Evolutionary genetics: evolution with foresight

Evolution has no foresight, but produces ad hoc solutions by tinkering with available variation. A new study demonstrates how evolution nevertheless prepares organisms for the future by increasing their evolvability.     

Evolutionary jumping and breakthrough in tree masting evolution

Many long-lived plants such as trees show masting or intermittent and synchronized reproduction. In a coupled chaos system describing the dynamics of individual-plant resource budgets, masting occurs when the resource depletion coefficient k (ratio of the reproductive expenditure to the excess resource reserve) is large. Here, we mathematically studied the condition for masting evolution. In an infinitely large population, we obtained a deterministic dynamical system, to which we applied the pairwise invasibility plot and convergence stability of evolutionary singularity analyses. We prove that plants reproducing at the same rate every year are not evolutionarily stable. The resource depletion coefficient k increases, and the system oscillates with a period of 2 years (high and low reproduction) if k<1. Alternatively, k may evolve further and jump to a value >1, resulting in the sudden start of intermittent reproduction. We confirm that a high survivorship of young plants (seedlings) in the light-limited understory favors masting evolution, as previously suggested by computer simulations and field observations. The stochasticity caused by the finiteness of population size also promotes masting evolution.     

Evolutionary suicide and evolution of dispersal in structured metapopulations

 We study the evolution of dispersal in a structured metapopulation model. The metapopulation consists of a large (infinite) number of local populations living in patches of habitable environment. Dispersal between patches is modelled by a disperser pool and individuals in transit between patches are exposed to a risk of mortality. Occasionally, local catastrophes eradicate a local population: all individuals in the affected patch die, yet the patch remains habitable. We prove that, in the absence of catastrophes, the strategy not to migrate is evolutionarily stable. Under a given set of environmental conditions, a metapopulation may be viable and yet selection may favor dispersal rates that drive the metapopulation to extinction. This phenomenon is known as evolutionary suicide. We show that in our model evolutionary suicide can occur for catastrophe rates that increase with decreasing local population size. Evolutionary suicide can also happen for constant catastrophe rates, if local growth within patches shows an Allee effect. We study the evolutionary bifurcation towards evolutionary suicide and show that a discontinuous transition to extinction is a necessary condition for evolutionary suicide to occur. In other words, if population size smoothly approaches zero at a boundary of viability in parameter space, this boundary is evolutionarily repelling and no suicide can occur. Received: 10 November 2000 / Revised version: 13 February 2002 / Published online: 17 July 2002     

Evolutionary framework for protein sequence evolution and gene pleiotropy

In this article, we develop an evolutionary model for protein sequence evolution. Gene pleiotropy is characterized by K distinct but correlated components (molecular phenotypes) that affect the organismal fitness. These K molecular phenotypes are under stabilizing selection with microadaptation (SM) due to random optima shifts, the SM model. Random coding mutations generate a correlated distribution of K molecular phenotypes. Under this SM model, we further develop a statistical method to estimate the "effective" number of molecular phenotypes (K(e)) of the gene. Therefore, for the first time we can empirically evaluate gene pleiotropy from the protein sequence analysis. Case studies of vertebrate proteins indicate that K(e) is typically approximately 6-9. We demonstrate that the newly developed SM model of protein evolution may provide a basis for exploring genomic evolution and correlations.     

Integrins during evolution: Evolutionary trees and model organisms

The integrins form a large family of cell adhesion receptors. All multicellular animals express integrins, indicating that the family evolved relatively early in the history of metazoans, and homologous sequences of the component domains of integrin α and β subunits are seen in prokaryotes. Some integrins, however, seem to be much younger. For example, the αI domain containing integrins, including collagen receptors and leukocyte integrins, have been found in chordates only. Here, we will discuss what conclusions can be drawn about integrin function by studying the evolutionary conservation of integrins. We will also look at how studying integrins in organisms such as the fruit fly and mouse has helped our understanding of integrin evolution-function relationships. As an illustration of this, we will summarize the current understanding of integrin involvement in skeletal muscle formation.     

Evolutionary genetics: the evolution of plumage patterns

The identification and sequencing of a gene affecting melanin production in the bananaquit, a bird species notable for its polymorphic plumage colour, paves the way for much greater understanding of the evolution of plumage patterns in birds, and the developmental modulations involved in producing new patterns.     

Evolutionary genomics: molecular evolution at the genomic scale

The Symposium on Evolutionary Genomics was held in Atami, Japan, from 4 to 6 November 2001.     

Evolutionary genomics: a dinosaur's view of genome-size evolution

Estimates of cell volume in fossilized bones of extinct dinosaurs indicate that genome size underwent a significant reduction in the early theropods, from which birds later evolved. This suggests that birds' small genomes are not an adaptation to metabolic demands associated with flight.     

Evolutionary dynamics of Candida albicans during in vitro evolution

While mechanisms of resistance to major antifungal agents have been characterized in Candida albicans, little is known about the evolutionary trajectories during the emergence of drug resistance. Here, we examined the evolutionary dynamics of C. albicans that evolved in vitro in the presence or absence of fluconazole using the visualizing evolution in real-time (VERT) method, a novel experimental approach that facilitates the systematic isolation of adaptive mutants that arise in the population. We found an increase in the frequency of adaptive events in the presence of fluconazole compared to the no-drug controls. Analysis of the evolutionary dynamics revealed that mutations that led to increased drug resistance appeared frequently and that mutants with increased levels of resistance arose in independent lineages. Interestingly, most adaptive mutants with increased fitness in the presence of the drug did not exhibit a significant fitness decrease in the absence of the drug, supporting the idea that rapid resistance can arise from mutations in strains maintained in the population prior to exposure to the drug.     

Fertilization alters the orientation of pigment granule saltations in Arbacia eggs.

Unfertilized eggs of the sea urchin Arbacia punctulata contain pigment granules distributed throughout their cytoplasm. During the first 15 minutes after fertilization, these vesicles move out to the cortex where they become firmly anchored. We have used time-lapse video differential interference microscopy to analyze the motility of these organelles in unfertilized and fertilized Arbacia eggs. Pigment granules exhibit saltatory movement in both unfertilized and fertilized eggs. Quantitation of vesicle saltations before and after fertilization demonstrates that while there is no significant difference in the speed or path-length of vesicle movement, there is a dramatic change in the orientation of these saltations. Saltations in the unfertilized egg are very non-radial and are as likely to be directed toward the cortex as away. In contrast, saltations in the fertilized egg are more radially oriented and more likely to be cortically directed. This transition must reflect underlying changes in the cellular structures necessary for pigment granule saltations. The change in the orientation of pigment granule saltations following fertilization requires both a transient increase in the cytoplasmic concentration of Ca2+ and an elevation of cytoplasmic pH. Similarly, the ability of pigment granules to adhere to the cortex requires both the transient elevation of cytoplasmic Ca2+ and the alkalinization of the cytoplasm. As the reorganization of cortical actin at fertilization is regulated by these ionic fluxes, and both movement and adhesion are sensitive to cytochalasins, we hypothesize that the alterations in directed motility and adhesion reflect underlying changes in the actin cytoskeleton.     

Evolutionary traction: the cost of adaptation and the evolution of sex

The advantage of sexual reproduction remains a puzzle for evolutionary biologists. Everything else being equal, asexual populations are expected to have twice the number of offspring produced by similar sexual populations. Yet, asexual species are uncommon among higher eukaryotes. In models assuming small populations, high mutation rates, or frequent environmental changes, sexual reproduction seems to have at least a two-fold advantage over asexuality. But the advantage of sex for large populations, low mutation rates, and rare or mild environmental changes remains a conundrum. Here we show that without recombination, rare advantageous mutations can result in increased accumulation of deleterious mutations ('evolutionary traction'), which explains the long-term advantage of sex under a wide parameter range.     

Polarized microtubule gliding and particle saltations produced by soluble factors from sea urchin eggs and embryos

In this report, we describe an in vitro system for analyzing microtubule-based movements in supernatants of sea urchin egg and embryo homogenates. Using video enhanced DIC microscopy, we have observed bidirectional saltatory particle movements on native taxol-stabilized microtubules assembled in low speed supernatants of Lytechinus egg homogenates, and gliding of these microtubules across a glass surface. A high speed supernatant of soluble proteins, depleted of organelles, microtubules, and their associated proteins supports the gliding of exogenous microtubules and translocation of polystyrene beads along these microtubules. The direction of microtubule gliding has been determined directly by observation of the gliding of flagellar axonemes in which the (+) and (-) ends could be distinguished by biased polar growth of microtubules off the ends. Microtubule gliding is toward the (-) end of the microtubule, is ATP sensitive, and inhibited only by high concentrations of vanadate. These characteristics suggest that the transport complex responsible for microtubule gliding in S2 is kinesin-like. The implications of these molecular interactions for mitosis and other motile events are discussed.     

Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis

Rubisco is responsible for the fixation of CO2 into organic compounds through photosynthesis and thus has a great agronomic importance. It is well established that this enzyme suffers from a slow catalysis, and its low specificity results into photorespiration, which is considered as an energy waste for the plant. However, natural variations exist, and some Rubisco lineages, such as in C4 plants, exhibit higher catalytic efficiencies coupled to lower specificities. These C4 kinetics could have evolved as an adaptation to the higher CO2 concentration present in C4 photosynthetic cells. In this study, using phylogenetic analyses on a large data set of C3 and C4 monocots, we showed that the rbcL gene, which encodes the large subunit of Rubisco, evolved under positive selection in independent C4 lineages. This confirms that selective pressures on Rubisco have been switched in C4 plants by the high CO2 environment prevailing in their photosynthetic cells. Eight rbcL codons evolving under positive selection in C4 clades were involved in parallel changes among the 23 independent monocot C4 lineages included in this study. These amino acids are potentially responsible for the C4 kinetics, and their identification opens new roads for human-directed Rubisco engineering. The introgression of C4-like high-efficiency Rubisco would strongly enhance C3 crop yields in the future CO2-enriched atmosphere.     

Evolutionary potential: A mathematical hypothesis of mouse hemoglobin beta chain evolution

Summary This paper examines the possibility that the linkage arrangements and regulatory properties of genes may be influenced by selection. A mathematical hypothesis is developed in order to show how selective properties of hemoglobin beta chains could have influenced the linkage and regulation of their structural genes. The hypothesis is applied to the case of mouse hemoglobin beta chains. In most mice, closely-linked pairs of loci (doublets) code for two structurally divergent beta chains in unequal amounts. Some mouse strains have singlet alleles, however, coding for another beta chain variant. With the mathematical hypothesis, one can show that selectively determined evolutionary potentials may have favored changes in proportions of major and minor chains produced by a doublet allele. In the extreme case, zero production of the minor chain may give a selective advantage, leading to a ringlet; conversely, selection may favor linking another gene to the singlet locus to give a doublet. A specific prediction of the model is the stable maintenance under certain conditions of multiple alleles at regulatory loci. The concept of evolutionary potential thus suggests that selection could have influenced the evolution of genotypic fitnesses, in addition to causing changes in gene frequencies as in standard population genetics models.     

Evolutionary anthropology and genes: Investigating the genetics of human evolution from excavated skeletal remains

The development of molecular tools for the extraction, analysis and interpretation of DNA from the remains of ancient organisms (paleogenetics) has revolutionised a range of disciplines as diverse as the fields of human evolution, bioarchaeology, epidemiology, microbiology, taxonomy and population genetics. The paper draws attention to some of the challenges associated with the extraction and interpretation of ancient DNA from archaeological material, and then reviews the influence of paleogenetics on the field of human evolution. It discusses the main contributions of molecular studies to reconstructing the evolutionary and phylogenetic relationships between extinct hominins (human ancestors) and anatomically modern humans. It also explores the evidence for evolutionary changes in the genetic structure of anatomically modern humans in recent millennia. This breadth of research has led to discoveries that would never have been possible using traditional approaches to human evolution.     

Development and evolution of lateral line placodes in amphibians. - II. Evolutionary diversification

The amphibian lateral line system develops from a series of lateral line placodes. The different phases of development from early induction, to pattern formation, differentiation, morphogenesis, and metamorphic fate were summarized in the first part of this review (Schlosser, 2002a). Here, a survey of the diversity of lateral line systems in amphibians is presented indicating that most phases of lateral line development have been subject to evolutionary changes. Several trends suggest important roles for both adaptive changes and internal constraints in amphibian lateral line evolution. Many of these trends involved the coordinated modification of different derivatives of lateral line placodes suggesting that these placodes are not only autonomous developmental modules, but also units of evolutionary variation that tend to be modified in a coherent and largely context-independent fashion.