Role In Selection Research Articles

Ash seedlings in a reciprocal transplant experiment—the extent of damage of mature forest stands affects ash offspring performance

In past decades, ash dieback has caused a rapid decline of European ash (Fraxinus excelsior) in temperate forests of Europe. Numerous studies focus on mitigating the negative impacts of ash dieback to forest ecosystems or identifying resistant genotypes. The role of natural selection toward genotypes withstanding ash dieback for ash regeneration has been less frequently studied with experimental means to date. This is, however, necessary in times of global change, because the preservation of ash in Europe’s forests will depend, above all, on the adaptability of the future generations of ash trees. To quantify the extent and effects of ash dieback severity for ash regeneration we selected five forest stands moderately damaged and five forest stands highly damaged by ash dieback, in Schleswig-Holstein, Germany. We reciprocally transplanted naturally regenerated ash seedlings sampled in the field between these 10 sites. A shading treatment added to each half of the plots per site was meant to test for effects of altered light conditions in the herb layer due to canopy opening caused by ash dieback. With this approach, we tested seedling survival, performance and fungal infection for an interacting effect of origin and target site in regard to ash dieback severity and environmental factors over 2 years and recorded leaf traits (specific leaf area, leaf dry matter content) in the second year. Reduced light conditions under the shading nets had strong effects, influencing first year performance and infection probability as well as second year survival, growth and leaf trait characteristics. Soil conditions had only a marginal influence on transplanted seedlings. Transplantation direction between moderately and highly damaged sites affected infection marginally during the first year and survival as well as leaf traits significantly during the second year. Most notably, seedlings transplanted from moderately damaged to severely damaged sites exhibited the highest infection probability and lowest SLA, while seedlings transplanted vice versa were least likely to be infected and exhibited the highest SLA. Results hint at a first filtering effect by the ash dieback history of a forest stand and might indicate a transition from ecologically to evolutionary driven differentiation of ash seedling responses.

Survival by Selection: The Role of Natural Selection in Developing Biological Radiation Defenses

Survival by Selection: The Role of Natural Selection in Developing Biological Radiation Defenses

Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus

Infectious bronchitis virus (IBV) is distributed worldwide and causes significant losses in the poultry industry. In recent decades, lineages GI-19 and GI-7 have become the most prevalent IBV strains in China. However, the molecular evolution and phylodynamics of the lineage GI-7 IBV strains remain largely unknown. In this study, we identified 19 IBV strains from clinical samples from January 2021 to June 2022 in China, including 12 strains of GI-19, 3 strains of GI-7, and 1 strain each of GI-1, GI-9, GI-13, and GI-28. These results indicated that lineages GI-19 and GI-7 IBVs are still the most prevalent IBVs in China. Here, we investigated the evolution and transmission dynamics of lineage GI-7 IBVs. Our results revealed that the Taiwan province might be the origin of lineage GI-7 IBVs and that South China plays an important role in the spread of IBV. Furthermore, we found low codon usage bias of the S1 gene in lineage GI-7 IBVs. This allowed IBV to replicate in the host during evolution as a result of reduced competition, mainly driven by natural selection and mutational pressure, where the role of natural selection is more prominent. Collectively, our results reveal the genetic diversity and evolutionary dynamics of lineage GI-7 IBVs, which could assist in the prevention and control of viral infection.

Genomic structural variation: A complex but important driver of human evolution.

Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.

Larger genomes show improved buffering of adult fitness against environmental stress in seed beetles.

Our general understanding of the evolution of genome size (GS) is incomplete, and it has long been clear that GS does not reflect organismal complexity. Here, we assess the hypothesis that larger genomes may allow organisms to better cope with environmental variation. It is, for example, possible that genome expansion due to proliferation of transposable elements or gene duplications may affect the ability to regulate and fine-tune transcriptional profiles. We used 18 populations of the seed beetle Callosobruchus maculatus, which differ in GS by up to 4.5%, and exposed adults and juveniles to environmental stress in a series of experiments where stage-specific fitness was assayed. We found that populations with larger genomes were indeed better buffered against environmental stress for adult, but not for juvenile, fitness. The genetic correlation across populations between GS and canalization of adult fitness is consistent with a role for natural selection in the evolution of GS.

Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley's classic species conundrum in Pipilo towhees.

Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley's (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (Pipilo maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. This towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages.

Admixture has obscured signals of historical hard sweeps in humans

The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.

Recentering forensic anthropology within a multifaceted body of evolutionary theory: Strengthening method by making theory explicit

AbstractThe discipline of forensic anthropology has been critiqued for its lack of a theoretical basis. In response, practitioners often assert that their analyses are implicitly grounded in evolutionary theory. However, the nature of this theoretical grounding is little discussed in the forensic anthropology literature, beyond, for example, statements indicating that sex‐based pelvic differences have evolved in response to increasing encephalization within the genusHomo, or that clinal variation in features like limb proportions have evolved within our species due to environmental pressures that differ on a gradient. Further, while the role of natural selection in shaping the morphologies analyzed in biological profile estimation is undeniable, adaptation in response to environmental pressures does not explain all variation within our species. Evolutionary theory is not monolithic; different perspectives on the primacy of functional adaptation versus factors like drift and phenotypic plasticity lead to differences in skeletal interpretations and lead researchers to novel approaches in creating new or improving current methodologies. Various theoretical perspectives underpin forensic anthropological analyses, and in order for forensic anthropology to be truly grounded in evolutionary theory, these theoretical perspectives must be not only made explicit but also interrogated in terms of how they inform forensic anthropological interpretations.

Gaining insights into the compositional constraints and molecular phylogeny of five silkworms mitochondrial genome

This study was performed to identify codon usage bias (CUB), genetic similarity and phylogenetic analysis of complete mitochondrial genomes along with separate sequences of 13 protein coding genes per each genome from five types of silkworm including Bombyx mori, Bombyx mandarina, Samia cynthia ricini, Antheraea pernyi and Antheraea assama. Nucleotide composition analysis suggested that AT content was higher than GC content and t-test analysis revealed significance difference (p < 0.01) between AT and GC content. Relative synonymous CUB analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed both natural selection and mutation pressure influenced CUB of mitochondrial genes while neutrality plot analysis suggested that role of natural selection was higher than mutation pressure. The effective number of codons (ENC) revealed the CUB was low among genes and genomes. In phylogenetic analysis of complete mitochondrial genomes, the Bombyx mori fell in a same cluster with Bombyx mandarina and showed the most similarity (96.7%). In terms of protein coding genes, COX1, COX2 and COX3 showed the most obvious differences. In conclusion, comparative analysis of mitochondrial genomes could be used to identify differences in gene organization, accurate phylogenetic analysis and clustering of different types of silkworms.

Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species.

The role of natural selection in shaping spatial patterns of genetic diversity in the Neotropics is still poorly understood. Here, we perform a genome scan with 24,751 probes targeting 11,026 loci in two Neotropical Bignoniaceae tree species: Handroanthus serratifolius from the seasonally dry tropical forest (SDTF) and Tabebuia aurea from savannas, and compared with the population genomics of H. impetiginosus from SDTF. OutFLANK detected 29 loci in 20 genes with selection signal in H. serratifolius and no loci in T. aurea. Using BayPass, we found evidence of selection in 335 loci in 312 genes in H. serratifolius, 101 loci in 92 genes in T. aurea, and 448 loci in 416 genes in H. impetiginosus. All approaches evidenced several genes affecting plant response to environmental stress and primary metabolic processes. The three species shared no SNPs with selection signal, but we found SNPs affecting the same gene in pair of species. Handroanthus serratifolius showed differences in allele frequencies at SNPs with selection signal among ecosystems, mainly between Caatinga/Cerrado and Atlantic Forest, while H. impetiginosus had one allele fixed across all populations, and T. aurea had similar allele frequency distribution among ecosystems and polymorphism across populations. Taken together, our results indicate that natural selection related to environmental stress shaped the spatial pattern of genetic diversity in the three species. However, the three species have different geographical distribution and niches, which may affect tolerances and adaption, and natural selection may lead to different signatures due to the differences in adaptive landscapes in different niches.

Selection and breeding work in northern reindeer husbandry (to change the development paradigm)

Purpose: Assessment of the current state of breeding and tribal work in northern reindeer herding.Due to the specifics of the content and incomplete dignification, breeding and tribal work in reindeer herding differs from other branches of animal husbandry. In the extreme natural conditions of the area, the interaction of the "genotype environment" has a significant impact on the realization of the genetic potential of the individual. The main selection feature of deer, determining all types of productivity - a living mass, an extremely variable phenotypic parameter, fluctuating in different years, by seasons of the year, by farms, which reduces the accuracy of the assessment of population-genetic parameters. In comparison with other pets, the role of natural selection in the microevolution of the reindeer is more substantial. The breeds of reindems relate to the aboriginal and so far do not have ingenust structures included in the state register of breeding achievements admitted to use. Methods for conducting reindeer tests for distinctness, homogeneity and stability, approved by the Government of the Silvering 24.11.2015, for No. 26-12-06, allows you to identify new types and raise breeding and tribal work in reindeer breeding to a higher level. Its main directions are the study, preservation and management of reindeer genetic resources in order to improve existing and creating new competitive types using high-performance genotyping technologies, accurate phenotyping, bio-information and digital technologies.Creation of methodological platforms and development of technologies that contribute to an increase in the implementation of the genetic potential of breeding forms of animals with improved parameters of economic and useful signs. Development of technologies for a lifetime management of meat quality to obtain high quality and safe food. Formation of a new paradigm of the selection process of creating highly productive forms, characterized by high quality indicators. Transformation of the paradigm "reindeer herding" in the conditions of a digital economy and global changes.

Studying the genetic basis of masting.

The mechanisms underlying mast seeding have traditionally been studied by collecting long-term observational data on seed crops and correlating seedfall with environmental variables. Significant progress in ecological genomics will improve our understanding of the evolution of masting by clarifying the genetic basis of masting traits and the role of natural selection in shaping those traits. Here, we summarize three important aspects in studying the evolution of masting at the genetic level: which traits govern masting, whether those traits are genetically regulated, and which taxa show wide variation in these traits. We then introduce recent studies on the molecular mechanisms of masting. Those studies measure seasonal changes in gene expression in natural conditions to quantify how multiple environmental factors combine to regulate floral initiation, which in many masting plant species is the single largest contributor to among-year variation in seed crops. We show that Fagaceae offers exceptional opportunities for evolutionary investigations because of its diversity at both the phenotypic and genetic levels and existing documented genome sequences. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

Prey preference of a wasp determined by nest size supports the role of natural selection in body size evolution in Cassidinae leaf beetles

Abstract The prey preference of a predator can impose natural selection on prey phenotypes, including body size. Despite evidence that large body size protects against predation in insects, the determinants of body size variation in Cassidinae leaf beetles are not well understood. We examined the prey preference of the digger wasp Cerceris albofasciata, a specialist predator of adult Cassidinae leaf beetles, and found evidence for natural selection on prey body size. The wasp hunted prey smaller than the size of their nest entrance. However, the wasp preferred larger prey species among those that could be carried into their nest. Thus, the benefits of large prey and the cost associated with nest expansion might determine the prey size preference. As expected from the prey species preference, the wasp preferred small individuals of the largest prey species, Thlaspida biramosa, and large individuals of the smallest prey species, Cassida piperata, resulting in natural selection on body sizes. In intermediate-sized prey species, however, there was no evidence for selection on body size. Natural selection on body size might explain the variation of prey morphologies that increase body size, such as explanate margins, in this group.

Genetic purging in captive endangered ungulates with extremely low effective population sizes

Inbreeding threatens the survival of small populations by producing inbreeding depression, but also exposes recessive deleterious effects in homozygosis allowing for genetic purging. Using inbreeding-purging theory, we analyze early survival in four pedigreed captive breeding programs of endangered ungulates where population growth was prioritized so that most adult females were allowed to contribute offspring according to their fitness. We find evidence that purging can substantially reduce inbreeding depression in Gazella cuvieri (with effective population size Ne = 14) and Nanger dama (Ne = 11). No purging is detected in Ammotragus lervia (Ne = 4), in agreement with the notion that drift overcomes purging under fast inbreeding, nor in G. dorcas (Ne = 39) where, due to the larger population size, purging is slower and detection is expected to require more generations. Thus, although smaller populations are always expected to show smaller fitness (as well as less adaptive potential) than larger ones due to higher homozygosis and deleterious fixation, our results show that a substantial fraction of their inbreeding load and inbreeding depression can be purged when breeding contributions are governed by natural selection. Since management strategies intended to maximize the ratio from the effective to the actual population size tend to reduce purging, the search for a compromise between these strategies and purging could be beneficial in the long term. This could be achieved either by allowing some level of random mating and some role of natural selection in determining breeding contributions, or by undertaking reintroductions into the wild at the earliest opportunity.

The Spectrum of Spontaneous Rifampin Resistance Mutations in the Bacillus subtilis rpoB Gene Depends on the Growth Environment.

Results from previous investigations into spontaneous rifampin resistance (Rifr) mutations in the Bacillus subtilis rpoB gene suggested that the spectrum of mutations depends on the growth environment. However, these studies were limited by low sample numbers, allowing for the potential distortion of the data by the presence of "jackpot" mutations that may have arisen early in the growth of a population. Here, we addressed this issue by performing fluctuation analyses to assess both the rate and spectrum of Rifr mutations in two distinct media: LB, a complete laboratory medium, and SMMAsn, a minimal medium utilizing l-asparagine as the sole carbon source. We cultivated 60 separate populations under each growth condition and determined the mutation rate to Rifr to be slightly but significantly higher in LB cultures. We then sequenced the relevant regions of rpoB to map the spectrum of Rifr mutations under each growth condition. We found a distinct spectrum of mutations in each medium; LB cultures were dominated by the H482Y mutation (27/53 or 51%), whereas SMMAsn cultures were dominated by the S487L mutation (24/51 or 47%). Furthermore, we found through competition experiments that the relative fitness of the S487L mutant was significantly higher in SMMAsn than in LB medium. We therefore conclude that both the spectrum of Rifr mutations in the B. subtilis rpoB gene and the fitness of resulting mutants are influenced by the growth environment. IMPORTANCE The rpoB gene encodes the beta subunit of RNA polymerase, and mutations in rpoB are key determinants of resistance to the clinically important antibiotic rifampin. We show here that the spectrum of mutations in Bacillus subtilis rpoB depends on the medium in which the cells are cultivated. The results show that the growth environment not only plays a role in natural selection and fitness but also influences the probability of mutation at particular bases within the target gene.

Random variations, gradualism and the role of natural selection.

While the modern synthesis has at its core the claim that evolution can be entirely explained by the natural selection of random variations, neither "random" nor "variation" is adequately defined. Neo-Darwinists explicitly deny that they use random with the meaning of haphazard, but it is what they assume in their work; if they did not, they could not justify their total concentration on selection and neglect of variations. They conflate variations in the genotype with those in the phenotype. This might be justifiable if the connection between the two were simple and straightforward, but it is not. Like Darwin, neo-Darwinists are committed to the belief that evolution is always gradual. Also like Darwin, they justify this on theoretical rather than empirical grounds and despite acknowledging that the evidence does not support them. The paradox could be resolved by relaxing the commitment to gradualism, but only at the cost of significant consequences for the paradigm.

Genetic structuring of Drosophila bipectinata in Indian natural populations based on the distribution of cosmopolitan inversions

Genetic differentiation among different natural populations of a species depends upon the environmental factors and the evolutionary forces that operate on them. In this study, seven Indian natural populations of D. bipectinata, two from north and five from south India, have been studied for their chromosomal inversion polymorphism. A total of nine paracentric autosomal inversions were recorded from these seven places but only three of them, present on the 2L, 2R and 3L were found to be cosmopolitan in distribution. In all the populations, the frequency of standard gene arrangement was found to be high than their respective cosmopolitan inversion gene arrangement. The average heterozygosity (Ho) of cosmopolitan inversions increases from north to south. There is a latitudinal cline in the distribution of three cosmopolitan inversion arrangements because their frequency increases with the decreasing latitude, i.e. from north to south India. A comparison of the genetic profile of two north Indian and five south Indian natural populations of D. bipectinata reveals the role of natural selection as well as bottleneck effect in the genetic structuring of these populations which may be due to their varying ecological conditions to which they are constantly encountered. Further, the presence of all kinds of paracentric inversions in individual populations was analysed following Poisson distribution to see whether these inversions occur randomly in natural populations or not and the results indicate that north Indian populations show the random occurrence of these inversions than the populations derived from the south.

Phylogenetically diverse diets favor more complex venoms in North American pitvipers

The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates over evolutionary timescales, with apparent increases and decreases in complexity, and yet the causes of this variation are unclear. We tested alternative hypotheses linking venom complexity and ecological sources of selection from diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths. We generated independent transcriptomic and proteomic measures of venom complexity and collated several natural history studies to quantify dietary variation. We then constructed genome-scale phylogenies for these snakes for comparative analyses. Strikingly, prey phylogenetic diversity was more strongly correlated to venom complexity than was overall prey species diversity, specifically implicating prey species' divergence, rather than the number of lineages alone, in the evolution of complexity. Prey phylogenetic diversity further predicted transcriptomic complexity of three of the four largest gene families in viper venom, showing that complexity evolution is a concerted response among many independent gene families. We suggest that the phylogenetic diversity of prey measures functionally relevant divergence in the targets of venom, a claim supported by sequence diversity in the coagulation cascade targets of venom. Our results support the general concept that the diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.

Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala - characterization and phylogenetic analysis.

Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species and scientific basis for phylogenetic revision of the genus Psittacula.

Pregnancy as a Factor of Adaptive Human Evolution. The Role of Natural Selection in the Origin of Preeclampsia

The review discusses the data on the significant role of pregnancy in adaptive evolution of modern humans. In the aspect of evolutionary medicine, the main attention is paid to preeclampsia (PE), a severe hypertensive pathology of pregnancy. The current evolutionary hypotheses about the origin and causes of racial and ethnic variability in the incidence of this pathology in human populations are summarized. Studies that suggest the contribution of adaptive evolution to the formation of a hereditary predisposition to the development of PE are presented. Our results which first showed the significant role of negative selection in the formation of the genetic architecture of PE via the regulatory single nucleotide polymorphisms of new candidate genes for this pathology are demonstrated.