Modern Evolutionary Biology Research Articles

Molecular evolution of ion channels: Amino acid sequences and 3D structures

An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

Neural nets

Although modern evolutionary biology has abandoned the use of 'lower' or 'higher' for animals, the quote of G.H. Parker captures quite well the current understanding of the nerve net as the evolutionarily oldest organization of the nervous system, the major organ system responsible for processing information and coordinating animal behaviour. The degree of complexity of a nervous system - in particular its organization into substructures such as brains and nerve cords - shows fascinating variations between animals. Even within an individual, the nervous system can show parallel existing types of organizations that are only partially connected, illustrated by the well-known central and peripheral nervous system. In general, the architecture of the nervous system is adapted to the specific needs and lifestyle of the individual species. How these diverse and complex nervous systems evolved is an ongoing debate among zoologists and evolutionary biologists.

Development of neuromuscular organization in the ctenophore Pleurobrachia bachei.

The phylogenetic position of the phylum Ctenophora and the nature of ctenphore nervous systems are highly debated topics in modern evolutionary biology. However, very little is known about the organization of ctenophore neural and muscular systems, and virtually nothing has been reported about their embryogenesis. Here we have characterized the neural and muscular development of the sea gooseberry, Pleurobrachia bachei, starting from the cleavage stages to posthatching larvae. Scanning electron microscopy and immunochemistry were used to describe the formation of the embryonic mouth, tentacles, combs, aboral organ, and putative sensory cells. The muscles started their specification at the end of the first day of Pleurobrachia development. In contrast, neurons appeared 2 days after myogenesis, just before the hatching of fully formed cydippid larvae. The first tubulin-immunoreactive neurons, a small group of four to six cells with neuronal processes, was initially recognized at the aboral pole during the third day of development. Surprisingly, this observed neurogenesis occurred after the emergence of distinct behavioral patterns in the embryos. Thus, the embryonic behavior associated with comb cilia beatings and initial muscle organization does not require morphologically defined neurons and their elongated neurites. This study provides the first description of neuromuscular development in the enigmatic ctenophores and establishes the foundation for future research using emerging genomic tools and resources.

Is geographic variation within species related to macroevolutionary patterns between species?

The relationship between microevolution and macroevolution is a central topic in evolutionary biology. An aspect of this relationship that remains very poorly studied in modern evolutionary biology is the relationship between within-species geographic variation and among-species patterns of trait variation. Here, we tested the relationship between climate and morphology among and within species in the salamander genus Plethodon. We focus on a discrete colour polymorphism (presence and absence of a red dorsal stripe) that appears to be related to climatic distributions in a common, wide-ranging species (Plethodon cinereus). We find that this trait has been variable among (and possibly within) species for >40million years. Furthermore, we find a strong relationship among species between climatic variation and within-species morph frequencies. These between-species patterns are similar (but not identical) to those in the broadly distributed Plethodon cinereus. Surprisingly, there are no significant climate-morphology relationships within most other polymorphic species, despite the strong between-species patterns. Overall, our study provides an initial exploration of how within-species geographic variation and large-scale macroevolutionary patterns of trait variation may be related.

A systemic approach for modeling biological evolution using Parallel DEVS

A new model for studying the evolution of living organisms is proposed in this manuscript. The proposed model is based on a non-neodarwinian systemic approach. The model is focused on considering several controversies and open discussions about modern evolutionary biology. Additionally, a simplification of the proposed model, named EvoDEVS, has been mathematically described using the Parallel DEVS formalism and implemented as a computer program using the DEVSLib Modelica library. EvoDEVS serves as an experimental platform to study different conditions and scenarios by means of computer simulations. Two preliminary case studies are presented to illustrate the behavior of the model and validate its results. EvoDEVS is freely available at http://www.euclides.dia.uned.es.

ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.

Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the correlation between multiple types of data, while simultaneously controlling for their unknown shared evolutionary history informed through molecular sequences. The latent formulation enables us to consider in a single model combinations of continuous traits, discrete binary traits, and discrete traits with multiple ordered and unordered states. Previous approaches have entertained a single data type generally along a fixed history, precluding estimation of correlation between traits and ignoring uncertainty in the history. We implement our model in a Bayesian phylogenetic framework, and discuss inference techniques for hypothesis testing. Finally, we showcase the method through applications to columbine flower morphology, antibiotic resistance in Salmonella, and epitope evolution in influenza.

Morphology is dead – long live morphology! Integrating MorphoEvoDevo into molecular EvoDevo and phylogenomics

Morphology, the description and analysis of organismal form, is one of the oldest biological disciplines that has significantly contributed to our understanding as to how animals function and how the overwhelming diversity of phenotypes evolved. The early discovery that comparative studies of morphogenesis add to our understanding of the evolutionary history and interrelationships of organisms led to the formulation of highly influential evolutionary principles, including Haeckel’s theory of recapitulation or Hatschek’s trochozoon-hypothesis, and established the intellectual foundation of a research area today termed EvoDevo. While the rapid integration of molecular techniques into systematics, phylogenetics, and developmental biology from the 1980s onwards made some consider morphology as having little to contribute to evolutionary research, methodological progress together with a revived focus on morphogenesis has resulted in an unexpected renaissance of evolutionary developmental morphology, here termed MorphoEvoDevo. Herein, I briefly summarize some classical landmark contributions and progress achieved by studies using the MorphoEvoDevo approach. I will focus on the role of morphology in modern evolutionary biology, especially with respect to the molecular-driven approaches such as phylogenetics and developmental genetics. I argue that, while MorphoEvoDevo may well survive as an independent field of research, in times of increased competition for funding it will significantly profit from integration of the molecular disciplines into research programs with a strong emphasis on morphology. After all, morphological data are indispensable for reconstruction of phenotypic ground patterns and character evolution, and only a holistic approach incorporating all major subdisciplines of the evolutionary biosciences may ultimately result in a deep understanding, from molecules to ecosystems, of the driving forces that have shaped our organismal world.

Chordate phylogeny and the meaning of categorial ranks in modern evolutionary biology.

In a recent review, Satoh et al. [[1][1]] discuss the evolutionary relationships among chordates and several of the scenarios that have been proposed to elucidate their origin. While we believe that the article is interesting in principle, as is the topic itself, we see, however, a major conceptual

The evolution of evolution Eternal Ephemera Adaptation and the Origin of Species from the Nineteenth Century Through Punctuated Equilibria and Beyond Niles Eldredge Columbia University Press, 2015. 398 pp.

Looking back at the theories that shaped modern evolutionary biology

Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies.

Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have undergone an adaptive radiation for wing-pattern mimicry and are influenced by distinct selection regimes. Using crosses between natural wing-pattern variants, we used genome-wide restriction site-associated DNA (RAD) genotyping, traditional linkage mapping and multivariate image analysis to study the evolution of the architecture of adaptive variation in two closely related species: Heliconius hecale and H. ismenius. We implemented a new morphometric procedure for the analysis of whole-wing pattern variation, which allows visualising spatial heatmaps of genotype-to-phenotype association for each quantitative trait locus separately. We used the H. melpomene reference genome to fine-map variation for each major wing-patterning region uncovered, evaluated the role of candidate genes and compared genetic architectures across the genus. Our results show that, although the loci responding to mimicry selection are highly conserved between species, their effect size and phenotypic action vary throughout the clade. Multilocus architecture is ancestral and maintained across species under directional selection, whereas the single-locus (supergene) inheritance controlling polymorphism in H. numata appears to have evolved only once. Nevertheless, the conservatism in the wing-patterning toolkit found throughout the genus does not appear to constrain phenotypic evolution towards local adaptive optima.

Social parasitism and the molecular basis of phenotypic evolution.

Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer—Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization.

Integrative and adaptive responses.

Darwin is considered the father of modern evolutionary biology by recognizing the importance of integrative and adaptive structural and physiological responses in living organisms. In his textbook Principles of Biology (1864), Herbert Spencer succinctly stated the essence of Darwin's theory of

Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies.

A major goal of modern evolutionary biology is to understand the causes and consequences of phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes in response to variable environments. While ecological and quantitative genetic studies have evaluated models of the evolution of adaptive plasticity, some long-standing questions about plasticity require more mechanistic approaches. Here, we address two of those questions: does plasticity facilitate adaptive evolution? And do physiological costs place limits on plasticity? We examine these questions by comparing genetically and plastically regulated behavioural variation in sailfin mollies (Poecilia latipinna), which exhibit striking variation in plasticity for male mating behaviour. In this species, some genotypes respond plastically to a change in the social environment by switching between primarily courting and primarily sneaking behaviour. In contrast, other genotypes have fixed mating strategies (either courting or sneaking) and do not display plasticity. We found that genetic and plastic variation in behaviour were accompanied by partially, but not completely overlapping changes in brain gene expression, in partial support of models that predict that plasticity can facilitate adaptive evolution. We also found that behavioural plasticity was accompanied by broader and more robust changes in brain gene expression, suggesting a substantial physiological cost to plasticity. We also observed that sneaking behaviour, but not courting, was associated with upregulation of genes involved in learning and memory, suggesting that sneaking is more cognitively demanding than courtship.

De Re Essentialism, Species, and Modal Ambiguity

Abstract I offer a concise critique of a recurring line of reasoning advanced by Joseph LaPorte and Samir Okasha that all modern species concepts render the view that biological organisms essentially belong to their species empirically untenable. The argument, I claim, trades on a crucial modal ambiguity that collapses the de re/de dicto distinction. Contra their claim that the continued adherence of such a view on behalf of contemporary metaphysicians stems from the latter’s ignorance of developments in modern biology, the modal ambiguity reveals the need to retrain in modal metaphysics.

Advances inEcologicalSpeciation: an integrative approach

The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference 'Advances in Ecological Speciation' organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation.

Engaging with Lyell: Alfred Russel Wallace’s Sarawak Law and Ternate papers as reactions to Charles Lyell’s Principles of Geology

Alfred Russel Wallace (1823-1913) and Charles Darwin (1809-1882) are honored as the founders of modern evolutionary biology. Accordingly, much attention has focused on their relationship, from their independent development of the principle of natural selection to the receipt by Darwin of Wallace's essay from Ternate in the spring of 1858, and the subsequent reading of the Wallace and Darwin papers at the Linnean Society on 1 July 1858. In the events of 1858 Wallace and Darwin are typically seen as central players, with Darwin's friends Charles Lyell (1797-1875) and Joseph Dalton Hooker (1817-1911) playing supporting roles. This narrative has resulted in an under-appreciation of a more central role for Charles Lyell as both Wallace's inspiration and foil. The extensive anti-transmutation arguments in Lyell's landmark Principles of Geology were taken as the definitive statement on the subject. Wallace, in his quest to solve the mystery of species origins, engaged with Lyell's arguments in his private field notebooks in a way that is concordant with his engagement with Lyell in the 1855 and 1858 papers. I show that Lyell was the object of Wallace's Sarawak Law and Ternate papers through a consideration of the circumstances that led Wallace to send his Ternate paper to Darwin, together with an analysis of the material that Wallace drew upon from the Principles. In this view Darwin was, ironically, intended for a supporting role in mediating Wallace's attempted dialog with Lyell.

Development and Prospect of Genetically Engineered Pharmaceutics

With the rapid development of modern biology and technology, Genetically Engineered Pharmaceutics has become the most important field in modern medicinal industry. Currently, we have taken concern that the Genetically Engineered Pharmaceutics has been a subject of research. As advanced genetically engineered technology, genetic therapy, the point mutation techniques, DNA shuffling, RNA interference (RNAi) technology, the bioinformatics for genome and proteome analyses, the high throughput screening technology, etc. can be applied in the treatment of cancer, and other targeted therapies. A great deal of advanced technologies accelerates the development of genetically engineered pharmaceutics, and plays a key role in genetically engineered pharmaceutics. With the advances in genetically engineered pharmaceutics, we look forward to finding more new drugs, such as the high-value peptides, small functional molecular groups, proteins, especially antibodies, vaccines, enzymes, and therapeutic peptides. These developments continue to secure greater health outcomes of human being at all aspects in the long run. In this article, the development and prospect of Genetically Engineered Pharmaceutics are reviewed, and furthermore, the potential development and huge prospects are also presented.

Systems Theory and the Role of Synergy in the Evolution of Living Systems

Living systems theory and other theory and research in the systems sciences and complexity science has illuminated many aspects of how living systems work—their mechanisms, processes and relationships. The Synergism Hypothesis, originally proposed in 1983, addresses the evolution of cooperative phenomena in nature and why there has been a secular trend over time toward increased complexity in living systems. This theory highlights the role of functional synergy—adaptively significant combined effects that are interdependent and otherwise unattainable—in shaping the ‘progressive’ emergence of complex living systems. This approach is entirely consistent with modern evolutionary biology and natural selection theory and is thus radically opposed to various orthogenetic/deterministic theories of complexity that have been proposed over the years. The Synergism Hypothesis has recently gained scientific support, and there is growing appreciation for the role of various kinds of synergy as an influence in the evolutionary process. Copyright © 2013 John Wiley & Sons, Ltd.

Museums' Role: Increasing Knowledge

Great natural history museums are among world's premier institutions of scientific research, training, and education. The research produced by these museums, based on their collections of biological, geological, and anthropological specimens, has been of incalculable importance in formulating and testing most fundamental theories and principles of these and related disciplines. In biological sciences, for instance, contributions from past curators of these collections form pillars of modern evolutionary biology [e.g., ([ 1 ][1]–[ 3 ][2])]. We therefore read with deep concern of plans to drastically reduce role of scientific research at one of world's greatest museums of natural history, Chicago's Field Museum (Budget crunch to shrink science programs at Chicago's Field V. Morell, News & Analysis, 4 January, p. [19][3]). The collections of Field Museum are an irreplaceable scientific resource, and scientists who care for, augment, and make them available for study by others are also renowned contributors to science in their own right. Their loss would be a blow not just to Museum, but to scientific enterprise as a whole. In making bequest that endowed Smithsonian, Smithson epitomized what has become mission of modern natural history museums: They are institutions for the increase and diffusion of knowledge ([ 4 ][4]). Many science museums can mount exhibits for diffusion of knowledge, but only museums such as Field, with its collections and scientists, can contribute so much to its increase. For Field Museum to abandon this duty would be unconscionable. We urge Museum's authorities and supporters to find a way to prevent such a calamity. 1. [↵][5]1. E. Mayr , Systematics and Origin of Species (Columbia Univ. Press, New York, 1942). 2. 1. G. G. Simpson , Tempo and Mode in Evolution (Columbia Univ. Press, New York, 1944). 3. [↵][6]1. B. Rensch , Neuere Probleme der Abstammungslehre (Enke, Stuttgart, 1947). 4. [↵][7]1. J. Smithson , James Smithson makes his will (1826); [http://siarchives.si.edu/collections/siris\_sic\_638][8]. [1]: #ref-1 [2]: #ref-3 [3]: http://www.sciencemag.org/content/339/6115/19.full [4]: #ref-4 [5]: #xref-ref-1-1 View reference 1 in text [6]: #xref-ref-3-1 View reference 3 in text [7]: #xref-ref-4-1 View reference 4 in text [8]: http://siarchives.si.edu/collections/siris_sic_638

Tandem-Repeat Patterns and Mutation Rates in Microsatellites of the Nematode Model OrganismPristionchus pacificus

Modern evolutionary biology requires integrative approaches that combine life history, population structure, ecology, and development. The nematode Pristionchus pacificus has been established as a model system in which these aspects can be studied in one organism. P. pacificus has well-developed genetic, genomic, and transgenic tools and its ecologic association with scarab beetles is well described. A recent study provided first mutation rate estimates based on mitochondrial genome sequencing and mutation accumulation line experiments that help resolve rather ancient evolutionary branches. Here, we analyzed the tandem-repeat pattern and studied spontaneous mutation rates for microsatellite markers by using the previously generated mutation accumulation lines. We found that 0.59%–3.83% of the genome is composed of short tandem repeats. We developed 41 microsatellite markers, randomly chosen throughout the genome and analyzed them in 82 mutation accumulation lines after 142 generations. A total of 31 mutations were identified in these lines. There was a strong correlation between allele size and mutation rate in P. pacificus, similar to Caenorhabditis elegans. In contrast to C. elegans, however, there is no evidence for a bias toward multistep mutations. The mutation spectrum of microsatellite loci in P. pacificus shows more insertions than deletions, indicating a tendency toward lengthening, a process that might have contributed to the increase in genome size. The mutation rates obtained for individual microsatellite markers provide guidelines for divergence time estimates that can be applied in P. pacificus next-generation sequencing approaches of wild isolates.