AUTECOLOGY AND THE FILLING OF ECOSPACE: KEY METAZOAN RADIATIONS

Abstract:  All possible combinations of six tiering positions in relation to the substratum/water interface, six motility levels and six feeding strategies define a complete theoretical ecospace of 216 potential modes of life for marine animals. The number of modes of life actually utilized specifies realized ecospace. Owing to constraints of effectiveness and efficiency the modern marine fauna utilizes only about half the potential number of modes of life, two-thirds of which (62 of 92) are utilized by animals with readily preserved, mineralized hard parts. Realized ecospace has increased markedly since the early evolution of animal ecosystems. The Ediacaran fauna utilized at most 12 modes of life, with just two practised by skeletal organisms. A total of 30 modes of life are recorded in the Early and Middle Cambrian, 19 of which were utilized by skeletal organisms. The other 11 are documented from soft-bodied animals preserved in the Chengjiang and Burgess Shale Konservat-Lagerstätten. The number of modes of life utilized by skeletal organisms increased by more than 50 per cent during the Ordovician radiation to a Late Ordovician total of 30. Between the Late Ordovician and the Recent the number of utilized modes of life has doubled again. The autecological and taxonomic diversity histories of the marine metazoa appear to be broadly parallel, and future studies of theoretical ecospace utilization should provide more detailed tests of pattern and process in the ecological history of the metazoa.     

Assessing the determinants of evolutionary rates in the presence of noise

Although protein sequences are known to evolve at vastly different rates, little is known about what determines their rate of evolution. However, a recent study using principal component regression (PCR) has concluded that evolutionary rates in yeast are primarily governed by a single determinant related to translation frequency. Here, we demonstrate that noise in biological data can confound PCRs, leading to spurious conclusions. When equalizing noise levels across 7 predictor variables used in previous studies, we find no evidence that protein evolution is dominated by a single determinant. Our results indicate that a variety of factors--including expression level, gene dispensability, and protein-protein interactions--may independently affect evolutionary rates in yeast. More accurate measurements or more sophisticated statistical techniques will be required to determine which one, if any, of these factors dominates protein evolution.     

A combined empirical and mechanistic codon model

The evolutionary selection forces acting on a protein are commonly inferred using evolutionary codon models by contrasting the rate of synonymous to nonsynonymous substitutions. Most widely used models are based on theoretical assumptions and ignore the empirical observation that distinct amino acids differ in their replacement rates. In this paper, we develop a general method that allows assimilation of empirical amino acid replacement probabilities into a codon-substitution matrix. In this way, the resulting codon model takes into account not only the transition-transversion bias and the nonsynonymous/synonymous ratio, but also the different amino acid replacement probabilities as specified in empirical amino acid matrices. Different empirical amino acid replacement matrices, such as secondary structure-specific matrices or organelle-specific matrices (e.g., mitochondria and chloroplasts), can be incorporated into the model, making it context dependent. Using a diverse set of coding DNA sequences, we show that the novel model better fits biological data as compared with either mechanistic or empirical codon models. Using the suggested model, we further analyze human immunodeficiency virus type 1 protease sequences obtained from drug-treated patients and reveal positive selection in sites that are known to confer drug resistance to the virus.     

A rose by any other name? Rethinking the similarities and differences between male and female genital cutting

In this article, we offer a critical examination of the tendency to segregate discussion of surgical alterations to the male and female genitals into separate compartments--the first known as circumcision, the second as genital mutilation. We argue that this fundamental problem of definition underlies the considerable controversy surrounding these procedures when carried out on minors, and that it hinders objective discussion of the alleged benefits, harms, and risks. We explore the variable effects of male and female genital surgeries, and we propose a scale of damage for male circumcision to complement the World Health Organization's categorization of female genital mutilation. The origins of the double standard identified are placed in historical perspective, and in a brief conclusion we make a plea for greater gender neutrality in the approach to this contentious issue.     

Explanations in evolutionary theory1

The theory of biological evolution is defined in many ways, leading to considerable confusion in its application and testing against objective empirical observations. Evolutionary change is usually defined as genetic which would exclude both cultural and template evolution; hence the qualifying adjective genetic should not be included in the definition of biological evolution. Darwin's theory, always described by him in the singular, is actually a bundle of five independent theories about evolution as advocated by Mayr. Furthermore only one of these theories, that of common descent, is historical, and the other four – evolution as such, gradualism, processes of phyletic evolution and of speciation, and causes of evolution – are nomological. Hence not all evolutionary theory is historical. Biological comparisons can be divided into horizontal and vertical ones and valid conclusions from one type of comparisons cannot be automatically extrapolated to the other. All phyletic evolutionary change, no matter how extensive it may be, never crosses species taxa boundaries; hence it is not possible to distinguish ‘trans‐specific evolution’ (= evolution beyond or above the level of the species) from evolution within the species level. Macroevolution does not differ from microevolution except in the scale of the overall change; no special causes or processes of macroevolution exist.     

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).     

The application of environmental ethics in biological conservation: a case study from the southernmost tip of the Americas

Biological conservation is not only about facts and technical measures concerning ecology, rather it must also consider values. This pertains to both the balancing of various human interests and also to the ethical evaluation of human actions towards nature. Here we discuss how environmental ethics can be incorporated into conservation decisions, and what implications the inclusion of ethical valuation has for the practice of conservation biology. While this is done mostly on a rather abstract level, we illustrate this here by applying ethical theory to a case study: the options for management of the introduced North American beaver (Castor canadensis) in the very south of Chile (Navarino Island). The beaver is an exotic species to the area and has substantially altered the ecological systems of the region. We discuss different options for dealing with the beaver (eradicate, control, tolerate, promote) from the viewpoint of anthropocentric environmental ethics and biocentric ethics. The results of our analysis demonstrate the value of ethical discussions in clarifying and underpinning arguments for and against specific actions. At the same time, they also show that ethical arguments do not decrease the need for sound scientific data but, on the contrary, may even increase this demand. We also highlight that the conclusions regarding adequate actions to be taken vary depending on the specific ethical theory embraced.

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.