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PubMed2006

Evolution of reproductive proteins from animals and plants.

Sexual reproduction is a fundamental biological process common among eukaryotes. Because of the significance of reproductive proteins to fitness, the diversity and rapid divergence of proteins acting at many stages of reproduction is surprising and suggests a role of adaptive diversification in reproductive protein evolution. Here we review the evolution of reproductive proteins acting at different stages of reproduction among animals and plants, emphasizing common patterns. Although we are just beginning to understand these patterns, by making comparisons among stages of reproduction for diverse organisms we can begin to understand the selective forces driving reproductive protein diversity and the functional consequences of reproductive protein evolution.

Animals↗
PubMed2003

A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae).

While Anartia butterflies have served as model organisms for research on the genetics of speciation, no phylogeny has been published to describe interspecific relationships. Here, we present a molecular phylogenetic analysis of Anartia species relationships, using both mitochondrial and nuclear genes. Analyses of both data sets confirm earlier predictions of sister species pairings based primarily on genital morphology. Yet both the mitochondrial and nuclear gene phylogenies demonstrate that Anartia jatrophae is not sister to all other Anartia species, but rather that it is sister to the Anartia fatima-Anartia amathea lineage. Traditional biogeographic explanations for speciation across the genus relied on A. jatrophae being sister to its congeners. These explanations invoked allopatric divergence of sister species pairs and multiple sympatric speciation events to explain why A. jatrophae flies alongside all its congeners. The molecular phylogenies are more consistent with lineage divergence due to vicariance, and range expansion of A. jatrophae to explain its sympatry with congeners. Further interpretations of the tree topologies also suggest how morphological evolution and eco-geographic adaptation may have set species range boundaries.

Animals↗
PubMed2002

[Phylogenetics of the immunosystem].

The human immune system is composed of two closely cooperating entities: innate, "unspecific" immune defense on one hand and adaptive, "specific" immunity on the other. Innate immune defense mechanisms were already developed very early in the evolution of the animal kingdom. By contrast, adaptive immunity exclusively evolved in jawed vertebrates within a surprisingly short time span. New data especially from genome sequencing projects now allow first glimpses on those events that resulted in the formation of adaptive immunity.

Animals↗
PubMed1994

Rapid exploration of alternatives via chaos.

Temporary chaos facilitates a rapid exploration of alternative asymptotic possibilities. The phenomenon of alternative-exploration via chaos is shown to have a finite probability of occurrence for a class of dynamical systems, the evolution of which is described by (complex) analytic maps. The ability to explore alternatives confers an adaptive advantage, and the possible relevance of temporary chaos to rapid mutations is discussed.

Adaptation, Biological↗
PubMed2026

Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change.

Understanding the genetic basis of rapid adaptation is key to predicting species' evolutionary responses to environmental change. However, it is still debatable whether many small-effect mutations or a few large-effect mutations underlie rapid adaptation, and how this knowledge can predict population survival or extinction. To address this question, we performed a series of ecologically grounded forward-in-time genetic simulations to study rapid adaptation and extinction with increasing magnitudes of environmental change. These simulations were seeded with genomic variation of the plant Arabidopsis thaliana to have a realistic genomic structure, with one (monogenic) to 1,000 (polygenic) variants with varying heritabilities contributing to an environmental adaptive trait. Our results revealed two distinct scenarios of rapid adaptation and population rescue. Under small-to-moderate environmental shifts, high polygenic traits increased evolutionary rescue probability. Under extreme environmental shifts, high polygenic traits lead predictably to extinction, yet monogenic traits sometimes produce one-off winning adaptive genotypes. We interpret our rapid evolutionary rescue findings in terms of the fundamental theorem of natural selection, where trait polygenicity shapes the distribution of genetic variance in fitness across replicates and, in turn, the probability of population survival, with polygenic architectures producing more stable and predictable fitness variance and monogenic architectures generating highly skewed and variable outcomes. These results highlight the insights genomics gives us into the (un)predictability of species' evolutionary responses to global change, with management implications for assisted adaptation and conservation.

Arabidopsis↗
PubMed1995

Evolution as a self-organized critical phenomenon.

We present a simple mathematical model of biological macroevolution. The model describes an ecology of adapting, interacting species. The environment of any given species is affected by other evolving species; hence, it is not constant in time. The ecology as a whole evolves to a "self-organized critical" state where periods of stasis alternate with avalanches of causally connected evolutionary changes. This characteristic behavior of natural history, known as "punctuated equilibrium," thus finds a theoretical explanation as a self-organized critical phenomenon. The evolutionary behavior of single species is intermittent. Also, large bursts of apparently simultaneous evolutionary activity require no external cause. Extinctions of all sizes, including mass extinctions, may be a simple consequence of ecosystem dynamics. Our results are compared with data from the fossil record.

Adaptation, Biological↗
PubMedDate not supplied

Evidence for nickel in the soluble hydrogenase from the unicellular green alga Scenedesmus obliquus.

Cultures of the green alga Scenedesmus obliquus were grown in the presence of either the chelating reagent EDTA or NiCl2 in various concentrations and assayed for hydrogenase catalyzed photohydrogen evolution after an anaerobic dark adaptation period. Cultivation of algae in the presence of 100 microM EDTA inhibited the formation of hydrogenase activity by 37%. After a cultivation of the cells in the presence of 5-20 microM NiCl2 photohydrogen evolution was increased by 20-40%. Addition of EDTA up to a final concentration of 1.5 mM had no effect on the activity of hydrogenase in cell-free hydrogenase preparations. Cultures grown in the presence of radioactive 63NiCl2 incorporated 63Ni in a parallel fashion to the cell growth. In radioactive labeled hydrogenase preparations a co-elution of radioactivity and hydrogenase activity could be observed using gel filtration chromatography.

Anaerobiosis↗
PubMed1988

Morphology and locomotor adaptations of the bovid femur in relation to habitat.

Extant bovids inhabit a wide diversity of environments that range from forest to savanna and display locomotor patterns that are habitat specific. I report here on an investigation of the linkage between these locomotor patterns and habitat based on a study of the morphology of the bovid femur. Femoral head shape, shaft dimensions, and knee structure are examined and support a statistically significant separation of the different morphological complexes present in bovids from forest, broken cover, and savanna habitats. Morphological differences are primarily related to locomotor patterns as reflected in the degree of cursoriality displayed by bovids in different habitats. Cursorial bovids from savanna environments have laterally expanded femoral heads that act to limit the degree of abduction and axial rotation at the hip, and elliptically shaped distal femora that increase the moment arm of the extensor muscles that cross the knee. Forest bovids have spherically shaped femoral heads. This morphology permits a much higher degree of abduction and axial rotation at the hip and appears to provide greater maneuverability in a vegetationally complex habitat. Bovids living in broken cover environments that fall between the extremes of closed canopy forest and savanna display an intermediate set of femoral characters. This approach to the relationship between habitat and locomotion offers a potentially powerful means with which to examine the interplay between structural form and function in bovid evolution.

Adaptation, Physiological↗
PubMed2005

Optimality and evolutionary tuning of the expression level of a protein.

Different proteins have different expression levels. It is unclear to what extent these expression levels are optimized to their environment. Evolutionary theories suggest that protein expression levels maximize fitness, but the fitness as a function of protein level has seldom been directly measured. To address this, we studied the lac system of Escherichia coli, which allows the cell to use the sugar lactose for growth. We experimentally measured the growth burden due to production and maintenance of the Lac proteins (cost), as well as the growth advantage (benefit) conferred by the Lac proteins when lactose is present. The fitness function, given by the difference between the benefit and the cost, predicts that for each lactose environment there exists an optimal Lac expression level that maximizes growth rate. We then performed serial dilution evolution experiments at different lactose concentrations. In a few hundred generations, cells evolved to reach the predicted optimal expression levels. Thus, protein expression from the lac operon seems to be a solution of a cost-benefit optimization problem, and can be rapidly tuned by evolution to function optimally in new environments.

Adaptation, Physiological↗
PubMed2005

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance.

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.

Adaptation, Biological↗
PubMed1991

Parallel evolution in mammalian and avian brains: comparative cytoarchitectonic and cytochemical analysis.

Comparative morphology, which is based on the selection theory of evolution, analyses the impact of function upon structure and, therefore, emphasizes the adaptive events and biological advantage during the evolution of organs. A comparison based on analogies is described here as an adequate method. The hypothesis is proposed that the evolution of the brain follows the same trends in birds as in mammals. This hypothesis is proved by (1) allometric studies of brain weight and brain structure volume in relation to body weight in mammals and birds; (2) architectonic studies using image analysis on cell and fibre stains as well as on histochemical preparations and receptor autoradiography; and (3) hodological studies with injections of [3H]leucin, HRP and WGA-HRP. The results reveal a vast amount of structural and functional similarities in avian and mammalian brain organization, especially an expansion of structures that permit multimodal integration capacity in the telencephalon. Thus, a parallel evolution occurred in these two groups of vertebrates. It is argued that this may be a general phenomenon in evolution. A cladistic approach, which is based on the concept of homologies (plesio-, apomorphies), pushes aside the existence of analogies. For this reason, cladism does not seem to be a method to answer questions of evolutionary morphology adequately.

Animals↗
PubMed2004

Genome data mining of lactic acid bacteria: the impact of bioinformatics.

Lactic acid bacteria (LAB) have been widely used in food fermentations and, more recently, as probiotics in health-promoting food products. Genome sequencing and functional genomics studies of a variety of LAB are now rapidly providing insights into their diversity and evolution and revealing the molecular basis for important traits such as flavor formation, sugar metabolism, stress response, adaptation and interactions. Bioinformatics plays a key role in handling, integrating and analyzing the flood of 'omics' data being generated. Reconstruction of metabolic potential using bioinformatics tools and databases, followed by targeted experimental verification and exploration of the metabolic and regulatory network properties, are the present challenges that should lead to improved exploitation of these versatile food bacteria.

Adaptation, Biological↗
PubMed2006

Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions.

The evolution of molecules, developmental circuits, and new species are all characterized by the accumulation of incompatibilities between ancestors and descendants. When specific interactions between components are necessary at any of these levels, this requires compensatory coevolution. Theoretical treatments of compensatory evolution that only consider the endpoints predict that it should be rare because intermediate states are deleterious. However, empirical data suggest that compensatory evolution is common at all levels of molecular interaction. A general solution to this paradox is provided by plausible neutral or nearly neutral intermediates that possess informational redundancy. These intermediates provide an evolutionary path between coadapted allelic combinations. Although they allow incompatible end points to evolve, at no point was a deleterious mutation ever in need of compensation. As a result, what appears to be compensatory evolution may often actually be "pseudocompensatory." Both theoretical and empirical studies indicate that pseudocompensation can speed the evolution of intergenic incompatibility, especially when driven by adaptation. However, under strong stabilizing selection the rate of pseudocompensatory evolution is still significant. Important examples of this process at work discussed here include the evolution of rRNA secondary structures, intra- and inter-protein interactions, and developmental genetic pathways. Future empirical work in this area should focus on comparing the details of intra- and intergenic interactions in closely related organisms.

Animals↗