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The evolution of plant nuclear genes.

We analyze the evolutionary dynamics of three of the best-studied plant nuclear multigene families. The data analyzed derive from the genes that encode the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS), the gene family that encodes the enzyme chalcone synthase (Chs), and the gene family that encodes alcohol dehydrogenases (Adh). In addition, we consider the limited evolutionary data available on plant transposable elements. New Chs and rbcS genes appear to be recruited at about 10 times the rate estimated for Adh genes, and this is correlated with a much smaller average gene family size for Adh genes. In addition, duplication and divergence in function appears to be relatively common for Chs genes in flowering plant evolution. Analyses of synonymous nucleotide substitution rates for Adh genes in monocots reject a linear relationship with clock time. Replacement substitution rates vary with time in a complex fashion, which suggests that adaptive evolution has played an important role in driving divergence following gene duplication events. Molecular population genetic studies of Adh and Chs genes reveal high levels of molecular diversity within species. These studies also reveal that inter- and intralocus recombination are important forces in the generation allelic novelties. Moreover, illegitimate recombination events appear to be an important factor in transposable element loss in plants. When we consider the recruitment and loss of new gene copies, the generation of allelic diversity within plant species, and ectopic exchange among transposable elements, we conclude that recombination is a pervasive force at all levels of plant evolution.

Alcohol Dehydrogenase↗

Prokaryotic evolution in light of gene transfer.

Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss, and other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm-some of whose implications we explore here. In particular, we discuss (1) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (2) the implications of these processes for the reconstruction and meaning of "phylogeny," and (3) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.

Evolution, Molecular↗

ADAPT: a developmental, asemantic, and procedural model for transcoding from verbal to arabic numerals.

This article presents a new model of transcoding numbers from verbal to arabic form. This model, called ADAPT, is developmental, asemantic, and procedural. The authors' main proposal is that the transcoding process shifts from an algorithmic strategy to the direct retrieval from memory of digital forms. Thus, the model is evolutive, adaptive, and particularly suited to account for learning and development. ADAPT, which has been implemented in a computer program, accounts for existing and new developmental data, for new data in adolescents with mild retardation, and for the neuropsychological cases described in the literature.

Aphasia↗

Climatic adaptation of Drosophila buzzatii populations in southeast Australia.

Variation in 19 traits possibly relevant for thermal adaptation was studied in 11 populations of Drosophila buzzatii collected in southeast Australia. Using stepwise multiple regression, the variation was compared to variation in geographic coordinates and to a set of climatic variables estimated for each collection site. For 13 of the traits, a significant part of the variation was explained by climatic variables and/or geographic coordinates, suggesting directional selection for adaptation to the environment in the majority of traits studied. In 10 of the traits, both geographic coordinates and climatic variables explained significant proportions of the variation, with R2 ranging from 0.075 to 0.58. Although larvae, pupae and adults of D. buzzatii share a common habitat, the measured traits were not correlated across life stages and gender. Also, there seemed to be special conditions in marginal populations near species borders, giving rise to nonlinear relations with latitude. Climate apparently does influence the adaptive evolution of the traits studied, but they also are affected by other factors that vary with latitude, longitude and distance to coast. These results highlight the complex challenges imposed by the environment on the adaptive process.

Acclimatization↗

Haplotype-resolved genome of Forsythia suspensa reveals the reticulate evolution in Oleaceae and a novel gene cluster regulating stamen development.

The olive family (Oleaceae) comprises numerous species of economic, horticultural, and medicinal importance. Despite its significance, the evolutionary history of this complex family remains enigmatic. Here, we generated a high-quality haplotype-resolved genome of Forsythia suspensa, a distylous species that occupies a key phylogenetic position in Oleaceae. The 2 haplotypes exhibit significant allelic divergence with potential allele-specific regulation. We reconstructed the polyploidization history of Oleaceae by confirming and precisely dating a shared whole-genome triplication and an independent whole-genome duplication event. We revealed a complex reticulate evolution that gave rise to the tribe Oleeae: an initial hybridization between Forsythieae (♂) and Jasmineae (♀), a subsequent backcrossing event, and a final whole-genome duplication. We identified a novel tandemly duplicated pectin methylesterase inhibitor gene cluster that regulates filament length and pollen size via restricting cell elongation in the long-styled morph. Dosage augmentation via stepwise cluster formation (0.99 to 3.83 Mya) may contribute to maintaining stamen traits of the long-styled morph. These FsPMEIs are co-expressed with many cell wall-related genes, suggesting a functional link in cell wall modification. Our study reveals the reticulate evolution in Oleaceae and a novel gene cluster controlling stamen development in F. suspensa and provides valuable haplotype-resolved genomic resources for heterostylous species, offering novel framework and molecular pathways to understand plant adaptive evolution.

Forsythia↗

Influence of tension reduction and peripheral dissection on histologic, biochemical and bioenergetic profiles, and kinetics of skeletal muscle fast-to-slow transformation.

Seven goat latissimus dorsi muscles were submitted to a progressive electrostimulation program through intramuscular electrodes (Medtronic SP5528). Group 1 (n = 3) consisted of muscles stimulated in situ, and group 2 (n = 4), of muscles dissected distally and reinserted on the chest wall with a reduced tension. In group 1, complete fiber switch from type II to I occurred within 60-100 days after the beginning of stimulation, as demonstrated by myosin isoforms and lactate dehydrogenase (LDH) isozymes pattern. Respiratory chain oxidases first increased within 30-70 days after stimulation, then progressively decreased to stabilized values, higher than the basal ones. Total LDH activity showed progressive decrease to one-fifth of the initial value. Morphological analysis confirmed the structural integrity and physical reinforcement of the muscles. In group 2, respiratory chain oxidases showed initial increase followed first by a fast reduction to values less than the starting ones, and then by a slow secondary increase between day 40 and 90. LDH activity displayed a sharp decrease between day 15 and 36. Myosin as well as LDH isoforms showed progressive conversion. This kinetic study suggests a three-phase adaptative evolution of the goat latissimus dorsi submitted to increased workload (group 1): a fast increase (phase I) in oxidative capacities is followed by the development of an efficient contractile machinery (phase II), with subsequent adaptation (phase III) of the terminal chemosmotic enzymes involved in energy production.+2

Adaptation, Physiological↗

Varying signals of the effects of natural selection during teleost growth hormone gene evolution.

The growth hormone (GH) gene of teleost fish exhibits a higher degree of variability compared with other vertebrate groups. However, the different selective constraints at the sequence level are not well understood. In this study, maximum-likelihood (ML) models of codon substitutions were used to investigate Darwinian adaptive evolution of the GH gene in teleost fishes. Complete GH gene sequences of 54 fish species were classified into 4 orders, and the variable nature of GH was examined by determining the dN and dS rate variation and the rates of molecular evolution for each teleost order. The results indicate that although the overall evolution rate for teleost GH is high ((1.15 +/- 0.01) x 10(-9) substitutions/(aa site x y)) compared with the "slow phases" in mammals ((0.21 to 0.28 +/- 0.05) x 10(-9)), the vital structure of this gene has been retained. While the majority of the amino acid changes appear to be due to relaxation of purifying selection, some positively selected sites were detected in regions with no specifically identified role in protein function. The positively selected regions observed in salmoniformes lineage suggests a possible role for positive selection driving functional divergence in paralogous forms of the GH gene after whole-genome duplication in this lineage.

Amino Acid Sequence↗

Molecular evolution and population genetic analysis of candidate female reproductive genes in Drosophila.

Molecular analyses in several taxa have consistently shown that genes involved in reproduction are rapidly evolving and subjected to positive selection. The mechanism behind this evolution is not clear, but several proposed hypotheses involve the coevolution between males and females. In Drosophila, several male reproductive proteins (Acps) involved in male-male and male-female interactions show evidence of rapid adaptive evolution. What has been missing from the Drosophila literature is the identification and analysis of female reproductive genes. Recently, an evolutionary expressed sequence tag analysis of Drosophila female reproductive tract genes identified 169 candidate female reproductive genes. Many of these candidate genes still await further molecular analysis and independent verification of positive selection. Our goal was to expand our understanding of the molecular evolution of Drosophila female reproductive genes with a detailed polymorphism and divergence study on seven additional candidate female reproductive genes and a reanalysis of two genes from the above study. We demonstrate that 6 candidate female genes of the 9 genes surveyed show evidence of positive selection using both polymorphism and divergence data. One of these proteins (CG17012) is modeled to reveal that the sites under selection fall around and within the active site of this protease, suggesting potential differences between species. We discuss our results in light of potential function as well as interaction with male reproductive proteins.

Animals↗

Unifying evolutionary dynamics: from individual stochastic processes to macroscopic models.

A distinctive signature of living systems is Darwinian evolution, that is, a propensity to generate as well as self-select individual diversity. To capture this essential feature of life while describing the dynamics of populations, mathematical models must be rooted in the microscopic, stochastic description of discrete individuals characterized by one or several adaptive traits and interacting with each other. The simplest models assume asexual reproduction and haploid genetics: an offspring usually inherits the trait values of her progenitor, except when a mutation causes the offspring to take a mutation step to new trait values; selection follows from ecological interactions among individuals. Here we present a rigorous construction of the microscopic population process that captures the probabilistic dynamics over continuous time of birth, mutation, and death, as influenced by the trait values of each individual, and interactions between individuals. A by-product of this formal construction is a general algorithm for efficient numerical simulation of the individual-level model. Once the microscopic process is in place, we derive different macroscopic models of adaptive evolution. These models differ in the renormalization they assume, i.e. in the limits taken, in specific orders, on population size, mutation rate, mutation step, while rescaling time accordingly. The macroscopic models also differ in their mathematical nature: deterministic, in the form of ordinary, integro-, or partial differential equations, or probabilistic, like stochastic partial differential equations or superprocesses. These models include extensions of Kimura's equation (and of its approximation for small mutation effects) to frequency- and density-dependent selection. A novel class of macroscopic models obtains when assuming that individual birth and death occur on a short timescale compared with the timescale of typical population growth. On a timescale of very rare mutations, we establish rigorously the models of "trait substitution sequences" and their approximation known as the "canonical equation of adaptive dynamics". We extend these models to account for mutation bias and random drift between multiple evolutionary attractors. The renormalization approach used in this study also opens promising avenues to study and predict patterns of life-history allometries, thereby bridging individual physiology, genetic variation, and ecological interactions in a common evolutionary framework.

Algorithms↗

Variable immune-driven natural selection in the attachment (G) glycoprotein of respiratory syncytial virus (RSV).

A maximum-likelihood analysis of selection pressures acting on the attachment (G) glycoprotein gene of respiratory syncytial virus (RSV) from humans (HRSV) and bovines (BRSV) is presented. Six positively selected sites were identified in both group A and group B of HRSV, although only one site was common between them, while no positively selected sites were detected in BRSV. All positively selected sites were located within the ectodomain of the G protein and showed some association with positions of immunoglobulin (Ig) epitopes and sites of O-glycosylation. These results suggest that immune (antibody)-driven natural selection is an important determinant of RSV evolution and that this selection pressure differs among strains. The passage histories of RSV strains were also shown to affect the distribution of positively selected sites, particularly in HRSV B, and should be considered whenever retrospective analysis of adaptive evolution is undertaken.

Amino Acid Sequence↗

Why are proteins marginally stable?

Most globular proteins are marginally stable regardless of size or activity. The most common interpretation is that proteins must be marginally stable in order to function, and so marginal stability represents the results of positive selection. We consider the issue of marginal stability directly using model proteins and the dynamical aspects of protein evolution in populations. We find that the marginal stability of proteins is an inherent property of proteins due to the high dimensionality of the sequence space, without regard to protein function. In this way, marginal stability can result from neutral, non-adaptive evolution. By allowing evolving protein sub-populations with different stability requirements for functionality to complete, we find that marginally stable populations of proteins tend to dominate. Our results show that functionalities consistent with marginal stability have a strong evolutionary advantage, and might arise because of the natural tendency of proteins towards marginal stability.

Models, Chemical↗

The modern synthesis, Ronald Fisher and creationism.

The 'modern evolutionary synthesis' convinced most biologists that natural selection was the only directive influence on adaptive evolution. Today, however, dissatisfaction with the synthesis is widespread, and creationists and antidarwinians are multiplying. The central problem with the synthesis is its failure to show (or to provide distinct signs) that natural selection of random mutations could account for observed levels of adaptation.

Journal Article↗

Beyond reinforcement: the evolution of premating isolation by direct selection on preferences and postmating, prezygotic incompatibilities.

The evolution of premating isolation after secondary contact is primarily considered in the guise of reinforcement, which relies on low hybrid fitness as the driving force for mating preference divergence. Here I consider two additional forces that may play a substantial role in the adaptive evolution of premating isolation, direct selection on preferences and indirect selection against postmating, prezygotic incompatibilities. First, I argue that a combination of ecological character displacement and sensory bias can cause direct selection on preferences that results in the pattern of reproductive character displacement. Both analytical and numerical methods are then used to demonstrate that, as expected from work in single populations, such direct selection will easily overwhelm indirect selection due to low hybrid fitness as the primary determinant of preference evolution. Second, postmating, prezygotic incompatibilities are presented as a driving force in the evolution of premating isolation. Two classes of these mechanisms, those increasing female mortality after mating but before producing offspring and those reducing female fertility, are shown to be identical in their effects on preference divergence. Analytical and numerical techniques are then used to demonstrate that postmating, prezygotic factors may place strong selection on preference divergence. These selective forces are shown to be comparable if not greater than those produced by the low fitness of hybrids.

Animals↗

Catalytic promiscuity and the evolution of new enzymatic activities.

Several contemporary enzymes catalyze alternative reactions distinct from their normal biological reactions. In some cases the alternative reaction is similar to a reaction that is efficiently catalyzed by an evolutionary related enzyme. Alternative activities could have played an important role in the diversification of enzymes by providing a duplicated gene a head start towards being captured by adaptive evolution.

Bacteria↗

Rapid evolution of muscle fibre number in post-glacial populations of Arctic charr Salvelinus alpinus.

Thingvallavatn, the largest and one of the oldest lakes in Iceland, contains four morphs of Arctic charr Salvelinus alpinus. Dwarf benthic (DB), large benthic (LB), planktivorous (PL) and piscivorous (PI) morphs can be distinguished and differ markedly in head morphology, colouration and maximum fork length (FL(max)), reflecting their different resource specialisations within the lake. The four morphs in Thingvallavatn are thought to have been isolated for approximately 10 000 years, since shortly after the end of the last Ice Age. We tested the null hypothesis that the pattern of muscle fibre recruitment was the same in all morphs, reflecting their recent diversification. The cross-sectional areas of fast and slow muscle fibres were measured at 0.7 FL in 46 DB morphs, 23 LB morphs, 24 PL morphs and 22 PI morphs, and the ages of the charr were estimated using sacculus otoliths. In fish larger than 10 g, the maximum fibre diameter scaled with body mass (M(b))(0.18) for both fibre types in all morphs. The number of myonuclei per cm fibre length increased with fibre diameter, but was similar between morphs. On average, at 60 mum diameter, there were 2264 nuclei cm(-1) in slow fibres and 1126 nuclei cm(-1) in fast fibres. The absence of fibres of diameter 4-10 mum was used to determine the FL at which muscle fibre recruitment stopped. Slow fibre number increased with body length in all morphs, scaling with M(b)(0.45). In contrast, the recruitment of fast muscle fibres continued until a clearly identifiable FL, corresponding to 18-19 cm in the dwarf morph, 24-26 cm in the pelagic morph, 32-33 cm in the large benthic morph and 34-35 cm in the piscivorous morph. The maximum fast fibre number (FN(max)) in the dwarf morph (6.97x10(4)) was 56.5% of that found in the LB and PI morphs combined (1.23x10(5)) (P<0.001). Muscle fibre recruitment continued until a threshold body size and occurred at a range of ages, starting at 4+ years in the DB morph and 7+ years in the LB and PI morphs. Our null hypothesis was therefore rejected for fast muscle and it was concluded that the dwarf condition was associated with a reduction in fibre number. We then investigated whether variations in development temperature associated with different spawning sites and periods were responsible for the observed differences in muscle cellularity between morphs. Embryos from the DB, LB and PL morphs were incubated at temperature regimes simulating cold subterranean spring-fed sites (2.2-3.2 degrees C) and the general lakebed (4-7 degrees C). Myogenic progenitor cells (MPCs) were identified using specific antibodies to Paired box protein 7 (Pax 7), Forkhead box protein K1-alpha (FoxK1-alpha), MyoD and Myf-5. The progeny showed no evidence of developmental plasticity in the numbers of either MPCs or muscle fibres. Juveniles and adult stages of the DB and LB morphs coexist and have a similar diet. We therefore conclude that the reduction in FN(max) in the dwarf morph probably has a genetic basis and that gene networks regulating myotube production are under high selection pressure. To explain these findings we propose that there is an optimal fibre size, and hence number, which varies with maximum body size and reflects a trade-off between diffusional constraints on fibre diameter and the energy costs of maintaining ionic gradients. The predictions of the optimal fibre size hypothesis and its consequences for the adaptive evolution of muscle architecture in fishes are briefly discussed.

Adaptation, Physiological↗

Spatially resolved single-cell atlas reveals the macroevolutionary trajectory of animal hearts.

Animal hearts display diverse anatomical structures during adaptive evolution. Here, we present a multiomics atlas of adult hearts from 27 species across chordates, arthropods, and mollusks. Joint analysis indicates that Bilateria hearts share a core gene repertoire, taking a stepwise "add-on" approach as a universal evolutionary strategy. The "proto-heart" is populated by key cell types, including cardiomyocytes, fibroblasts, endothelial cells, and neural cells, which maintained core signatures while evolving with shifts in living environments and corresponding adaptations in the cardiovascular system. Additionally, we reveal an evolutionarily conserved cardiomyocyte state dynamic potentially linked to cardiac development and stress responses. Finally, we identify a common molecular program underpinning chamber evolution from a ventricular foundation. This work establishes a resource for understanding the intrinsic mechanisms of heart evolution.

Animals↗

The conversion of variance and the evolutionary potential of restricted recombination.

Genetic recombination is usually considered to facilitate adaptive evolution. However, recombination prevents the reliable cotransmission of interacting gene combinations and can disrupt complexes of coadapted genes. If interactions between genes have important fitness effects, restricted recombination may lead to evolutionary responses that are different from those predicted from a purely additive model and could even aid adaptation. Theory and data have demonstrated that phenomena that limit the effectiveness of recombination via increasing homozygosity, such as inbreeding and population subdivision and bottlenecks, can temporarily increase the additive genetic variance available to these populations. This effect has been attributed to the conversion of nonadditive to additive genetic variance. Analogously, phenomena such as chromosomal inversions and apomictic parthenogenesis that physically restrict recombination in part or all of the genome may also result in a release of additive variance. Here, we review and synthesize literature concerning the evolutionary potential of populations with effectively or physically restricted recombination. Our goal is to emphasize the common theme of increased short-term access to additive genetic variance in all of these situations and to motivate research directed towards a more complete characterization of the relevance of the conversion of variance to the evolutionary process.

Animals↗