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PubMed2006

The paranoid optimist: an integrative evolutionary model of cognitive biases.

Human cognition is often biased, from judgments of the time of impact of approaching objects all the way through to estimations of social outcomes in the future. We propose these effects and a host of others may all be understood from an evolutionary psychological perspective. In this article, we elaborate error management theory (EMT; Haselton & Buss, 2000). EMT predicts that if judgments are made under uncertainty, and the costs of false positive and false negative errors have been asymmetric over evolutionary history, selection should have favored a bias toward making the least costly error. This perspective integrates a diverse array of effects under a single explanatory umbrella, and it yields new content-specific predictions.

Animals↗

PubMed1995

Evolutionary-conserved enhancers direct region-specific expression of the murine Hoxa-1 and Hoxa-2 loci in both mice and Drosophila.

The HOM-C/Hox complexes are an evolutionary related family of genes that have been shown to direct region-specific development of the animal body plan. We examined in transgenic mice the DNA regulatory elements that determine the temporal and spatially restricted expression of two of the earliest and most anteriorly expressed murine genes, Hoxa-1 and Hoxa-2, which are homologues of the labial and proboscipedia genes of Drosophila. In both mouse and Drosophila, these genes have been shown to play a critical role in head development. We identified three independent enhancers which direct distinct portions of the Hoxa-1 and Hoxa-2 expression domains during early murine embryogenesis. Two enhancers mediate hindbrain-specific expression, being active in either rhombomere 2, the most anterior rhombomere expressing Hoxa-2, or in rhombomere 4, a region where Hoxa-1 and Hoxa-2 have been shown to exert critical developmental roles. The third enhancer is essential for the most extensive expression domain of Hoxa-1 and contains a retinoic acid response element. Point mutations within the retinoic acid response element abolish expression in neuroepithelium caudal to rhombomere 4, supporting a natural role for endogenous retinoids in patterning of the hindbrain and spinal cord. Analysis of the murine Hoxa-2 rhombomere 2-specific enhancer in Drosophila embryos revealed a distinct expression domain within the arthropod head segments, which parallels the expression domain of the Hoxa-2 homologue proboscipedia. These results suggest an evolutionary conservation between HOM-C/Hox family members, which includes a conservation of certain DNA regulatory elements and possible regulatory cascades.

Animals↗

PubMed1997

Evolutionary changes of developmental mechanisms in the absence of cell lineage alterations during vulva formation in the Diplogastridae (Nematoda).

The origin of novelty is one of the least understood evolutionary phenomena. One approach to study evolutionary novelty comes from developmental biology. During developmental cell fate specification of the nematode Pristionchus pacificus (Diplogastridae), five cell fates can be distinguished within a group of twelve ventral epidermal cells. The differentiation pattern of individual cells includes programmed cell death, cell fusion and vulval differentiation after induction by the gonad. A cell lineage comparison among species of seven different genera of the Diplogastridae indicates that the differentiation pattern of ventral epidermal cells is highly conserved. Despite this morphological conservation, cell ablation experiments indicate many independent alterations of underlying mechanisms of cell fate specification. Cell fusion and individual cell competence change during evolution as well as the differentiation property in response to inductive signaling. These results suggest that developmental mechanisms, some of which are redundantly involved in vulval fate specification of the genetic model organism Caenorhabditis elegans, can evolve without concomitant morphological change.

Animals↗

PubMed2006

Biomimetic evolutionary analysis: testing the adaptive value of vertebrate tail stiffness in autonomous swimming robots.

For early vertebrates, a long-standing hypothesis is that vertebrae evolved as a locomotor adaptation, stiffening the body axis and enhancing swimming performance. While supported by biomechanical data, this hypothesis has not been tested using an evolutionary approach. We did so by extending biomimetic evolutionary analysis (BEA), which builds physical simulations of extinct systems, to include use of autonomous robots as proxies of early vertebrates competing in a forage navigation task. Modeled after free-swimming larvae of sea squirts (Chordata, Urochordata), three robotic tadpoles (;Tadros'), each with a propulsive tail bearing a biomimetic notochord of variable spring stiffness, k (N m(-1)), searched for, oriented to, and orbited in two dimensions around a light source. Within each of ten generations, we selected for increased swimming speed, U (m s(-1)) and decreased time to the light source, t (s), average distance from the source, R (m) and wobble maneuvering, W (rad s(-2)). In software simulation, we coded two quantitative trait loci (QTL) that determine k: bending modulus, E (Nm(-2)) and length, L (m). Both QTL were mutated during replication, independently assorted during meiosis and, as haploid gametes, entered into the gene pool in proportion to parental fitness. After random mating created three new diploid genotypes, we fabricated three new offspring tails. In the presence of both selection and chance events (mutation, genetic drift), the phenotypic means of this small population evolved. The classic hypothesis was supported in that k was positively correlated (r(2)=0.40) with navigational prowess, NP, the dimensionless ratio of U to the product of R, t and W. However, the plausible adaptive scenario, even in this simplified system, is more complex, since the remaining variance in NP was correlated with the residuals of R and U taken with respect to k, suggesting that changes in k alone are insufficient to explain the evolution of NP.

Animals↗

PubMed1994

ARE MITOCHONDRIA SUBJECT TO EVOLUTIONARY TEMPERATURE ADAPTATION?

Thermal tolerance and the respiratory properties of isolated red muscle mitochondria were investigated in Oreochromis alcalicus grahami from the alkaline hot-springs, Lake Magadi, Kenya. Populations of O. a. grahami were resident in pools at 42.8 °C and migrated into water reaching temperatures of 44.8 °C for short periods. The maximum respiration rates of mitochondria with pyruvate as substrate were 217 and 284 natom O mg-1 mitochondrial protein min-1 at 37 °C and 42 °C, respectively (Q10=1.71). Fatty acyl carnitines (chain lengths C8, C12 and C16), malate and glutamate were oxidised at 7080 % of the rate for pyruvate. In order to assess evolutionary temperature adaptation of maximum mitochondrial oxidative capacities, the rates of pyruvate and palmitoyl carnitine utilisation in red muscle mitochondria were measured from species living at other temperatures: Notothenia coriiceps from Antarctica (-1.5 to +1 °C); summer-caught Myoxocephalus scorpius from the North Sea (1015 °C); and Oreochromis andersoni from African lakes and rivers (2230 °C). State 3 respiration rates had Q10 values in the range 1.82.7. At the lower lethal temperature of O. andersoni (12.5 °C), isolated mitochondria utilised pyruvate at a similar rate to mitochondria from N. coriiceps at 2.5 °C (30 natom O mg-1 mitochondrial protein min-1). Rates of pyruvate oxidation by mitochondria from M. scorpius and N. coriiceps were similar and were higher at a given temperature than for O. andersoni. At their normal body temperature (-1.2 °C), mitochondria from the Antarctic fish oxidised pyruvate at 5.5 % and palmitoyl-dl-carnitine at 8.8 % of the rates of mitochondria from the hot-spring species at 42 °C. The results indicate only modest evolutionary adjustments in the maximal rates of mitochondrial respiration in fish living at different temperatures.

Journal Article↗

PubMed1996

Genetic basis, mode of inheritance and evolutionary changes of migratory directions in palaearctic warblers (Aves: Sylviidae)

The genetic basis, mode of inheritance and recent evolutionary changes of migratory directions in birds are discussed on the basis of published and new experimental evidence. Displacement experiments with wild-caught migrants and orientation tests with hand-reared passerines illustrate that inexperienced young birds possess genetic information about the direction and approximate distance of migration, but not about the geographic location of the winter quarters. Hand-raised blackcaps Sylvia atricapilla from east and west of the Central European migratory divide, when tested under identical conditions, exibited population-specific migratory directions in orientation cages. Cross-breeding of birds from these two populations demonstrated an intermediate mode of inheritance of this behavioural character. New data on the orientation of an F2 generation suggest that the directional information is encoded by only a few major genes. Migratory adaptations may have evolved recently, in some cases rapidly, as is illustrated by the establishment of a new migration route of central European blackcaps to winter quarters in the British Isles. This new route is shown (in a captive breeding experiment) to be based on a novel, genetically programmed westnorthwesterly migratory direction. It must have spread from almost zero to 7-11 % frequency in parts of central Europe within only three decades. The novel direction is also inherited phenotypically intermediately; its rapid evolution may be mediated by assortative mating based on differential arrival times at the breeding grounds. The evolutionary flexibility of migratory adaptations is discussed in relation to changes in the environment, both natural and accelerated by man.

Journal Article↗

PubMed1993

Evolutionary position of n-alkane-assimilating yeast Candida maltosa shown by nucleotide sequence of small-subunit ribosomal RNA gene.

We clarified the evolutionary position of Candida maltosa, an n-alkane-assimilating yeast, by sequencing the nucleotides of the small-subunit ribosomal RNA gene. Phylogenetic analyses showed the close evolutionary relationships of C. maltosa with C. tropicalis, C. viswanathii, C. albicans, C. parapsilosis, and C. guilliermondii, forming a sub-group within this genus.

Alkanes↗

PubMed2006

Evoecotoxicology: environmental changes and life features development during the evolutionary process-the record of the past at developmental stages of living organisms.

For most of evolutionary history, scientific understanding of the environment and life forms is extremely limited. In this commentary I discuss the hypothesis that ontogenetic features of living organisms can be considered biomarkers of coevolution between organisms and physicochemical agents during Earth's history. I provide a new vision of evolution based on correlations between metabolic features and stage-dependent susceptibility of organisms to physicochemical agents with well-known environmental signatures. Thus, developmental features potentially reflect environmental changes during evolution. From this perspective, early multicellular life forms would have flourished in the anoxic Earth more than 2 billion years ago, which is at least 1.2 billion years in advance of available fossil evidence. The remarkable transition to aerobic metabolism in gastrula-stage embryos potentially reflects evolution toward tridermic organisms by 2 billion years ago. Noteworthy changes in embryonic resistance to physicochemical agents at different developmental stages that can be observed in living organisms potentially reflect the influence of environmental stress conditions during different periods of evolutionary history. Evoecotoxicology, as a multidisciplinary and transdisciplinary approach, can enhance our understanding of evolution, including the phylogenetic significance of differences in susceptibility/resistance to physicochemical agents in different organisms.

Animals↗

PubMed2005

Self-criticism and major depression: an evolutionary perspective.

OBJECTIVES: This study sought to incorporate the personality style of self-criticism within an evolutionary framework to help explain its relationship to major depression. It was expected that self-critics would engage in poor social comparisons and have greater feelings of internal entrapment, which are both processes related to depression by evolutionary thinkers. DESIGN: A cross-sectional design was employed such that participants were first interviewed and then completed several questionnaires. METHODS: The sample consisted of 146 graduate students who had experienced at least one prior episode of major depression, which was confirmed using the Structured Clinical Interview for DSM-IV (SCID). Participants were subsequently administered the Center for epidemiological studies depression scale (CESD), Depressive Experiences Questionnaire (DEQ), Social comparison rating scale (SCRS), and Entrapment scale (ES). RESULTS: Regression analyses revealed that self-criticism significantly predicted internal entrapment and social comparison when controlling for mood and for levels of dependency. Subsequent Structural Equation Modelling (SEM) revealed that a factor of self-reported entrapment and social comparison mediated the effect of self-criticism on the number of previous episodes of depression. CONCLUSION: These findings suggest that part of the reason self-critics are vulnerable to clinical episodes of depression lies in their subjective experience of entrapment and in their negative social comparisons.

Attitude↗

PubMed2001

Acne: a biopsychosocial and evolutionary perspective with a focus on shame.

PURPOSE: Hypotheses regarding the psychological factors implicated in the development and maintenance of acne first emerged in the middle of the eighteenth century. However, the psychodermatological literature from this date relating to acne has variously been described as confusing, overly prone to conjecture and, in particular, atheoretical. The current paper has two key objectives; first, to present a biopsychosocial model of acne development and maintenance and, secondly, to understand the psychosocial strain imposed by acne from an evolutionary perspective with a particular emphasis on body shame reactions. METHODS: The psychodermatological literature relating to acne is reviewed with the data analysed for potential biopsychosocial interactions and shame eliciting responses. RESULTS: The review indicates that acne can be reconceptualized as a biopsychosocial phenomena which, in turn, provides the field with innovative hypotheses for empirical inquiry and the potential for expanding and evaluating treatment options. The evolutionary analysis illustrates that acne provides the potential for distressing body shame reactions due to the skin disease's potential for damaging self-other evaluations of attractiveness. CONCLUSIONS: Acne has tended to be viewed as a minor dermatological complaint which imposes minimal psychological distress upon sufferers. The paper concludes that acne has the ability to elicit in some sufferers significant mental health concerns due to a heightened sense of shame relating to appearance.

Journal Article↗

PubMed2005

Evolutionary trace analysis of eukaryotic DNA topoisomerase I superfamily: identification of novel antitumor drug binding site.

The studies of novel inhibitors of DNA topoisomerase I (Topo I) have already become very promising in cancer chemotherapy. Identifying the new drug-binding residues is playing an important role in the design and optimization of Topo I inhibitors. The designed compounds may have novel scaffolds, thus will be helpful to overcome the toxicities of current camptothecin (CPT) drugs and may provide a solution to cross resistance with these drugs. Multiple sequence alignments were performed on eukaryotic DNA topoisomerase I superfamily and thus the evolutionary tree was constructed. The Evolutionary Trace method was applied to identify functionally important residues of human Topo I. It has been demonstrated that class-specific hydrophobic residues Ala351, Met428, Pro431 are located around the 7,9-position of CPT, indicating suitable substitution of hydrophobic group on CPT will increase antitumor activity. The conservative residue Lys436 in the superfamily is of particular interest and new CPT derivatives designed based on this residue may greatly increase water solubility of such drugs. It has also been demonstrated that the residues Asn352 and Arg364 were conservative in the superfamily, whose mutation will render CPT resistance. As our molecular docking studies demonstrated they did not make any direct interaction with CPT, they are important drug-binding site residues for future design of novel non-camptothecin lead compounds. This work provided a strong basis for the design and synthesis of novel highly potent CPT derivatives and virtual screening for novel lead compounds.

Amino Acid Sequence↗

PubMed2006

Evolutionary potential of a duplicated repressor-operator pair: simulating pathways using mutation data.

Ample evidence has accumulated for the evolutionary importance of duplication events. However, little is known about the ensuing step-by-step divergence process and the selective conditions that allow it to progress. Here we present a computational study on the divergence of two repressors after duplication. A central feature of our approach is that intermediate phenotypes can be quantified through the use of in vivo measured repression strengths of Escherichia coli lac mutants. Evolutionary pathways are constructed by multiple rounds of single base pair substitutions and selection for tight and independent binding. Our analysis indicates that when a duplicated repressor co-diverges together with its binding site, the fitness landscape allows funneling to a new regulatory interaction with early increases in fitness. We find that neutral mutations do not play an essential role, which is important for substantial divergence probabilities. By varying the selective pressure we can pinpoint the necessary ingredients for the observed divergence. Our findings underscore the importance of coevolutionary mechanisms in regulatory networks, and should be relevant for the evolution of protein-DNA as well as protein-protein interactions.

Computational Biology↗

PubMed2005

The evolutionary value of recombination is constrained by genome modularity.

Genetic recombination is a fundamental evolutionary mechanism promoting biological adaptation. Using engineered recombinants of the small single-stranded DNA plant virus, Maize streak virus (MSV), we experimentally demonstrate that fragments of genetic material only function optimally if they reside within genomes similar to those in which they evolved. The degree of similarity necessary for optimal functionality is correlated with the complexity of intragenomic interaction networks within which genome fragments must function. There is a striking correlation between our experimental results and the types of MSV recombinants that are detectable in nature, indicating that obligatory maintenance of intragenome interaction networks strongly constrains the evolutionary value of recombination for this virus and probably for genomes in general.

Evolution, Molecular↗

PubMed2025

Meta-evolutionary exome analysis identifies novel type 2 diabetes mellitus genes in the UK Biobank and all of us.

Type 2 diabetes mellitus (T2DM) risk is heavily influenced by genetics, yet current association tests have explained only parts of its heritability. We developed MEVA (Meta-Evolutionary Action), a meta-analytic framework that integrates three complementary methods-EAML, Sigma-Diff, and GeneEMBED-to assess the functional burden of protein-coding variants using evolutionary data. MEVA was applied to exome data from 28,115 T2DM cases and 28,115 controls in the UK Biobank (UKB), identifying 101 genes (p < 1e-5). MEVA outperformed its component methods, each of which substantially outperformed a conventional burden test (MAGMA), in recovering known T2DM genes (AUROC = 0.925) and maintaining robustness in progressively smaller cohorts (AUROC = 0.917). MEVA showed significant enrichment for T2DM-related loci (p = 6.8e-10, p = 2.0e-34), protein interactions (z = 4.6, z = 4.2), pathways (p = 1.3e-6, z = 2.0), phenotypes (p = 1.3e-21, z = 9.1), and literature mentions (z = 7.2). Replication in 16,915 T2DM cases and 16,915 controls from All of Us (AoU) yielded 99 genes (p < 1e-5), 23 of which were also recovered in the UKB cohort - far exceeding random chance. These included established genes (SLC30A8, WFS1, HNF1A) and less-characterized candidates (NRIP1, ADAM30, CALCOCO2, TUBB1, ZFP36L2, WDR90). Notably, NRIP1 loss-of-function variants were associated with increased T2DM risk in both the UKB (OR = 1.09, FDR = 5.4e-4) and AoU (OR = 1.09, FDR = 0.046), and TUBB1 and CALCOCO2 gain-of-function variants showed consistent risk effects (FDR < 0.05). Pathway analyses revealed convergence on endoplasmic reticulum chaperone complexes (FDR = 0.02) and Hippo signaling (FDR = 8.5e-4). Finally, all 177 candidate genes were functionally prioritized using ten orthogonal criteria to guide experimental follow-up. These results demonstrate that combining complementary, impact-aware association tests increases sensitivity, improves replication, and expands the catalog of genetic risk factors for T2DM.

Humans↗

PubMed2001

Evolutionary lines of cysteine peptidases.

The proteolytic enzymes that depend upon a cysteine residue for activity have come from at least seven different evolutionary origins, each of which has produced a group of cysteine peptidases with distinctive structures and properties. We show here that the characteristic molecular topologies of the peptidases in each evolutionary line can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. Clan CA contains the families of papain (C1), calpain (C2), streptopain (C10) and the ubiquitin-specific peptidases (C12, C19), as well as many families of viral cysteine endopeptidases. Clan CD contains the families of clostripain (C11), gingipain R (C25), legumain (C13), caspase-1 (C14) and separin (C50). These enzymes have specificities dominated by the interactions of the S1 subsite. Clan CE contains the families of adenain (C5) from adenoviruses, the eukaryotic Ulp1 protease (C48) and the bacterial YopJ proteases (C55). Clan CF contains only pyroglutamyl peptidase I (C15). The picornains (C3) in clan PA have probably evolved from serine peptidases, which still form the majority of enzymes in the clan. The cysteine peptidase activities in clans PB and CH are autolytic only. In conclusion, we suggest that although almost all the cysteine peptidases depend for activity on catalytic dyads of cysteine and histidine, it is worth noting some important differences that they have inherited from their distant ancestral peptidases.

Animals↗

PubMedDate not supplied

Green paramecia as an evolutionary winner of oxidative symbiosis: a hypothesis and supportive data.

A single cell of the green paramecia (Paramecium bursaria) harbors several hundreds of endo-symbiotic Chlorella-like algae in its cytoplasm. Removal of algae from the host organism and re-association of ex-symbiotic host paramecia with ex-symbiotic algae can be experimentally demonstrated in the laboratory. However, the mechanism precisely governing the alga-protozoan association is not fully understood, and the origin of symbiosis in the evolutionary view has not been given. Here, we propose the possible biochemical models (models 1 and 2) explaining the co-evolution between Paramecium species and algal symbionts by pointing out that algal photosynthesis in the host paramecia plays a dual role providing the energy source and the risk of oxidative damage to the host. Model 1 lays stress on the correlation between the (re)greening ability of the paramecia and the tolerance to oxidative stress whereas model 2 emphasizes the cause of evolutionary selection leading to the emergence of Paramecium species tolerant against reactive oxygen species.

Animals↗

PubMed2004

Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm.

Understanding the evolution of biopolymers is a key element in rationalizing their structures and functions. Simple exact models (SEMs) are well-positioned to address general principles of evolution as they permit the exhaustive enumeration of both sequence and structure (conformational) spaces. The physics-based models of the complete mapping between genotypes and phenotypes afforded by SEMs have proven valuable for gaining insight into how adaptation and selection operate among large collections of sequences and structures. This study compares the properties of evolutionary landscapes of a variety of SEMs to delineate robust predictions and possible model-specific artifacts. Among the models studied, the ruggedness of evolutionary landscape is significantly model-dependent; those derived from more protein-like models appear to be smoother. We found that a common practice of restricting protein structure space to maximally compact lattice conformations results in (i.e., "designs in") many encodable (designable) structures that are not otherwise encodable in the corresponding unrestrained structure space. This discrepancy is especially severe for model potentials that seek to mimic the major role of hydrophobic interactions in protein folding. In general, restricting conformations to be maximally compact leads to larger changes in the model genotype-phenotype mapping than a moderate shifting of reference state energy of the model potential function to allow for more specific encoding via the "designing out" effects of repulsive interactions. Despite these variations, the superfunnel paradigm applies to all SEMs we have tested: For a majority of neutral nets across different models, there exists a funnel-like organization of native stabilities for the sequences in a neutral net encoding for the same structure, and the thermodynamically most stable sequence is also the most robust against mutation.

Biophysics↗

PubMed2004

Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection.

Genes whose products are involved in reproduction include some of the fastest-evolving genes found within the genomes of several organisms. Drosophila has long been used to study the function and evolutionary dynamics of genes thought to be involved in sperm competition and sexual conflict, two processes that have been hypothesized to drive the adaptive evolution of reproductive molecules. Several seminal fluid proteins (Acps) made in the Drosophila male reproductive tract show evidence of rapid adaptive evolution. To identify candidate genes in the female reproductive tract that may be involved in female-male interactions and that may thus have been subjected to adaptive evolution, we used an evolutionary bioinformatics approach to analyze sequences from a cDNA library that we have generated from Drosophila female reproductive tracts. We further demonstrate that several of these genes have been subjected to positive selection. Their expression in female reproductive tracts, presence of signal sequences/transmembrane domains, and rapid adaptive evolution indicate that they are prime candidates to encode female reproductive molecules that interact with rapidly evolving male Acps.

Animals↗