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Publications related to Evolutionary Biology (10,000)
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Although gene expansion plays an important role in evolution, its identification remains a challenge due to potential errors in genome assembly and annotation. Here, we describe a detailed step-by-step protocol for gene annotation, prediction of genomic gene expansion, and its computational and experimental validation. Finally, we also detail steps...
Article
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Intelligent Personal Assistants (IPAs), such as Amazon's Alexa, are now widely used for an ample variety of tasks, ranging from personal management to education. These tools have shown considerable promise for student-educator interactions, especially at a distance, a potential that has come to the forefront during the ongoing COVID-19 pandemic. Ev...
Article
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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 t...
Article
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In evolutionary biology, speciation is often perceived as a gradual evolutionary process spanning thousands of generations; however, the emergence of the London Underground mosquito (Culex pipiens molestus) from the common house mosquito (Culex pipiens) illustrates a recent, observable speciation event. Via allopatric speciation, the mosquito popul...
Preprint
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In this article, I put forward the idea that the neoplastic process (NP) has deep evolutionary roots and make specific predictions about the connection between cancer and the formation of the first embryo, which allowed for the evolutionary radiation of metazoans. My main hypothesis is that the NP is at the heart of cellular mechanisms responsible...
Article
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Cichlid fishes are an important model system in evolutionary biology, primarily because of their exceptional diversity. However , while some cichlid assemblages, such as the ones of the African Great Lakes, have received considerable attention, others are not well studied, including many riverine species. Here, we focus on the Australoheros autrani...
Article
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Although its role in the functioning of aquatic systems is widely recognized, the contribution of freshwater metazooplankton (metazoan plankton) to ecosystem services (ES) is seldom considered. Here we aim at providing a first overview of how this group contributes to ecosystem services according to the Millennium Ecosystem Assessment framework. We...
Article
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O objetivo deste artigo é avaliar o naturalismo biológico à luz do debate adaptacionista. Como é notório, Searle busca fundamentar explicitamente a sua teoria da mente nas ciências biológicas. Entretanto, a biologia evolutiva recebe pouco destaque no interior de sua obra, o que resulta em importantes confusões teóricas quanto ao adaptacionismo. Nes...
Article
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In this short paper, we argue that there is a fundamental connection between the medical sciences and evolutionary biology as both are sciences of biological variation. Medicine studies pathological variation among humans (and domestic animals in veterinary medicine) and evolutionary biology studies variation within and among species in general. A...
Article
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We are honored to present this special issue of Palaeoentomology in celebration of our dear friend, mentor, and collaborator, David A. Grimaldi (Fig. 1), and on the occasion of his 65th birthday on 22 September 2022. This issue has been compiled in recognition of David’s remarkable ongoing impact on the fields of paleontology, entomology, and evolu...
Article
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This paper deals in detail with a fairly recent philosophical debate centered around the ability of the theory of natural selection to account for those phenotypical changes which can be argued to make organisms better adapted to their environments. The philosopher and cognitive scientist Jerry Fodor started the debate by claiming that natural sele...
Article
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The HHUMTL22 cruise onboard R/V Helmer Hanssen was an initiative by The Arctic University Museum of Norway (UMAK) aimed at sampling marine fauna for the museum collections and various research projects undertaken at the museum. Researchers from the Swedish Museum of Natural History and the Department of Evolutionary Biology at the University of Vie...
Article
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What controls species diversity and diversification is one of the major questions in evolutionary biology and paleontology. Previous studies have addressed this issue based on various plant and animal groups, geographic regions, and time intervals. However, as most previous research focused on terrestrial or marine ecosystems, our understanding of...
Article
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Understanding the evolution of genitalic traits and their co-evolution between sexes is at the core of Evolutionary Biology. Cross-species reproductive trait co-variation can be the outcome of hybrid avoidance and/or sexual selection. Although the outcome of these two phenomena will look similar, they yield distinct patterns of species co-occurrenc...
Preprint
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Many life-history traits are used as proxies of fitness in Drosophila. Egg size is an adaptive trait that can be used for fitness measurement. However, the low throughput of manual measurement of egg size has hampered the widespread use of this trait in evolutionary biology. We established a method for accurate and high throughout measurement of Dr...
Preprint
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Morphological integration is relevant to evolutionary biology and paleontology because the structure of variation within populations determines the ways in which a population can respond to selective pressures. However, understanding the macroevolutionary consequences of morphological integration is elusive because the adaptive landscape is dynamic...
Article
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Background The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cau...
Article
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This article introduces and defends the “pathological complexity thesis” as a hypothesis about the evolutionary origins of minimal consciousness, or sentience, that connects the study of animal consciousness closely with work in behavioral ecology and evolutionary biology. I argue that consciousness is an adaptive solution to a design problem that...
Preprint
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Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservat...
Article
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The scaling of respiratory structures has been hypothesized to be a major driving factor in the evolution of many aspects of animal physiology. Here we provide the first assessment of the scaling of the spiracles in insects using ten scarab beetle species differing 180x in mass, including some of the most massive extant insect species. Using X-ray...
Preprint
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Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, which limits scalability. We present TOGA, the first method that integrates gene annotation and orthology inference. TOGA implements a novel paradigm to infer orthologous genes, improv...
Conference Paper
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Se presentan los resultados preliminares de un estudio sobre la enseñanza de la teoría de la evolución (TE) y su representatividad en los Grados en Biología del territorio nacional. Como ya otros trabajos señalan, existe una deficiencia educativa relativa a estos contenidos en la Educación Primaria y Secundaria. Sin embargo, poco se ha explorado en...
Article
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Understanding the mechanisms by which mutations affect fitness and the distribution of mutational effects are central goals in evolutionary biology. Mutation accumulation (MA) lines have long been an important tool for understanding the effect of new mutations on fitness, phenotypic variation, and mutational parameters. However, there is a clear ga...
Article
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Here, we build on earlier work concerning notions of engineering design and investigate their conceptual connection to evolutionary biology. The basis for this work is an engineering design schema covering the central concepts of function, working principle and construction. Its relevance for evolutionary biology is explored by connecting these con...
Article
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The environment of the religious mind and behaviour is social, cultural, and natural. Hence, their scientific study has to account for these aspects as well as for religion itself. This paper is focused upon biological and cultural evolution as a framework for religious evolution. It considers the progress of evolutionary biology towards an Extende...
Article
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How new genes evolve has become an interesting problem in biology, particularly in evolutionary biology [...]
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Individual-based studies where animals are monitored through space and time enable explorations of ecology, demography, evolutionary biology, movements, and behavior. Here, we review 70 years of research on an endangered African herbivore, the giraffe, based on individual spot pattern recognition, and profile an example of a long-term photographic...
Article
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Professor of St. Petersburg State University Archil K. Dondua (1929–2021) is known for his pioneering work in the developmental biology of annelids and vertebrates, the kinetics of cell populations in ontogenesis, and comparative embryological aspects of animal evolution. Prof. Dondua created and led an academic school and paid a special attention...
Article
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Drawing on the perspectives of cognitive linguistics and evolutionary biology, this contribution revisits the meaning of the Homeric formula ὑπόδρα ἰδών, literally ‘looking from below’, which is generally acknowledged as an indication of anger in epic poetry. A detailed examination of the phrase suggests that the facial expression it refers to was...
Article
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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 dif-ferent ways, and attempts to quantify RI have used very different approaches. After showing t...
Preprint
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An important question in evolutionary biology is whether and in what ways genotype-phenotype (GP) map biases can influence evolutionary trajectories. Untangling the relative roles of natural selection and biases (and other factors) in shaping phenotypes can be difficult. Because RNA secondary structure (SS) can be analysed in detail mathematically...
Article
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Solute carriers are an operationally defined diverse family of membrane proteins involved in the transport of nutrients, metabolites, xenobiotics and drugs. Here, we provide an integrative classification of solute carriers by combining evolutionary information with proteome-wide structure models recently made available through the AlphaFold resourc...
Article
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Plesiosaurs are a group of Mesozoic marine diapsids. Most derived plesiosaurs fall into one of two typical body forms: those with proportionately small heads, short snouts, and elongated necks, and those with large heads, elongated snouts, and short necks. Serpentisuchops pfisterae is a polycotylid plesiosaur from the Upper Cretaceous Pierre Shale...
Article
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Punishment as a response to impairment of individual or group welfare may be found not only among humans but also among a wide range of social animals. In some cases, acts of punishment serve to increase social cooperation among conspecifics. Such phenomena motivate the search for the biological foundations of punishment among humans. Of special in...
Article
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Being one of Freud’s most famous contributions to psychoanalysis, the Oedipus complex is still a topic of heated interest. It has been disputed in many different disciplines ranging from anthropology to biology. This theoretical paper aimed to explain the phenomena that are represented by children’s affectionate and assertive attitudes towards thei...
Article
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As a key parameter in population genetics, relatedness has found wide applications in molecular ecology, evolutionary biology, conservation, forensics and in studies of human inheritable diseases. It is defined as the probability that two individuals share an allele due to recent common ancestry. Many estimators have been developed to estimate rela...
Article
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Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (...
Article
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Cancer genomes exhibit surprisingly weak signatures of negative selection 1,2 . This may be because selective pressures are relaxed or because genome-wide linkage prevents deleterious mutations from being removed (Hill-Robertson interference) ³ . By stratifying tumors by their genome-wide mutational burden, we observe negative selection (dN/dS ~ 0....
Article
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Annotation highlights and segmentation isolates features in cryogenic electron tomograms to improve visualization and quantification of features (for example, their size and abundance, and spatial relationships with other features), facilitating phenotypic structural analyses of cellular tomograms. Here, we present a manual annotation protocol usin...
Article
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A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes...
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In animals with slow ontogeny and long-term maternal investment, immatures are likely to experience the birth of a younger sibling before reaching maturity. In these species, the birth of a sibling marks a major event in an offspring's early life, as the older siblings experience a decrease in maternal support. The transition to siblinghood (TTS) i...
Article
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There are numerous children and adolescents throughout the world who are either diagnosed with speech and language disorders or manifest any of them as a result of another disorder. Meanwhile, since the emergence of language as an innate capability, the question of whether it constitutes a behaviour or an innate ability has been debated for decades...
Article
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De novo gene birth is the process by which new genes emerge in sequences that were previously non‐coding. Over the past decade, researchers have taken advantage of the power of yeast as a model and a tool to study the evolutionary mechanisms and physiological implications of de novo gene birth. We summarize the mechanisms that have been proposed to...
Book
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[https://link.springer.com/book/10.1007/978-3-031-09206-0] This book explores the evolutionary and cognitive foundations of human communication, focusing on narrative as its distinctive dimension. Within a framework of continuity with both the communication of our hominin predecessors and that of non-human animals, the book is about a twofold propo...
Article
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Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The 'success', or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that...
Article
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The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing bacteria are far lar...
Article
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Gestures during speaking are typically understood in a representational framework: they represent absent or distal states of affairs by means of pointing, resemblance, or symbolic replacement. However, humans also gesture along with the rhythm of speaking, which is amenable to a non-representational perspective. Such a perspective centers on the ph...
Preprint
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Living cells evolve under specific ecological conditions. The mass of our planet setting a constant gravitational pull and its daily rotation on its axis setting a circadian rhythm are two examples of universal ecological parameters that shape the physiology of every living creature on earth. In the ocean, gravity plays a critical role in shaping t...
Preprint
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The oldest authenticated peptide sequences to date were reported in 2016 from 3.8 Ma old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we demonstrate survival of the same sequences in 6.5-9 Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in ext...
Poster
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In the field of macrobiology including taxonomy, ecology, and evolutionary biology, we frequently confront missing values both in phenotype and genotype data, leaving it an important issue how to treat missing data. In particular, it is common to encounter a case where either genotype or phenotype data does not exist for an individual sample due to...
Thesis
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A majority (~60%) of the global belowground organic carbon (OC) pool is trapped in a perennially frozen state in permafrost soils underlying the Arctic tundra. Climate warming has initiated thaw in large regions of permafrost. Such thaw will likely trigger increased microbial activity leading to faster degradation of previously frozen OC and its re...
Article
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The evolution of gametic sex (meiosis and fertilization) and subsequent transition from isogamy (fusion between two equal-sized gametes) to anisogamy (dimorphism into eggs and sperm, namely, females and males) is one of the largest enigmas of evolutionary biology. Meiosis entails genome-dilution cost and anisogamy entails male-production cost. Desp...
Article
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Background and aims – Understanding whether variation in plant attributes is primarily driven by selection or historical contingencies is a main goal in evolutionary biology. We characterize leaf diversity in Euphorbia tithymaloides and identify patterns related to taxonomy, geography, biogeography, and climate that provide insights on the role of...
Article
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Fitness landscape mapping and the prediction of evolutionary trajectories on these landscapes are major tasks in evolutionary biology research. Evolutionary dynamics is tightly linked to the landscape topography, but this relation is not straightforward. Here, we analyze a fitness landscape of a yeast tRNA gene, previously measured under four diffe...
Article
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Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identi...
Article
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The rise of animals represents a major but enigmatic event in the evolutionary history of life. In recent years, numerous studies have aimed at understanding the genetic basis of this transition. However, genome comparisons of diverse animal and protist lineages suggest that the appearance of gene families that were previously considered animal spe...
Article
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The Early Cretaceous diversification of birds was a major event in the history of terrestrial ecosystems, occurring during the earliest phase of the Cretaceous Terrestrial Revolution, long before the origin of the bird crown-group. Frugivorous birds play an important role in seed dispersal today. However, evidence of fruit consumption in early bird...
Book
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The homo neanderthalis had a cerebellar dominant brain and a philosophy of intuition, subjectivity and magical realism consequent to archaeal endosymbiosis. Retroviral symbiosis in sapiens led to evolution and expansion of neocortex resulting in scientific temper, reasoning and logic. The evolutionary biology of neurophilosophy depends upon symbios...
Book
Full-text available
The homo neanderthalis had a cerebellar dominant brain and a philosophy of intuition, subjectivity and magical realism consequent to archaeal endosymbiosis. Retroviral symbiosis in sapiens led to evolution and expansion of neocortex resulting in scientific temper, reasoning and logic. The evolutionary biology of neurophilosophy depends upon symbios...
Book
Full-text available
The homo neanderthalis had a cerebellar dominant brain and a philosophy of intuition, subjectivity and magical realism consequent to archaeal endosymbiosis. Retroviral symbiosis in sapiens led to evolution and expansion of neocortex resulting in scientific temper, reasoning and logic. The evolutionary biology of neurophilosophy depends upon symbios...
Article
Full-text available
The protein kinases PAK4, PAK5 and PAK6 comprise a family of ohnologues. In multiple cancers including melanomas PAK5 most frequently carries non-synonymous mutations; PAK6 and PAK4 have fewer; and PAK4 is often amplified. To help interpret these genomic data, initially we compared the cellular regulation of the sister kinases and their roles in me...
Article
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Why sex has evolved and is maintained is an open question in evolutionary biology. The Red Queen hypothesis predicts that host lineages subjected to more intense parasite pressure should invest more in sexual reproduction to continuously create novel defences against their rapidly evolving natural enemies. In this comparative study across the angio...
Article
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Bacterial pathogens show high levels of chromosomal genetic diversity, but the influence of this diversity on the evolution of antibiotic resistance by plasmid acquisition remains unclear. Here, we address this problem in the context of colistin, a 'last line of defence' antibiotic. Using experimental evolution, we show that a plasmid carrying the...
Article
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Metazoans function as individual organisms but also as “colonies” of cells whose single-celled ancestors lived and reproduced independently. Insights from evolutionary biology about multicellular group formation help us understand the behavior of cells: why they cooperate, and why cooperation sometimes breaks down. Current explanations for multicel...
Article
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The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in...
Article
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Finite element analysis (FEA) is no longer a new technique in the fields of palaeontology, anthropology, and evolutionary biology. It is nowadays a well-established technique within the virtual functional-morphology toolkit. However, almost all the works published in these fields have only applied the most basic FEA tools i.e ., linear materials in...
Article
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Telomere dynamics are linked with both cellular and organismal senescence, and life history, individual quality and health. Telomere dynamics, particularly telomere length, have therefore garnered much research interest in evolutionary biology. To examine the evolution of telomere length, it is important to quantify its heritability, the proportion...
Article
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Larger animals studied during ontogeny, across populations, or across species, usually have lower mass-specific metabolic rates than smaller animals (hypometric scaling). This pattern is usually observed regardless of physiological state (e.g. basal, resting, field, maximally-active). The scaling of metabolism is usually highly correlated with the...