Exploring macroevolution using modern and fossil data

Macroevolution, encompassing the deep-time patterns of the origins of modern biodiversity, has been discussed in many contexts. Non-Darwinian models such as macromutations have been proposed as a means of bridging seemingly large gaps in knowledge, or as a means to explain the origin of exquisitely adapted body plans. However, such gaps can be spanned by new fossil finds, and complex, integrated organisms can be shown to have evolved piecemeal. For example, the fossil record between dinosaurs and Archaeopteryx has now filled up with astonishing fossil intermediates that show how the unique plexus of avian adaptations emerged step by step over 60 Myr. New numerical approaches to morphometrics and phylogenetic comparative methods allow palaeontologists and biologists to work together on deep-time questions of evolution, to explore how diversity, morphology and function have changed through time. Patterns are more complex than sometimes expected, with frequent decoupling of species diversity and morphological diversity, pointing to the need for some new generalizations about the processes that lie behind such patterns.     

The concept of matter in modern atomic theory

In biology the idea of matter as something passive has been abandoned in favour of the idea that matter has the capacity of self-activity. In modern physics too matter functions more as an agent, with which the experimenter has a relation, than as passive material which he can handle as he likes. So in both fields of study the antithesis between idealism and materialism has been given up, so that the relation instead of the difference between man and nature became the starting point of scientific inquiry.     

The continuity of microevolution and macroevolution

A persistent debate in evolutionary biology is one over the continuity of microevolution and macroevolution – whether macroevolutionary trends are governed by the principles of microevolution. The opposition of evolutionary trends over different time scales is taken as evidence that selection is uncoupled over these scales. I argue that the paradox inferred by trend opposition is eliminated by a hierarchical application of the ‘geometric‐mean fitness’ principle, a principle that has been invoked only within the limited context of microevolution in response to environmental variance. This principle implies the elimination of well adapted genotypes – even those with the highest arithmetic mean fitness over a shorter time scale. Contingent on premises concerning the temporal structure of environmental variance, selectivity of extinction, and clade‐level heritability, the evolutionary outcome of major environmental change may be viewed as identical in principle to the outcome of minor environmental fluctuations over the short‐term. Trend reversals are thus recognized as a fundamental property of selection operating at any phylogenetic level that occur in response to event severities of any magnitude over all time scales. This ‘bet‐hedging’ perspective differs from others in that a specified, single hierarchical selective process is proposed to explain observed hierarchical patterns of extinction.     

The organizer concept and modern embryology: Anglo-American perspectives

This paper analyses the origins of the Spemann-Mangold organizer concept of 1924 in relation to his earlier background and concepts. It traces the consequences and fate of the organizer, and related concepts (embryonic induction, gradients, fields) through subsequent phases in the evolution of developmental biology up to the present, primarily from a UK perspective, but also in the USA. The origins of Wolpert's concept of positional information of around 1970 are analysed; this markedly different model of embryogenesis effectively took the place of the organizer, following on from a generally assumed out-datedness of the corpus of Spemann's data and concepts. Explanations in terms of historical forces are suggested; events are seen as a historical causal chain. A crucial factor appears to have been the long-term neglect of morphogenetic cell movement as an integral component of an adequate induction-based model. The paper discusses the general inter-relation of history and science, and particularly the implications for current scientific practice, including the potential for conceptual distortions due to historical factors. It is argued that historical considerations need to be included as part of the use and critical assessment of basic concepts in science.     

The importance of protistan phylogeny for macroevolution

Explicit estimates of protist phylogeny should play a key role in the development of macroevolutionary theory. Nearly half the evolutionary history of living systems involved only protists, and many trends and traits of macroevolutionary significance originated in protist groups. Special areas of research that can make use of protist phylogenies include: (1) origin of life studies, (2) biotic aspects of the evolution of the environment, (3) developmental biology and evolution, and (4) macroevolutionary trends in the diversification of life.     

Molecular mechanisms of macroevolution

The present paper is devoted to the evolutionary role of genetic modules shuffing. The mechanisms capable to produce new molecular functions and significant complications of ontogenesis are reviewed. Two-step model of macroevolution is proposed. This model comprises: (1) Arising of a new combination of genetic modules. This step does not result in formation of a new taxon but makes necessary ground for that process. (2) Precise structure completing of the new combination of modules and corresponding genome optimization by use of various mechanisms including point mutations. This step concerns many genes and finally leads to formation of a new taxon. It is shown that arising of new combinations of genetic modules might work out as molecular basis for progressive evolution, while alternative structural completing of the same combination might result in adaptive radiation.     

Differential adhesion in morphogenesis: a modern view

The spreading of one embryonic tissue over another, the sorting out of their cells when intermixed and the formation of intertissue boundaries respected by the motile border cells all have counterparts in the behavior of immiscible liquids. The 'differential adhesion hypothesis' (DAH) explains these liquid-like tissue behaviors as consequences of the generation of tissue surface and interfacial tensions arising from the adhesion energies between motile cells. The experimental verification of the DAH, the recent computational models simulating adhesion-mediated morphogenesis, and the evidence concerning the role of differential adhesion in a number of morphodynamic events, including teleost epiboly, the specification of boundaries between rhombomeres in the developing vertebrate hindbrain, epithelial-mesenchymal transitions in embryos, and malignant invasion are reviewed here.     

The organic codes. The basic mechanism of macroevolution.

The origin of the genetic code coincided with the origin of life, while the human codes of cultural evolution emerged almost four billion years later. Modern biology does not recognize any other organic code in nature, and is bound therefore to conclude that the whole of cellular evolution consisted of informational changes. Semantic transformations, natural conventions and biological meaning are things that officially do not exist in the organic world, and play no part in our reconstruction of development and evolution. And yet the properties of organic codes are beginning to emerge in various biological processes. Here it is shown that splicing, signal transduction and pattern formation can be accounted for precisely by the existence of organic codes. It is also shown that those processes were instrumental in bringing about major changes in the history of life, and it is concluded that every main step of macroevolution corresponded to the origin of a new organic code.     

The role of herbivory in the macroevolution of vertebrate hormone dynamics

Vertebrates have high species‐level variation in circulating hormone concentrations, and the functional significance of this variation is largely unknown. We tested the hypothesis that interspecific differences in hormone concentrations are partially driven by plant consumption, based on the prediction that herbivores should have higher basal hormone levels to ‘outcompete’ plant endocrine disruptors. We compared levels of glucocorticoids (GCs), the hormones with the most available data, across 166 species. Using phylogenetically informed comparisons, we found that herbivores had higher GC levels than carnivores. Furthermore, we found that the previously described negative relationship between GC levels and body mass only held in herbivores, not carnivores, and that the effect of diet was greatest at extreme body sizes. These findings demonstrate the far‐reaching effects of diet on animal physiology, and provide evidence that herbivory influences circulating hormone concentrations. We urge future direct testing of the relationship between phytochemical load and GC levels.     

Species selection and random drift in macroevolution

Species selection resulting from trait‐dependent speciation and extinction is increasingly recognized as an important mechanism of phenotypic macroevolution. However, the recent bloom in statistical methods quantifying this process faces a scarcity of dynamical theory for their interpretation, notably regarding the relative contributions of deterministic versus stochastic evolutionary forces. I use simple diffusion approximations of birth‐death processes to investigate how the expected and random components of macroevolutionary change depend on phenotype‐dependent speciation and extinction rates, as can be estimated empirically. I show that the species selection coefficient for a binary trait, and selection differential for a quantitative trait, depend not only on differences in net diversification rates (speciation minus extinction), but also on differences in species turnover rates (speciation plus extinction), especially in small clades. The randomness in speciation and extinction events also produces a species‐level equivalent to random genetic drift, which is stronger for higher turnover rates. I then show how microevolutionary processes including mutation, organismic selection, and random genetic drift cause state transitions at the species level, allowing comparison of evolutionary forces across levels. A key parameter that would be needed to apply this theory is the distribution and rate of origination of new optimum phenotypes along a phylogeny.     

A modern view of phenylalanine ammonia lyase.

Phenylalanine ammonia lyase (PAL; E.C.4.3.1.5), which catalyses the biotransformation of L-phenylalanine to trans-cinnamic acid and ammonia, was first described in 1961 by Koukol and Conn. Since its discovery, much knowledge has been gathered with reference to the enzyme's catabolic role in microorganisms and its importance in the phenyl propanoid pathway of plants. The 3-dimensional structure of the enzyme has been characterized using X-ray crystallography. This has led to a greater understanding of the mechanism of PAL-catalyzed reactions, including the discovery of a recently described cofactor, 3,5-dihydro-5-methyldiene-4H-imidazol-4-one. In the past 3 decades, PAL has gained considerable significance in several clinical, industrial, and biotechnological applications. The reversal of the normal physiological reaction can be effectively employed in the production of optically pure L-phenylalanine, which is a precursor of the noncalorific sweetener aspartame (L-phenylalanyl-L-aspartyl methyl ester). The enzyme's natural ability to break down L-phenylalanine makes PAL a reliable treatment for the genetic condition phenylketonuria. In this mini-review, we discuss prominent details relating to the physiological role of PAL, the mechanism of catalysis, methods of determination and purification, enzyme kinetics, and enzyme activity in nonaqueous media. Two topics of current study on PAL, molecular biology and crystal structure, are also discussed.     

The macroevolution of climatic niches and its role in ant diversification

1. Investigating how climatic niches change over evolutionary timescales is a necessary step to understanding the current distribution of lineages, yet few studies have addressed this issue using comprehensive datasets. In this study, the evolution of ant climatic niches is investigated at a global scale based on bioclimatic data associated with 163 481 ant occurrence records. The resulting dataset was subjected to principal component analysis, and the scores obtained were used to characterise the main axes of ant climatic niche evolution. 2. Principal component axis 1 (PC1) reflected variation in average temperature and seasonality – consistent with typical tropical/temperate gradients – whereas PC2 was associated with varying levels of aridity. Evolution along these two niche axes was markedly different: differences in the amount of explained variance between PC1 (65%) and PC2 (19%) suggest that climatic niche evolution was nearly three times more pronounced along a tropical–temperate climate axis. 3. There was statistically significant phylogenetic signal on PC1, with genera occupying more tropical conditions diversifying at a faster rate, yet neither of these results is significant on PC2. In addition, most of the ancient ant lineages are associated with conditions of low seasonality and high temperatures. 4. These results provide partial support for the tropical conservatism hypothesis as an explanation for geographical patterns of ant species richness.     

Environmental change drove macroevolution in cupuladriid bryozoans

Most macroevolutionary events are correlated with changes in the environment, but more rigorous evidence of cause and effect has been elusive. We compiled a 10 Myr record of origination and extinction, changes in mode of reproduction, morphologies and abundances of cupuladriid bryozoan species, spanning the time when primary productivity collapsed in the southwestern Caribbean as the Isthmus of Panama closed. The dominant mode of reproduction shifted dramatically from clonal to aclonal, due in part to a pulse of origination followed by extinction that was strongly selective in favour of aclonal species. Modern-day studies predict reduced clonality in increasingly oligotrophic conditions, thereby providing a mechanistic explanation supporting the hypothesis that the collapse in primary productivity was the cause of turnover. However, whereas originations were synchronous with changing environments, extinctions lagged 1–2 Myr. Extinct species failed to become more robust and reduce their rate of cloning when the new environmental conditions arose, and subsequently saw progressive reductions in abundance towards their delayed demise. Environmental change is therefore established as the root cause of macroevolutionary turnover despite the lag between origination and extinction.