Influence Of Natural Selection Research Articles

The Promise of Inferring the Past Using the Ancestral Recombination Graph.

The ancestral recombination graph (ARG) is a structure that represents the history of coalescent and recombination events connecting a set of sequences (Hudson RR. In: Futuyma D, Antonovics J, editors. Gene genealogies and the coalescent process. In: Oxford Surveys in Evolutionary Biology; 1991. p. 1 to 44.). The full ARG can be represented as a set of genealogical trees at every locus in the genome, annotated with recombination events that change the topology of the trees between adjacent loci and the mutations that occurred along the branches of those trees (Griffiths RC, Marjoram P. An ancestral recombination graph. In: Donnelly P, Tavare S, editors. Progress in population genetics and human evolution. Springer; 1997. p. 257 to 270.). Valuable insights can be gained into past evolutionary processes, such as demographic events or the influence of natural selection, by studying the ARG. It is regarded as the "holy grail" of population genetics (Hubisz M, Siepel A. Inference of ancestral recombination graphs using ARGweaver. In: Dutheil JY, editors. Statistical population genomics. New York, NY: Springer US; 2020. p. 231-266.) since it encodes the processes that generate all patterns of allelic and haplotypic variation from which all commonly used summary statistics in population genetic research (e.g. heterozygosity and linkage disequilibrium) can be derived. Many previous evolutionary inferences relied on summary statistics extracted from the genotype matrix. Evolutionary inferences using the ARG represent a significant advancement as the ARG is a representation of the evolutionary history of a sample that shows the past history of recombination, coalescence, and mutation events across a particular sequence. This representation in theory contains as much information, if not more, than the combination of all independent summary statistics that could be derived from the genotype matrix. Consistent with this idea, some of the first ARG-based analyses have proven to be more powerful than summary statistic-based analyses (Speidel L, Forest M, Shi S, Myers SR. A method for genome-wide genealogy estimation for thousands of samples. Nat Genet. 2019:51(9):1321 to 1329.; Stern AJ, Wilton PR, Nielsen R. An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data. PLoS Genet. 2019:15(9):e1008384.; Hubisz MJ, Williams AL, Siepel A. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet. 2020:16(8):e1008895.; Fan C, Mancuso N, Chiang CWK. A genealogical estimate of genetic relationships. Am J Hum Genet. 2022:109(5):812-824.; Fan C, Cahoon JL, Dinh BL, Ortega-Del Vecchyo D, Huber C, Edge MD, Mancuso N, Chiang CWK. A likelihood-based framework for demographic inference from genealogical trees. bioRxiv. 2023.10.10.561787. 2023.; Hejase HA, Mo Z, Campagna L, Siepel A. A deep-learning approach for inference of selective sweeps from the ancestral recombination graph. Mol Biol Evol. 2022:39(1):msab332.; Link V, Schraiber JG, Fan C, Dinh B, Mancuso N, Chiang CWK, Edge MD. Tree-based QTL mapping with expected local genetic relatedness matrices. bioRxiv. 2023.04.07.536093. 2023.; Zhang BC, Biddanda A, Gunnarsson ÁF, Cooper F, Palamara PF. Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nat Genet. 2023:55(5):768-776.). As such, there has been significant interest in the field to investigate 2 main problems related to the ARG: (i) How can we estimate the ARG based on genomic data, and (ii) how can we extract information of past evolutionary processes from the ARG? In this perspective, we highlight 3 topics that pertain to these main issues: The development of computational innovations that enable the estimation of the ARG; remaining challenges in estimating the ARG; and methodological advances for deducing evolutionary forces and mechanisms using the ARG. This perspective serves to introduce the readers to the types of questions that can be explored using the ARG and to highlight some of the most pressing issues that must be addressed in order to make ARG-based inference an indispensable tool for evolutionary research.

Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses.

Hemorrhagic fever with renal syndrome (HFRS) is an acute viral zoonosis carried and transmitted by infected rodents through urine, droppings, or saliva. The etiology of HFRS is complex due to the involvement of viral factors and host immune and genetic factors which hinder the development of potential therapeutic solutions for HFRS. Hantaan virus (HTNV), Dobrava-Belgrade virus (DOBV), Seoul virus (SEOV), and Puumala virus (PUUV) are predominantly found in hantaviral species that cause HFRS in patients. Despite ongoing prevention and control efforts, HFRS remains a serious economic burden worldwide. Furthermore, recent studies reported that the hantavirus nucleocapsid protein is a multi-functional protein and plays a major role in the replication cycle of the hantavirus. However, the precise mechanism of the nucleoproteins in viral pathogenesis is not completely understood. In the framework of the current study, various in silico approaches were employed to identify the factors influencing the codon usage pattern of hantaviral nucleoproteins. Based on the relative synonymous codon usage (RSCU) values, a comparative analysis was performed between HFRS-causing hantavirus and their hosts, suggesting that HTNV, DOBV, SEOV, and PUUV, were inclined to evolve their codon usage patterns that were comparable to those of their hosts. The results indicated that most of the overrepresented codons had AU-endings, which revealed that mutational pressure is the major force shaping codon usage patterns. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Further analysis also demonstrated that HFRS causing hantaviruses adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts. To our knowledge, no study to date reported the factors influencing the codon usage pattern within hantaviral nucleoproteins. Thus, the proposed computational scheme can help in understanding the underlying mechanism of codon usage patterns in HFRS-causing hantaviruses which lend a helping hand in designing effective anti-HFRS treatments in future. This study, although comprehensive, relies on in silico methods and thus necessitates experimental validation for more solid outcomes. Beyond the identified factors influencing viral behavior, there could be other yet undiscovered influences. These potential factors should be targets for further research to improve HFRS therapeutic strategies.

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC).

The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC strains followed a trend of antagonistic codon usage with respect to the human host. The identified CUBs divergence would help to understand the virus evolution and its host adaptation, thus help design novel vaccine strategies against the emerging VOC strains. To the best of our knowledge, this is the first report for identifying the evolution of CUBs pattern in all the currently identified VOC.

Approaching the domesticated plant holobiont from a community evolution perspective.

Plants establish a pivotal relationship with their microbiome and are often conceptualized as holobionts. Nonetheless, holobiont theories have attracted much criticism, especially concerning the fact that the holobiont is rarely a unit of selection. In previous work, we discussed how the plant microbiome can be considered to be an 'ecosystem on a leash', which is subject to the influence of natural selection acting on plant traits. We proposed that in domesticated plants the assembly of the plant microbiome can usefully be conceptualized as being subject to a 'double leash', which encompasses both the effect of artificial selection imposed by the domesticator on plant traits and the leash from the plant to the microbiome. Here we approach the domesticated plant holobiont, simply defined as a community of organisms, from a community evolution point of view, and show how community heritability (a measure of community selection) complements the 'double-leash' framework in providing a community-level view of plant domestication and its impact on plant-microbe interactions. We also propose simple experiments that could be performed to investigate whether plant domestication has altered the potential for community selection at the holobiont level.

Selection and demography drive range-wide patterns of MHC-DRB variation in mule deer

BackgroundStanding genetic variation is important especially in immune response-related genes because of threats to wild populations like the emergence of novel pathogens. Genetic variation at the major histocompatibility complex (MHC), which is crucial in activating the adaptive immune response, is influenced by both natural selection and historical population demography, and their relative roles can be difficult to disentangle. To provide insight into the influences of natural selection and demography on MHC evolution in large populations, we analyzed geographic patterns of variation at the MHC class II DRB exon 2 locus in mule deer (Odocoileus hemionus) using sequence data collected across their entire broad range.ResultsWe identified 31 new MHC-DRB alleles which were phylogenetically similar to other cervid MHC alleles, and one allele that was shared with white-tailed deer (Odocoileus virginianus). We found evidence for selection on the MHC including high dN/dS ratios, positive neutrality tests, deviations from Hardy–Weinberg Equilibrium (HWE) and a stronger pattern of isolation-by-distance (IBD) than expected under neutrality. Historical demography also shaped variation at the MHC, as indicated by similar spatial patterns of variation between MHC and microsatellite loci and a lack of association between genetic variation at either locus type and environmental variables.ConclusionsOur results show that both natural selection and historical demography are important drivers in the evolution of the MHC in mule deer and work together to shape functional variation and the evolution of the adaptive immune response in large, well-connected populations.

Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination.

In eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Our results demonstrate that this bias was in part due to the action of restriction–modification systems, whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that recombination occurred uniformly across the genome without concentration into hotspots. Notably, our results show that species-level genetic distance did not affect genome-wide recombination. This study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.

The Influence of Natural Selection and Other Disciplines on Ecological Economic Values

The motives behind the economic value in human behavior are a topic of longstanding foci of research interest. Two motives, self-interest and altruism influence in different degrees in form of inclusive fitness in natural selection and contribute in determining and reasoning the values in human societies. We elaborate how inclusive fitness (self-interest and altruism) shapes the values, and behavior resulting sustainability of species and ecosystems. We argue self-interest and altruism combine in different scales that determine human values. The concept of value in economic analysis changes over time with the development and influence of other disciplines and in economics, propagates in more multi-disciplinary way per se in ecological economics currently. Animal behavior studies provide examples that value originated as result of natural selection in animals as a biological process. The paper contributes to the debate on how natural selection generates the mechanism of surviving which in turn originates in particular existence value, option value and values which support the sustainability of ecosystems.

Mutational spectrum of SARS-CoV-2 during the global pandemic

Viruses accumulate mutations under the influence of natural selection and host–virus interactions. Through a systematic comparison of 351,525 full viral genome sequences collected during the recent COVID-19 pandemic, we reveal the spectrum of SARS-CoV-2 mutations. Unlike those of other viruses, the mutational spectrum of SARS-CoV-2 exhibits extreme asymmetry, with a much higher rate of C>U than U>C substitutions, as well as a higher rate of G>U than U>G substitutions. This suggests directional genome sequence evolution during transmission. The substantial asymmetry and directionality of the mutational spectrum enable pseudotemporal tracing of SARS-CoV-2 without prior information about the root sequence, collection time, and sampling region. This shows that the viral genome sequences collected in Asia are similar to the original genome sequence. Adjusted estimation of the dN/dS ratio accounting for the asymmetrical mutational spectrum also shows evidence of negative selection on viral genes, consistent with previous reports. Our findings provide deep insights into the mutational processes in SARS-CoV-2 viral infection and advance the understanding of the history and future evolution of the virus.

Positive selection and intrinsic disorder are associated with multifunctional C4(AC4) proteins and geminivirus diversification

Viruses within the Geminiviridae family cause extensive agricultural losses. Members of four genera of geminiviruses contain a C4 gene (AC4 in geminiviruses with bipartite genomes). C4(AC4) genes are entirely overprinted on the C1(AC1) genes, which encode the replication-associated proteins. The C4(AC4) proteins exhibit diverse functions that may be important for geminivirus diversification. In this study, the influence of natural selection on the evolutionary diversity of 211 C4(AC4) genes relative to the C1(AC1) sequences they overlap was determined from isolates of the Begomovirus and Curtovirus genera. The ratio of nonsynonymous (dN) to synonymous (dS) nucleotide substitutions indicated that C4(AC4) genes are under positive selection, while the overlapped C1(AC1) sequences are under purifying selection. Ninety-one of 200 Begomovirus C4(AC4) genes encode elongated proteins with the extended regions being under neutral selection. C4(AC4) genes from begomoviruses isolated from tomato from native versus exotic regions were under similar levels of positive selection. Analysis of protein structure suggests that C4(AC4) proteins are entirely intrinsically disordered. Our data suggest that non-synonymous mutations and mutations that increase the length of C4(AC4) drive protein diversity that is intrinsically disordered, which could explain C4/AC4 functional variation and contribute to both geminivirus diversification and host jumping.

The ecological causes and consequences of hard and soft selection.

Interactions between natural selection and population dynamics are central to both evolutionary-ecology and biological responses to anthropogenic change. Natural selection is often thought to incur a demographic cost that, at least temporarily, reduces population growth. However, hard and soft selection clarify that the influence of natural selection on population dynamics depends on ecological context. Under hard selection, an individual's fitness is independent of the population's phenotypic composition, and substantial population declines can occur when phenotypes are mismatched with the environment. In contrast, under soft selection, an individual's fitness is influenced by its phenotype relative to other interacting conspecifics. Soft selection generally influences which, but not how many, individuals survive and reproduce, resulting in little effect on population growth. Despite these important differences, the distinction between hard and soft selection is rarely considered in ecology. Here, we review and synthesize literature on hard and soft selection, explore their ecological causes and implications and highlight their conservation relevance to climate change, inbreeding depression, outbreeding depression and harvest. Overall, these concepts emphasise that natural selection and evolution may often have negligible or counterintuitive effects on population growth-underappreciated outcomes that have major implications in a rapidly changing world.

Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to the Coronaviridae Family.

Viruses belonging to the Coronaviridae family have a single-stranded positive-sense RNA with a poly-A tail. The genome has a length of ~29.9 kbps, which encodes for genes that are essential for cell survival and replication. Different evolutionary constraints constantly influence the codon usage bias (CUB) of different genes. A virus optimizes its codon usage to fit the host environment on which it savors. This study is a comprehensive analysis of the CUB for the different genes encoded by viruses of the Coronaviridae family. Different methods including relative synonymous codon usage (RSCU), an Effective number of codons (ENc), parity plot 2, and Neutrality plot, were adopted to analyze the factors responsible for the genetic evolution of the Coronaviridae family. Base composition and RSCU analyses demonstrated the presence of A-ended and U-ended codons being preferred in the 3rd codon position and are suggestive of mutational selection. The lesser ENc value for the spike ‘S’ gene suggests a higher bias in the codon usage of this gene compared to the other structural genes. Parity plot 2 and neutrality plot analyses demonstrate the role and the extent of mutational and natural selection towards the codon usage pattern. It was observed that the structural genes of the Coronaviridae family analyzed in this study were at the least under 84% influence of natural selection, implying a major role of natural selection in shaping the codon usage.

A Cretaceous bug with exaggerated antennae might be a double-edged sword in evolution.

SummarySexual selection can favor production of exaggerated features, but the high cost of such features in terms of energy consumption and enemy avoidance makes them go to extinction under the influence of natural selection. However, fossils preserved with specialized features are very rare. Here, we report a new nymph from Burmese amber, Magnusantena wuae Du & Chen gen. et sp. nov., which has exaggerated leaf-like expanded antennae. Such bizarre antennae indicate that sensitive and delicate sensory system and magnificent appearance in Hemiptera have been already established in mid-Cretaceous. Our findings may provide evidence for Darwin's view that sensory organs play an important role in sexual selection. This nymph with the leaf-like antennae may also represents a new camouflage pattern. However, the oversized antennae are costly to develop and maintain, increasing the risks from predators. Such unparalleled expanded antennae might be the key factor for the evolutionary fate of the coreid.

The Emergence of Complex Dynamics during the Evolution of a Structured Limited Population

The paper considers a microevolution model of two-stage population with limitation under the influence of natural selection that regulates juvenile survival rate. An analytical and numerical study of the model is performed; the parametric areas of various dynamic modes are determined. It is shown that an emergence of new alleles (for example, as a result of mutations) providing a greater reproductive potential of individuals leads to a natural selection of these alleles and evolutionary growth of the average value of the reproductive potential in the population. However, in the case of density dependent regulation of birth rate, the increase in the average value of reproductive potential leads to destabilization of the dynamics for the age group sizes. Scenarios of changes in the dynamics are various and depend on the parameter values of the model, but the main result is always the same: the dynamics become more and more complex and, as a rule, chaotic.

Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection

Bluetongue virus (BTV) is a double-stranded RNA virus with multiple segments and belongs to the genus Orbivirus within the family Reoviridae. BTV is spread to livestock through its dominant vector, biting midges of genus Culicoides. Although great progress has been made in genomic analyses, it is not fully understood how BTVs adapt to their hosts and evade the host’s immune systems. In this study, we retrieved BTV genome sequences from the National Center for Biotechnology Information (NCBI) database and performed a comprehensive research to explore the codon usage patterns in 50 BTV strains. We used bioinformatic approaches to calculate the relative synonymous codon usage (RSCU), codon adaptation index (CAI), effective number of codons (ENC), and other indices. The results indicated that most of the overpreferred codons had A-endings, which revealed that mutational pressure was the major force shaping codon usage patterns in BTV. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Based on the RSCU values, we performed a comparative analysis between BTVs and their hosts, suggesting that BTVs were inclined to evolve their codon usage patterns that were comparable to those of their hosts. Such findings will be conducive to understanding the elements that contribute to viral evolution and adaptation to hosts.

Ontogenetic changes in the targets of natural selection in three plant defenses.

The evolution of plant defenses has traditionally been studied at single plant ontogenetic stages, overlooking the fact that natural selection acts continuously on organisms along their development, and that the adaptive value of phenotypes can change along ontogeny. We exposed 20 replicated genotypes of Turnera velutina to field conditions to evaluate whether the targets of natural selection on different defenses and their adaptative value change across plant development. We found that low chemical defense was favored in seedlings, which seems to be explained by the assimilation efficiency and the ability of the specialist herbivore to sequester cyanogenic glycosides. Whereas trichome density was unfavored in juvenile plants, it increased relative plant fitness in reproductive plants. At this stage we also found a positive correlative gradient between cyanogenic potential and sugar content in extrafloral nectar. We visualize this complex multi-trait combination as an ontogenetic defensive strategy. The inclusion of whole-plant ontogeny as a key source of variation in plant defense revealed that the targets and intensity of selection change along the development of plants, indicating that the influence of natural selection cannot be inferred without the assessment of ontogenetic strategies in the expression of multiple defenses.

Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin (Kajikia audax), a broadly distributed and highly migratory pelagic species.

Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site‐associated DNA to characterize genome‐wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual‐based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F ST = 0.0137–0.0819). F ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m R ≤ 0.37) compared with most populations in the Pacific Ocean (m R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long‐distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome‐wide markers enable inference of population‐level relationships using sample sizes practical for large pelagic fishes of conservation concern.

Study of the Role of the Main Factors of Population Dynamics in the Mechanism of Differentiation and Formation of Diversity and Genetic Load of Hereditary Diseases in Subpopulations of the Karachay-Cherkess Republic

The generalized results of the genetic and epidemiological study of the genetic structure of various ethnic groups of the Karachay-Cherkess Republic (KChR) through various genetic systems are presented: by the genes causing AD, AR, and X-linked hereditary diseases and by nonbiological parameters estimated by the methods of population statistics (random inbreeding FST, Malecot’s isolation-by-distance parameters, migration index, and Crow index and its components). The total size of the investigated population was 410 367 individuals (city of Cherkessk, Ust-Dzhegutinsky, Karachayevsky, Malokarachayevsky, Prikubansky, Khabezsky, Nogaysky, Adyge-Khablsky, Urupsky, and Zelenchuksky districts). On the basis of the study of correlations between different characteristics of the population genetic structure, it is assumed that the main cause of genetic differentiation of KChR subpopulations in terms of diversity and load of hereditary diseases (AD, AR, and X-linked) is genetic drift and migration under decreased influence of natural selection and mutational process.

Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host.

Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host–virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.

Genetic Consequences of Interspecific Hybridization, Its Role in Speciation and Phenotypic Diversity of Plants

The review focuses on the genetic consequences of interspecific hybridization and discusses its role in speciation and increasing the genetic diversity of plants, including the diversity of species and varieties of cultivated crops and garden plants. The combination of two or more genomes of different origin in the first-generation hybrids is usually accompanied by a phenomenon referred to as genomic shock, which results in different genetic and epigenetic changes. As a result, a material appears which is unique in providing multiple variants for natural selection of organisms, in different degrees adapted to new environmental conditions. In isolated plant populations with various destabilized genomes of hybrid origin under the influence of natural selection and due to genetic drift, gene and chromosomal differences will accumulate, triggering new reproductive isolating mechanisms that increase genetic isolation of a new race or species. Progressive establishment of genome stabilization at the eupolyploid stage and subsequent repeated genome and karyotype diploidization facilitate the retention of selected new genomic and epigenomic combinations. It seems likely that the evolutionary history of all agricultural crops and garden plant varieties, as well as of many invasive alien species and the components of adventive flora, was marked by interspecific crossings purposefully carried out by breeders during the creation of modern varieties and crossings between previously geographically isolated plants that were unintentionally united in apothecary and botanical gardens, in fields and backyards, and on disturbed lands around settlements. At the same time, phenotypic and genetic diversity of cultivars not only results from the combination of different alleles that already existed in the genomes of the parental species but also is a consequence of the appearance in the first-generation hybrids of new genomic and epigenomic variants that are direct or distant effects of post-hybridization genomic shock, the creative role of which we would like to emphasize.

The Comparative Method in Biology and the Essentialist Trap

The comparative method is at the centre of a complex view of biology, according to which organisms are seen as historical products. This is a dynamic view of nature, where genotypes and phenotypes change over evolutionary time under the influence of natural selection. Organisms (species) and groups of them (clades) are defined by their uniqueness, and their comparison provides insight into patterns of diversification. The alternative, mechanistic approach is enormously powerful, and has led to our understanding of basic molecular mechanisms underlying biological processes. However, because of intrinsic practical difficulties, this latter approach has only been applied to a very small cohort of animal systems, the so-called “model systems”. While this approach has been enormously productive, it has brought with it as a by-product a narrow view of biological diversity; and the assumption that with just a handful of well-studied animals we “understand” development and evolution. Nothing could be further from the truth, as indicated by many recent studies, which have shown that the development of animals is highly plastic. The lack of appreciation of this simple fact has brought me (and others) to see the field of developmental biology as caught within an “essentialist trap” from which many contemporary evo-devo approaches try to free it.