Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuitry

A large body of experimental evidence indicates that the specific molecular interactions and/or chemical conversions depicted as links in the conventional diagrams of cellular signal transduction and metabolic pathways are inherently probabilistic, ambiguous and context-dependent. Being the inevitable consequence of the dynamic nature of protein structure in solution, the ambiguity of protein-mediated interactions and conversions challenges the conceptual adequacy and practical usefulness of the mechanistic assumptions and inferences embodied in the design charts of cellular circuitry. It is argued that the reconceptualization of molecular recognition and cellular organization within the emerging interpretational framework of self-organization, which is expanded here to include such concepts as bounded stochasticity, evolutionary memory, and adaptive plasticity offers a significantly more adequate representation of experimental reality than conventional mechanistic conceptions do. Importantly, the expanded framework of self-organization appears to be universal and scale-invariant, providing conceptual continuity across multiple scales of biological organization, from molecules to societies. This new conceptualization of biological phenomena suggests that such attributes of intelligence as adaptive plasticity, decision-making, and memory are enforced by evolution at different scales of biological organization and may represent inherent properties of living matter.     

The role of two LEAFY paralogs from Idahoa scapigera (Brassicaceae) in the evolution of a derived plant architecture

Idahoa scapigera produces solitary flowers in the axils of rosette leaves without elongation of the shoot axis, a rosette-flowering architecture. Previous work with one of the two I. scapigera LFY paralogs, IscLFY1, showed that this gene caused aerial flowering rosettes in Arabidopsis thaliana. In this paper, we report that after three generations IscLFY1 transgenic lines are phenotypically indistinguishable from wild-type Arabidopsis, indicating that IscLFY1 protein is able to replace normal LFY function. Additionally, we found that ectopic LFY expression late in development can phenocopy aspects of the aerial rosette phenotype, suggesting that shoot compression caused by IscLFY1 could be caused by localized overexpression of a functional IscLFY protein. We also characterized the expression and function of the second I. scapigera LFY paralog, IscLFY2, in A. thaliana. In contrast to IscLFY1, this paralog was expressed in floral meristems and the shoot apical meristem (SAM). In I. scapigera, LFY-specific antibodies detected high protein levels in developing flowers but not in the apex, suggesting trans-regulatory differences between I. scapigera and A. thaliana. Most IscLFY2 transgenic A. thaliana plants were indistinguishable from wild type, but in a minority of lines the SAM was converted to a terminal flower as would be expected from the reporter-expression pattern. Taken together these results show that both I. scapigera paralogs have conserved LFY function, both proteins can rescue lfy and both can modify inflorescence architecture in an A. thaliana background: either by affecting internode elongation (IscLFY1) or by causing homeotic conversion of shoots into flowers (IscLFY2).     

Cuckoos, cowbirds and hosts: adaptations, trade-offs and constraints

The interactions between brood parasitic birds and their host species provide one of the best model systems for coevolution. Despite being intensively studied, the parasite-host system provides ample opportunities to test new predictions from both coevolutionary theory as well as life-history theory in general. I identify four main areas that might be especially fruitful: cuckoo female gentes as alternative reproductive strategies, non-random and nonlinear risks of brood parasitism for host individuals, host parental quality and targeted brood parasitism, and differences and similarities between predation risk and parasitism risk. Rather than being a rare and intriguing system to study coevolutionary processes, I believe that avian brood parasites and their hosts are much more important as extreme cases in the evolution of life-history strategies. They provide unique examples of trade-offs and situations where constraints are either completely removed or particularly severe.     

Molecular ecophysiology of Antarctic notothenioid fishes

The notothenioid fishes of the Southern Ocean surrounding Antarctica are remarkable examples of organismal adaptation to extreme cold. Their evolution since the mid-Miocene in geographical isolation and a chronically cold marine environment has resulted in extreme stenothermality of the extant species. Given the unique thermal history of the notothenioids, one may ask what traits have been gained, and conversely, what characters have been lost through change in the information content of their genomes. Two dramatic changes that epitomize such evolutionary transformations are the gain of novel antifreeze proteins, which are obligatory for survival in icy seawater, by most notothenioids and the paradoxical loss of respiratory haemoproteins and red blood cells, normally deemed indispensable for vertebrate life, by the species of a highly derived notothenioid family, the icefishes. Here, we review recent advances in our understanding of these traits and their evolution and suggest future avenues of investigation.The formerly coherent paradigm of notothenioid freeze avoidance, developed from three decades of study of antifreeze glycoprotein (AFGP) based cold adaptation, now faces challenges stemming from the recent discovery of antifreeze-deficient, yet freeze-resistant, early notothenioid life stages and from definitive evidence that the liver is not the physiological source of AFGPs in notothenioid blood. The resolution of these intriguing observations is likely to reveal new physiological traits that are unique to the notothenioids. Similarly, the model of AFGP gene evolution from a notothenioid pancreatic trypsinogen-like gene precursor is being expanded and refined based on genome-level analyses of the linked AFGP loci and their ancestral precursors. Finally, the application of comparative genomics to study evolutionary change in the AFGP genotypes of cool-temperate notothenioids from sub-Antarctic habitats, where these genes are not necessary, will contribute to the mechanistic understanding of the dynamics of AFGP gene gain and loss.In humans and most vertebrates, mutations in the alpha- or beta-globin genes or defects in globin chain synthesis are causes of severe genetic disease. Thus, the 16 species of haemoglobinless, erythrocyte-null icefishes are surprising anomalies -- in fact, they could only have evolved and thrived due to relaxed selection pressure for oxygen-binding proteins in the cold, oxygen-rich waters of the Southern Ocean. Fifteen of the sixteen icefish species have lost most of the adult alphabeta-globin locus and retain only a small 3' fragment of the alpha-globin gene. The only exception to this pattern occurs in Neopagetopsis ionah, which possesses a disrupted alphabeta-globin gene complex that probably represents a non-functional intermediate on the evolutionary pathway to near total globin gene extinction. By contrast, six of the icefish species fail to express myoglobin. The absence of myoglobin expression has occurred by several independent mutations and distinct mechanisms. Haemoprotein loss is correlated with dramatic increases in cellular mitochondrial density, heart size, blood volume and capillary bed volume. Evolution of these compensatory traits was probably facilitated by the homeostatic activity of nitric oxide, a key modulator of angiogenesis and mitochondrial biogenesis. These natural knockouts of the red blood cell lineage are an excellent genomic resource for erythroid gene discovery by comparative genomics, as illustrated for the newly described gene, bloodthirsty.     

Do constructional constraints influence cichlid craniofacial diversification?

Constraints on form should determine how organisms diversify. Owing to competition for the limited space within the body, investment in adjacent structures may frequently represent an evolutionary compromise. For example, evolutionary trade-offs between eye size and jaw muscles in cichlid fish of the African great lakes are thought to represent a constructional constraint that influenced the diversification of these assemblages. To test the evolutionary independence of these structures in Lake Malawi cichlid fish, we measured the mass of the three major adductor mandibulae (AM) muscles and determined the eye volume in 41 species. Using both traditional and novel methodologies to control for resolved and unresolved phylogenetic relationships, we tested the evolutionary independence of these four structures. We found that evolutionary change in the AM muscles was positively correlated, suggesting that competition for space in the head has not influenced diversification among these jaw muscles. Furthermore, there was no negative relationship between change in total AM muscle mass and eye volume, indicating that there has been little effect of the evolution of eye size on AM evolution in Lake Malawi cichlids. The comparative approach used here should provide a robust method to test whether constructional constraints frequently limit phenotypic change in adaptive radiations.     

A primary role of developmental instability in sexual selection

In evolutionary biology, fluctuating asymmetry (FA) is thought to reveal developmental instability (DI, inability to buffer development against perturbations), but its adaptive and genetic bases are being debated. In other fields, such as human clinical genetics, DI is being assessed as incidence of minor morphological abnormalities (MMAs) and used to predict certain fitness outcomes. Here, for the first time, we combine these complementary measures of DI in sexual selection and quantitative genetic studies of a natural population. Comprehensive multivariate analyses demonstrate that FA and MMAs in a condition-dependent sexual ornament, the male Drosophila bipectinata sex comb used in courtship, are sole significant targets of selection favouring their reduced expression in New Caledonia. Comb FA and MMAs are positively correlated, confirming that each are linked to a common buffering system. Ornament size and DI (as FA and MMAs) are positively correlated, genetically and phenotypically, contrary to theoretical expectation of negative size-FA scaling under the assumption that FA reveals overall genetic quality. There exists significant additive genetic variance for MMAs, demonstrating their evolutionary potential. Ornament DI in New Caledonia is markedly elevated compared with populations where such selection was not detected, suggesting that the increased population-level DI is capacitating adaptive evolution.     

Springs and wire plants: anachronistic defences against Madagascar's extinct elephant birds

The extinction of large vertebrates in the last few millennia has left a legacy of evolutionary anachronisms. Among these are plant structural defences that persist long after the extinction of the browsers. A peculiar, and controversial, example is a suite of traits common in divaricate (wide-angled branching) plants from New Zealand. Divaricate architecture has been interpreted as an adaptive response to cold climates or an anachronistic defence against the extinct moas. Madagascar, a larger tropical island, also had a fauna of large flightless birds, the elephant birds. If these extinct ratites selected for similar plant defences, we expected to find convergent features between New Zealand and Malagasy plants, despite their very different climates. We searched the southern thickets of Madagascar for plants with putative anti-ratite defences and scored candidate species for a number of traits common to many New Zealand divaricates. We found many Malagasy species in 25 families and 36 genera shared the same suite of traits, the 'wire plant' syndrome, as divaricates in New Zealand that resist ratite browsing. Neither ecologically, nor phylogenetically, matched species from South Africa shared these traits. Malagasy wire plants differ from many New Zealand divaricates in lacking the distinctive concentration of leaves in the interior of shrubs. We suggest that New Zealand divaricates have a unique amalgam of traits that acted as defences and also confer tolerance to cold. We conclude that many woody species in the thickets of southern Madagascar share, with New Zealand, anachronistic structural defences against large extinct bird browsers.     

Cooperation is less likely to evolve in a finite population with a highly skewed distribution of family size

In the context of the finitely repeated Prisoner's Dilemma with the possibility of cooperating or defecting each time, the strategy tit-for-tat (TFT) consists in cooperating the first time and copying the strategy previously used by the opponent the next times. Assuming random pairwise interactions in a finite population of always defecting individuals, TFT can be favoured by selection to go to fixation following its introduction as a mutant strategy. We deduce the condition for this to be the case under weak selection in the framework of a general reproduction scheme in discrete time. In fact, we show when and why the one-third rule for the evolution of cooperation holds, and how it extends to a more general rule. The condition turns out to be more stringent when the numbers of descendants left by the individuals from one time-step to the next may substantially differ. This suggests that the evolution of cooperation is made more difficult in populations with a highly skewed distribution of family size. This is illustrated by two examples.     

Insilco analysis of functionally important residues in folate receptors

Lack of crystal structure data of folate binding proteins has left so many questions unanswered (for example, important residues in active site, binding domain, important amino acid residues involved in interactions between ligand and receptor). With sequence alignment and PROSITE motif identification, we attempted to answer evolutionarily significant residues that are of functional importance for ligand binding and that form catalytic sites. We have analyzed 46 different FRs and FBP sequences of various organisms obtained from Genbank. Multiple sequence alignment identified 44 highly conserved identical amino acid residues with 10 cysteine residues and 12 motifs including ECSPNLGPW (which might help in the structural stability of FR).     

鸟类羽色多态现象：概念及其进化机制假说

多态现象对了解物种的遗传、变异和进化有着重要意义,鸟类羽色多态现象的进化机制,是多态现象研究中非常重要的内容。鸟类羽色多态现象的进化机制假说主要有：分化选择假说、异类选择假说和非随机性交配假说等。本文对鸟类羽色多态现象的概念和以上进化机制假说进行了综述,并针对鸟类羽色多态现象进化机制研究中存在争议的问题及研究的不足提出了自己的看法。