Concept In Evolutionary Biology Research Articles

Genetic enhancement from the perspective of transhumanism: exploring a new paradigm of transhuman evolution.

Transhumanism is a movement that advocates for the enhancement of human capabilities through the use of advanced technologies such as genetic enhancement. This article explores the definition, history, and development of transhumanism. Then, it compares the stance on genetic enhancement from the perspectives of bio-conservatism, bio-liberalism, and transhumanism. This article posits that transhuman evolution has twofold implications, allowing for the integration of transhumanist research and evolutionary biology. First, it offers a compelling scientific framework for understanding genetic enhancement, avoiding technological progressivism, and incorporating concepts of evolutionary biology. Second, it represents a new evolutionary paradigm distinct from traditional Lamarckism and Darwinism. It marks the third synthesis of evolutionary biology, offering fresh perspectives on established concepts such as artificial selection and gene-culture co-evolution. In recent decades, human enhancement has captivated not only evolutionary biologists, neurobiologists, psychologists, and philosophers, but also those in fields such as cybernetics and artificial intelligence. In addition to genetic enhancement, other human enhancement technologies, including brain-computer interfaces and brain uploading, are currently under development, which the paradigm of transhuman evolution can better integrate into its framework.

The improbability of detecting trade-offs and some practical solutions.

Trade-offs are a fundamental concept in evolutionary biology because they are thought to explain much of nature's biological diversity, from variation in life-histories to differences in metabolism. Despite the predicted importance of trade-offs, they are notoriously difficult to detect. Here we contribute to the existing rich theoretical literature on trade-offs by examining how the shape of the distribution of resources or metabolites acquired in an allocation pathway influences the strength of trade-offs between traits. We further explore how variation in resource distribution interacts with two aspects of pathway complexity (i.e., the number of branches and hierarchical structure) affects tradeoffs. We simulate variation in the shape of the distribution of a resource by sampling 106 individuals from a beta distribution with varying parameters to alter the resource shape. In a simple "Y-model" allocation of resources to two traits, any variation in a resource leads to slopes less than -1, with left skewed and symmetrical distributions leading to negative relationships between traits, and highly right skewed distributions associated with positive relationships between traits. Adding more branches further weakens negative and positive relationships between traits, and the hierarchical structure of pathways typically weakens relationships between traits, although in some contexts hierarchical complexity can strengthen positive relationships between traits. Our results further illuminate how variation in the acquisition and allocation of resources, and particularly the shape of a resource distribution and how it interacts with pathway complexity, makes its challenging to detect trade-offs. We offer several practical suggestions on how to detect trade-offs given these challenges.

Testing the form-function paradigm: body shape correlates with kinematics but not energetics in selectively-bred birds

A central concept of evolutionary biology, supported by broad scale allometric analyses, asserts that changing morphology should induce downstream changes in locomotor kinematics and energetics, and by inference selective fitness. However, if these mechanistic relationships exist at local intraspecific scales, where they could provide substrate for fundamental microevolutionary processes, is unknown. Here, analyses of selectively-bred duck breeds demonstrate that distinct body shapes incur kinematic shifts during walking, but these do not translate into differences in energetics. A combination of modular relationships between anatomical regions, and a trade-off between limb flexion and trunk pitching, are shown to homogenise potential functional differences between the breeds, accounting for this discrepancy between form and function. This complex interplay between morphology, motion and physiology indicates that understanding evolutionary links between the avian body plan and locomotor diversity requires studying locomotion as an integrated whole and not key anatomical innovations in isolation.

Deciphering climate resilience in Indian cattle breeds by selection signature analyses.

The signature of selection is a crucial concept in evolutionary biology that refers to the pattern of genetic variation which arises in a population due to natural selection. In the context of climate adaptation, the signature of selection can reveal the genetic basis of adaptive traits that enable organisms to survive and thrive in changing environmental conditions. Breeds living in diverse agroecological zones exhibit genetic "footprints" within their genomes that mirror the influence of climate-induced selective pressures, subsequently impacting phenotypic variance. It is assumed that the genomes of animals residing in these regions have been altered through selection for various climatic adaptations. These regions are known as signatures of selection and can be identified using various summary statistics. We examined genotypic data from eight different cattle breeds (Gir, Hariana, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, and Tharparkar) that are adapted to diverse regional climates. To identify selection signature regions in thisinvestigation, we used four intra-population statistics: Tajima's D, CLR, iHS, and ROH. In this study, we utilized Bovine 50K chip data and four genome scan techniques to assess the genetic regions of positive selection for high-temperature adaptation. We have also performed a genome-wide investigation of genetic diversity, inbreeding, and effective population size in our target dataset. We identified potential regions for selection that are likely to be caused by adverse climatic conditions. We observed many adaptation genes in several potential selection signature areas. These include genes like HSPB2, HSPB3, HSP20, HSP90AB1, HSF4, HSPA1B, CLPB, GAP43, MITF, and MCHR1 which have been reported in the cattle populations that live in varied climatic regions. The findings demonstrated that genes involved in disease resistance and thermotolerance were subjected to intense selection. The findings have implications for marker-assisted breeding, understanding the genetic landscape of climate-induced adaptation, putting breeding andconservation programs into action.

Darwin's 'mystery of mysteries': the role of sexual selection in plant speciation.

Sexual selection is considered one of the key processes that contribute to the emergence of new species. While the connection between sexual selection and speciation has been supported by comparative studies, the mechanisms that mediate this connection remain unresolved, especially in plants. Similarly, it is not clear how speciation processes within plant populations translate into large-scale speciation dynamics. Here, we review the mechanisms through which sexual selection, pollination, and mate choice unfold and interact, and how they may ultimately produce reproductive isolation in plants. We also overview reproductive strategies that might influence sexual selection in plants and illustrate how functional traits might connect speciation at the population level (population differentiation, evolution of reproductive barriers; i.e. microevolution) with evolution above the species level (macroevolution). We also identify outstanding questions in the field, and suitable data and tools for their resolution. Altogether, this effort motivates further research focused on plants, which might potentially broaden our general understanding of speciation by sexual selection, a major concept in evolutionary biology.

Abiraterone-Docetaxel scheduling for metastatic castration-resistant prostate cancer based on evolutionary dynamics.

Patients with metastatic castration-resistant prostate cancer (mCRPC) are divided into three groups based on their response to Abiraterone treatment: best responder, responder, and non-responder. In the latter two groups, successful outcomes may not be achieved due to the development of drug-resistant cells in the tumor environment during treatment. To overcome this challenge, a secondary drug can be used to control the population of drug-resistant cells, potentially leading to a longer period of disease inhibition. This paper proposes using a combination of Docetaxel and Abiraterone in some polytherapy methods to control both the overall cancer cell population and the drug-resistant subpopulation. To investigate the competition and evolution of mCRPC cancer phenotypes, as in previous studies, the Evolutionary Game Theory (EGT) has been used as a mathematical modeling of evolutionary biology concepts.

The Selfish Gene as a Possible Driving Force Behind HIIT

Purpose: High-Intensity Interval Training (HIIT) is a training method aimed at increasing the fitness of individuals. It is based on a combination of periods in which high-intensity alternate with low-intensity exercise or passive rest. The topic of this paper is a reflection on the benefits and risks of HIIT health use in recreational athletes. We investigate humans' conscious and unconscious motivations for choosing this specific method in the philosophical discourse. Problem: HIIT is a method that, in some ways and with particular approaches, strongly reflects the imperative of the postmodern age - to get as much as possible, as quickly as possible. Martin Heidegger perceives three fundamental existentials in the context of temporality – historicity, everydayness, and within-time-ness. Here conscious motivation may be linked to the temporal characteristic of human being. As Richard Dawkins presents, unconscious motivation may be related to the application of the selfish gene theory. The philosophical approach to the problem: The Heideggerian concept of temporality leads us to research the authenticity and inauthenticity of the Dasein phenomenon. Some features of motivation for applying HIIT can be examined as inauthentic forms of being. In focusing on possible elements of unconscious motivation, the concept of evolutionary biology, namely Dawkins's theory of the selfish gene, provides a unique platform. It is primarily (a human) effort to spread genes. Here, in connection with HIIT, we build on the concepts of replicator and vehicle and deal with the basic selection unit of evolution and its form. Conclusions: HIIT presents an exciting training method that is examined in the context of effectivity of sports training, social benefits, or health aspects. Here we would like to offer the HIIT concept as the reflection of philosophical (mainly ontological, partly ethical) discourse.

Evaluating the dissemination of evolutionary biology concepts in medicine.

Darwin's theory of evolution, which is based on variation, heredity, and selection, includes all biological fields and spreads to other areas such as philosophy. Medicine is an example of how the evolutionary perspective can greatly improve the understanding of concepts in an area, as human health and pathological conditions are under the effect of evolution. Evolutionary medicine is an emerging paradigm for understanding human heterogeneity, health, and diseases. Nevertheless, there are indications that medical research and practice are only marginally affected by these ideas. Here, we investigate how concepts of biological evolution are employed in medical research. We use a bibliometric approach to look for the presence and frequency of biological evolution-related concepts in medical articles. The distribution of these concepts over the years is analyzed according to the medical specialty and the impact of the journal. Our data showed that: i) only a small percentage of articles in medical journals have an evolutionary perspective; ii) medical journals where these evolution-based articles are published focus on basic science, theoretical medicine, and less frequently, on applied medicine; iii) these articles are mostly from the microbiology, immunology, neurology, psychology, behavior, and oncology fields; and iv) viruses are the most frequently covered microorganisms, followed by bacteria, fungi, and protozoans. The collection of our results, considering the importance of evolutionary medicine in the medical field, highlights the need for a decisive change in perspective in medical research.

The female orgasm and the homology concept in evolutionary biology.

The definition of homology and its application to reproductive structures, external genitalia, and the physiology of sexual pleasure has a tortuous history. While nowadays there is a consensus on the developmental homology of genital and reproductive systems, there is no agreement on the physiological translation, or the evolutionary origination and roles, of these structural correspondences and their divergent histories. This paper analyzes the impact of evolutionary perspectives on the homology concept as applied to the female orgasm, and their consequences for the biological and social understanding of female sexuality and reproduction. After a survey of the history of pre-evolutionary biomedical views on sexual difference and sexual pleasure, we examine how the concept of sexual homology was shaped in the new phylogenetic framework of the late 19th century. We then analyse the debates on the anatomical locus of female pleasure at the crossroads of theories of sexual evolution and new scientific discourses in psychoanalysis and sex studies. Moving back to evolutionary biology, we explore the consequences of neglecting homology in adaptive explanations of the female orgasm. The last two sections investigate the role played by different articulations of the homology concept in evolutionary developmental explanations of the origin and evolution of the female orgasm. These include the role of sexual, developmental homology in the byproduct hypothesis, and a more recent hypothesis where a phylogenetic, physiological concept of homology is used to account for the origination of the female orgasm. We conclude with a brief discussion on the social implications for the understanding of female pleasure derived from these different homology frameworks.

A special issue of Essays in Biochemistry on evolutionary developmental biology.

Evolutionary developmental biology (or evo devo) is a broad field that aims to understand how developmental processes evolve and how this underpins phenotypic change and organismal diversification. This encompasses a need to understand theoretical concepts in evolutionary biology and how tissues, cells, genes, proteins and regulatory elements function and evolve. The articles in this special issue review key topics in the field of evo devo including advances in theory and methodology as well as our latest knowledge about molecular, cellular and organismal functionality and diversification.

What is reproductive isolation?

Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches.

Active Learning Strategies for Biodiversity Science

Organismal courses are inherently integrative, incorporating concepts from genetics, physiology, ecology and other disciplines linked through a comparative and phylogenetic framework. In a comprehensive organismal course, the organisms themselves are a lens through which students view and learn major concepts in evolutionary biology. Here, we present the learning goals of five core concepts (phylogenetics, biogeography, biodiversity, evo-devo, and key traits) we are using to transform organismal courses. We argue that by focusing on organismal knowledge and authentic examples, students learn foundational concepts and investigate biological hypotheses through the content that is unique to individual organismal groups. By using active learning strategies to teach core concepts, instructors can promote an inclusive classroom designed to engage students from diverse backgrounds and facilitate mastery and retention to test understanding of core biological concepts. This paper provides justification for why organismal biology needs to be kept as part of the biology curriculum, outlines the framework we are using to transform organismal courses, and provides examples of different ways instructors can incorporate active learning strategies and in-class activities in organismal courses in ways that enable their application to further investigation of both foundational and translational sciences for students.

Developing the BETTSI: A tree-thinking diagnostic tool to assess individual elements of representational competence.

Phylogenies are a ubiquitous visual representation of core concepts in evolutionary biology and it is important that students develop an ability to read and correctly interpret these diagrams. However, as with any representation of complex disciplinary information, learning to correctly interpret phylogenies can be challenging, requiring that a diversity of educational strategies be deployed. Representational competence is the ability to develop and effectively use abstract representations. Accurately interpreting a phylogenetic tree as a presentation of evolutionary relationships requires that students develop general representational competence as well as knowledge of specific technical aspects of tree interpretation, such as knowing the graphical components of trees and what they represent. Here, we report on the development of a basic diagnostic tool of students’ representational competence and technical skills with phylogenies, the Basic Evolutionary Tree‐Thinking Skills Instrument (BETTSI). This short, multiple‐choice instrument was designed to provide instructors with a quick diagnostic of students’ ability to read and interpret phylogenies. It has been checked for reliability and validity and provides a convenient formative and summative assessment of students’ understanding of evolutionary trees.

Numerical Simulation of Gas Lift Optimization Uses Genetic Algorithm

This article, written by JPT Technology Editor Chris Carpenter, contains highlights of paper IPTC 20254, “Numerical Simulation of Gas Lift Optimization Using Genetic Algorithm for a Middle East Oil Field: Feasibility Study,” by Mustafa AlJuboori and Mofazzal Hossain, SPE, Curtin University, and Omar Al-Fatlawi, SPE, University of Baghdad, et al. The paper has not been peer reviewed. Copyright 2021 International Petroleum Technology Conference. Reproduced by permission. Optimal allocation of gas-injection rates in large fields through a gas lift network is a challenging task. Traditional gas lift optimization programs may prove inefficient or incapable of modeling gas lift optimization in extremely large networks. The key objective of the complete paper is to assess the feasibility of using the genetic algorithm (GA) technique to optimize the allocation of continuous gas lift injection rate in a network of a Middle Eastern oil field with 43 gas lift injected wells through numerical modeling and simulation studies. GA GA is an optimization technique that solves constrained and unconstrained optimization problems through a natural-selection process based on the concept of evolutionary biology, including the fundamental processes of selection, crossover, and mutation. Instead of considering a single point or solution, a population of solutions is designed. The algorithm modifies the population of individual solutions repetitively, selects individuals randomly from the current population as parents, and uses these parents to produce the children for the next generation. The population evolves over successive generations toward an optimal solution. The solution process of GA follows different principles as compared with conventional approaches. These fundamental differences are as follows: - GA uses objective function. - Instead of using a single point, it uses a population of design points or variables that avoid a local optimum solution. - Strings of binary numbers represent the design variables, which are similar to chromosomes in genetics, so discrete and integer problems are naturally applicable to GA. GA avoids falling into local optimums by sustaining multiple points to multiple-point approaches of each generation. In such a method, the probability of surviving the best, fittest solution is high as compared with a low-fitness solution. As a result, the GA mostly will result in a global optimal solution. GA techniques consists of five basic phases: - Initial population - Fitness function - Selection - Crossover - Mutation The process begins with an initial population comprising a set of individuals (i.e., solutions) within a search space. An individual is characterized by a range of combinations of the design variables (or parameters) termed “genes,” which are joined into a string to form a chromosome (or solution). For each solution, the objective function is assessed with regard to its level of fitness. Each solution is paired with another to form a mating pair, used for reproduction of subsequent populations. The mating pairs produce new solutions as offspring, which retain values of the design variables generated by crossover of the parents’ values. In addition, random mutation is introduced to some of the new solution’s values. The process of GA technique is random, even though its optimization permits one solution to establish the level of control.

Genie: an interactive real-time simulation for teaching genetic drift

Neutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is especially challenging. Here we present Genie, a browser-based educational tool that demonstrates population-genetic concepts such as genetic drift, population isolation, gene flow, and genetic mutation. Because it does not need to be downloaded and installed, Genie can scale to large groups of students and is useful for both in-person and online instruction. Genie was used to teach genetic drift to Evolution students at Arizona State University during Spring 2016 and Spring 2017. The effectiveness of Genie to teach key genetic drift concepts and misconceptions was assessed with the Genetic Drift Inventory developed by Price et al. (CBE Life Sci Educ 13(1):65–75, 2014). Overall, Genie performed comparably to that of traditional static methods across all evaluated classes. We have empirically demonstrated that Genie can be successfully integrated with traditional instruction to reduce misconceptions about genetic drift.

Differential effects of steroid hormones on levels of broad-sense heritability in a wild bird: possible mechanism of environment × genetic variance interaction?

Genetic variation is one of the key concepts in evolutionary biology and an important prerequisite of evolutionary change. However, we know very little about processes that modulate its levels in wild populations. In particular, we still are to understand why genetic variances often depend on environmental conditions. One of possible environment-sensitive modulators of observed levels of genetic variance are maternal effects. In this study we attempt to experimentally test the hypothesis that maternally transmitted agents (e.g. hormones) may influence the expression of genetic variance in quantitative traits in the offspring. We manipulated the levels of steroid hormones (testosterone and corticosterone) in eggs laid by blue tits in a wild population. Our experimental setup allowed for full crossing of genetic and rearing effects with the experimental manipulation. We observed that birds treated with corticosterone exhibited a significant decrease in broad-sense genetic variance of tarsus length, and an increase in this component in body mass on the 2nd day post-hatching. Our study indicates, that maternally transmitted substances such as hormones may have measurable impact on the levels of genetic variance and hence, on the evolutionary potential of quantitative traits.

Directional selection shifts trait distributions of planted species in dryland restoration

Abstract The match between species trait values and local abiotic filters can restrict community membership. An often‐implicit assumption of this relationship is that abiotic filters select for a single locally optimal strategy, though difficulty in isolating effects of the abiotic environment from those of dispersal limitation and biotic interactions has resulted in few empirical tests of this assumption. Similar constraints have made it difficult to assess whether the type and intensity of abiotic filters shift along gradients of environmental harshness, as predicted by the stress‐dominance hypothesis. We planted 9,216 plants of 29 perennial grass and forb species that had a range of functional trait values and were assigned to a warm, intermediate or cool temperature tolerance pool across eight sites on the Colorado Plateau. We compared the distributions of traits of surviving individuals to null distributions to evaluate whether there were shifts in trait means and variation. Borrowing from phenotypic selection concepts in evolutionary biology, we assessed support for stabilizing, directional and disruptive abiotic filtering of trait distributions and whether these types of filtering varied with initial species pool. Functional composition was significantly different from null distributions for nearly all traits at all sites, with trait variation more restricted in harsher abiotic conditions, supporting the stress‐dominance hypothesis. Contrary to expectations, we primarily found evidence for directional selection, which increased in frequency in warm species pools while disruptive selection was found more often in cool and intermediate species pools. Synthesis. This study provides a controlled experimental approach to test the effect of the abiotic environment on plant trait filtering. We found that opportunistic strategies allowing for rapid water acquisition during favourable periods improved survival at warmer sites. Species with these strategies may be expected to benefit from increasing aridity and may be selected for active management efforts. More generally, the prevalence of directional selection may have important implications for dynamic vegetation models that rely on trait distributions for translating environmental variation into ecosystem processes.

Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish.

Concepts of evolutionary biology suggest that morphological change may occur by rare punctual but rather large changes, or by more steady and gradual transformations. It can therefore be asked whether genetic changes underlying morphological, physiological, and/or behavioral innovations during evolution occur in a punctual manner, whereby a single mutational event has prominent phenotypic consequences, or if many consecutive alterations in the DNA over longer time periods lead to phenotypic divergence. In the marine teleost, sablefish (Anoplopoma fimbria), complementary genomic and genetic studies led to the identification of a sex locus on the Y Chromosome. Further characterization of this locus resulted in identification of the transforming growth factor, beta receptor 1a (tgfbr1a) gene, gonadal somatic cell derived factor (gsdf), as the main candidate for fulfilling the master sex determining (MSD) function. The presence of different X and Y Chromosome copies of this gene indicated that the male heterogametic (XY) system of sex determination in sablefish arose by allelic diversification. The gsdfY gene has a spatio-temporal expression profile characteristic of a male MSD gene. We provide experimental evidence demonstrating a pivotal role of a transposable element (TE) for the divergent function of gsdfY. By insertion within the gsdfY promoter region, this TE generated allelic diversification by bringing cis-regulatory modules that led to transcriptional rewiring and thus creation of a new MSD gene. This points out, for the first time in the scenario of MSD gene evolution by allelic diversification, a single, punctual molecular event in the appearance of a new trigger for male development.

EvALLution: making basic evolution concepts accessible to people with visual impairment through a multisensory tree of life

BackgroundPeople with visual impairment have benefitted from recent developments of assistive technology that aim to decrease socio-economic inequality. However, access to post-secondary education is still extremelly challenging, especially for scientific areas. The under representation of people with visual impairment in the evolution research community is connected with the vision-based communication of evolutionary biology knowledge and the accompanying lack of multisensory alternatives for learning.ResultsHere, we describe the development of an inclusive outreach activity based on a multisensory phylogeny representing 20 taxonomic groups. We provide a tool kit of materials and ideas that allow both the replication of this activity and the adaptation of others, to include people with visual impairment. Furthermore, we provide activity evaluation data, a discussion of the lessons learned and an inclusive description of all figures and visual data presented.The presented baseline data show that people with visual impairment indeed have lack of access to education but are interested in and apt to understand evolutionary biology concepts and predict evolutionary change when education is inclusive.ConclusionsWe show that, with creative investment, basic evolutionary knowledge is perfectly possible to be transmitted through multisensory activities, which everyone can benefit from. Ultimately, we hope this case study will provide a baseline for future initiatives and a more inclusive outreach community.

Developing & Testing Curricula for Teaching Evolutionary Concepts at the Elementary School Level

Evolution by natural selection is key to understanding life and of considerable practical importance in public health, medicine, biotechnology, and agriculture. The Next Generation Science Standards (NGSS) include natural selection among several evolutionary concepts that all third-graders should know. This article explores a novel approach to developing and testing curricula for teaching natural selection and related concepts to children. College students developed lesson plans with specific evolutionary learning objectives based on the NGSS and taught them at elementary schools. Learning was assessed with a pre/post-test design, and a subset of students was retested after two years. After just two hours of instruction and active-learning activities, students of all three grade levels tested (grades 3–5) demonstrated substantial improvement in their understanding of evolutionary concepts. Students who were retested in grade 5 scored higher than fifth-graders who had not participated previously. The most challenging concepts for all grade levels were common ancestry and natural selection, but fifth-graders showed more improvement than third- and fourth-graders. If this finding is substantiated by further research, an adjustment to the NGSS schedule might be warranted. Spacing evolutionary biology concepts out might be a better strategy than concentrating them all in grade 3.