substitutions tended to be less common in the basal parts of haplotype trees, suggesting that they are selected against over evolutionary time. Thus, the pattern of selection is consistent with a model of mildly deleterious haplotypes. To investigate the significance of this selection, the ND2 gene was subdivided into surface and transmembrane portions, and synonymous-non-synonymous sites, and$F_{ST}-values$(the amount of variance distributed among populations) computed for each. Among sampling localities in P. major, both partitions gave similar estimates of$F_{ST}$, which is consistent with demographic expansion as the cause of the shallow trees. In P. montanus, two localities contained high percentages of individuals that had a single replacement substitution in the transmembrane portion of the gene, which inflated$F_{ST}-values$relative to the surface sites. Thus, the interpretation of the genetic differentiation of these two sites could be either geographical isolation or selection. Given that the sole substitution causing the high$F_{ST}-values$was a replacement one, selection is implicated. However, this substitution occurred in only 2 of 12 localities, revealing that overall the phylogeographic pattern was not biased by selection, once the cause of the two high pairwise$F_{ST}-comparisons$was recognized. Investigators should consider the source of significant genetic heterogeneity within species, to determine if the variation is likely caused by demographic isolation or selection. However, it seems unlikely that most phylogeographic analyses are invalidated by the effects of natural selection.

I examined mitochondrial ND2 sequences in species of tits (genus Parus) to determine whether substitutions were neutral or under selection. Haplotype trees in these species are shallow and geographically unstructured, which could be a signature of recent demographic expansion or purifying selection. McDonald-Kreitman tests revealed a pattern of excess replacement polymorphisms for closely related taxa. Replacement substitutions tended to be less common in the basal parts of haplotype trees, suggesting that they are selected against over evolutionary time. Thus, the pattern of selection is consistent with a model of mildly deleterious haplotypes. To investigate the significance of this selection, the ND2 gene was subdivided into surface and transmembrane portions, and synonymous-non-synonymous sites, and FST-values (the amount of variance distributed among populations) computed for each. Among sampling localities in P.major, both partitions gave similar estimates of FST, which is consistent with demographic expansion as the cause of the shallow trees. In P.montanus, two localities contained high percentages of individuals that had a single replacement substitution in the transmembrane portion of the gene, which inflated FST-values relative to the surface sites. Thus, the interpretation of the genetic differentiation of these two sites could be either geographical isolation or selection. Given that the sole substitution causing the high FST-values was a replacement one, selection is implicated. However, this substitution occurred in only 2 of 12 localities, revealing that overall the phylogeographic pattern was not biased by selection, once the cause of the two high pairwise FST-comparisons was recognized. Investigators should consider the source of significant genetic heterogeneity within species, to determine if the variation is likely caused by demographic isolation or selection. However, it seems unlikely that most phylogeographic analyses are invalidated by the effects of natural selection.

Even though, from Darwin onwards, interisland evolution has been a cornerstone of evolutionary theory it has not been possible to determine to what extent this geographic variation reflects the phylogeny (e.g., pattern of island colonization) or ecogenetic adaptation to different ecological conditions on each island. Using the morphology of western Canary Island lacertids (Gallotia galloti) as an example, a procedure is explored that gives a preliminary answer to this problem when there are a limited number of islands. The phylogenetic component (represented by patristic distances derived from 1005 mitochondrial DNA [mtDNA] base pairs) can be separated from two potential ecogenetic factors (environmental richness and climate) by partial Mantel tests. This reveals that, although these components interact, some characters are correlated primarily to biodiversity/paucity (e.g., size), others are correlated to wet and lush environments (e.g., dorsal pattern), and others are correlated primarily to the phylogeny (e.g., sexual leg markings). The former two correlations may be due to ecogenetic adaptation to current ecological conditions, wheras the latter reflects historical processes.

Assume a population is distributed in an infinite lattice of colonies in a migration and random-mating model in which all creatures are selectively equivalent. In one and two dimensions, the population tends to consolidate into larger and larger blocks, each of which is composed of the descendents of a single initial individual. The purpose here is to describe the variation of the size and shape of these blocks with time. Specifically, we obtain asymptotic results for (1) the expected number of individuals in, (2) the approximate radius of, and (3) the distribution of the individuals within a typical block for large time. These results depend on the dimension, and most extend to three or more dimensions.

Partisans hold unfavorable views of media they associate with the other party. They also avoid out-party news sources. We link these developments and argue that partisans assess out-party media based on negative and inaccurate stereotypes. This means cross-cutting exposure that challenges these misperceptions can improve assessments of out-party media. To support this argument, we use survey-linked web browsing data to show that the public has hostile views of out-party news sources they rarely encounter. We conduct three survey experiments that demonstrate cross-cutting exposure to nonpolitical or neutral political stories, forms of news widely available from online partisan sources, reduces oppositional media hostility. This explains how perceptions of rampant bias from out-party media coexist with more modest differences in the online content of major partisan news outlets. More broadly, we illustrate how negative misperceptions can sustain animus towards an out-group when people avoid encounters with them.

This paper examines the effects of our modern media environment on affective polarization. We conducted an experiment during the last month of the 2012 presidential election varying both the choice of media sources available about the major presidential candidates, and the tone of political advertisements presented to subjects. We posit that voters in a high-choice, ideologically-diverse media environment will exhibit greater affective polarization than those in a “mainstream” ideologically neutral environment. We also hypothesize that subjects who are exposed to negative rather than positive political advertisements will show increased affective polarization. We provide causal evidence that the combination of a high-choice ideologically diverse media environment and exposure to negative political ads, significantly increases affective polarization. We also find that both overall information search and selective exposure to information are influenced by our experimental manipulations, with the greatest amount of search, and the most biased search, conducted by Romney supporters in the Negative Ads, Diverse Media condition.

Recently, global warming is proving to be an increasing challenge for the sustainable human survival on planet earth. Worldwide, researchers are putting their efforts into controlling carbon emissions and have set the aim to achieve levels of overall carbon neutrality. Different industrial processes, especially oil refinery processes, release large amounts of low-carbon alkanes as gaseous byproducts directly into the air and pollute clean environments, which is one of the major reasons for sudden climate changes, ocean acidification, loss of biodiversity, and rising sea levels. The conversion of lighter alkanes, especially n-butane, into value-added chemicals can be beneficial for green economies and green environments. Presently, heterogeneous vanadium phosphorus oxide catalysts (VPOs) are considered potential candidates for n-butane selective oxidation toward maleic anhydride (MA). In this research, we developed a VPO catalyst with the assistance of copper-based ionic liquids (Cu-ILs), including [Bmim][OAc]–[Cu(OAc)2], [Bmim][Cl]–[CuCl], and [Bmim][Cl]–[CuCl2]. We observed significant improvement in the MA selectivity; meanwhile, the COx (CO and CO2) selectivity was decreased. Compared to the unpromoted catalyst (Blank-VPO), the Cu-IL-promoted catalyst, i.e., [Bmim][Cl]–[CuCl2]-VPO remarkably increased the MA selectivity (11%) and n-butane conversion (9.2%) and minimized the COx selectivity (11%). In addition to this the ratio of CO/CO2 has been reduced from 2.01 to 1.32. Therefore, this can be a helpful process for achieving carbon neutrality goals.

HIV is one of the fastest evolving organisms known. It evolves about 1 million times faster than its host, humans. Because HIV establishes chronic infections, with continuous evolution, its divergence within a single infected human surpasses the divergence of the entire humanoid history. Yet, it is still the same virus, infecting the same cell types and using the same replication machinery year after year. Hence, one would think that most mutations that HIV accumulates are neutral. But the picture is more complicated than that. HIV evolution is also a clear example of strong positive selection, that is, mutants have a survival advantage. How do these facts come together?