Self-inflicted Fear of Evolution

Commonly calculated zero probabilities for synthesis of a given protein sequence by chance are that small because the sizes of the proteins taken for the calculations are too large (over 100 residues). Same estimate for 20 - 30 residue chains makes the chance close to 1. Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005.     

A congruent phylogenomic signal places eukaryotes within the Archaea

Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook ‘three domains’ tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.     

Science and the Concept of Evolution: From the Big Bang to the Origin and Evolution of Life

The common thread of evolution runs through all science disciplines, and the concept of evolution enables students to better understand the nature of the universe and our origins. “Science and the Concept of Evolution” is one of two interdisciplinary science Core courses taken by Dowling College undergraduates as part of their General Education requirements. The course examines basic principles and methods of science by following the concept of evolution from the big bang to the origin and evolution of life. Case studies of leading scientists illustrate how their ideas developed and contributed to the evolution of our understanding of the world. Evidences for physical, chemical, and biological evolution are explored, and students learn to view the evolution of matter and of ideas as a natural process of change over space and time.     

The ecological benefits of larger colony size may promote polygyny in ants

How polygyny evolved in social insect societies is a long‐standing question. This phenomenon, which is functionally similar to communal breeding in vertebrates, occurs when several queens come together in the same nest to lay eggs that are raised by workers. As a consequence, polygyny drastically reduces genetic relatedness among nestmates. It has been suggested that the short‐term benefits procured by group living may outweigh the costs of sharing the same nesting site and thus contribute to organisms rearing unrelated individuals. However, tests of this hypothesis are still limited. To examine the evolutionary emergence of polygyny, we reviewed the literature to build a data set containing life‐history traits for 149 Palearctic ant species and combined this data set with a reconstructed phylogeny. We show that monogyny is the ancestral state and that polygyny has evolved secondarily and independently throughout the phylogenetic tree. The occurrence of polygyny is significantly correlated with larger colony size, dependent colony founding and ecological dominance. Although polydomy (when a colony simultaneously uses several connected nests) tends to occur more frequently in polygynous species, this trend is not significant when phylogenetic history is accounted for. Overall, our results indicate that polygyny may have evolved in ants in spite of the reduction in nestmate relatedness because large colony size provides immediate ecological advantages, such as the more efficient use of temporal food resources. We suggest that the competitive context of ant communities may have provided the conditions necessary for the evolution of polygyny in some clades.     

Maternal effects and heritability of annual productivity

Within-individual consistency and among-individual heterogeneity in fitness are prerequisites for selection to take place. Within-individual variation in productivity between years, however, can vary considerably, especially when organisms become older and more experienced. We examine individual consistency in annual productivity, the covariation between survival and annual productivity, and the sources of variation in annual productivity, while accounting for advancing age, to test the individual-quality and resource-allocation life-history theory hypotheses. We use long-term data from a pedigreed, wild population of house sparrows. Within-individual annual productivity first increased and later decreased with age, but there were no selective mortality due to individual quality and no correlation between lifespan and productivity. Individuals were consistent in their annual productivity (C = 0.49). Narrow-sense heritability was low (h(2) = 0.09), but maternal effects explained much of the variation (M = 0.33). Such effects can influence evolutionary processes and are of major importance for our understanding of how variation in fitness can be maintained.     

The adaptive legacy of human evolution: A search for the environment of evolutionary adaptedness

The growth of evolutionary psychology has led to renewed interest in what might be the significant evolutionary heritage of people living today, and in the extent to which humans are suited to a particular adaptive environment—the EEA. The EEA, though, is a new tool in the battery of evolutionary concepts, and it is important both that it is scrutinized for its utility, and that the actual reconstructions of the environments in which humans and hominids evolved are based on sound palaeobiological inference and an appropriate use of the phylogenetic context of primate evolution.     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

Life history influences rates of climatic niche evolution in flowering plants

Across angiosperms, variable rates of molecular substitution are linked with life-history attributes associated with woody and herbaceous growth forms. As the number of generations per unit time is correlated with molecular substitution rates, it is expected that rates of phenotypic evolution would also be influenced by differences in generation times. Here, we make the first broad-scale comparison of growth-form-dependent rates of niche evolution. We examined the climatic niches of species on large time-calibrated phylogenies of five angiosperm clades and found that woody lineages have accumulated fewer changes per million years in climatic niche space than related herbaceous lineages. Also, climate space explored by woody lineages is consistently smaller than sister lineages composed mainly of herbaceous taxa. This pattern is probably linked to differences in the rate of climatic niche evolution. These results have implications for niche conservatism; in particular, the role of niche conservatism in the distribution of plant biodiversity. The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets.     

Comets: Chemistry and chemical evolution

Summary Lasting commitment to cosmic chemistry and an awareness of the fascinating role of comets in that study was a consequence of an association with Harold Urey early in my astronomical career. Urey's influence on cometary research spread as colleagues with whom I was associated, in turn, developed their own programs in cometary chemistry. One phase of the Chicago research shows that Whipple's icy nucleus would be below about 250 K. This property, combined with their small internal pressure, means cometary interiors remain essentially unchanged during their lifetime. Observations of cometary spectra indicate that they are rich in simple organic species. Experiments on comet-like ice mixture suggests that the extensive array of interstellar molecules also may be found in comets. The capture of cometary debris by the earth or the impact of comets would have been an early source of biochemically significant molecules. Recent hypotheses on radiogenic heating and melting of water ice in the central zone of nuclei do not seem consistent with recent observations or ideas of structure. Thus comets are not a likely place for life to develop.     

The evolution of embryonic patterning mechanisms in animals

Animals exhibit an enormous diversity of life cycles and larval morphologies. The developmental basis for this diversity is not well understood. It is clear, however, that mechanisms of pattern formation in early embryos differ significantly among and within groups of animals. These differences show surprisingly little correlation with phylogenetic relationships; instead, many are correlated with ecological factors, such as changes in life histories.     

Emergent Robustness in Competition Between Autocatalytic Chemical Networks

The origin of auto-catalytic networks has been proposed as an initial step in pre-biotic evolution. It is possible to derive simple models where auto-catalytic networks naturally arise from simple chemical mixtures. In order for such a system to develop, there needs to be some degree of stability, what is characterised as `robustness'. We demonstrate that competing systems generate this robustness as they create a distributed network of catalytic pathways.     

REVIEW: Optimality models in the age of experimental evolution and genomics

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well‐researched organism allows dissection of the evolutionary process to identify causes of model failure – whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation – an especially useful augmentation to well‐researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.     

Brooding of pelagic-type larvae in Ophiopeza spinosa: reproduction and development in a tropical ophiodermatid brittlestar

Abstract. Ophiopeza spinosa , a small ophiodermatid ophiuroid, is locally abundant in shallow water rubble habitat at Lizard Island, northern Great Barrier Reef, Australia. This species is a protantric hermaphrodite. The switch from reproduction as a male to a female is progressive, involving a simultaneous hermaphrodite as a transitional stage. Members of O. spinosa brood their young in the respiratory bursae. Cohorts of eggs (280 μm diameter) develop synchronously in the gonad and are spawned as a group into the bursa. Despite non-pelagic development, the larvae of O. spinosa are a vitellaria type typical of broadcast-spawning ophiodermatids, providing a link to an ancestral form with a dispersive larva. The vitellaria has prominent ciliary bands and swims in the same manner as pelagic vitellaria. In vitro , the larvae developed to the juvenile stage independent of the parent. There was no evidence of extraembryonic nutrition; a proportion of the maternal provisions were retained through metamorphosis. This is the first ophiuroid known to brood a pelagic-type vitellaria larva. Juveniles appear to leave the parent at the two- to three-arm segment stage, slightly larger than the newly settled juveniles of ophiodermatids with pelagic vitellariae. The presence of functional larvae in the bursa suggests a recent switch to the incubatory life history in O. spinosa and the possibility of a reversal back to a dispersive life history. O. spinosa have the potential to both brood and broadcast their young.     

Evolutionarily optimal age schedule of repair: Computer modelling of energy partition between current and future survival and reproduction

The aim of this study was to clarify the relationships between environmental conditions and physiological constraints that persist during the evolution of a species on the one hand, and the strategies of energy investment used by an individual to repair on the other. We take as a basis for our study the evolutionary optimization approach and use as a criterion of optimality the individual's lifetime reproductive success. Using methods of mathematical theory of optimal control, we calculated some optimal strategies of energy partition between repair, current survival and reproduction for various levels of uncontrollable (external) mortality. The results are presented in the form of dependencies of mortality on age and dependencies of optimal energy partitioning on age and accumulated mortality risk. Three cases of energy partitioning were considered: that between reproduction and current survival, that between reproduction and repair, and that between current survival and repair. In the case of the trade-off between reproduction and current survival, we noted opposite influences of the levels of increase of uncontrollable and controllable sources of mortality on the strategy of energy partitioning, and the crucial role of the finiteness of maximum lifespan when age-independent sources of mortality only were present. In the case of the trade-off between reproduction and repair, we noted that controllable repair leads to the emergence of accelerated growth of mortality with age, which may be considered one possible cause of the accelerated ageing often observed in nature and expressed sometimes in the form of a Gompertz-Makeham equation. In the case of the trade-off between current survival and repair, we found that, in the case of increasing mortality, repair is sacrificed not only in favour of reproduction, but also in favour of current survival, so that accelerated ageing should be expected even when investment in reproduction does not increase with age. In general, we conclude that when mortality increases, the priority when expending energy is shifted primarily in favour of reproduction, then in favour of current survival, with repair having the lowest priority. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogenomics reveal a robust fungal tree of life

Our understanding of the tree of life (TOL) is still fragmentary. Until recently, molecular phylogeneticists have built trees based on ribosomal RNA sequences and selected protein sequences, which, however, usually suffered from lack of support for the deeper branches and inconsistencies probably due to limited subsampling of the entire genome. Now, phylogenetic hypotheses can be based on the analysis of full genomes. We used available complete genome data as well as the eukaryote orthologous group (KOG) proteins to reconstruct with confidence basal branches of the fungal TOL. Phylogenetic analysis of a core of 531 KOGs shared among 21 fungal genomes, three animal genomes and one plant genome showed a single tree with high support resulting from four different methods of phylogenetic reconstruction. The single tree that we inferred from our dataset showed excellent nodal support for each branch, suggesting that it reflects the true phylogenetic relationships of the species involved.     

Evolution of the capacity to evolve

Abstract During the past two decades, the fields of molecular biology and genetics have enabled study of far broader and more detailed aspects of evolutionary change than were possible when the evolutionary synthesis was elaborated in the mid‐twentieth century. The capacity for complete sequencing of both genes and proteins of all groups of organisms provide, simultaneously, the means to determine both the patterns and processes of evolution throughout the history of life. Increased knowledge of the genome documents the changing nature of its composition, mode of transmission, and the nature of the units of selection. Advances in evolutionary developmental biology demonstrate the conservation of genetic elements throughout multicellular organisms, and explain how control of the timing, position and nature of their expression has produced the extraordinary diversity of living plants and animals. The next generation of evolutionary biologists will benefit greatly from the increased integration of these new fields of research with those that are currently emphasized in the standard textbooks and journals.     

Time‐limited environments affect the evolution of egg–body size allometry

Initial offspring size is a fundamental component of absolute growth rate, where large offspring will reach a given adult body size faster than smaller offspring. Yet, our knowledge regarding the coevolution between offspring and adult size is limited. In time‐constrained environments, organisms need to reproduce at a high rate and reach a reproductive size quickly. To rapidly attain a large adult body size, we hypothesize that, in seasonal habitats, large species are bound to having a large initial size, and consequently, the evolution of egg size will be tightly matched to that of body size, compared to less time‐limited systems. We tested this hypothesis in killifishes, and found a significantly steeper allometric relationship between egg and body sizes in annual, compared to nonannual species. We also found higher rates of evolution of egg and body size in annual compared to nonannual species. Our results suggest that time‐constrained environments impose strong selection on rapidly reaching a species‐specific body size, and reproduce at a high rate, which in turn imposes constraints on the evolution of egg sizes. In combination, these distinct selection pressures result in different relationships between egg and body size among species in time‐constrained versus permanent habitats.