Changes In Gene Frequencies Research Articles

Selenium alters the gene content but not the taxonomic composition of the soil microbiome

Abstract Background Microbiomes, essential to ecosystem processes, face strong selective forces that can drive rapid evolutionary adaptation. However, our understanding of evolutionary processes within natural systems remains limited. We investigated evolution in response to naturally occurring selenium in soils of different geological parental materials on the Western Slope of Colorado. Our study focused on examining changes in gene frequencies within microbial communities in response to selenium exposure. Results Despite expectations of taxonomic composition shifts and increased gene content changes at high-selenium sites, we found no significant alterations in microbial diversity or community composition. Surprisingly, we observed a significant increase in differentially abundant genes within high-selenium sites. Conclusions These findings are suggestive that selection within microbiomes primarily drives the accumulation of genes among existing microbial taxa, rather than microbial species turnover, in response to strong stressors like selenium. Our study highlights an unusual system that allows us to examine evolution in response to the same stressor annually in a non-model system, contributing to understanding microbiome evolution beyond model systems.

Recentering evolution for sustainability science

Abstract Non-technical summary Evolutionary biology considers how organisms and populations change over multiple generations, and so is naturally focused on issues of sustainability through time. Yet, sustainability science rarely incorporates evolutionary thinking and most scientists and policy makers do not account for how evolutionary processes contribute to sustainability. Understanding the interplay between evolutionary processes and nature's contribution to people is key to sustaining life on Earth. Technical summary Evolution, the change in gene frequencies within populations, is a process of genetically based modification by descent, providing the raw material essential for adaptation to environmental change. Therefore, it is crucial that we understand evolutionary processes if we aim for a sustainable planet. We here contribute to this development by describing examples of contemporary, rapid evolutionary changes of concern for sustainability, specifically highlighting the global spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and how the evolutionary toolbox allowed tracking the origins and evolution of SARS-CoV-2 in real time and predicting potential future outbreaks. We also consider how urban development accelerates evolutionary processes such as altered phenotypic and physiological changes and the spread of infectious and zoonotic diseases. We show the importance of evolutionary concepts and techniques for public-health decision making. Many examples of the potential of evolutionary insights contributing to crucial sustainability challenges exist, including infectious and zoonotic diseases, ecosystem and human health, and conservation of natural resources. We thus join recent calls advocating for a stronger collaboration between evolutionary biologists and the sustainability community, increasing interdisciplinarity and the awareness about the knowledge of evolutionary processes for decision making and policies. Social media summary Evolution is fundamental to sustaining life on Earth and should be incorporated in sustainability measures and policies.

Biodiversity change under adaptive community dynamics.

Compositional change is a ubiquitous response of ecological communities to environmental drivers of global change, but is often regarded as evidence of declining "biotic integrity" relative to historical baselines. Adaptive compositional change, however, is a foundational idea in evolutionary biology, whereby changes in gene frequencies within species boost population-level fitness, allowing populations to persist as the environment changes. Here, we present an analogous idea for ecological communities based on core concepts of fitness and selection. Changes in community composition (i.e., frequencies of genetic differences among species) in response to environmental change should normally increase the average fitnessof community members. We refer to compositional changes that improve the functional match, or "fit," between organisms' traits and their environment as adaptive community dynamics. Environmental change (e.g., land-use change) commonly reduces the fit between antecedent communities and new environments. Subsequent change in community composition in response to environmental changes, however, should normally increase community-level fit, as the success of at least some constituent species increases. We argue that adaptive community dynamics are likely to improve or maintain ecosystem function (e.g., by maintaining productivity). Adaptive community responses may simultaneously produce some changes that are considered societally desirable (e.g., increased carbon storage) and others that are undesirable (e.g., declines of certain species), just as evolutionary responses within species may be deemed desirable (e.g., evolutionary rescue of an endangered species) or undesirable (e.g., enhanced virulence of an agricultural pest). When assessing possible management interventions, it is important to distinguish between drivers of environmental change (e.g., undesired climate warming) and adaptive community responses, which may generate some desirable outcomes. Efforts to facilitate, accept, or resist ecological change require separate consideration of drivers and responses, and may highlight the need to reconsider preferences for historical baseline communities over communities that are better adapted to the new conditions.

Modeling and analysis of the Haldane genetic model under Brownian motion using stochastic differential equation

Heterozygote advantage as a natural consequence of adaptation in diploid organisms is an attractive mechanism by which two alleles are maintained in natural populations. It has significant effects on biodiversity conservation and plant and animal breeding programs. The mathematical modeling of this biological mechanism is important for eco-evolutionary dynamics studies and genetics investigations. In this paper, I aimed to formalize the changes of gene frequency in time v(t), and in time and space v(t,x) with additive effects in a birth and death process of the Haldane genetic model using Brownian motion under fluctuations of habitat. In addition, the gene-environment interactions were evaluated under the mechanism. The mathematical model was investigated in both deterministic and white noise forms. It was shown that if the environmental random processes in the Haldane genetic model changed quickly and smoothly, then the diffusion approximation of the allele frequencies could be modeled and analyzed by a stochastic partial differential equation. It was revealed that the mathematical model used in this paper belonged to a more general model. The mathematical model was analyzed and since the modeling by the Cauchy problem had not had a usual global solution, the qualitative behavior of the solutions was considered. Besides, the generalizations of ItÔ integral were defined as the integrals of Wick products of random parameters and noise components. It was found that if v(t,x) behaved like a super-Brownian motion and the fatal mutations took place, as a consequence a tiny group of alleles was quickly disappeared. The v(t,x) was unstable when it was close to one. The stationary phase appeared and v(t,x) tended to the stationary situation in the intermediate region under the stabilizing selection. This was a condition under additive gene effect, but with the presence of dominance gene effect, it might be ambidirectional without considering the epistatic effects. The emergence of the dominance and epistatic effects was due to the directional selection. Since Falconer and MacKay had already introduced a deterministic model to study the frequency of genes with no spatial spreading of the population and no stochastic processes, another model was explained to study their equation in the case of heterozygote intermediate for diffusion approximation of frequency of genes, including white noise. It was shown that if the rates of mutation and selection became very small, then the model would be more deterministic and predictable. On the other hand, if the rates of mutation and selection became large, then the model would be more stochastic, and more fluctuations occurred because of the strong effective noise strength. In this case, the stationary situation did not take place. The outlook can help to model the similar biological mechanisms in eco-evolutionary community genetics for studying the indirect genetic effects via the systems of stochastic partial differential equations, and white noise calculus.

PHYLOGENETIC PROCESSES IN EUROPEAN AND ASIAN PIG POPULATIONS

As a result of evolution, a gradual change in the hereditary structure of a species, not only the number of genes changes, but also their properties, frequency, and direction of variability. Changes in gene frequencies occurring over a relatively small period of time belong to microevolution. The breeding process in pig breeding is the microevolutionary processes originating from the ancestral forms of Sus scrofa to the modern specialized breeds of pigs. Genetic monitoring of the genetic systems of blood groups makes it possible to assess the genetic structure and processes occurring in populations. The microevolutionary process of transformation of wild ancestral forms over the last 10-12 thousand years from transitional forms of local aboriginal to factory breeds has occurred with significant genetic and phenotypic transformations in animal populations. In this connection, it is important to clarify the correct understanding of the terms 'population' and 'breed'. Naturally, any breed is a population, but not any population is not a breed, especially since both population and population as taxonomic terms have different interpretations. In the first place, a distinction must be made between wild populations, in which microevolution takes place only by means of natural selection, and breed populations, in the development of which artificial selection was involved as a fundamental factor in microevolution. Depending on the level of methods and forms of selection, we have to distinguish local indigenous populations (e.g., Kakhetian and Mangali breeds) and basic factory breeds (Large White, Berkshire, Landrace, Duroc, etc.), which have been created for decades and centuries. The concept of a breed is closely linked to the size of the reproductive population and the range of distribution. According to FAO, in 2006 there were some 730 breeds and lines of pigs worldwide, most of which are bred in China and Europe, and 270 of which are regarded as rare breeds. At the same time, 58 breeds (25 regional and 33 international) are registered as common, i.e. occurring in more than one country. Five international breeds are now widely distributed: Large White (117 countries), Duroc (93 countries), Landrace (91 countries), Hampshire (54 countries) and Petren (35 countries).

Maternal-Offspring Interactions: Reciprocally Coevolving Social Environments.

Maternal-zygotic co-evolution is one of the most common examples of indirect genetic effects. I investigate how maternal-zygotic gene interactions affect rates of evolution and adaptation. Using comparably parameterized population genetic models, I compare evolution to an abiotic environment with genotype-by-environment interaction (G × E) to evolution to a maternal environment with offspring genotype-by-maternal environment interaction (G × Gmaternal). There are strong parallels between the 2 models in the components of fitness variance but they differ in their rates of evolution measured in terms of ∆p, gene frequency change, or of ∆W, change in mean fitness. The Price Equation is used to partition ∆W into 2 components, one owing to the genetic variance in fitness by natural selection and a second owing to change in environment. Adaptive evolution is faster in the 2-locus model with G × Gmaternal with free recombination, than it is in the 1-locus model with G × E, because in the former the maternal genetic environment coevolves with the zygotic phenotype adapting to it. I discuss the relevance of these findings for the evolution of genes with indirect genetic effects.

When is Offspring Viability Fitness a Measure of Paternal Fitness and When is it not?

We use population genetics to model the evolution of a gene with an indirect effect owing to paternal care and with a second pleiotropic, direct effect on offspring viability. We use the model to illustrate how the common empirical practice of considering offspring viability as a component of parent fitness can confound a gene’s direct and indirect fitness effects. We investigate when this confounding results in a distorted picture of overall evolution and when it does not. We find that the practice has no effect on mean fitness, W, but it does have an effect on the dynamics of gene frequency change, ∆q. We also find that, for some regions of parameter space associated with fitness trade-offs, the distortion is not only quantitative but also qualitative, obscuring the direction of gene frequency change. Because it affects the evolutionary dynamics, it also affects the expected amount of genetic variation at mutation-selection balance, an important consideration in molecular evolution. We discuss empirical techniques for separating direct from indirect effects and how field studies measuring the value of male paternal care might be improved by using them.

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding.

The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.

2La Paracentric Chromosomal Inversion and Overexpressed Metabolic Genes Enhance Thermotolerance and Pyrethroid Resistance in the Major Malaria Vector Anopheles gambiae.

Simple SummaryWhile shifts in temperature may promote the spread of insects, exacerbating the intensity of vector-borne diseases like malaria, very high temperatures exert deleterious effects in insect vectors, forcing them to evolve/adapt genetically. These genetic adaptations may facilitate insecticide resistance through common genes involved in both processes. Here, the impact of thermal tolerance on pyrethroid resistance in the major malaria vector Anopheles gambiae s.l. from four localities spanning the savanna and sub-Sahel of northern Nigeria was investigated. In all four localities, An. coluzzii and An. gambiae s.s. were the only malaria vectors found. The populations were highly thermotolerant, with ~50% of mosquitoes in two sites surviving 44 °C. Thermotolerant larvae and adult mosquitoes (survivors of 44 °C) were significantly more resistant to permethrin, suggesting that prior heat-hardening facilitates insecticide resistance. Thermal tolerance and permethrin resistance were found to be associated with the 2La rearrangement (a form of chromosomal inversion). Transcriptional analysis revealed six major genes commonly overexpressed in the highly thermotolerant mosquitoes and those resistant to permethrin, suggesting common mechanisms involved in thermotolerance and insecticide resistance. These findings highlight challenges associated with insecticide-based malaria vector control, stressing the need to take environmental variables and other pleiotropic mechanisms into account for the choice of control measures.Changes in global temperature are impacting the spread/intensity of vector-borne diseases, including malaria, and accelerating evolutionary/adaptive changes in vector species. These changes, including chromosomal inversions and overexpression and/or changes in allele frequencies of thermotolerance-associated genes, may facilitate insecticide resistance through pleiotropy. This study investigated the impact of thermotolerance on pyrethroid resistance in four populations of the malaria vector An. gambiae s.l., from the savanna/sub-Sahel of northern Nigeria. Anopheles coluzzii and An. gambiae s.s. were the only malaria vectors found, sympatric in all the sites, with the former species predominant. High thermotolerance was observed, with no mortality at 38 °C, and LT50 of ~44 °C. Significantly high permethrin resistance was observed (mortality < 50%) in 44 °C heat-hardened (exposure to an intermediately high temperature provides protection to a more severe temperature or insecticide) larvae from two sites, BUK and Pantami, compared with the control, and heat-hardened adult females from Auyo (mortality = 3.00% ± 1.20, χ2 = 5.83, p < 0.01) compared with the control (12.00% ± 4.65). The 2La chromosomal inversion was detected at ~50% in subset of larvae and 58% in subset of adult females genotyped. A significant association was observed (OR = 7.2, p < 0.03) between permethrin resistance and the 2La/+a rearrangement compared with 2L+a/+a, in BUK larvae. For all sites, permethrin resistance correlated with 2La/a homozygosity in adult females (R = 5.02, p = 0.01). qRT-PCR identified six genes commonly induced/overexpressed, including the heat shock protein 70 (AGAP004581) which was 2468× and 5× overexpressed in heat-hardened and permethrin-resistant females, respectively; trehalose-6-phosphate synthase (AGAP008227); and the ionotropic glutamate receptor genes, IR25a (AGAP010272) and IR21a (AGAP008511). This study highlights challenges associated with insecticide-based malaria vector control, and the epidemiological significance of taking climate variables into account for the design/choice of control measures.

Extending the range of additivity in using inclusive fitness.

Inclusive fitness is a concept widely utilized by social biologists as the quantity organisms appear designed to maximize. However, inclusive fitness theory has long been criticized on the (uncontested) grounds that other quantities, such as offspring number, predict gene frequency changes accurately in a wider range of mathematical models. Here, we articulate a set of modeling assumptions that extend the range of scenarios in which inclusive fitness can be applied. We reanalyze recent formal analyses that searched for, but did not find, inclusive fitness maximization. We show (a) that previous models have not used Hamilton's definition of inclusive fitness, (b) a reinterpretation of Hamilton's definition that makes it usable in this context, and (c) that under the assumption of probabilistic mixing of phenotypes, inclusive fitness is indeed maximized in these models. We also show how to understand mathematically, and at an individual level, the definition of inclusive fitness, in an explicit population genetic model in which exact additivity is not assumed. We hope that in articulating these modeling assumptions and providing formal support for inclusive fitness maximization, we help bridge the gap between empiricists and theoreticians, which in some ways has been widening, demonstrating to mathematicians why biologists are content to use inclusive fitness, and offering one way to utilize inclusive fitness in general models of social behavior.

The evolutionary genetics of paternal care: How good genes and extrapair copulation affect the trade-off between paternal care and mating success.

We investigate the evolution of a gene for paternal care, with pleiotropic effects on male mating fitness and offspring viability, with and without extrapair copulations (EPCs). We develop a population genetic model to examine how pleiotropic effects of a male mating advantage and paternal care are affected by “good genes” and EPCs. Using this approach, we show that the relative effects of each on fitness do not always predict the evolutionary change. We then find the line of combinations of mating success and paternal care that bisects the plane of possible values into regions of positive or negative gene frequency change. This line shifts when either good genes or EPCs are introduced, thereby expanding or contracting the region of positive gene frequency change and significantly affecting the evolution of paternal care. Predictably, a direct viability effect of “good genes” that enhances offspring viability constrains or expands the parameter space over which paternal care can evolve, depending on whether the viability effect is associated with the paternal care allele or not. In either case, the effect of a “good gene” that enhances offspring viability is substantial; when strong enough, it can even facilitate the evolution of poor paternal care, where males harm their young. When nonrandom mating is followed by random EPCs, the genetic regression between sire and offspring is reduced and, consequently, the relative strengths of selection are skewed away from paternal care and toward the male mating advantage. However, when random mating is followed by nonrandom EPCs, a situation called “trading up” by females, we show that selection is skewed in the opposite direction, away from male mating advantage and toward paternal care across the natural range of EPC frequencies.

Sepsis: An Evolutionary Perspective (Sepsis through the Eyes of a Microbe vs Clinical Sepsis through the Eyes of an Intensivist).

“Change of gene frequency in population” is the most fundamental concept of evolutionary biology. Human sepsis is a quantitative biological war between microbial genes and human genes, fought through their respective phenotypes. The prize of this war is an increase of gene frequency. Stating that sepsis is caused by a dysregulated host response is missing one half of the septic syndrome. Clinicians may gain a different perspective into the many intricacies of sepsis by conceptualizing it as an adaptive evolutionary process, rather than an abnormal physiological state. Clinicians may also get a deeper perspective by seeing it as a genotypic evolutionary process of natural selection rather than a phenotypic pathophysiological event.How to cite this article: Kapadia FN. Sepsis: An Evolutionary Perspective (Sepsis through the Eyes of a Microbe vs Clinical Sepsis through the Eyes of an Intensivist). Indian J Crit Care Med 2020;24(12):1165–1168.

O PERFIL GENÉTICO DO POVO CUNHAMA

O presente trabalho faz uma análise sobre o perfil genético do povo Cunhama, tendo como objectivo avaliar as características genotípicas de 15 marcadores STRs, no grupo étnico Cuanhama. O povo Cuanhama é residente na sua maioria no Sul de Angola e a Norte da Namíbia, visto que nos últimos tempos a população humana cresce num ritmo acelerado, com ela aumenta cada vez mais o processo de migração populacional, contribuindo de certa medida para a alteração das características genotípicas da população. Do mesmo modo que a deriva genética, as migrações têm um efeito evolutivo porque são capazes de promover alterações das frequências génicas, tanto nas populações da qual se originam os imigrantes quanto naquelas que os recebem. O povo Cuanhama foi, durante muito tempo, considerado um povo homogéneo, isto é, o envolvimento com outros povos era expressamente proibido; daí a necessidade de conhecer os efeitos dos movimentos migratórios no pool genético do povo. Para tal, estudaremos o perfil genético deste povo usando microssatélites, que constituem uma das mais importantes classes de marcadores moleculares utilizados atualmente em estudos populacionais.

Climate change and the genetics of insecticide resistance.

Changes in global temperature and humidity as a result of climate change are producing rapid evolutionary changes in many animal species, including agricultural pests and disease vectors, leading to changes in allele frequencies of genes involved in thermotolerance and desiccation resistance. As some of these genes have pleiotropic effects on insecticide resistance, climate change is likely to affect insecticide resistance in the field. In this review, we discuss how the interactions between adaptation to climate change and resistance to insecticides can affect insecticide resistance in the field using examples in phytophagous and hematophagous pest insects, focusing on the effects of increased temperature and increased aridity. We then use detailed genetic and mechanistic studies in the model insect, Drosophila melanogaster, to explain the mechanisms underlying this phenomenon. We suggest that tradeoffs or facilitation between adaptation to climate change and resistance to insecticides can alter insecticide resistance allele frequencies in the field. The dynamics of these interactions will need to be considered when managing agricultural pests and disease vectors in a changing climate. © 2019 Society of Chemical Industry.

Quantifying evolution by natural selection

The theme of this paper is that Fisher's “Fundamental Theorem of Natural Selection” has various deficiencies as a quantification of the effect of natural selection in a Mendelian population which are not shared by a new different theorem described in this paper. The deficiencies in Fisher's theorem are listed in this paper. The new theorem focuses on the implications of changes in gene frequencies under natural selection and not, as does the Fundamental Theorem of Natural Selection, on changes in mean population fitness. Whereas the algebra in the new theorem corresponds in places to that in the Fundamental Theorem of Natural Selection, the approach, perspective and conclusion of the new theorem are different from those of the Fundamental Theorem of Natural Selection.

Inclusive fitness as a criterion for improvement

I distinguish two roles for a fitness concept in the context of explaining cumulative adaptive evolution: fitness as a predictor of gene frequency change, and fitness as a criterion for phenotypic improvement. Critics of inclusive fitness argue, correctly, that it is not an ideal fitness concept for the purpose of predicting gene-frequency change, since it relies on assumptions about the causal structure of social interaction that are unlikely to be exactly true in real populations, and that hold as approximations only given a specific type of weak selection. However, Hamilton took this type of weak selection, on independent grounds, to be responsible for cumulative assembly of complex adaptations. In this special context, I argue that inclusive fitness is distinctively valuable as a criterion for improvement and a standard for optimality. Yet to call inclusive fitness a criterion for improvement and a standard for optimality is not to make any claim about the frequency with which inclusive fitness optimization actually occurs in nature. This is an empirical question that cannot be settled by theory alone. I close with some reflections on the place of inclusive fitness in the long running clash between ‘causalist’ and ‘statisticalist’ conceptions of fitness.

LearnPopGen: An R package for population genetic simulation and numerical analysis.

Here, I briefly present a new R package called learnPopGen that has been designed primarily for the purposes of teaching evolutionary biology, population genetics, and evolutionary theory. Functions of the package can be used to conduct simulations and numerical analyses of a wide range of evolutionary phenomena that would typically be covered in advanced undergraduate through graduate‐level curricula in population genetics or evolution. For instance, learnPopGen functions can be used to visualize gene frequency changes through time under multiple deterministic and stochastic processes, to compute and animate the changes in phenotypic trait values or distributions under natural selection, to numerically analyze and graph the outcome of simple game theory models, and to plot coalescence within a population experiencing genetic drift, along with a number of other things. Functions have been designed to be maximally didactic and frequently employ compelling animated visualizations. Furthermore, it is straightforward to export plots and animations from R in the form of flat or animated graphics, or as videos. For maximum flexibility, students working with the package can run functions directly in R; however, instructors may choose to guide students less adept in the R environment to one of various web interfaces that I have built for a number of the functions of the package and that are already available online.

Inclusive fitness is an indispensable approximation for understanding organismal design.

For some decades most biologists interested in design have agreed that natural selection leads to organisms acting as if they are maximizing a quantity known as “inclusive fitness.” This maximization principle has been criticized on the (uncontested) grounds that other quantities, such as offspring number, predict gene frequency changes accurately in a wider range of mathematical models. Here, we adopt a resolution offered by Birch, who accepts the technical difficulties of establishing inclusive fitness maximization in a fully general model, while concluding that inclusive fitness is still useful as an organizing framework. We set out in more detail why inclusive fitness is such a practical and powerful framework, and provide verbal and conceptual arguments for why social biology would be more or less impossible without it. We aim to help mathematicians understand why social biologists are content to use inclusive fitness despite its theoretical weaknesses. Here, we also offer biologists practical advice for avoiding potential pitfalls.

The left-hand side of the Fundamental Theorem of Natural Selection: A reply

In a recent paper, Grafen (2018) discussed the left-hand side in the equation stating Fisher’s (1930, 1958) “Fundamental Theorem of Natural Selection” (FTNS). Fisher’s original statement of the FTNS is, in effect, “The rate of increase in fitness of any organism is equal to its genetic variance in fitness at that time” with the rate of increase in fitness understood as the one “due to all changes in gene ratios” (Fisher, 1930, p. 35). For purposes of exposition, Grafen (2018) considered what is today called the analogous discrete-time model, and restated the FTNS on p. 181 as “The increase in population [mean fitness] due to changes in gene frequencies [is equal to the] additive genetic variance in fitness [divided by the] mean fitness”. Allowing for the fact that Grafen’s statement of the FTNS relates to a discrete-time model, his statement is in effect a discrete-time version of Fisher’s. It has however been widely accepted for many years, ever since Price’s (1972) deep analysis of the FTNS, that Fisher’s wording does not correctly describe the content of the FTNS. The same is therefore true of Grafen’s statement. The confusion caused by these misstatements is unfortunate and adds to a continuing misunderstanding of the FTNS, whose source can also be found in Fisher’s (1941) own explanation. Our purpose is to review the detailed analysis of the calculations leading to the FTNS to clarify the points at issue.

Changes in gene and genotype frequencies during the development of the grass carp Ctenopharyngodon idella.

In this study, a full-sib population of Ctenopharyngodon idella was constructed and approximately 500 C. idella individuals were sampled at four early developmental stages (hatching, first feeding, juvenile fish and young fish). Four DNA pools were constructed and subjected to next-generation sequencing. On the basis of the identification of single nucleotide polymorphisms (SNP), changes in gene and genotype frequencies during the developmental progress of C. idella were revealed, which indicates that death during the early developmental stage is not a random process. These findings will establish the basis for further studies performed for identifying superior alleles or genotypes as target markers for molecular breeding.