Development of evolutionary biomedicine as a novel direction of biological science

This review analyzes the data obtained for the last decade on invertebrate animals (insects, round worms, molluscs) as models of various human diseases. As illustration, there are considered advances in studying of the invertebrate system of insulin-like peptides and signaling mechanisms of their action—evolutionary conservative homologues of the mammalian insulin/IGF-1 system. Results are presented of studies on the nematode Caenorhabditis elegans, Drosophila Drosophila melanogaster, and mollusks, which “model” individual aspects of some human diseases—diabetes, neurodegenerative dysfunction, carcinogenesis, as well as aging. A conclusion is made about the development of a new, synthetic direction combining evolutionary science and molecular biology and medicine, which we call evolutionary biomedicine. The roots of the appearance of this synthetic direction are to be searched for in L.A. Orbeli’s evolutionary ideas, methods, and scientific predictions.     

Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex

Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature.     

Recent findings in evolution and function of insect innexins

The past decade has seen significant advances in the field of innexin biology, particularly in the model invertebrate organisms, the nematode Caenorhabditis elegans and the fly Drosophila melanogaster. However, advances in genomics and functional techniques during this same period are ushering in a period of comparative innexin biology. Insects are the most diverse metazoan taxa in terms of species number, as well as in developmental, physiological, and morphological processes. Combined with genomics data, the study of innexins should rapidly advance. In this review, we consider the current state of knowledge regarding innexins in insects, focusing on innexin diversity, both evolutionary and functional. We also consider an unusual set of innexins, known as vinnexins, that have been isolated from mutualistic viruses of some parasitoid wasps. We conclude with a call to study insect innexins from a broader, evolutionary perspective. Knowledge derived from such comparative studies will offer significant insight into developmental and evolutionary physiology, as well as specific functional processes in a taxon that has huge biomedical and ecological impact on humans.     

New fossils of ascomycetous anamorphic fungi from Baltic amber

Three new fossils of saprotrophic fungi are presented and described from Baltic amber, dated to Eocene epoch (Paleogene, upper to mid-Eocene). All belong to Ascomycota and are represented by hyphae as well as asexual reproduction structures allowing to assign them to present genera, respectively Periconia, Penicillium and Scopulariopsis. These material provide both the first and the oldest known fossil record of the mentioned taxa, making these data valuable for the knowledge about the evolutionary history of the Ascomycota.     

General survey of hAT transposon superfamily with highlight on hobo element in Drosophila

The hAT transposons, very abundant in all kingdoms, have a common evolutionary origin probably predating the plant-fungi-animal divergence. In this paper we present their general characteristics. Members of this superfamily belong to Class II transposable elements. hAT elements share transposase, short terminal inverted repeats and eight base-pairs duplication of genomic target. We focus on hAT elements in Drosophila, especially hobo. Its distribution, dynamics and impact on genome restructuring in laboratory strains as well as in natural populations are reported. Finally, the evolutionary history of hAT elements, their domestication and use as transgenic tools are discussed.     

On Darwin's palaeontology in The Origin of Species

I investigate the role of palaeontology within Darwin's works through an analysis of the two chapters of The Origin of Species most especially devoted to this science. Palaeontology may occupy several places within the structure of the argumentative logic of Darwinism, but these places have remained to some extent ancillary. Indeed, palaeontology could well document evolutionary patterns, showing the actual occurrence of evolution as a general “historical fact”, but it was poorly adapted to demonstrate the main point of Darwinism: the actual evolutionary process: natural selection acting among individuals. I also show, in agreement with Gould, that Darwin had great confidence in the ultimate ability of palaeontology to support his theory, and that in interpreting palaeontological evidence, he expressed a vision of natural selection much wider and more eclectic than that which has generally been ascribed to him.     

Evolution of structure and function of Class I peroxidases

The phylogenetics of Class I of the heme peroxidase-catalase superfamily currently representing over 940 known sequences in all available genomes of prokaryotes and eukaryotes has been analysed. The robust reconstructed tree for 193 Class I peroxidases with 6 selected Class II representatives reveals all main trends of molecular evolution. It suggests how the ancestral peroxidase gene might have been transferred from prokaryotic into eukaryotic genomes. Besides well known families of catalase-peroxidases, cytochrome c peroxidases and ascorbate peroxidases, the phylogenetic analysis shows for the first time the presence of two new well separated clades of hybrid-type peroxidases that might represent evolutionary bridges between catalase-peroxidases and cytochrome c peroxidases (type A) as well as between ascorbate peroxidases and Class II peroxidases (type B). Established structure-function relationships are summarized. Presented data give useful hints on the origin and evolution of catalytic promiscuity and specificity and will be a valuable basis for future functional analysis of Class I enzymes as well as for de novo design.     

Evolution of nutrient acquisition: when adaptation fills the gap between contrasting ecological theories

Although plant strategies for acquiring nutrients have been widely studied from a functional point of view, their evolution is still not well understood. In this study, we investigate the evolutionary dynamics of these strategies and determine how they influence ecosystem properties. To do so, we use a simple nutrient-limited ecosystem model in which plant ability to take up nutrients is subject to adaptive dynamics. We postulate the existence of a trade-off between this ability and mortality. We show that contrasting strategies are possible as evolutionary outcomes, depending on the shape of the trade-off and, when nitrogen is considered as the limiting nutrient, on the intensity of symbiotic fixation. Our model enables us to bridge these evolutionary outcomes to classical ecological theories such as Hardin''s tragedy of the commons and Tilman''s rule of R*. Evolution does not systematically maximize plant biomass or primary productivity. On the other hand, each evolutionary outcome leads to a decrease in the availability of the limiting mineral nutrient, supporting the work of Tilman on competition between plants for a single resource. Our model shows that evolution can be used to link different classical ecological results and that adaptation may influence ecosystem properties in contrasted ways.     

The Evolution and Origin of Animal Toll-Like Receptor Signaling Pathway Revealed by Network-Level Molecular Evolutionary Analyses

Genes carry out their biological functions through pathways in complex networks consisting of many interacting molecules. Studies on the effect of network architecture on the evolution of individual proteins will provide valuable information for understanding the origin and evolution as well as functional conservation of signaling pathways. However, the relationship between the network architecture and the individual protein sequence evolution is yet little known. In current study, we carried out network-level molecular evolution analysis on TLR (Toll-like receptor ) signaling pathway, which plays an important role in innate immunity in insects and mammals, and we found that: 1) The selection constraint of genes was negatively correlated with its position along TLR signaling pathway; 2) all genes in TLR signaling pathway were highly conserved and underwent strong purifying selection; 3) the distribution of selective pressure along the pathway was driven by differential nonsynonymous substitution levels; 4) The TLR signaling pathway might present in a common ancestor of sponges and eumetazoa, and evolve via the TLR, IKK, IκB and NF-κB genes underwent duplication events as well as adaptor molecular enlargement, and gene structure and conservation motif of NF-κB genes shifted in their evolutionary history. Our results will improve our understanding on the evolutionary history of animal TLR signaling pathway as well as the relationship between the network architecture and the sequences evolution of individual protein.     

Spatiotemporal Evolution of the Global Species Diversity of Rhododendron

Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here, we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3,437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multispecies subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southward from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, that is, elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.     

The economic approach to ‘theory of mind’

Theory of mind (ToM) is a great evolutionary achievement. It is a special intelligence that can assess not only one''s own desires and beliefs, but also those of others. Whether it is uniquely human or not is controversial, but it is clear that humans are, at least, significantly better at ToM than any other animal. Economists and game theorists have developed sophisticated and powerful models of ToM and we provide a detailed summary of this here. This economic ToM entails a hierarchy of beliefs. I know my preferences, and I have beliefs (a probabilistic distribution) about your preferences, beliefs about your beliefs about my preferences, and so on. We then contrast this economic ToM with the theoretical approaches of neuroscience and with empirical data in general. Although this economic view provides a benchmark and makes useful suggestions about empirical tendencies, it does not always generate a close fit with the data. This provides an opportunity for a synergistic interdisciplinary production of a falsifiable theory of bounded rationality. In particular, a ToM that is founded on evolutionary biology might well be sufficiently structured to have predictive power, while remaining quite general. We sketch two papers that represent preliminary steps in this direction.     

Neglected features of probable taxonomic value in Podostemaceae: The case of Polypleurum

The paper reports on hitherto largely neglected discriminative characters in Polypleurum stylosum, P. elongatum, P. minus, as well as the problematic P. munnarense (Podostemaceae, subfam. Podostemoideae) from India and Sri Lanka. The characters discussed include dimorphism of floriferous and vegetative shoots, leaf dimorphism, presence of peculiar floating trichomes on vegetative leaves, and presence of silica bodies in root and shoot tissue. In addition, anatomical pecularities (well-developed cuticle covering the ovary and ovules, cell inclusions in the form of droplets, and presence of idioblasts with firm inclusions of unknown compounds) and specific morphological features (presence of an apical septum in the gynoecium) are documented. All these features point to different developmental and physiological properties of the species concerned, thus signaling separate evolutionary pathways. They may help to elucidate phylogenetic relationships at various taxonomic levels and may prove useful for the delimitation of the genus.     

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History

The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.     

Evolutionary reorganizations of ontogenesis in ascidians of the genus Molgula

The data on comparative, experimental, and molecular embryology of ascidians (genus Molgula) published during the last 15 years have been reviewed. Some representatives of this genus evolved from development with a tailed larva (tadpole) to direct development associated with the loss of larval structures, such as tail, notochord, sensory organs, and differentiated muscles. The data on evolutionary reorganizations of ontogenesis in ascidians of the genus Molgula have been compared with those in sea urchins, anuran amphibians, and some other organisms.     

Conservation and evolutionary modifications of neuroblast expression patterns in insects

One of the major questions in evolutionary developmental neurobiology is how neuronal networks have been adapted to different morphologies and behaviour during evolution. Analyses of neurogenesis in representatives of all arthropod species have revealed evolutionary modifications of various developmental mechanisms. Among others, variations can be seen in mechanisms that are associated with changes in neural progenitor identity, which in turn determines the neuronal subtype of their progeny. Comparative analyses of the molecular processes that underlie the generation of neuronal identity might therefore uncover the steps of evolutionary changes that eventually resulted in modifications in neuronal networks. Here we address this question in the flour beetle Tribolium castaneum by analyzing and comparing the development and expression profile of neural stem cells (neuroblasts) to the published neuroblast map of the fruit fly Drosophila melanogaster. We show that substantial changes in the identity of neuroblasts have occurred during insect evolution. In almost all neuroblasts the relative positions in the ventral hemi-neuromeres are conserved; however, in over half of the neuroblasts the time of formation as well as the gene expression profile has changed. The neuroblast map presented here can be used for future comparative studies on individual neuroblast lineages in D. melanogaster and T. castaneum and additional markers and information on lineages can be added. Our data suggest that evolutionary changes in the expression profile of individual neuroblasts might have contributed to the evolution of neural diversity and subsequently to changes in neuronal networks in arthropod.     

Phylogenetic analysis of protein sequences based on a novel k-mer natural vector method

Based on the k-mer model for protein sequence, a novel k-mer natural vector method is proposed to characterize the features of k-mers in a protein sequence, in which the numbers and distributions of k-mers are considered. It is proved that the relationship between a protein sequence and its k-mer natural vector is one-to-one. Phylogenetic analysis of protein sequences therefore can be easily performed without requiring evolutionary models or human intervention. In addition, there exists no a criterion to choose a suitable k, and k has a great influence on obtaining results as well as computational complexity. In this paper, a compound k-mer natural vector is utilized to quantify each protein sequence. The results gotten from phylogenetic analysis on three protein datasets demonstrate that our new method can precisely describe the evolutionary relationships of proteins, and greatly heighten the computing efficiency.     

根据叶表皮微形态特征试论新麦草属、芒麦草属和三柄麦属间的系统关系

观察了禾本科新麦草属、芒麦草属和三柄麦属主要代表种的叶片表皮形态学特征,总结了三属植物叶表皮结构的异同,探讨了叶表皮特征的分类学意义。同时,根据三属植物叶表皮性状的演化趋势,分析了各属的演化关系和系统位置。结果表明,新麦草属最原始,芒麦草属较进化,三柄麦属最高级;新麦草属可能直接派生了较进化的芒麦草属,并在芒麦草属的基础上进而产生了最高级的三柄麦属。三柄麦属、芒麦草属和新麦草属的这一系统关系同它们外部形态上三联小穗的演化趋势是相互印证的。     

Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms

To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.     

How evolutionary biology challenges the classical theory of rational choice

A fundamental philosophical question that arises in connection with evolutionary theory is whether the fittest patterns of behavior are always the most rational. Are fitness and rationality fully compatible? When behavioral rationality is characterized formally as in classical decision theory, the question becomes mathematically meaningful and can be explored systematically by investigating whether the optimally fit behavior predicted by evolutionary process models is decision-theoretically coherent. Upon investigation, it appears that in nontrivial evolutionary models the expected behavior is not always in accord with the norms of the standard theory of decision as ordinarily applied. Many classically irrational acts, e.g. betting on the occurrence of one event in the knowledge that the probabilities favor another, can under certain circumstances constitute adaptive behavior. One interesting interpretation of this clash is that the criterion of rationality offered by classical decision theory is simply incorrect (or at least incomplete) as it stands, and that evolutionary theory should be called upon to provide a more generally applicable theory of rationality. Such a program, should it prove feasible, would amount to the logical reduction of the theory of rational choice to evolutionary theory.