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The Neutral Theory Of Molecular Evolution
Abstract
Motoo Kimura, as founder of the neutral theory, is uniquely placed to write this book. He first proposed the theory in 1968 to explain the unexpectedly high rate of evolutionary change and very large amount of intraspecific variability at the molecular level that had been uncovered by new techniques in molecular biology. The theory - which asserts that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants - has caused controversy ever since. This book is the first comprehensive treatment of this subject and the author synthesises a wealth of material - ranging from a historical perspective, through recent molecular discoveries, to sophisticated mathematical arguments - all presented in a most lucid manner.
... The SNP A/S ratio was calculated over the longest open reading frame predicted for each transcript in each species. In order to identify putative positively selected genes (PSGs), we first retained those with A/S values exceeding 1, the threshold usually considered as evidence for positive selection (Kimura, 1983), and applied a Characteristics of the seven conifer species analyzed in this study. The approximate natural range of each species is represented in green besides its associated tree silhouette, and populations sampled are mapped as red dots. ...
... After these adjustments, SNP diversity was estimated for Detection of genes with high SNP A/S ratios and relationship with overall SNP diversity Synonymous and nonsynonymous sites were identified and rates of synonymous (S) and nonsynonymous SNPs (A) were estimated to calculate the gene SNP A/S ratio (see Methods). A ratio above 1 is indicative of positive or balancing selection related to adaptive evolution (Kimura, 1983;Fay et al., 2001). Ratios above 1 were found in around 19% and 25% of genes depending on the species (Supplementary Table S8.2). ...
... However, in relation to the neutral theory of evolution which assumes that much of the standing genetic variation derives from neutral or nearly neutral mutations (e.g. Kimura, 1983;Ohta, 1992), part of the observed interspecific differences in molecular genetic diversity likely relates to historical effective population sizes (Bousquet et al., 1992). Indeed, the minimum historical population size (Ne) of Picea glauca and Picea mariana, the most diverse species group in this study, was estimated at~1 00,000 or more individuals (Bouilléand Bousquet, 2005;Chen et al., 2010), while that of Pinus strobus, which belongs to the low diversity group, has been estimated to be an order of magnitude lower (5000 to 10,000 individuals; Zinck and Rajora, 2016). ...
Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are archaic species of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species (118 individuals from 67 populations) populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. The analysis of sequence homology also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of ~350 Mya between conifers and Angiosperms, we also uncovered a set of 17 key genes presumably under positive selection in both lineages.
... The threshold at which mutations behave as though neutral equivalent depends directly on the effective population size. So long as 4N e s > 1, selection rules the day to weed out detrimental variation [1,2] and cause beneficial alleles to spread efficiently in deterministic selective sweeps [3,4,5,6] (where N e is the effective population size and s is the selection coefficient). When 4N e s < 1, forces of drift can allow mildly detrimental variation to spread under stochastic fluctuations [1,2]. ...
... So long as 4N e s > 1, selection rules the day to weed out detrimental variation [1,2] and cause beneficial alleles to spread efficiently in deterministic selective sweeps [3,4,5,6] (where N e is the effective population size and s is the selection coefficient). When 4N e s < 1, forces of drift can allow mildly detrimental variation to spread under stochastic fluctuations [1,2]. Hence, the threshold of variation that will be tolerated as nearly neutral polymorphism is expected to shift when population sizes drop [2]. ...
... Nearly neutral models were initially envisioned with an eye toward single basepair changes in DNA [1,2], but modern evolutionary genomics has expanded the predictions to encompass new expectations for mutations that modify larger segments of DNA at once. Gene duplications are expected on average to be neutral or detrimental resulting in their accumulation in smaller populations [9,10]. ...
Nearly neutral theory predicts that evolutionary processes will differ in small populations compared to large populations, a key point of concern for endangered species. The nearly-neutral threshold, the span of neutral variation, and the adaptive potential from new mutations all differ depending on . To determine how genomes respond in small populations, we have created a reference genome for a US federally endangered IUCN Red List freshwater mussel, \emph{Elliptio spinosa}, and compare it to genetic variation for a common and successful relative, \emph{Elliptio crassidens}. We find higher rates of background duplication rates in \emph{E. spinosa} consistent with proposed theories of duplicate gene accumulation according to nearly-neutral processes. Along with these changes we observe fewer cases of adaptive gene family amplification in this endangered species. However, TE content is not consistent with nearly-neutral theory. We observe substantially less recent TE proliferation in the endangered species with over 500 Mb of newly copied TEs in \emph{Elliptio crassidens}. These results suggest a more complex interplay between TEs and duplicate genes than previously proposed for small populations. They further suggest that TEs and duplications require greater attention in surveys of genomic health for endangered species.
... In small populations, genetic drift can help populations traverse the valleys between a low peak and a higher peak, raising the question of whether small populations may attain higher peaks 1,94 . We simulated adaptive walks with an approach pioneered by Kimura 88,95 that allows us to calculate the fixation probability of any mutation as a function of population size and the selection coefficient s, i.e., the difference in repression strength between neighboring genotypes 88,96 . We used this approach to simulate adaptive evolution in populations with 10 8 , 10 5 and 10 2 individuals, and found that 20%, 25%, 20% of walks attained high peaks, respectively ( Supplementary Fig. S19). ...
... Both types of adaptive walks ignore the possibility of genetic drift, which allows mutations with no or negative fitness effects to become fixed in a population. A well-established model for random walks that permit genetic drift uses fixation probabilities computed by Kimura 88,95,96 i.e., f ij = (1-e −2s )/(1-e −2Ns ), where f ij is the probability of fixing mutation j in the background of genotype i, N is the effective population size, and s is the selection coefficient, i.e. the difference in repression strengths between genotypes i and j 88,96 . For a given pair of genotypes, the only parameter of this model is the effective population size N, for which we explored values of N = 10 8 , N = 10 5 and N = 10 2 . ...
... Both types of adaptive walks ignore the possibility of genetic drift, which allows mutations with no or negative fitness effects to become fixed in a population. A well-established model for random walks that permit genetic drift uses fixation probabilities computed by Kimura 88,95,96 i.e., f ij = (1-e −2s )/(1-e −2Ns ), where f ij is the probability of fixing mutation j in the background of genotype i, N is the effective population size, and s is the selection coefficient, i.e. the difference in repression strengths between genotypes i and j 88,96 . For a given pair of genotypes, the only parameter of this model is the effective population size N, for which we explored values of N = 10 8 , N = 10 5 and N = 10 2 . ...
Transcription factor binding sites (TFBSs) are important sources of evolutionary innovations. Understanding how evolution navigates the sequence space of such sites can be achieved by mapping TFBS adaptive landscapes. In such a landscape, an individual location corresponds to a TFBS bound by a transcription factor. The elevation at that location corresponds to the strength of transcriptional regulation conveyed by the sequence. Here, we develop an in vivo massively parallel reporter assay to map the landscape of bacterial TFBSs. We apply this assay to the TetR repressor, for which few TFBSs are known. We quantify the strength of transcriptional repression for 17,765 TFBSs and show that the resulting landscape is highly rugged, with 2092 peaks. Only a few peaks convey stronger repression than the wild type. Non-additive (epistatic) interactions between mutations are frequent. Despite these hallmarks of ruggedness, most high peaks are evolutionarily accessible. They have large basins of attraction and are reached by around 20% of populations evolving on the landscape. Which high peak is reached during evolution is unpredictable and contingent on the mutational path taken. This in-depth analysis of a prokaryotic gene regulator reveals a landscape that is navigable but much more rugged than the landscapes of eukaryotic regulators.
... In this context, understanding the combined influence of genetic drift, mutations and natural selection on the dynamics of the allele frequency is clearly an issue of fundamental importance in evolutionary biology (Crow and Kimura (1970); Kimura and Ohta (1971); Kimura (1983); Ewens (2000); Gillespie (2004)). A large body of studies dedicated to gene frequency is based on the diffusion approximation [see, e.g., (Crow and Kimura (1970); Ewens (2000))]. ...
... A situation of particular relevance in population genetics arises when the selection intensity s is weak and the mutation rate v is much weaker, i.e. 0 < v ≪ s ≪ 1, where v is several order of magnitudes smaller than s (Ewens (2000); Crow and Kimura (1970); Kimura (1983); Kimura and Ohta (1971)) 4 . The MFT of this model where the mutant allele A ′ is either dominant, recessive or semi-dominant was treated both analytically and numerically within the diffusion approach in (Kimura (1980)), while the non-dominant case was considered in (Li and Nei (1977)). ...
... While it is generally a very demanding task to extract accurate and useful information from Eq. (3), the latter can be investigated within various approaches. One very popular and insightful approximation is provided by the diffusion theory (see, e.g., Crow and Kimura (1970); Kimura (1983); Ewens (2000)), that is based on a Taylor-expansion in N −1 ≪ 1 of the master equation leading to a Fokker-Planck or Kolomogorov equation (KE) (Gardiner (2002); van Kampen (1992); Risken (1989)). For the problem at hand, the backward KE associated with the birth-death process (3) for the probability density P(x, t) ≡ N P n (t), see below, is given by ...
The mean fixation time of a deleterious mutant allele is studied beyond the diffusion approximation. As in Kimura's classical work [M. Kimura, Proc. Natl. Acad. Sci. U.S.A. Vol.77, 522 (1980)], that was motivated by the problem of fixation in the presence of amorphic or hypermorphic mutations, we consider a diallelic model at a single locus comprising a wild-type A and a mutant allele A' produced irreversibly from A at small uniform rate v. The relative fitnesses of the mutant homozygotes A'A', mutant heterozygotes A'A and wild-type homozygotes AA are 1-s, 1-h and 1, respectively, where it is assumed that v<< s. Here, we adopt an approach based on the direct treatment of the underlying Markov chain (birth-death process) obeyed by the allele frequency (whose dynamics is prescribed by the Moran model), which allows to accurately account for the effects of large fluctuations. After a general description of the theory, we focus on the case of a deleterious mutant allele (i.e. s>0) and discuss three situations: when the mutant is (i) completely dominant (s=h); (ii) completely recessive (h=0), and (iii) semi-dominant (h=s/2). Our theoretical predictions for the mean fixation time and the quasi-stationary distribution of the mutant population in the coexistence state, are shown to be in excellent agreement with numerical simulations. Furthermore, when s is finite, we demonstrate that our results are superior to those of the diffusion theory that is shown to be an accurate approximation only when N_e s^2 << 1, where N_e is the effective population size.
... In this paper we have evaluated the fitness and fitness related traits of white eye mutant and discussed their implication to understanding the evolutionary concept of 'the neutral theory of molecular evolution' (Kimura, 1968(Kimura, , 1983(Kimura, , 1991) that suggests no affect/effect of mutations on fitness of the organism bearing them. We have assessed the effect of white eye mutation on important life history traits namely, pre-adult development time, egg to adult viability, adult weight, lipid content in adult fly, adult longevity, and life time egg production. ...
... Our results show that white eye mutation does not significantly affect the fitness of the organisms, yet has the potential to alter the course of evolution through drift. This is the first study that provides experimental support to neutral theory of molecular evolution (Kimura, 1968(Kimura, , 1983(Kimura, , 1991. ...
White eye mutation in Drosophila melanogaster resulted in significant reduction in pre-adult development time. However, this reduction in pre-adult development time was accompanied by non-significant reduction in adult dry weight, lifetime oviposition, and longevity lending a fortuitous support to the 'neutral theory of molecular evolution'.
... Kimura tested this remarkable prediction by comparing the rate of amino-acid substitutions in the coding sequences for proteins during the evolutionary history of different vertebrate species, finding evidence that this rate is indeed conserved [28,29]. ...
... The concept that variation within a population can be explained by mutation-drift balance played a central part in a stochastic, view of evolution that emerged in the latter half of the 20th century, pioneered by the Japanese biologist Motoo Kimura (1924Kimura ( -1994. Kimura argued that at a molecular level, i.e. at the level of molecular changes in DNA or protein sequences, evolution is mostly driven by neutral genetic drift rather than by selection [28,29]. Modern molecular techniques allow us to sequence genomes of multiple individuals from the same species rapidly and affordably. ...
Population genetics lies at the heart of evolutionary theory. This topic forms part of many biological science curricula but is rarely taught to physics students. Since physicists are becoming increasingly interested in biological evolution, we aim to provide a brief introduction to population genetics, written for physicists. We start with two background chapters: chapter 1 provides a brief historical introduction to the topic, while chapter 2 provides some essential biological background. We begin our main content with chapter 3 which discusses the key concepts behind Darwinian natural selection and Mendelian inheritance. Chapter 4 covers the basics of how variation is maintained in populations, while chapter 5 discusses mutation and selection. In chapter 6 we discuss stochastic effects in population genetics using the Wright-Fisher model as our example, and finally we offer concluding thoughts and references to textbooks in chapter 7.
... We then show that several statistical properties of the system have been stable for the past few years, including the number of active cryptocurrencies, the market share distribution, the stability of the ranking, and the birth and death rate of new cryptocurrencies. We adopt an "ecological" perspective on the system of cryptocurrencies and notice that several observed distributions are well described by the so-called "neutral model" of evolution [33,34], which also captures the decrease of Bitcoin market share. ...
... In order to account for the empirical properties of the dynamics of cryptocurrencies we have discussed above, we adopt the view of a "cryptocurrency ecology" and consider the neutral model of evolution, a prototypical model in population-genetics and ecology [33,34]. ...
The cryptocurrency market surpassed the barrier of \$100 billion market capitalization in June 2017, after months of steady growth. Despite its increasing relevance in the financial world, however, a comprehensive analysis of the whole system is still lacking, as most studies have focused exclusively on the behaviour of one (Bitcoin) or few cryptocurrencies. Here, we consider the history of the entire market and analyse the behaviour of 1,469 cryptocurrencies introduced between April 2013 and June 2017. We reveal that, while new cryptocurrencies appear and disappear continuously and their market capitalization is increasing (super-)exponentially, several statistical properties of the market have been stable for years. These include the number of active cryptocurrencies, the market share distribution and the turnover of cryptocurrencies. Adopting an ecological perspective, we show that the so-called neutral model of evolution is able to reproduce a number of key empirical observations, despite its simplicity and the assumption of no selective advantage of one cryptocurrency over another. Our results shed light on the properties of the cryptocurrency market and establish a first formal link between ecological modelling and the study of this growing system. We anticipate they will spark further research in this direction.
... Picos de mutação podem atuar como um motor de rápida adaptação, onde mutações mitocondriais desempenham um papel chave na evolução humana [13] [16]. No entanto, o acúmulo de mutações deletérias no genoma humano, conforme observado em vários bancos de dados genéticos, levanta preocupações sobre a degeneração genética. ...
A discrepância entre as taxas de acúmulo de mutações mitocondriais estimadas a partir de dados antigos e modernos representa um enigma na biologia evolutiva. Este artigo propõe que eventos catastróficos, particularmente aqueles associados à radiação intensa e estresse ambiental severo, induzem picos de mutação que explicam essa discrepância. Além disso, explora as implicações desse(s) pico(s) de mutação para a degeneração humana e a acumulação de mutações deletérias no genoma humano. A discrepância nas taxas de mutação pode ser interpretada à luz da teoria de que eventos catastróficos induzem picos de mutações. A radiação, como um agente mutagênico, pode explicar o aumento observado nas mutações modernas em comparação com as antigas. A seleção natural pode atuar sobre essas mutações, favorecendo aquelas que conferem vantagens adaptativas em ambientes alterados [1]. No entanto, o acúmulo de mutações deletérias também pode levar à degeneração genética e ao aumento da suscetibilidade a doenças. Os dados sugerem que um pico de mutações durante catástrofe em torno de 5115 anos atrás, é uma explicação viável para a discrepância nas taxas de acúmulo de mutações mitocondriais histórica versus atuais. A compreensão desses mecanismos é crucial para a biologia evolutiva do tipo degenerativa e para a interpretação da diversidade genética nas populações modernas, bem como para entender como reverter a perda de longevidade e aumento exponencial de doenças na humanidade ao editar genes mutados priorizando corrigir genes usando modelos de genes de nossos ancestrais, recuperando inclusive sistemas de reparo. Introdução As mutações mitocondriais desempenham um papel fundamental na sub especiação do tipo degenerativa, diversidade genética e morfológica e adaptação das populações. No entanto, a disparidade entre as taxas de mutação observadas em estudos modernos e as estimativas de taxas derivadas de comparação de acúmulo de mutações no DNAmt de amostras antigas com atuais, levanta questões significativas. As taxas modernas variam de 1 a 2 mutações por milhão de pares de bases por geração, enquanto as taxas estimadas em amostras antigas , que variam de 200 a 300 mutações acumuladas [2] quando comparadas as mutações atuais (~19k)[3] gera uma taxa de ~24 mutações mitocondriais por geração. Essa discrepância sugere que houve um ou vários picos de mutação no intervalo entre hoje e 5 mil anos atrás, justificando assim este aumento exponencial, o que poderia ocorrer se houvesse um evento catastrófico repleto de radiações ionizantes seguido de efeito gargalo sob muitas mudanças ambientais abruptas.
... These traits are also observed in large Bovids and are associated with an increase in size and mass (Figs. 2, 4). Nonetheless, neutral evolution can take place on structures free of physical and mechanical constraints, and provide essential information for phylogeny 47,50 . Bovidae tend to display larger proximal trochlear ridges than other Pecora (Fig. 5), while Moschidae have a more prominent posterior process and their LRPT exhibits a peculiar morphology with its central part wider laterally (Figs. ...
The astragalus is a hinged bony organ common to many tetrapods. Several factors, including allometry, phylogeny, and environment, constrain its morphology. Due to the underlying risk of these factors being confounding, previous works have frequently highlighted the difficulty in discerning the specific influence of each factor. Here, we conducted allometric and size-adjusted clade and ecomorphological analyses to assess the contribution of each of these three parameters to the morphological variation of the astragalus in ruminant artiodactyls. 3D geometric morphometric analyses confirm the astragalus’ highly integrated structure and multifactorial morphological responses. Sturdier astragali are correlated with heavier bodies. Bovids tend to display larger proximal trochlear ridges, and moschids show a prominent posterior process. The degree of development of areas where joints and ligaments intersect reflects the degree of freedom of the ankle and the locomotion type. This study provides new perspectives on the evolution of ruminants and their interactions with their environment.
... Gaps were edited in the BioEdit program [16]. The evolutionary distances were calculated using the Kimura two-parameter model [17]. The phylogenetic trees were constructed based on 16S rRNA gene sequences using the neighbour-joining (NJ) [18], and the maximum-likelihood (ML) algorithms in the mega 7.0 program [19], with bootstrap values based on 1000 replications. ...
A Gram-stain-negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-64 T , was isolated from the rhizosphere of rice. The colonies were observed to be creamy white-coloured, smooth, spherical and 0.5–1.1 mm in diameter when grown on Reasoner’s 2A agar medium for 2 days. Strain MAHUQ-64 T was able to grow at 10–40 °C, at pH 5.0–9.5 and in the presence of 0–2.0% NaCl (w/v). The strain was positive for both catalase and oxidase tests. The strain was positive for hydrolysis of l -tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Vogesella and is closely related to Vogesella oryzae L3B39 T (98.6% sequence similarity) and Vogesella facilis TTM-24 T (98.2%). The novel strain MAHUQ-64 T has a draft genome size of 3 827 146 bp (22 contigs), annotated with 3612 protein-coding genes, 74 tRNA and 4 rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-64 T and its closest member V. oryzae L3B39 T were 86.5 and 33.4%, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAHUQ-64 T . The genomic DNA G+C content was determined to be 63.4 mol%. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as summed feature 3 (comprising C 16 : 1 ω 7 c and/or C 16 : 1 ω 6 c ) and C 16 : 0 . Based on dDDH, ANI value, genotypic analysis and chemotaxonomic and physiological data, strain MAHUQ-64 T represents a novel species within the genus Vogesella , for which the name Vogesella oryzagri sp. nov. is proposed, with MAHUQ-64 T (=KACC 22245 T =CGMCC 1.19000 T ) as the type strain.
... Ka and Ks nucleotide substitution patterns were very important indicators in gene evolution [31]. The selection pressure of genes was reflected by the ratio of Ka/ Ks. ...
Background
Poplars are important woody plants, which are widely distributed in the forests from the subtropics to the north of the Northern Hemisphere. Poplars have high ecological and economic value. However, there are frequent interspecific and intraspecific hybrids in Populus, resulting in a large number of intermediate taxa, which makes the morphological identification of Populus very challenging. Plastid genome is an important tool to study the evolutionary relationship of plants. Therefore, comparison and phylogenetic analysis were carried out based on the population chloroplast genomes of 34 individuals from 7 taxa.
Results
In this study, seven newly assembled and annotated chloroplast genomes of Populus were reported. They all had typical quadripartite structures with the same GC content (37.6%), but there were differences within the population, and the genome size ranged from 155,736 bp to 156,812 bp. In all Populus species, 134 genes were identified, including 88 protein coding genes (PCGs), 37 tRNA and 8 rRNA genes. The gene sequences alignment of different taxa showed that the gene sequences and content were relatively conservative, there was no gene rearrangement, and only 3 highly variable regions (psbZ-trnG, ndhC-trnV and trnN-trnR) were identified, which can be used as molecular markers. Most PCGs had high codon usage bias and 3 positive selection genes (rps7, rps12 and rpl16) have been identified. The analysis of population genetic structure and phylogeny showed that the chloroplast genomes supported that Populus was a monophyletic taxon, which could be divided into four sections (Abaso, Turanga, Populus and ATL (Aigeiros, Tacamahaca and Leucoides)). Among them, P. dafengensis, P. butuoensis and P. szechuanica had the closest genetic relationship, P. gonggaensis and P. cathayana had the closest genetic relationship, it was speculated that the taxa of Sect. Tacamahaca may be the main female parent of the three new taxa from Sect. Leucoides.
Conclusion
In general, this study provides valuable insights for new species identification, phylogenetic relationships, breeding and resource development, and genetic diversity of Populus.
... Hence, the relaxation of natural selection dominates genome evolution in the common ancestor of Triplophysa. The consequence of relaxed selection is that the genome will accumulate more slightly deleterious mutations [29][30][31]. ...
High-altitude environments are inhospitable, but Triplophysa, the largest taxon among the three major fish groups in the Qinghai-Tibetan Plateau (QTP), is an exception. However, the evolutionary profiling of the common ancestor and its contribution to the adaptation of existing QTP native species is unclear.We researched the comparative genomics of Triplophysa species and found that the genome-wide genes of Triplophysa and its ancestry have the characteristics of rapid evolution.Moreover, the rapid evolution of the ancestral genes was caused by relaxed selection. Natural selection analysis showed that more ancestral relaxed selection genes were under strongly purifying selection and showed higher expression in QTP endemic Triplophysa species.The change in natural selection might be associated with the adaptation to QTP. It should be noted that SPT5 homolog, DSIF elongation factor subunit (supt5h) experienced relaxed selection in common ancestral populations of Triplophysa but under purifying selection in extant species, which might be related to hypoxia adaptation of QTP. In summary, the extant species in different environments were used to infer the evolutionary profile of the common ancestor and to identify candidate genes based on changes in natural selection. Our work might provide new clues for understanding adaptation to extreme environments.
... With this regard, it is essential to examine key evolutionary pressures such as "neutral selection", "positive selection", and "purifying selection". Neutral selection involves no impact on fitness, positive selection favors advantageous mutations, and purifying selection eliminates deleterious variants to maintain the functional integrity of genes [61,62]. Detection of these selective pressures may offer insights into the genetic diversification and functional specialization of MADS-box genes in the genus Oryza. ...
To investigate the evolutionary trajectory during the recent speciation of AA-genome Oryza species, we conducted a comprehensive analysis of the MADS-box gene family across eight Oryza species. We identified 1093 MADS-box genes in total and systematically examined their evolutionary history, gene family expansion, and expression divergence. Our results revealed that extensive lineage-specific expansions occurred in AA-genome Oryza species, which were primarily generated by proximal and tandem duplications, with a particularly notable episode in Type-I genes. Despite the significant expansion, Type-I genes were generally expressed at low levels or not expressed across various organs. In contrast, the expansion of Type-II genes was primarily observed in the AG, AGL12, SOC1, GGM13, and MIKC* subfamilies, which exhibited high levels of expression in reproductive organs such as panicles and stigmas. Additionally, we found species-specific gene expression in the two out-crossing wild rice species, Oryza rufipogon and Oryza longistaminata. Notably, a unique MADS-box gene in O. longistaminata exhibited high expression levels in rhizomes and stems, which may be associated with the species’ distinctive rhizomatous growth habit.
... Climate variables in the RDA model accounted for ∼0.63% of the genetic variation, identifying 482 climate-associated RDA loci, with temperature annual range (bio7) and precipitation of the wettest month (bio13) as the main climate drivers of the detected genetic variation (Fig. 2). Although the observed proportion of genetic variation explained by climate variables was relatively low, it aligns with expectations under the neutral theory of molecular evolution (Kimura 1983). Therefore, only a small subset of loci are expected to show significant relationships with environmental variables. ...
Orphan crops serve as essential resources for both nutrition and income in local communities and offer potential solutions to the challenges of food security and climate vulnerability. Tef [Eragrostis tef (Zucc.)], a small-grained allotetraploid, C4 cereal mainly cultivated in Ethiopia, stands out for its adaptability to marginal conditions and high nutritional value, which holds both local and global promise. Despite its significance, tef is considered an orphan crop due to limited genetic improvement efforts, reliance on subsistence farming, and its nutritional, economic, and cultural importance. Although pre-Semitic inhabitants of Ethiopia have cultivated tef for millennia (4000–1000 BCE), the genetic and environmental drivers of local adaptation remain poorly understood. To address this, we resequenced a diverse collection of traditional tef varieties to investigate their genetic structure and identify genomic regions under environmental selection using redundancy analysis, complemented by differentiation-based methods. We identified 145 loci associated with abiotic environmental factors, with minimal geographic influence observed in the genetic structure of the sample population. Overall, this work contributes to the broader understanding of local adaptation and its genetic basis in tef, providing insights that support efforts to develop elite germplasms with improved environmental resilience.
... The number of generations during which genetic degeneration has been evolving in each stratum can be estimated using Y-X or Z-W divergence, given enough genes that retain Y-or W-linked sequences (termed gametolog pairs). Synonymous mutations, or mutations at fourfold degenerate sites, are ideal, as they evolve similarly to neutral variants, for which divergence accumulates linearly over generations 16 . If close relatives are available, inter-species divergence can be used to correct for possible rate differences between strata. ...
A recent paper found that the sex chromosomes of the crested ibis have more gametolog pairs than many other birds. This Comment discusses that this finding suggets that WZ recombination stopped independently in the sex chromosomes in different bird lineages.
... This implies a mutational bias toward the low noise allele in that case. As always, it is critical to establish the baseline mutational expectation before ascribing a selective effect [Kimura 1983]. ...
Noise is intrinsic to information transmission, and information transmission is intrinsic to life. Critically, while biological noise is random, its amount is in part genetically determined. Here, we explore the population genetics of alleles that heritably influence the amount of noise in any biological mechanism. We argue that biological noise is a double-edged sword: almost always inducing deleterious phenotypes but also occasionally yielding high fitness outcomes. We further suggest that this implies the existence of an equilibrium amount of noise, at which the advantage of producing additional, rare beneficial phenotypes is balanced by the cost of producing the vastly more common deleterious phenotypes. The location of this equilibrium will reflect the rate at which its environment is changing, the persistence of association between noise-modifying alleles and the phenotypic perturbations they induce, the mode of selection, and the population size. The population genetics of alleles that heritable change mean trait values have been established for nearly a century, but to our knowledge, this is the first general treatment of the evolution of heritable changes in the statistical distribution around that mean. Our framework generalizes modifier theory in the sense used by Altenberg, Feldman and others, and resolves teleological criticisms of the hypothesis that evolvability can evolve via natural selection. We conclude with an outline of open theoretical and empirical questions posed by our framework.
... Phylogenetic trees were reconstructed using the neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) methods using the software Seaview version 5.0.5 (Gouy et al., 2010). The evolutionary distances for the NJ, MP and ML methods were respectively calculated using the Kimura two-parameters, the Dnapars and the GTR models (Kimura, 1983;Saitou and Nei, 1987;Dereeper et al., 2008;Gouy et al., 2010;Guindon et al., 2010). The robustness of the inferred topology was assessed by bootstrap analyses based on 1000 replications. ...
A novel bacterial strain, HK31-GT, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland)
and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along
with phylogenomic position indicated that the novel strain belongs to the genus Phenylobacterium. Cells are
motile Gram-negative thin rods. Physiological characterization showed that strain HK31-GT is a mesophilic
bacterium able to grow from 10 to 30 ◦C, at pH values between 6 and 8 and at NaCl concentrations between
0 and 0.5 %. Optimal growth was observed without sodium chloride at 25 ◦C and pH 6. Strain HK31-GT is
chemoorganoheterotroph and its major saturated fatty acids are C18:1ω7c, C16:1ω6c and C16:0, the predominant
quinone is Q-10 and the major polar lipid is phosphatidylglycerol. The new strain also possesses the capacity to
use ferrous iron (Fe(II)) as the sole energy source and can also be considered as a chemolithoautotrophic
microorganism. The overall genome of strain HK31-GT was estimated to be 4.46 Mbp in size with a DNA G + C
content of 67.95 %. Genes involved in iron metabolism were identified, but no genes typically involved in Fe(II)-
oxidation were found. According to the overall genome relatedness indices (OGRI) values, six MAGs from
groundwater have been assigned to the same species as the new strain HK31-GT. Furthermore, OGRI values
between the genome of strain HK31-GT and the genomes of its closest relatives are below the species delineation
threshold. Therefore, given the polyphasic approach used, strain HK31-GT represents a novel species of the genus
Phenylobacterium, for which the name Phenylobacterium ferrooxidans sp. nov. is proposed. The type strain is HK31-
GT (DSM 116432T = UBOCC-M-3429T = LMG 33376T).
... Comparative genomics has been traditionally used to annotate functional genomic sequences, and is highly dependent on the principles described by Kimura (1983) 34 . Said theory does not undermine Darwinian selection, but highlights another important aspect of molecular evolution, where most silent changes in the DNA and protein sequences are not adaptive in nature but are in fact the result of random drift of neutral or nearly neutral mutants. ...
Tuberculosis remains a burden to this day, due to the rise of multi and extensively drug-resistant bacterial strains. The genome of Mycobacterium tuberculosis (Mtb) strain H37Rv underwent an annotation process that excluded small Open Reading Frames (smORFs), which encode a class of peptides and small proteins collectively known as microproteins. As a result, there is an overlooked part of its proteome that is a rich source of potentially essential, druggable molecular targets. Here, we employed our recently developed proteogenomics pipeline to identify novel microproteins encoded by non-canonical smORFs in the genome of Mtb using hundreds of mass spectrometry experiments in a large-scale approach. We found protein evidence for hundreds of unannotated microproteins and identified smORFs essential for bacterial survival and involved in bacterial growth and virulence. Moreover, many smORFs are co-expressed and share operons with a myriad of biologically relevant genes and play a role in antibiotic response. Together, our data presents a resource of unknown genes that play a role in the success of Mtb as a widespread pathogen.
Supplementary Information
The online version contains supplementary material available at 10.1038/s41598-024-82465-w.
... Both neutral evolution (105) and positive selection (106)(107)(108) are known to drive sequence divergence following gene duplication. What drove the divergence of ancestral Sfx following its duplication? ...
Conjugative plasmids are widespread among prokaryotes, highlighting their evolutionary success. Conjugation systems on most natural plasmids are repressed by default. The negative regulation of F-plasmid conjugation is partially mediated by the chromosomal nucleoid-structuring protein (H-NS). Recent bioinformatic analyses have revealed that plasmid-encoded H-NS homologs are widespread and exhibit high sequence diversity. However, the functional roles of most of these homologs and the selective forces driving their phylogenetic diversification remain unclear. In this study, we characterized the functionality and evolution of Sfx, a H-NS homolog encoded by the model IncX2 plasmid R6K. We demonstrate that Sfx, but not chromosomal H-NS, can repress R6K conjugation. Notably, we find evidence of positive selection acting on the ancestral Sfx lineage. Positively selected sites are located in the dimerization, oligomerization, and DNA-binding interfaces, many of which contribute to R6K repression activity—indicating that adaptive evolution drove the functional divergence of Sfx. We additionally show that Sfx can physically interact with various chromosomally encoded proteins, including H-NS, StpA, and Hha. Hha enhances the ability of Sfx to regulate R6K conjugation, suggesting that Sfx retained functionally important interactions with chromosomal silencing proteins. Surprisingly, the loss of Sfx does not negatively affect the stability or dissemination of R6K in laboratory conditions, reflecting the complexity of selective pressures favoring conjugation repression. Overall, our study sheds light on the functional and evolutionary divergence of a plasmid-borne H-NS-like protein, highlighting how these loosely specific DNA-binding proteins evolved to specifically regulate different plasmid functions.
IMPORTANCE
Conjugative plasmids play a crucial role in spreading antimicrobial resistance and virulence genes. Most natural conjugative plasmids conjugate only under specific conditions. Therefore, studying the molecular mechanisms underlying conjugation regulation is essential for understanding antimicrobial resistance and pathogen evolution. In this study, we characterized the conjugation regulation of the model IncX plasmid R6K. We discovered that Sfx, a H-NS homolog carried by the plasmid, represses conjugation. Molecular evolutionary analyses combined with gain-of-function experiments indicate that positive selection underlies the conjugation repression activity of Sfx. Additionally, we demonstrate that the loss of Sfx does not adversely affect R6K maintenance under laboratory conditions, suggesting additional selective forces favoring Sfx carriage. Overall, this work underscores the impact of protein diversification on plasmid biology, enhancing our understanding of how molecular evolution affects broader plasmid ecology.
... These fitnesses determine the replication or death rates of each individual. This selective advantage leads to a dynamical competition in which selection dominates for large populations, while random genetic drift [7,8] occurs for small populations or weak selection. ...
The evolution of two species with different fitness is investigated on degree-heterogeneous graphs. The population evolves either by one individual dying and being replaced by the offspring of a random neighbor (voter model (VM) dynamics) or by an individual giving birth to an offspring that takes over a random neighbor node (invasion process (IP) dynamics). The fixation probability for one species to take over a population of N individuals depends crucially on the dynamics and on the local environment. Starting with a single fitter mutant at a node of degree k, the fixation probability is proportional to k for VM dynamics and to 1/k for IP dynamics.
... Under mild demographic assumptions (namely: no selection [18], random mating, constant population size, and uniform recombination rate [3]), the joint distribution of the mutations in a population is given by a process known as the coalescent with recombination [19]. Briefly, the coalescent with recombination is given as follows: the ancestry of N genetic sequences in a population is formed by tracing their lineage backwards in time and placing coalescent events with rate 2 Ne k(ℓ) ! 2 , where k(ℓ) is the number of distinct lineages existing at time ℓ, and N e is the effective population size [3]. ...
Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self transitions. We develop a new nonparametric model of genetic sequence data, based on the hierarchical Dirichlet process, which supports these self transitions and nonhomogeneity. Our model provides a parameterization of the genetic process that is more parsimonious than other more general nonparametric models which have previously been applied to population genetics. We provide truncation-free MCMC inference for our model using a new auxiliary sampling scheme for Bayesian nonparametric HMMs. In a series of experiments on male X chromosome data from the Thousand Genomes Project and also on data simulated from a population bottleneck we show the benefits of our model over the popular finite model fastPHASE, which can itself be seen as a parametric truncation of our model. We find that the number of HMM states found by our model is correlated with the time to the most recent common ancestor in population bottlenecks. This work demonstrates the flexibility of Bayesian nonparametrics applied to large and complex genetic data.
... Natural selection is a process through which organisms that possess advantageous adaptations to their environment are more likely to survive and reproduce, whereas those that are less welladapted face a higher risk of elimination. The comparison of nonsynonymous (d N ) to synonymous (d S ) substitution ratios has emerged as a valuable method for quantifying the effects of natural selection on molecular evolution (Kimura 1983;Yang et al. 2000); namely, the ω value, serves as an indicator of the molecular evolutionary rate. Specifically, values of ω < 1, = 1, and > 1 are indicative of purifying selection, neutral evolution, and positive selection, respectively. ...
Birds exhibit remarkable variations in body size, making them an ideal group for the study of adaptive evolution. However, the genetic mechanisms underlying body size evolution in avian species remain inadequately understood. This study investigates the evolutionary patterns of avian body size by analyzing 15 body‐size‐related genes, including GHSR , IGF2BP1 , and IGFBP7 from the growth hormone/insulin‐like growth factor axis, EIF2AK3 , GALNS , NCAPG , PLOD1 , and PLAG1 associated with tall stature, and ACAN , OBSL1 , and GRB10 associated with short stature, four genes previously reported in avian species: ATP11A , PLXDC2 , TNS3 , and TUBGCP3 . The results indicate significant adaptive evolution of body size‐related genes across different avian lineages. Notably, in the IGF2BP1 gene, a significant positive correlation was observed between the evolutionary rate and body size, suggesting that larger bird species exhibit higher evolutionary rates of the IGF2BP1 gene. Furthermore, the IGFBP7 and PLXDC2 genes demonstrated accelerated evolution in large‐ and medium‐sized birds, respectively, indicating distinct evolutionary patterns for these genes among birds of different sizes. The branch‐site model analysis identified numerous positively selected sites, primarily concentrated near functional domains, thereby reinforcing the critical role of these genes in body size evolution. Interestingly, extensive convergent evolution was detected in lineages with larger body sizes. This study elucidates the genetic basis of avian body size evolution for the first time, identifying adaptive evolutionary patterns of body size‐related genes across birds of varying sizes and documenting patterns of convergent evolution. These findings provide essential genetic data and novel insights into the adaptive evolution of body size in birds.
... The importance of selective neutrality as a significant factor in evolution was stressed by Kimura [12] in the context of evolutionary theory. The relevance and benefits of neutrality for the robustness and evolvability in living systems have been recently discussed by Wagner [23]. ...
VEGAS (Varying Evolvability-Guided Adaptive Search) is a new methodology proposed to deal with the neutrality property of some optimization problems. ts main feature is to consider the whole neutral network rather than an arbitrary solution. Moreover, VEGAS is designed to escape from plateaus based on the evolvability of solution and a multi-armed bandit. Experiments are conducted on NK-landscapes with neutrality. Results show the importance of considering the whole neutral network and of guiding the search cleverly. The impact of the level of neutrality and of the exploration-exploitation trade-off are deeply analyzed.
... continent) versus smaller (e.g. island) populations (Kimura 1983). However, conclusions are hard to draw due to the limited number of island samples included. ...
Cladonia sandstedei forms cushion-shaped lichens that colonize open environments and is distributed throughout the Caribbean and the south-eastern United States. It co-occurs in parts of its range with C. subtenuis , a morphologically similar taxon that is distinguished from the former by the presence of usnic acid. Preliminary phylogenetic analysis with the RPB 2 and TEF -1α loci revealed that these taxa were closely related, but relationships were inconsistent among markers. Here, we combined phylogenetic and population genomic analyses based on RADseq data to clarify the evolutionary relationships and phylogeography of these taxa. Both approaches indicate that the taxa cannot be separated based on secondary metabolites, as previously proposed, but instead form a complex composed of several lineages, largely unrelated to chemistry but with a strong geographical structure in their genetic variation. Continental populations formerly separated under the names C. sandstedei and C. subtenuis were closely related to each other. A similar pattern was observed in the Jamaican counterparts of these taxa, suggesting homoplasy of secondary chemistry. Discriminant Analysis of Principal Components (DAPC) hinted at potential conspecificity between populations in Cuba and Puerto Rico on one hand, and between Jamaica and the continental US on the other; however, phylogenetic analysis and other population-level analyses (PCA and fineRADstructure) suggested that both insular and continental populations were more likely to be reproductively isolated from each other. Based on this, we propose to recognize only one species for the entire complex, under the older name C. sandstedei , with the four spatially structured clades as subspecies: C. sandstedei subsp. sandstedei (restricted to Jamaica) and C . sandstedei subsp. subtenuis comb. nov. (restricted to continental North America) exhibit several chemosyndromes variably containing usnic acid and/or atranorin. The two additional subspecies described here as new, C. sandstedei subsp. cubana and C. sandstedei subsp. landroniana , exhibit the atranorin chemosyndrome and are restricted to Cuba and Puerto Rico, respectively. Our work reaffirms the power of combining RADseq-based phylogenetics and population genetics to disentangle taxonomic and evolutionary histories in poorly understood, closely related and phenotypically similar lichen-forming fungal species.
... In the evolutionary field, neutral models were first proposed by Kimura [11]as the main driving force in evolution. In the ecology field, Hubbell [12] used a special version of the neutral model (UNTB), called the infinite allele model [13], to explain the pattern of biodiversity in nature in terms of neutral mutations . ...
The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual based model of Wright and Fisher, we compute the amplitude of neutral aggregation in the genome space, i.e., the probability of finding two individuals at genetic (hamming) distance k as a function of genome size L, population size N and mutation probability per base \nu. In well mixed populations, we show that for N\nu\textless{}1/L, neutral aggregation is the dominant force and most individuals are found at short genetic distances from each other. For N\nu\textgreater{}1 on the contrary, individuals are randomly dispersed in genome space. The results are extended to geographically dispersed population, where the controlling parameter is shown to be a combination of mutation and migration probability. The theory we develop can be used to test the neutrality hypothesis in various ecological and evolutionary systems.
The common-cause hypothesis says that factors regulating the sedimentary record also exert macroevolutionary controls on speciation, extinction, and biodiversity. I show through computational modeling that common cause factors can, in principle, also control microevolutionary processes of trait evolution. Using Bermuda and its endemic land snail Poecilozonites , I show that the glacial–interglacial sea-level cycles that toggle local sedimentation between slow pedogenesis and rapid eolian accumulation could also toggle evolution rates between long slow phases associated with large geographic ranges and short rapid phases associated with small, fragmented ranges and “genetic surfing” events. Patterns produced by this spatially driven process are similar to the punctuated equilibria patterns that Gould inferred from the fossil record of Bermuda, but without speciation or true stasis. Rather, the dynamics of this modeled system mimic a two-rate Brownian motion process (even though the rate parameter is technically constant) in which the contrast in rate and duration of the phases makes the slower one appear static. The link between sedimentation and microevolution in this model is based on a sediment-starved island system, but the principles may apply to any system where physical processes jointly control the areal extents of sedimentary regimes and species’ distributions.
Given the many levels of biological variation in mutation rates observed to date in primates—spanning from species to individuals to genomic regions—future steps in our understanding of mutation rate evolution will not only be aided by a greater breadth of species coverage across the primate clade but also by a greater depth as afforded by an evaluation of multiple trios within individual species. In order to help bridge these gaps, we here present an analysis of a species representing one of the most basal splits on the primate tree (aye-ayes), combining whole-genome sequencing of seven parent–offspring trios from a three-generation pedigree with a novel computational pipeline that takes advantage of recently developed pan-genome graphs, thereby circumventing the application of (highly subjective) quality metrics that has previously been shown to result in notable differences in the detection of de novo mutations and ultimately estimates of mutation rates. This deep sampling has enabled both a detailed picture of parental age effects and sex dependency in mutation rates, which we here compare with previously studied primates, but has also provided unique insights into the nature of genetic variation in one of the most endangered primates on the planet.
Analyses of codon usage in eukaryotes suggest that amino acid usage responds to GC pressure so AT-biased substitutions drive higher usage of amino acids with AT-ending codons. Here, we combine single-cell transcriptomics and phylogenomics to explore codon usage patterns in foraminifera, a diverse and ancient clade of predominantly uncultivable microeukaryotes. We curate data from 1,044 gene families in 49 individuals representing 28 genera, generating perhaps the largest existing dataset of data from a predominantly uncultivable clade of protists, to analyze compositional bias and codon usage. We find extreme variation in composition, with a median GC content at fourfold degenerate silent sites below 3% in some species and above 75% in others. The most AT-biased species are distributed among diverse non-monophyletic lineages. Surprisingly, despite the extreme variation in compositional bias, amino acid usage is highly conserved across all foraminifera. By analyzing nucleotide, codon, and amino acid composition within this diverse clade of amoeboid eukaryotes, we expand our knowledge of patterns of genome evolution across the eukaryotic tree of life.
IMPORTANCE
Patterns of molecular evolution in protein-coding genes reflect trade-offs between substitution biases and selection on both codon and amino acid usage. Most analyses of these factors in microbial eukaryotes focus on model species such as Acanthamoeba, Plasmodium, and yeast, where substitution bias is a primary contributor to patterns of amino acid usage. Foraminifera, an ancient clade of single-celled eukaryotes, present a conundrum, as we find highly conserved amino acid usage underlain by divergent nucleotide composition, including extreme AT-bias at silent sites among multiple non-sister lineages. We speculate that these paradoxical patterns are enabled by the dynamic genome structure of foraminifera, whose life cycles can include genome endoreplication and chromatin extrusion.
Haematococcus lacustris is an important natural source of astaxanthin for the pharmaceutical and nutraceutical industries. However, its slow growth and susceptibility to contamination by other microalgae pose challenges for commercial astaxanthin production. The bacterial communities associated with microalgae can affect biomass yield and the production of value-added compounds. This study explored the dynamic shifts and functional characteristics in the microbial communities associated with H. lacustris during the aplanospore stage using 16S rRNA metabarcoding. As H. lacustris reached the aplanospore stage, the bacterial communities underwent significant shifts. At the genus level, Massilia dominated the early stages but was later replaced by Sphingomonas in both the microalgae-attached and particle-attached bacterial communities. In contrast, Sphingomonas dominated free-living bacterial communities. Functional predictions suggest that these bacterial communities may support the cultivation of H. lacustris by potentially supplying essential growth factors, including auxins, vitamins, and heme. Network analysis identified that Sphingomonas species can be a key regulator of the microbiome of H. lacustris culture, facilitating the development of H. lacustris during the inductive stage. Overall, these findings highlighted the potential role of the microbiome in supporting the development of H. lacustris at this stage.
Two novel Gram-stain-negative, aerobic, heterotrophic, non-motile bacterial strains, designated as AS3R-12 T and PS1R-30 T , were isolated from freshwater in South Korea. To determine their taxonomic positions, the strains were thoroughly characterized. Genomic analyses, based on 16S rRNA gene and draft genome sequence data, revealed that the two novel isolates, AS3R-12 T and PS1R-30 T , belonged to the genus Novosphingobium . AS3R-12 T showed the highest 16S rRNA gene similarity (97.7%) with Novosphingobium flavum UCT-28 T . In addition, PS1R-30 T showed 97.9% 16S rRNA gene similarity with Novosphingobium lentum NBRC 107847 T . The draft genome of strains AS3R-12 T and PS1R-30 T consisted of 4 149 275 and 4 969 838 bps, with DNA G+C content of 63.1 and 66.1 mol%, respectively. The average nucleotide identity between two strains and other related species was below 76.2%, and the digital DNA–DNA hybridization values with closely related species were below 20.8%, both lower than the species delineation threshold. Strains AS3R-12 T and PS1R-30 T contained the ubiquinone Q-10 as the major quinone and displayed a polyamine pattern with spermidine as the predominant polyamine. Additionally, their major fatty acids were characterized by C 16:1 ω7c /C 16:1 ω6c (summed feature 3) and C 18:1 ω7c /C 18:1 ω6c (summed feature 8). The major polar lipids of AS3R-12 T and PS1R-30 T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), sphingoglycolipid (SGL) and phosphatidylcholine (PC). Moreover, physiological and biochemical results allowed the phenotypic and genotypic differentiation of strains AS3R-12 T and PS1R-30 T from their closest and other species of the genus Novosphingobium with validly published names. Therefore, AS3R-12 T and PS1R-30 T represented novel species of the genus Novosphingobium , for which the names Novosphingobium aquae sp. nov. (type strain AS3R-12 T =KACC 23096 T =LMG 32950 T ) and Novosphingobium anseongense sp. nov. (type strain PS1R-30 T =KACC 23097 T =LMG 32951 T ) are proposed.
Although multigenic traits are often assumed to be under some form of stabilizing selection, numerous aspects of the population-genetic environment can cause mean phenotypes to deviate from presumed optima, often in ways that effectively transform the fitness landscape to one of directional selection. Focusing on an asexual population, we consider the ways in which such deviations scale with the relative power of selection and genetic drift, number of linked genomic sites, magnitude of mutation bias, and the location of optima with respect to possible genotypic space. Even in the absence of mutation bias, mutation will influence evolved mean phenotypes unless the optimum happens to coincide exactly with the mean expected under neutrality. In the case of directional mutation bias and large numbers of selected sites, effective population sizes (Ne) can be dramatically reduced by selective-interference effects, leading to further mismatches between phenotypic means and optima. Situations in which the optimum is outside or near the limits of possible genotypic space (e.g., a half-Gaussian fitness function) can lead to particularly pronounced gradients of phenotypic means with respect to Ne, but such gradients can also occur when optima are well within the bounds of attainable phenotypes. These results help clarify the degree to which mean phenotypes can vary among populations experiencing identical mutation and selection pressures but differing in Ne, and yield insight into how the expected scaling relationships depend on the underlying features of the genetic system.
Do the properties of amino acids affect their rates of substitution? The neutral theory predicts that greater selective constraint leads to slower rates of evolution; similarly, we expect amino acids that are more different from each other to have lower rates of exchange because such changes are most likely to affect protein structure and function. Here we test these predictions, using substitution rates estimated from empirical amino acid exchangeability matrices. To measure degree of amino acid difference, we focussed on two physicochemical properties, hydrophobicity and molecular weight, uncorrelated metrics that are known to have important implications for protein structure and function. We find that for both hydrophobicity and molecular weight, amino acid pairs with large differences had lower rates of substitution. We also found that amino acids that differed in both properties had the lowest rates of substitution, suggesting that both physicochemical properties are under selective constraint. Mutation properties, such as the number of mutations or the number of transitions as opposed to transversions separating amino acid pairs, were also important predictors of substitution rates. The relationship between amino acid substitution rates and differences in their physiochemical properties holds across several taxonomically restricted datasets. This finding suggests that purifying selection affects amino acid substitution rates in a similar manner across taxonomic groups with different effective population sizes.
The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.
Changes in gene expression underlie much of evolution and occur via either cis-acting mutations, which lie near the affected gene and act in a context specific manner, or trans-acting mutations, which may be far from the affected gene and act through diffusible molecules such as transcription factors. A commonly held view is that most expression variation within species is controlled in trans- while expression differences between species are largely controlled in cis-. Here, we summarize recent intraspecific gene regulation studies and find, contrary to this widely held view, that many studies in diverse taxa have revealed a large role for cis-acting mutations underlying expression variation within species. A review of the existing literature also shows that preparations using whole organisms rather than individual tissues may be biased towards identifying trans-regulation. Moreover, we note several examples of predominantly cis-acting regulation in recently diverged populations adapted to different environments. We highlight the challenges of drawing general conclusions from comparisons among studies that use different methodologies and we offer suggestions for studies that will address outstanding questions concerning the evolution of gene regulation.
Purifying selection is a critical factor in shaping genetic diversity. Current theoretical models mostly address scenarios of either very weak or strong selection, leaving a significant gap in our knowledge. The effects of purifying selection on patterns of genomic diversity remain poorly understood when selection against deleterious mutations is weak to moderate, particularly when recombination is limited or absent. In this study, we extend an existing approach, the fitness-class coalescent, to incorporate arbitrary levels of purifying selection in haploid populations. This model offers a comprehensive framework for exploring the influence of purifying selection in a wide range of demographic scenarios. Moreover, our research reveals potential sources of qualitative and quantitative biases in demographic inference, highlighting the significant risk of attributing genetic patterns to past demographic events rather than purifying selection. This work expands our understanding of the complex interplay between selection, drift, and population dynamics, and how purifying selection distorts demographic inference.
GenProg implemented a novel method for automatically evolving patches to repair test suite failures in legacy C programs. It combined insights from genetic programming and software engineering. Many of the original design decisions in GenProg were ultimately less important than its impact as an existence proof. In particular, it demonstrated that useful patches for non-trivial bugs and programs could be generated automatically. Since the original publication, research in automated program repair has expanded to consider and evaluate many new methods, contexts and defects. As code synthesis and debugging techniques based on machine learning have become popular, it is informative to consider how views on perennial issues in program repair have changed, or remained static, over time. This retrospective discusses the issues of repair quality (including the role of tests), use cases for automated repairs (including the role of humans), and why these approaches work at all.
We are witnessing an ongoing global biodiversity crisis, and an increasing number of mammalian populations are at risk of decline. Species that have survived severe historic bottlenecks, such as the cheetah (Acinonyx jubatus) exhibit symptoms of inbreeding depression including reproductive and developmental defects. Although it has long been suggested that such defects stem from an accumulation of weakly deleterious mutations, the implications of such mutations leading to pseudogenization has not been assessed.
Here, we use comparative analysis of eight felid genomes to better understand the impacts of deleterious mutations in the cheetah. We find novel pseudogenization events specific to the cheetah. Through careful curation, we identify 65 genes with previously unreported premature termination codons that likely affect gene function. With the addition of population data (n=6) we find 22 of these premature termination codons in at least one resequenced individual, four of which (DEFB116, ARL13A, CFAP119 and NT5DC4) are also found in a more recent reference genome. Mutations within three of these genes are linked with sterility, including azoospermia, which is common in cheetahs. Our results highlight the power of comparative genomic approaches for the discovery of novel causative variants in declining species.
Protein sequence evolution in the presence of epistasis makes many previously acceptable amino acid residues at a site unfavorable over time. This phenomenon of entrenchment has also been observed with neutral substitutions using Potts Hamiltonian models. Here, we show that simulations using these models often evolve non-neutral proteins. We introduce a Neutral-with-Epistasis (NxE) model that incorporates purifying selection to conserve fitness, a requirement of neutral evolution. NxE protein evolution revealed a surprising lack of entrenchment, with site-
specific amino-acid preferences remaining remarkably conserved, in biologically realistic time frames despite extensive residue coupling. Moreover, we found that the overdispersion of the molecular clock is caused by rate variation across sites introduced by epistasis in individual
lineages, rather than by historical contingency. Therefore, substitutional entrenchment and rate contingency may indicate that adaptive and other non-neutral evolutionary processes were at play during protein evolution.
The evolution of brain-expressed genes is notably slower than that of genes expressed in other tissues, a phenomenon likely due to high-level functional constraints. One such constraint might be the integration of information by neuron assemblies, enhancing environmental adaptability. This study explores the physiological mechanisms of information integration in neurons through three types of synchronization: chemical, electromagnetic, and quantum. Chemical synchronization involves the diffuse release of neurotransmitters like dopamine and acetylcholine, causing transmission delays of several milliseconds. Electromagnetic synchronization encompasses action potentials, electrical gap junctions, and ephaptic coupling. Electrical gap junctions enable rapid synchronization within cortical GABAergic networks, while ephaptic coupling allows structures like axon bundles to synchronize through extracellular electromagnetic fields, surpassing the speed of chemical processes. Quantum synchronization is hypothesized to involve ion coherence during ion channel passage and the entanglement of photons within the myelin sheath. Unlike the finite-time synchronization seen in chemical and electromagnetic processes, quantum entanglement provides instantaneous non-local coherence states. Neurons might have evolved from slower chemical diffusion to rapid temporal synchronization, with ion passage through gap junctions within cortical GABAergic networks potentially facilitating both fast gamma band synchronization and quantum coherence. This mini-review compiles literature on these three synchronization types, offering new insights into the physiological mechanisms that address the binding problem in neuron assemblies.
The divergence rate between the alignable genomes of humans and chimpanzees is as little as 1.23%. Their phenotypical difference was hypothesized to be accounted for by gene regulation. We construct the cis‐regulatory element frequency (CREF) matrix to represent the proximal regulatory sequences for each species. Each CREF matrix is further decomposed into dual eigen‐modules. By comparing the CREF modules of four existing hominid species, we examine their quantitative and qualitative changes along evolution. We identified two saltations: one between the 4th and 5th, the other between the 9th and 10th eigen‐levels. The cognition and intelligence unique to humans are thus found from the saltations at the molecular level. They include long‐term memory, cochlea/inner ear morphogenesis that enables the development of human language/music, social behavior that allows us to live together peacefully and to work collaboratively, and visual/observational/associative learning. Moreover, we found exploratory behavior crucial for humans’ creativity, the GABA‐B receptor activation that protects our neurons, and serotonin biosynthesis/signaling that regulates our happiness. We observed a remarkable increase in the number of motifs present on Alu elements on the 4th/9th motif‐eigenvectors. The cognition and intelligence unique to humans can, by and large, be identified using only the CREF profiles without any a priori. Although gradual evolution might be the only mode in the mutations of protein sequences, the evolution of gene regulation has both gradual and saltational modes, which could be explained by the framework of CREF eigen‐modules.
Contingency (or “luck”) in early life plays an important role in shaping individuals’ development. By comparing the developmental trajectories of functionally genetically identical free-living mice who either experienced high levels of resource competition (males) or did not (females), we show that competition magnifies early contingency. Male resource competition results in a feedback loop that magnifies the importance of early contingency and pushes individuals onto divergent, self-reinforcing life trajectories, while the same process appears absent in females. Our results indicate that the strength of sexual selection may be self-limiting, and they highlight the potential for contingency to lead to differences in life outcomes, even in the absence of any underlying differences in ability (“merit”).
Fisher was the first of the founding fathers of the modern synthesis. The two tenets of his evolutionary work were that natural selection acted slowly on populations that were large and panmictic, and that the effects of natural selection could be gauged by focusing on individual genes. In 1918, Fisher wrote a fundamental paper on biometrical (quantitative) genetics. His 1922 paper introduced the concepts of balancing selection and diffusion equations. It also investigated equilibria under different evolutionary scenarios. Fisher first clashed with Wright in 1928 on the issue of the evolution of dominance. One of Fisher’s most controversial contributions to evolutionary genetics is the fundamental theorem of natural selection, which he first enunciated in 1930.
Understanding the genetic diversity–area relationship (GAR) is essential for comprehending how species adapt to environmental changes, as genetic diversity is an indicator of a species' adaptive potential. Variation in environmental adaptation capacity exists among species and animal taxa with different distribution areas, highlighting the importance of understanding the GAR. To obtain a more comprehensive understanding of the GAR in terrestrial vertebrates, we assessed both haplotype diversity–area and nucleotide diversity–area relationships using 25,453 cytochrome c oxidase subunit I (COI) sequences from 142 amphibian species, 574 bird species, and 342 mammal species. We found that both measures of genetic diversity increased with species range size across major animal groups. Nevertheless, the GAR did not differ among animal groups, while haplotype diversity performed better than nucleotide diversity in profiling the GAR, as indicated by higher R2 values. The difference in the modelling fit may stem from the distinct biological and mathematical significance of nucleotide diversity and haplotype diversity. These results suggest that the GAR follows similar rules among different animal taxa. Furthermore, haplotype diversity may serve as a more reliable indicator for assessing the potential effects of area size changes on animal populations and provide better guidance for conserving genetic diversity.
Global adaptation occurs when all populations of a species undergo selection toward a common optimum. This can occur by a hard selective sweep with the emergence of a new globally advantageous allele that spreads throughout a species’ natural range until reaching fixation. This evolutionary process leaves a temporary trace in the region affected, which is detectable using population genomic methods. While selective sweeps have been identified in many species, there have been few comparative and systematic studies of the genes involved in global adaptation. Building upon recent findings showing repeated genetic basis of local adaptation across independent populations and species, we asked whether certain genes play a more significant role in driving global adaptation across plant species. To address this question, we scanned the genomes of 17 plant species to identify signals of repeated global selective sweeps. Despite the substantial evolutionary distance between the species analyzed, we identified several gene families with strong evidence of repeated positive selection. These gene families tend to be enriched for reduced pleiotropy, consistent with predictions from Fisher’s evolutionary model and the cost of complexity hypothesis. We also found that genes with repeated sweeps exhibit elevated levels of gene duplication. Our findings contrast with recent observations of increased pleiotropy in genes driving local adaptation, consistent with predictions based on the theory of migration-selection balance.
Most comprehensive simulations of population dynamics use origin-fixation approaches to modeling mutations, specifically modeling mutation using the framework of the modern synthesis. However, modern advances in understanding mutations have brought into focus new modalities of mutation that do not fully align with this vision of population dynamics. These other modes of mutation, such as cyclical mutation, have not so far been represented in models of population dynamics despite representing a significant fraction of mutations that occur in vivo. Problematic results of current attempts to create total models of population dynamics may be due to this incompleteness. In addition, we will present how a cyclical mutation modality can be modeled in population dynamics and how this can, at least partially, resolve problematic long-term trends predicted by current comprehensive simulations.
Previously, we developed a dynamic magnetic field (DMF) device using neodymium magnets that induced c-fos expression in cortical neurons, while activity-regulated cytoskeleton-associated protein (Arc), and brain-derived neurotrophic factor (BDNF) remained unaffected. The precise signal transduction pathway for c-fos induction under DMF was unclear. This study aimed to investigate the mechanism of immediate early gene (IEG) induction using calcium channel blockers (CCBs). Six experiments were conducted with cortical neurons, employing an NMDA receptor antagonist and an L-type voltage-dependent calcium channel blocker as CCBs. Neuronal cultures were exposed to DMF, CCBs, or both, and IEG expression (Arc, c-fos, BDNF) was measured through polymerase chain reaction. Results showed a tendency for increased c-fos expression with DMF exposure, which was unaffected by CCBs. In contrast, Arc and BDNF were not induced under DMF exposure but were significantly inhibited by CCBs. These findings suggest that c-fos induction under DMF involves a distinct pathway, potentially relevant to stress resistance and drug discovery.
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