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DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data with a user-friendly Windows 95/98/2000/NT interface. DAMBE is free and can be downloaded from http://web.hku.hk/~xxia/software/software.htm. The current version is 4.0.36.
We show how cultural selection for learnability during the process of linguistic evolution can be visualized using a simple iterated learning model. Computational models of linguistic evolution typically focus on the nature of, and conditions for, stable states. We take a novel approach and focus on understanding the process of linguistic evolution itself. What kind of evolutionary system is this process? Using visualization techniques, we explore the nature of replicators in linguistic evolution, and argue that replicators correspond to local regions of regularity in the mapping between meaning and signals. Based on this argument, we draw parallels between phenomena observed in the model and linguistic phenomena observed across languages. We then go on to identify issues of replication and selection as key points of divergence in the parallels between the processes of linguistic evolution and biological evolution.
We investigate stochastic resonance in the nonlinear, one-dimensional Fisher-Eigen model (FEM), which represents an archetypal model for biological evolution based on a global coupling scheme. In doing so we consider different periodically driven fitness functions which govern the evolution of a biological phenotype population. For the case of a simple harmonic fitness function we are able to derive the exact analytic solution for the asymptotic probability density. A distinct feature of this solution is a phase lag between the driving signal and the linear response of the system. Furthermore, for more complex systems a general perturbation theory (linear response approximation) is put forward. Using the latter approach, we investigate stochastic resonance in terms of the spectral amplification measure for a quadratic, a quartic single-peaked, and for a bistable fitness function. Our analytical results are also compared with those of detailed numerical simulations. Our findings vindicate that stochastic resonance does occur in these nonlinear, globally coupled biological systems.
3.5 billion years (byr) ago, when it is thought that Mars and Earth had similar climates, biological evolution on Earth had made considerable progress, such that life was abundant. It is therefore surmised that prior to this time period the advent of chemical evolution and subsequent origin of life occurred on Earth and may have occurred on Mars. Analysis for organic compounds in the soil buried beneath the Martian surface may yield useful information regarding the occurrence of chemical evolution and possibly biological evolution. Calculations based on the stability of amino acids lead to the conclusion that remnants of these compounds, if they existed on Mars 3.5 byr ago, might have been preserved buried beneath the surface oxidizing layer. For example, if phenylalanine, an amino acid of average stability, existed on Mars 3.5 byr ago, then 1.6% would remain buried today, or 25 pg-2.5 ng of C g-1 Martian soil may exist from remnants of meteoritic and cometary bombardment, assuming that 1% of the organics survived impact.
Studies of the biology of music (as of language) are highly interdisciplinary and demand the integration of diverse strands of evidence. In this paper, I present a comparative perspective on the biology and evolution of music, stressing the value of comparisons both with human language, and with those animal communication systems traditionally termed "song". A comparison of the "design features" of music with those of language reveals substantial overlap, along with some important differences. Most of these differences appear to stem from semantic, rather than structural, factors, suggesting a shared formal core of music and language. I next review various animal communication systems that appear related to human music, either by analogy (bird and whale "song") or potential homology (great ape bimanual drumming). A crucial comparative distinction is between learned, complex signals (like language, music and birdsong) and unlearned signals (like laughter, ape calls, or bird calls). While human vocalizations clearly build upon an acoustic and emotional foundation shared with other primates and mammals, vocal learning has evolved independently in our species since our divergence with chimpanzees. The convergent evolution of vocal learning in other species offers a powerful window into psychological and neural constraints influencing the evolution of complex signaling systems (including both song and speech), while ape drumming presents a fascinating potential homology with human instrumental music. I next discuss the archeological data relevant to music evolution, concluding on the basis of prehistoric bone flutes that instrumental music is at least 40,000 years old, and perhaps much older. I end with a brief review of adaptive functions proposed for music, concluding that no one selective force (e.g., sexual selection) is adequate to explaining all aspects of human music. I suggest that questions about the past function of music are unlikely to be answered definitively and are thus a poor choice as a research focus for biomusicology. In contrast, a comparative approach to music promises rich dividends for our future understanding of the biology and evolution of music.
The Adelgidae form a small clade of insects within the Aphidoidea (Hemiptera) that includes some of the most destructive introduced pest species threatening North American forest ecosystems. Despite their importance, little is known about their evolutionary history and their taxonomy remains unresolved. Adelgids are cyclically parthenogenetic and exhibit multigeneration complex life cycles. They can be holocyclic, with a sexual generation and host alternation, or anholocyclic, entirely asexual and without host alternation. We discuss adelgid behavior and ecology, emphasizing plant-insect interactions, and we explore ways that the biogeographic history of their host plants may have affected adelgid phylogeny and evolution of adelgid life cycles. Finally, we highlight several areas in which additional research into speciation, population genetics, multitrophic interactions, and life-history evolution would improve our understanding of adelgid biology and evolution.
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The principles of biological evolution of photosynthesis are established, but the ways of chemical evolution are unclear yet. The model systems will help to elucidate the problem. Every type of photosynthesis requires photoreceptor absorbing solar radiation. We studied as photoreceptors inorganic components of Earth crust, some coenzymes and porphyrins of abiogenic and biogenic origin. By the aid of inorganic photosensitizers (TiO2, ZnO) the models of photosystems I and II were constructed. Photochemical activation of some coenzymes may serve as an intermediate step from heterotrophic 'dark' to 'light' metabolism. The further evolution led to the separation of catalytic and photosensitizing functions. Porphin, chlorin and bacteriochlorin were formed by abiogenic synthesis. Magnesium complexes of porphyrins are active being excited by light. They are capable to reversible acceptance or donation of an electron to partner molecule. Excited Mg-complexes of porphyrins (P) are capable to transfer an electron from electron-donor (D) to electron-acceptor (A) accompanied by conversion of light quanta energy into potential chemical energy. The primary electron transfer unit (D-P-A) was incorporated into primary membrane. The transition from random to anisotropic arrangement of (D-P-A) in the membrane was plausable as a step of evolution; charge translocation appeared. (D-P-A) units created in the period of chemical evolution were probably used in the course of biological evolution. The (D-P-A) units were coupled with noncyclic and cyclic electron transfer resulting in ATP formation; coupling of two (D-P-A) units led to H2O oxidation and NADP reduction in photosynthetic organisms. The improvement of pigments biosynthesis created the phenomenon of excitation energy migration from the bulk of the pigment to (D-P-A) unit, being reactive center. The models described points the plausible steps of chemical evolution; the real sequence of events will be probably disclosed in the studies of precambrian rocks and space exploration.
The first three decades of the subdiscipline of biology known as "molecular evolution" have generated large amounts of new information that illuminate the nature of evolutionary pattern and process. Major progress has been made in identifying primary sequence variation in genes and their protein products, initially from biochemically tractable systems (from large or culturable organisms and from highly-reiterated genes or highly-expressed gene products). In the 1980s, these techniques that had been limited to specialists, to relatively few representatives of the diversity of life, and to a small number of those organisms' genes, were extended through advances in molecular genetics and biochemistry, resulting in an explosion of molecular information and a proliferation of molecular trees. Studies of variation in molecular characters also were rarely linked with studies of anatomical, behavioral or ecological diversity. More sophisticated molecular genetic and biochemical techniques, currently being applied to long-standing questions in cell and developmental biology in model systems, should be applicable to more diverse lineages in the next decade. Molecular trees produced from one or more "housekeeping genes" can identify key lineages (species, populations, genomes or gene families) which, by comparison to model systems, may illuminate important aspects of higher level variability. Thus, the next phase of research in the field of molecular evolution should see greater linkage between studies of simple molecular and more complex developmental characters, and increased functional testing of genes and gene products in an evolutionary context. This review highlights some comparative experimental approaches that I believe will be most effective in extending our understanding of molecular evolution and better linking the field to other areas of science in the next few years.
BACKGROUND: MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. RESULTS: We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. CONCLUSION: MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454
In the history of evolution, biologic organisms have formed traits with both adaptive and sometimes maladaptive significance to their surrounding environments. The sickle cell mutation genes conferring resistance to malarial infection in human heterozygotes is an example of how certain genetic abnormalities can serve adaptive significance to an organism. Schizophrenia and the "Odyssyian personality" have often been cited as a neuropsychiatric correlate for evolutionary adaptive benefit in an organism. This article re-examines the possibility that schizophrenia-related genes can serve a beneficial adaptive role and that altered function of the N-methyl-D-aspartate receptor is the molecular correlate of such adaptive significance.
Author pay attention to polyvariantness of expectative consequences of hotbed effect, to evolution-biological aspect of problem, and to evolution prognosis difficulties. The perspective of biosphere and mankind survival is mutual adaptation in coevolution process. Creation of complete biological evolution theory is becoming more and more urgent. Evolution prognosis and biosphere management will be realized on evolution theory base.
On the basis of paleological evidence, it has been suggested that biological evolution need not necessarily be characterized by gradual change. Rather, evolutionary history may display saltatory periods of rapid speciation alternating with periods of relative quiescence, the whole dynamic being called punctuated equilibria. The empirical evidence that has been presented in support of this hypothesis has been the object of a vigorous dispute. Mathematical investigations of complex models of biological evolution that contain random elements have demonstrated that these systems can display saltatory behavior. In this paper we address a more abstract question: can saltations occur in the evolution of very simple, deterministic mathematical systems that function in a constant environment? The answer appears to be yes. Saltations appear as a natural dynamical behavior in the evolution of simplistic information processing networks. We stress that these networks do not constitute a model of biological evolution. However, the appearance of saltations in such simple systems suggests that their appearance in a process as complex as biological evolution is not surprising.
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While biological evolution is a well-defined and accepted phenomenon, the notion of conceptual evolution, however implicit in biomedical progress, remains less well-defined and accepted. Frameworks are provided which portray conceptual evolution in terms of the spatio-temporal and hierarchical cognitive embrace of the human external and internal environments.
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The human chromosomal growth hormone locus contained on cloned DNA and spanning approximately 66,500 bp was sequenced in its entirety to provide a framework for the analysis of its biology and evolution. This locus evolved by a series of duplications and contains in its present form five genes which display a remarkably high degree of sequence identity (approximately 95%) in all their domains. The DNA sequence of the locus reveals the presence of 48 middle repetitive sequence elements of the Alu type and one member of the KpnI family, all located in the intergenic regions. The expression of each gene was examined by screening pituitary and placental cDNA libraries by using gene-specific oligonucleotides. According to this analysis, the hGH-N gene is transcribed exclusively in the pituitary, whereas the other four genes (hCS-L, hCS-A, hGH-V, hCS-B) are expressed only in placental tissue, at levels characteristic for each gene. Particular DNA sequences found upstream of the individual promoter regions might account for the observed tissue specificity and different transcriptional activity of the genes. The hCS-L gene carries a G to A transition in a sequence used by the other four genes as an intronic 5' splice donor site. This mutation results in a different splicing pattern and, hence, in a novel sequence of the hCS-L gene mRNA and the deduced polypeptide.
Biological diversity is driven mainly by gene duplication followed by mutation and selection. This divergence in either regulatory or protein-coding sequences can result in quite different biological functions for even closely related genes. This concept is exemplified by the mammalian Hox gene complex, a group of 39 genes which are located on 4 linkage groups, dispersed on 4 chromosomes. The evolution of this complex began with amplification in cis of a primordial Hox gene to produce 13 members, followed by duplications in trans of much of the entire unit. As a consequence, Hox genes that occupy the same relative position along the 5' to 3' chromosomal coordinate (trans-paralogous genes) share more similarity in sequence and expression pattern than do adjacent Hox genes on the same chromosome. Studies in mice indicate that although individual family members may have unique biological roles, they also share overlapping functions with their paralogues. Here we show that the proteins encoded by the paralogous genes, Hoxa3 and Hoxd3, can carry out identical biological functions, and that the different roles attributed to these genes are the result of quantitative modulations in gene expression.