Model Of Biological Evolution Research Articles

Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.

The Sackin index and depth of leaves in generalized Schröder trees

. Schröder trees are biological models of evolution, with internal nodes having two or three children. We generalize the model to grow from an arbitrary stochastic process of independent nonnegative integers (not necessarily identically distributed). We call such a process the building sequence. We study the depth of leaves and the Sackin index for some specific building sequences, such as constant additions, Bernoulli, and Poisson-like models. We include an example that shows that the methods can be extended to exchangeable sequences.

Cooperative genes in smart systems: Toward an inclusive new synthesis in evolution

For more than half a century, biologist Julian Huxley's term, the “Modern Synthesis”, has been used as a label for a model of biological evolution where genetic influences are viewed as a principal source of creativity and change. Over the years, as evidence has accumulated that there are many other, far more important factors at work in evolution, theoretical “compromises,” such as the so-called “Extended Synthesis”, have been proposed. This is no longer tenable. It is time to abandon the Modern Synthesis, and its doppelganger “The Selfish Gene”. Here is the case for a new, multi-faceted, open-ended, “inclusive” evolutionary synthesis, where living systems themselves are recognized as purposeful (teleonomic) “agents” and cooperative effects (synergies) of various kinds are seen as all-important influences.

Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Parasitoid wasps are rapidly developing as a model for evolutionary biology. Here we present chromosomal genomes of two Anastatus wasps, A. japonicus and A. fulloi, and leverage these genomes to study two fundamental questions—genome size evolution and venom evolution. Anastatus shows a much larger genome than is known among other wasps, with unexpectedly recent bursts of LTR retrotransposons. Importantly, several genomic innovations, including Piwi gene family expansion, ubiquitous Piwi expression profiles, as well as transposable element-piRNA coevolution, have likely emerged for transposable element silencing to maintain genomic stability. Additionally, we show that the co-option evolution arose by expression shifts in the venom gland plays a dominant role in venom turnover. We also highlight the potential importance of non-venom genes that are coexpressed with venom genes during venom evolution. Our findings greatly advance the current understanding of genome size evolution and venom evolution, and these genomic resources will facilitate comparative genomics studies of insects in the future.

A Fish of Multiple Faces, Which Show Us Enigmatic and Incredible Phenomena in Nature: Biology and Cytogenetics of the Genus Carassius.

Sexual vs. asexual reproduction—unisexual vs. bisexual populations—diploid vs. polyploid biotypes—genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. This review places emphasis on two Carassius entities with completely different biological characteristics: one globally widespread and invasive Carassius gibelio, and the other C. carassius with a decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance the advantages of highly invasive and disadvantages of threatened species. For example, the benefits of a wide-ranged colonization can lead to the extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and the importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for the identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Furthermore, the review focuses on the consequences of the co-occurrence of native and non-native species and outlines future perspectives of Carassius research.

Mitochondrial DNA variation of Drosophila obscura (Diptera: Drosophilidae) across Europe

Drosophila obscura is a common fruit fly that inhabits the temperate forests of Europe. While it is abundant in the north compared to other Drosophila, its density decreases southwards, where it is gradually replaced by other Drosophila species. This study describes variation in the mitochondrial Cyt b gene of D. obscura from several European populations. We observed a large number of haplotypes, together with the structuring of genetic variation. Genetic variation is higher in the west where O1 and related divergent haplotypes dominate. In the east, the O2 haplotype is most frequent, together with haplotypes that recently arose from it. In the central part of the species range, both O1 and O2 are equally present, along with many others. These data reveal signs of population expansions that probably happened earlier in the west, and more recently in the east. Though our conclusions are based on only one genetic marker, limiting the power of the analysis, the results imply either postglacial expansion from two unique sources or, more likely, eastwards stepping-stone expansion. This study adds important information on genetic variation and phylogeography to the obscure biology of D. obscura, a species that has the potential to become an interesting model in evolutionary biology and conservation genetics.

Physicochemical characterization of the anatomical structures of teosinte (Zea mays subsp. mexicana) covered caryopses

Teosinte is the wild ancestor of maize and is used as a study model in evolutionary biology. Information about the physicochemical properties of teosinte caryopses is scarce. Therefore, the aim of this study was to determine the physical properties and chemical composition of teosinte (Zea mays subsp. mexicana, race Chalco) covered caryopses per anatomical structure. Covered caryopses were dissected into cupule, outer glume, and endosperm-germ prior to analysis. Covered caryopses showed a thousand kernel weight, test weight, and flotation index values of 116.4 g, 82.3 kg/hL, and 13.3%, respectively. Chalco teosinte covered caryopses contained protein, fat, dietary fiber, and total starch contents of 7.8%, 2.8%, 54.9%, and 39.2% (dw), respectively. The endosperm-germ fraction accounted for 41% of the covered caryopsis weight and showed high protein and fat contents. It contained 86% and 87% of the total protein and fat contents of covered caryopses. Low total and resistant starch contents were detected in the endosperm-germ fraction. High contents of insoluble dietary fiber were detected in the cupule and outer glume, contributing to the high total dietary fiber content present in covered caryopses. This research is the most recent update on the chemical composition of the anatomical structures comprising teosinte covered caryopses.

Application of a resonance-based model of biological evolution

Application of a resonance-based model of biological evolution

The mirror of physics: on how the Price equation can unify evolutionary biology

Due to its high degree of complexity and its historical nature, evolutionary biology has been traditionally portrayed as a messy science. According to the supporters of such a view, evolutionary biology would be unable to formulate laws and robust theories, instead just delivering coherent narratives and local models. In this article, our aim is to challenge this view by showing how the Price equation can work as the core of a general theoretical framework for evolutionary phenomena. To support this claim, we outline some unnoticed structural similarities between physical theories (in particular, classical mechanics) and evolutionary biology. More specifically, we shall argue that the Price equation, in the same way as fundamental formalisms in physics, can serve as a heuristic principle to formulate and systematise different theories and models in evolutionary biology.

Genetic divergence in transcriptional regulators of defense metabolism: insight into plant domestication and improvement.

A number of mutational changes in transcriptional regulators of defense metabolism have occurred during plant domestication and improvement. Plant domestication and improvement entail genetic changes that underlie divergence in development and metabolism, providing a tremendous model of biological evolution. Plant metabolism produces numerous specialized alkaloids, terpenoids, phenolics, and cyanogenic glucosides with indispensable roles in defense against herbivory and microbial infection. Many compounds toxic or deterrent to predators have been eliminated through domestication and breeding. Series of genes involved in defense metabolism are coordinately regulated by transcription factors that specifically recognize cis-regulatory elements in promoter regions of downstream target genes. Recent developments in DNA sequencing technologies and genomic approaches have facilitated studies of the metabolic and genetic changes in chemical defense that have occurred via human-mediated selection, many of which result from mutations in transcriptional regulators of defense metabolism. In this article, we review such examples in almond (Prunus dulcis), cucumber (Cucumis sativus), pepper (Capsicum spp.), potato (Solanum tuberosum), quinoa (Chenopodium quinoa), sorghum (Sorghum bicolor), and related species and discuss insights into the evolution and regulation of metabolic pathways for specialized defense compounds.

Cooperative Equilibrium in Biosphere Evolution: Reconciling Competition and Cooperation in Evolutionary Ecology.

As our understanding of biological evolution continues to deepen, tension still surrounds the relationship between competition and cooperation in the evolution of the biosphere, with rival viewpoints often associated with the Red Queen and Black Queen hypotheses respectively. This essay seeks to reconcile these viewpoints by integrating observations of some general trends in biosphere evolution with concepts from game theory. It is here argued that biodiversity and ecological cooperation are intimately related, and that both tend to cyclically increase over biological history; this is likely due to the greater relative stability of cooperation over competition as a means of long-term conflict resolution within ecosystems. By integrating this view of the biosphere with existing models such as Niche Game Theory, it may be argued that competition and cooperation in ecosystems coexist at equilibria which shift preferentially towards increasing cooperation over biological history. This potentially points to a state of "cooperative equilibrium" as a limit or endpoint in long-term biosphere evolution, such that Black Queen and Red Queen behavior dominate different phases in an evolutionary movement towards optimal cooperative stability in ecological networks. This concept, if accepted, may also bear implications for developing future mathematical models in evolutionary biology, as well as for resolving the perennial debate regarding the relative roles of conflict and harmony in nature.

Total body and regional surface area: Quantification with low-cost three-dimensional optical imaging systems.

Body surface area (SA) is a widely used physical measure incorporated into multiple thermophysiology and evolutionary biology models currently estimated in humans either with empirical prediction equations or costly whole-body laser imaging systems. The introduction of low-cost 3D scanners provides a new opportunity to quantify total body (TB) and regional SA, although a critical question prevails: can these devices acquire the quality of depth information and process this initial data to form a mesh that has the fidelity needed to generate accurate SA estimates? This question was answered by comparing SA estimates calculated using images from four commercial 3D scanners in 108 adults to corresponding estimates acquired with a whole-body laser system. This was accomplished by processing initial mesh data from all devices, including the laser system, with the same universal software adapted specifically for repairing mesh gaps, identifying landmarks, and generating SA measurements. TB SA measured on all four 3D scanners was highly correlated with corresponding laser system estimates (R2 s, 0.98-0.99; all p< 0.001) with some small but significant mean differences (-0.19 to 0.06 m2 ); root-mean square errors (RMSEs) were small (0.02-0.03 m2 ); and significant bias was present for one device. Qualitatively similar results (e.g., R2 s, 0.78-0.95; mean Δs, -0.05 to 0.02 m2 ; RMSEs, 0.01-0.03 m2 ) were present for trunk, arm, and leg SA comparisons. The current study observations demonstrate that low-cost and practical 3D optical scanners are capable of accurately quantifying TB and regional SA, thus opening new opportunities for evaluating human phenotypes and related physiological characteristics.

Gradient Flow Formulations of Discrete and Continuous Evolutionary Models: A Unifying Perspective

We consider three classical models of biological evolution: (i) the Moran process, an example of a reducible Markov Chain; (ii) the Kimura Equation, a particular case of a degenerated Fokker-Planck Diffusion; (iii) the Replicator Equation, a paradigm in Evolutionary Game Theory. While these approaches are not completely equivalent, they are intimately connected, since (ii) is the diffusion approximation of (i), and (iii) is obtained from (ii) in an appropriate limit. It is well known that the Replicator Dynamics for two strategies is a gradient flow with respect to the celebrated Shahshahani distance. We reformulate the Moran process and the Kimura Equation as gradient flows and in the sequel we discuss conditions such that the associated gradient structures converge: (i) to (ii), and (ii) to (iii). This provides a geometric characterisation of these evolutionary processes and provides a reformulation of the above examples as time minimisation of free energy functionals.

A Place for Viruses on the Tree of Life.

Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.

The expansion of the Acheulian to the Southeastern Ethiopian Highlands: Insights from the new early Pleistocene site-complex of Melka Wakena

Current models of early hominin biological and cultural evolution are shaped almost entirely by the data accumulated from the East African Rift System (EARS) over the last decades. In contrast, little is known about the archaeological record from the high-elevation regions on either side of the Rift. Melka Wakena is a newly discovered site-complex on the Southeastern Ethiopian Highlands (SEH) (>2300 m above mean sea level) just east of the central sector of the Main Ethiopian Rift (MER), where eight archaeological and two paleontological localities were discovered to date. Nine archaeological horizons from three localities were tested so far, all dated to the second half of the early Pleistocene (∼1.6 to >0.7 Ma). All the lithic assemblages belong to the Acheulian technocomplex. Here we report on geochronological, stratigraphic, paleontological and lithic technological aspects of the tested localities and contextualize them in the broader framework of hominin cultural evolution in eastern Africa. Findings from Melka Wakena, assessed against the backdrop of the few other highland sites (Melka Kunture and Gadeb), support a scenario of expansion rather than dispersal from the Rift to the highlands. When considered in the context of the Rift-highlands interface, results of the first-phase research at Melka Wakena help to parse existing general models into archaeologically testable hypotheses and demonstrate the site’s potential to contribute to research of early prehistory and to understanding the dynamics of early Pleistocene hominin populations in eastern Africa.

Export sales forecasting using artificial intelligence

Sales forecasting is important in production and supply chain management. It affects firms’ planning, strategy, marketing, logistics, warehousing and resource management. While traditional time series forecasting methods prevail in research and practice, they have several limitations. Causal forecasting methods are capable of predicting future sales behavior based on relationships between variables and not just past behavior and trends. This research proposes a framework for modeling and forecasting export sales using Genetic Programming, which is an artificial intelligence technique derived from the model of biological evolution. Analyzing an empirical case of an export company, an export sales forecasting model is suggested. Moreover, a sales forecast for a period of six weeks is conducted, the output of which is compared with the real sales data. Finally, a variable sensitivity analysis is presented for the causal forecasting model.

A Central Limit Theorem for punctuated equilibrium

Current evolutionary biology models usually assume that a phenotype undergoes gradual change. This is in stark contrast to biological intuition, which indicates that change can also be punctuated—the phenotype can jump. Such a jump could especially occur at speciation, i.e., dramatic change occurs that drives the species apart. Here we derive a Central Limit Theorem for punctuated equilibrium. We show that, if adaptation is fast, for weak convergence to normality to hold, the variability in the occurrence of change has to disappear with time.

Learning Problem for Functional Programming and Model of Biological Evolution

The approach “genome as a program” is discussed. We suggest that a genome is a functional program and biological evolution can be described by machine learning for functional programming. We introduce learning model for functional programming at non-zero temperature and discuss relation to scaling laws observed in genomics.

Why mountains matter for biodiversity

AbstractMountains are arguably Earth's most striking features. They play a major role in determining global and regional climates, are the source of most rivers, act as cradles, barriers and bridges for species, and are crucial for the survival and sustainability of many human societies. The complexity of mountains is tightly associated with high biodiversity, but the processes underlying this association are poorly known. Solving this puzzle requires researchers to generate more primary data, and better integrate available geological and climatic data into biological models of diversity and evolution. In this perspective, we highlight emerging insights, which stress the importance of mountain building through time as a generator and reservoir of biodiversity. We also discuss recently proposed parallels between surface uplift, habitat formation and species diversification. We exemplify these links and discuss other factors, such as Quaternary climatic variations, which may have obscured some mountain‐building evidence due to erosion and other processes. Biological evolution is complex and the build‐up of mountains is certainly not the only explanation, but biological and geological processes are probably more intertwined than many of us realize. The overall conclusion is that geology sets the stage for speciation, where ecological interactions, adaptive and non‐adaptive radiations and stochastic processes act together to increase biodiversity. Further integration of these fields may yield novel and robust insights.

The diversity and evolution of odorant receptors in beetles (Coleoptera).

The insect odorant receptors (ORs) are amongst the largest gene families in insect genomes and the primary means by which insects recognize volatile compounds. The evolution of ORs is thus instrumental in explaining the chemical ecology of insects and as a model of evolutionary biology. However, although ORs have been described from numerous insect species, their analysis within and amongst the insect orders has been hindered by a combination of limited genomic information and a tendency of the OR family toward rapid divergence, gain, and loss. We addressed these issues in the insect order Coleoptera through a targeted genomic annotation effort that included 1181 ORs from one species of the sister order Strepsiptera and 10 species representing the four coleopteran suborders. The numbers of ORs in each species varied from hundreds to fewer than 10, but coleopteran ORs could nevertheless be represented within a scheme of nine monophyletic subfamilies. We observed many radiations and losses of genes amongst OR subfamilies, and the diversity of ORs appeared to parallel the host breadth of the study species. However, some small lineages of ORs persisted amongst many coleopteran families, suggesting receptors of key function that underlie the olfactory ecology of beetles.