Arboreal locomotor adaptation in primates and its relevance to human evolution. Proceedings of a workshop. March 5-7, 1999.
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Adaptation, Physiological↗
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Serine carboxypeptidase-like acyltransferases.
In plant secondary metabolism, an alternative pathway of ester formation is facilitated by acyltransferases accepting 1-O-beta-acetal esters (1-O-beta-glucose esters) as acyl donors instead of coenzyme A thioesters. Molecular data indicate homology of these transferases with hydrolases of the serine carboxypeptidase type defining them as serine carboxypeptidase-like (SCPL) acyltransferases. During evolution, they apparently have been recruited from serine carboxypeptidases and adapted to take over acyl transfer function. SCPL acyltransferases belong to the highly divergent class of alpha/beta hydrolases. These enzymes make use of a catalytic triad formed by a nucleophile, an acid and histidine acting as a charge relay system for the nucleophilic attack on amide or ester bonds. In analogy to SCPL acyltransferases, bacterial thioesterase domains are known which favour transferase activity over hydrolysis. Structure elucidation reveals water exclusion and a distortion of the oxyanion hole responsible for the changed activity. In plants, SCPL proteins form a large family. By sequence comparison, a distinguished number of Arabidopsis SCPL proteins cluster with proven SCPL acyltransferases. This indicates the occurrence of a large number of SCPL proteins co-opted to catalyse acyltransfer reactions. SCPL acyltransferases are ideal systems to investigate principles of functional adaptation and molecular evolution of plant genes.
Acyltransferases↗
The genetics of plant morphological evolution.
Considerable progress has been made in identifying genes that are involved in the evolution of plant morphologies. Elements of the ABC model of flower development are conserved throughout angiosperms, and homologous MADS-box genes function in gymnosperm reproduction. Candidate gene and mapping analyses of floral symmetry, sex determination, inflorescence architecture, and compound leaves provide intriguing glimpses into the evolution of morphological adaptations.
ATP-Binding Cassette Transporters↗
Imprinting and transgenerational modulation of gene expression; human growth as a model.
It is proposed that transgenerational modulation of gene expression might be possible, if the metabolic response of the parent to some physiological or social stress modified imprint setting. Transcription regulators could theoretically mediate this process. The nature of imprinted genes poised, as it were, between a transcriptionally active and silent state, makes them good candidates for incorporation into the evolution of transgenerational adaption systems where coordinated changes in gene expression over the generations is a selective advantage. The coordination of human fetal (head) growth with the existing size of the mother's pelvis is suggested as just such a circumstance. The reduce birth weight of Dutch babies where their grandmothers suffered acute starvation in mid pregnancy, supports the notion of transgenerational adaption to nutrition, as does the secular change (increase) in child growth over the last century. The recent indication that there may be functional polymorphism in the imprinting of the human IGF2 and IGF2R genes suggests these ideas could be explored using association studies at the population and individual level.
Adaptation, Physiological↗
Robustness, evolvability, and optimality of evolutionary neural networks.
In a typical optimization problem, the main goal is to search for the appropriate values of the variables that provide the optimal solution of the given function. In artificial neural networks (ANN), this translates to the minimization of the error surface during training such that misclassification is minimized during generalization. However, since optimal training performance does not necessarily imply optimal generalization due to the possibility of overfitting or underfitting, we developed SEPA (Structure Evolution and Parameter Adaptation) which addressed these issues by simultaneously evolving ANN structure and weights. Since SEPA primarily relies on the perturbation function to bring variation in its population, this follow-up study aims to find out SEPAs evolvability, optimality, and robustness in other perturbation functions. Our findings indicate that SEPAs optimal generalization performances are stable and robust from the effect of the different perturbation functions. This is due to the feedback loop between its architecture evolution and weight adaptation such that any shortcoming of the former is compensated by the latter, and vice versa. Our results strongly suggest that proper ANN design requires simultaneous adaptation of ANN structure and weights to avoid one-sided or bias convergence to either the weight or architecture space.
Algorithms↗
The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes.
When facing the challenge of developing an individual that best fits its environment, nature demonstrates an interesting combination of two fundamentally different adaptive mechanisms: genetic evolution and phenotypic plasticity. Following numerous computational models, it has become the accepted wisdom that lifetime acclimation (e.g. via learning) smooths the fitness landscape and consequently accelerates evolution. However, analytical studies, focusing on the effect of phenotypic plasticity on evolution in simple unimodal landscapes, have often found that learning hinders the evolutionary process rather than accelerating it. Here, we provide a general framework for studying the effect of plasticity on evolution in multipeaked landscapes and introduce a rigorous mathematical analysis of these dynamics. We show that the convergence rate of the evolutionary process in a given arbitrary one-dimensional fitness landscape is dominated by the largest descent (drawdown) in the landscape and provide numerical evidence to support an analogous dominance also in multidimensional landscapes. We consider several schemes of phenotypic plasticity and examine their effect on the landscape drawdown, identifying the conditions under which phenotypic plasticity is advantageous. The lack of such a drawdown in unimodal landscapes vs. its dominance in multipeaked landscapes accounts for the seemingly contradictory findings of previous studies.
Adaptation, Biological↗
Evolution of the pregnane x receptor: adaptation to cross-species differences in biliary bile salts.
The pregnane X receptor (PXR) regulates the metabolism and elimination of bile salts, steroids, and xenobiotics. The sequence of the PXR ligand-binding domain diverges extensively between different animals, suggesting interspecies differences in ligands. Of the endogenous ligands known to activate PXR, biliary bile salts vary the most across vertebrate species, ranging from 27-carbon (C27) bile alcohol sulfates (early fish, amphibians) to C24 bile acids (birds, mammals). Using a luciferase-based reporter assay, human PXR was activated by a wide variety of bile salts. In contrast, zebrafish PXR was activated efficiently only by cyprinol sulfate, the major zebrafish bile salt, but not by recent bile acids. Chicken, mouse, rat, and rabbit PXRs were all activated by species-specific bile acids and by early fish bile alcohol sulfates. In addition, phylogenetic analysis using maximum likelihood demonstrated evidence for nonneutral evolution of the PXR ligand-binding domain. PXR activation by bile salts has expanded from narrow specificity for C27 bile alcohol sulfates (early fish) to a broader specificity for recent bile acids (birds, mammals). PXR specificity for bile salts has thus paralleled the increasing complexity of the bile salt synthetic pathway during vertebrate evolution, an unusual example of ligand-receptor coevolution in the nuclear hormone receptor superfamily.
Animals↗
Hypothesis: human cysticercosis is an adaptational advantage of Taenia solium rather than an error of phylogenetic evolution.
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Adaptation, Physiological↗
Cranial kinesis in the amphibia: a review.
All extant orders of amphibians are characterized by kinetic skulls. Main type of intracranial movability in amphibians is pleurokinetism, that is supplemented in different amphibian groups by various types of rhyncho- and prokinetism. The most primitive pattern of cranial kinesis is revealed in the stegocrotaphic gymnophions. More paedomorphic species retain general cranial flexibility that is characteristic of larval skull. That is unfavourable for evolution of well-regulated (adult) cranial kinesis and related feeding adaptations. Kinetism is also reduced in the species with heavily ossified skulls. Adaptive role and evolution of cranial kinesis in amphibians are discussed.
Amphibians↗
Darwinian adaptation, population genetics and the streetcar theory of evolution.
This paper investigates the problem of how to conceive a robust theory of phenotypic adaptation in non-trivial models of evolutionary biology. A particular effort is made to develop a foundation of this theory in the context of n-locus population genetics. Therefore, the evolution of phenotypic traits is considered that are coded for by more than one gene. The potential for epistatic gene interactions is not a priori excluded. Furthermore, emphasis is laid on the intricacies of frequency-dependent selection. It is first discussed how strongly the scope for phenotypic adaptation is restricted by the complex nature of 'reproduction mechanics' in sexually reproducing diploid populations. This discussion shows that one can easily lose the traces of Darwinism in n-locus models of population genetics. In order to retrieve these traces, the outline of a new theory is given that I call 'streetcar theory of evolution'. This theory is based on the same models that geneticists have used in order to demonstrate substantial problems with the 'adaptationist programme'. However, these models are now analyzed differently by including thoughts about the evolutionary removal of genetic constraints. This requires consideration of a sufficiently wide range of potential mutant alleles and careful examination of what to consider as a stable state of the evolutionary process. A particular notion of stability is introduced in order to describe population states that are phenotypically stable against the effects of all mutant alleles that are to be expected in the long-run. Surprisingly, a long-term stable state can be characterized at the phenotypic level as a fitness maximum, a Nash equilibrium or an ESS. The paper presents these mathematical results and discusses - at unusual length for a mathematical journal - their fundamental role in our current understanding of evolution.
Animals↗
Rapid evolution of the ribonuclease A superfamily: adaptive expansion of independent gene clusters in rats and mice.
The two eosinophil ribonucleases, eosinophil-derived neurotoxin (EDN/RNase 2) and eosinophil cationic protein (ECP/RNase 3), are among the most rapidly evolving coding sequences known among primates. The eight mouse genes identified as orthologs of EDN and ECP form a highly divergent, species-limited cluster. We present here the rat ribonuclease cluster, a group of eight distinct ribonuclease A superfamily genes that are more closely related to one another than they are to their murine counterparts. The existence of independent gene clusters suggests that numerous duplications and diversification events have occurred at these loci recently, sometime after the divergence of these two rodent species ( approximately 10-15 million years ago). Nonsynonymous substitutions per site (d(N)) calculated for the 64 mouse/rat gene pairs indicate that these ribonucleases are incorporating nonsilent mutations at accelerated rates, and comparisons of nonsynonymous to synonymous substitution (d(N) / d(S)) suggest that diversity in the mouse ribonuclease cluster is promoted by positive (Darwinian) selection. Although the pressures promoting similar but clearly independent styles of rapid diversification among these primate and rodent genes remain uncertain, our recent findings regarding the function of human EDN suggest a role for these ribonucleases in antiviral host defense.
Amino Acid Motifs↗
Viral evolution toward change in receptor usage: adaptation of a major group human rhinovirus to grow in ICAM-1-negative cells.
Major receptor group common cold virus HRV89 was adapted to grow in HEp-2 cells, which are permissive for minor group human rhinoviruses (HRVs) but which only marginally support growth of major-group viruses. After 32 blind passages in these cells, each alternating with boosts of the recovered virus in HeLa cells, HRV89 acquired the capacity to effectively replicate in HEp-2 cells, attaining virus titers comparable to those in HeLa cells although no cytopathic effect was observed. Several clones were isolated and shown to replicate in HeLa cells whose ICAM-1 was blocked with monoclonal antibody R6.5 and in COS-7 cells, which are devoid of ICAM-1. Blocking experiments with recombinant very-low-density lipoprotein receptor fragments and enzyme-linked immunosorbent assays indicated that the mutants bound a receptor different from that used by minor-group viruses. Determination of the genomic RNA sequence encoding the capsid protein region revealed no changes in amino acid residues at positions equivalent to those involved in the interaction of HRV14 or HRV16 with ICAM-1. One mutation was within the footprint of a very-low-density lipoprotein receptor fragment bound to minor-group virus HRV2. Since ICAM-1 not only functions as a vehicle for cell entry but has also a "catalytic" function in uncoating, the use of other receptors must have important consequences for the entry pathway and demonstrates the plasticity of these viruses.
Evolution, Molecular↗
Adaptation and conservation of physiological systems in the evolution of human hypoxia tolerance.
Analysis of human responses to hypobaric hypoxia in different lineages (lowlanders, Andean natives, Himalayan natives, and East Africans) indicates 'conservative' and 'adaptable' physiological characters involved in human responses to hypoxia. Conservative characters, derived by common descent, dominate and indeed define human physiology, but in five hypoxia response systems analyzed, we also found evidence for 'adaptable' characters at all levels of organization in all three high altitude lineages. Since Andeans and Himalayans have not shared common ancestry with East Africans for most of our species history, we suggest that their similar hypoxia physiology may represent the 'ancestral' condition for humans--an interpretation consistent with recent evidence indicating that our species evolved under 'colder, drier, and higher' conditions in East Africa where the phenotype would be simultaneously advantageous for endurance performance and for high altitude hypoxia. It is presumed that the phenotype was retained in low capacity form in highlanders and in higher capacity form in most lowland lineages (where it would be recognized by most physiologists as an endurance performance phenotype). Interestingly, it is easier for modern molecular evolution theory to account for the origin of 'adaptable' characters through positive selection than for conserved traits. Many conserved physiological systems are composed of so many gene products that it seems difficult to account for their unchanging state (for unchanging structure and function of hundreds of proteins linked in sequence to form the physiological system) by simple models of stabilizing selection.
Adaptation, Physiological↗
Analysis of ribosomal RNA genes suggests that trypanosomes are monophyletic.
To further investigate the phylogeny of protozoa from the order Kinetoplastida we have sequenced the small subunit (SSU) and a portion of the large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences were determined from a lizard trypanosome, Trypanosoma scelopori and a bodonid, Rhynchobodo sp., and the LSU sequences were determined from an insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigella trypaniformis. Contrary to previous results, in which trypanosomes were found to be paraphyletic, with Trypanosoma brucei representing the earliest-diverging lineage, we have now found evidence for the monophyly of trypanosomes. Addition of new taxa which subdivide long branches (such as that of T. brucei) have helped to identify homoplasies responsible for the paraphyletic trees in previous studies. Although the monophyly of the trypanosome clade is supported in the bootstrap analyses for maximum likelihood at 97% and maximum parsimony at 92%, there is only a small difference in ln-likelihood value or tree length between the most optimal monophyletic tree and the best suboptimal paraphyletic tree. Within the trypanosomatid subtree, the clade of trypanosomes is a sister group to the monophyletic clade of the nontrypanosome genera. Different groups of trypanosomes group on the tree according to their mode of transmission. This suggests that the adaptation to invertebrate vectors plays a more important role in the trypanosome evolution than the adaptation to vertebrate hosts.
Animals↗
Temperature adaptation of enzymes: lessons from laboratory evolution.
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Catalysis↗
Deficit in schizophrenia: the relationship between negative symptoms and neurocognition.
The aim of the study was to analyze the role of clinical and neuropsychological variables in the psychosocial functioning and evolution of negative schizophrenia. We examined a sample of 49 negative schizophrenic outpatients who were pharmacologically stabilized. The subjects were evaluated clinically with the Positive and Negative Syndrome Scale (PANSS) and the Schedule for Affective Disorders and Schizophrenia (SADS), and neuropsychologically with a broad neuropsychological test battery. The correlations between all of the variables were studied and their predictive capacity assessed by linear regression methods. When the neuropsychological impairment criterion was established, we were able to distinguish two groups of patients with similar psychopathologies, but different neuropsychological and prognostic characteristics. Schizophrenic patients with neuropsychological impairment showed worse prognosis, worse evolution, and worse psychosocial adaptation than nonneuropsychologically impaired schizophrenics. Cognitive variables are statistically good predictors of evolution, prognosis, and adaptation. In conclusion, the negative syndrome of schizophrenia is neuropsychologically heterogeneous. Although negative patients present a similar clinical profile, their neuropsychological and prognostic characteristics may differ.
Adult↗
The application of statistical physics to evolutionary biology.
A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.
Adaptation, Biological↗
Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic.
Over the past quarter century, detailed genus- and species-level similarities in cellular morphology between described taxa of Precambrian microfossils and extant cyanobacteria have been noted and regarded as biologically and taxonomically significant by numerous workers world-wide. Such similarities are particularly well documented for members of the Oscillatoriaceae and Chroococcaceae, the two most abundant and widespread Precambrian cyanobacterial families. For species of two additional families, the Entophysalidaceae and Pleurocapsaceae, species-level morphologic similarities are supported by in-depth fossil-modern comparisons of environment, taphonomy, development, and behavior. Morphologically and probably physiologically as well, such cyanobacterial "living fossils" have exhibited an extraordinarily slow (hypobradytelic) rate of evolutionary change, evidently a result of the broad ecologic tolerance characteristic of many members of the group and a striking example of G. G. Simpson's [Simpson, G.G. (1944) Tempo and Mode in Evolution (Columbia Univ. Press, New York)] "rule of the survival of the relatively unspecialized." In both tempo and mode of evolution, much of the Precambrian history of life--that dominated by microscopic cyanobacteria and related prokaryotes--appears to have differed markedly from the more recent Phanerozoic evolution megascopic, horotelic, adaptationally specialized eukaryotes.
Animals↗