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Results for “Evolutionary adaptability”

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PubMed2002

Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza Rufipogon Griff., into indica rice (Oryza sativa L.).

This study was conducted to identify and map the quantitative trait locus (QTL) controlling Al tolerance in rice using molecular markers. A population of 171 F(6) recombinant inbred lines (RILs) derived from the cross of Oryza sativa (IR64), the Al susceptible parent, and Oryza rufipogon, the Al tolerant parent, was evaluated for Al tolerance using a nutrient solution with and without 40 ppm of active Al(+3). A genetic map, consisting of 151 molecular markers covering 1,755 cM with an average distance of 11.6 cM between loci, was constructed. Nine QTLs were dentified including one for root length under non-stress conditions (CRL), three for root length under Al stress (SRL) and five for relative root length (RRL). O. rufipogon contributed favorable alleles for each of the five QTLs for RRL, which is a primary parameter for Al tolerance, and individually they explained 9.0-24.9% of the phenotypic variation. Epistatic analysis revealed that CRL was conditioned by an epistatic effect, whereas SRL and RRL were controlled by additive effects. Comparative genetic analysis showed that QTLs for RRL, which mapped on chromosomes 1 and 9, appear to be consistent among different rice populations. Interestingly, a major QTL for RRL, which explained 24.9% of the phenotypic variation, was found on chromosome 3 of rice, which is conserved across cereal species. These results indicate the possibilities to use marker-assisted selection and pyramiding QTLs for enhancing Al tolerance in rice. Positional cloning of such QTLs introgressed from O. rufipogon will provide a better understanding of the Al tolerance mechanism in rice and the evolutionary genetics of plant adaptation to acid-soil conditions across cereal species.

Alleles↗

PubMed2026

Development and Characterization of Microsatellite Markers for the Euryhaline Polychaete Laeonereis acuta (Annelida: Nereididae) in the Southwestern Brazilian Coast.

Laeonereis acuta is a polychaete species typically found at high abundance in estuarine and coastal lagoon environments. Due to its association with polluted habitats, it is commonly used in ecotoxicological studies. Moreover, its occurrence in spatially discontinuous environments with high environmental variability makes it a suitable model for evolutionary studies of local adaptation, genetic landscape, and early stages of speciation. This study aimed to develop primers and characterize microsatellite markers for L. acuta sampled from three coastal lagoons in southwestern Brazil. A total of 10 loci were characterized based on the genotyping of 40 individuals. The number of alleles per locus ranged from 2 to 19. Evidence of null alleles was detected at five loci, although their frequency decreased when coastal lagoons were analyzed separately. When considering all individuals as a single population, five loci showed positive and significant FIS values, and seven loci deviated from Hardy-Weinberg equilibrium. Maricá and Guarapina exhibited heterozygote excess at several loci, whereas Jaconé showed evidence of population genetic isolation. The 10 microsatellite loci were polymorphic and suitable for population genetic analysis in L. acuta, although these patterns may not necessarily be representative of other geographic regions. These markers may contribute to ecotoxicological studies by clarifying whether physiological responses to pollutants are associated with genetic differentiation among populations. Furthermore, they provide valuable tools for investigating genetic structure and connectivity in discontinuous environments.

Animals↗

PubMed1992

Domain-specific reasoning: social contracts, cheating, and perspective change.

What counts as human rationality: reasoning processes that embody content-independent formal theories, such as propositional logic, or reasoning processes that are well designed for solving important adaptive problems? Most theories of human reasoning have been based on content-independent formal rationality, whereas adaptive reasoning, ecological or evolutionary, has been little explored. We elaborate and test an evolutionary approach. Cosmides' (1989) social contract theory, using the Wason selection task. In the first part, we disentangle the theoretical concept of a "social contract" from that of a "cheater-detection algorithm". We demonstrate that the fact that a rule is perceived as a social contract--or a conditional permission or obligation, as Cheng and Holyoak (1985) proposed--is not sufficient to elicit Cosmides' striking results, which we replicated. The crucial issue is not semantic (the meaning of the rule), but pragmatic: whether a person is cued into the perspective of a party who can be cheated. In the second part, we distinguish between social contracts with bilateral and unilateral cheating options. Perspective change in contracts with bilateral cheating options turns P & not-Q responses into not-P & Q responses. The results strongly support social contract theory, contradict availability theory, and cannot be accounted for by pragmatic reasoning schema theory, which lacks the pragmatic concepts of perspectives and cheating detection.

Adult↗

PubMed2006

A kinetic-dynamic model for regulatory RNA processing.

A kinetic-dynamic model was proposed to simulate RNA processing by determining four essential reaction rates, including the rates of transcription, pre-mRNA turnover, pre-mRNA splicing, and mRNA decay. A family competition evolutionary algorithm (FCEA) was adapted herein to approximate these rates. Several artificial datasets were used to verify the correctness and robustness of the FCEA. The model was finally applied on time series data of yeast prp4-l mutant cells for determination of rates of RNA processing. Based on the FCEA, the model indicated that the pre-mRNA splicing was decreased in the mutant cells as well as the possible effects on transcription, pre-mRNA turnover, and mRNA decay, which was consistent with surveyed literature.

Kinetics↗

PubMed2000

Trace elements in regulation of NF-kappaB activity.

In recent years several studies have shown that NF-kappaB might be a very important therapeutic target in the treatment ot various chronic inflammatory, degenerative and tumour diseases. Trace elements play essential roles in the regulation ot cell signaling mechanisms via transcription tactors and a large number of genes. An important aspect of the present review is the description ot the mechanisms by which trace elements might influence transcription factor NF-kappaB. DNA-binding activity of NF-kappaB is regulated by the redox state of the cysteine residue (Gys-62) in the DNA binding domain of the p50 subunit and impaired by different metals (Go, Cr, Ni, Cd, Pb). It has been hypothesised that the broad speciticity of interrelationships between NF-kappaB. AP-1 and various metals results from interactions of metals with specific moieties of transcription factors and IkappaB-kinases, as well as trom the existence of a metal-governed redox system. The hypothetical targets in the NF-kappaB signaling pathway affected by metals are: IkappaB-kinases, IkappaBs, NF-kappaB, proteasome degradation of NF-kappaB, kappaB-sites in DNA. Possibly, this system is required by the cell for adequate regulation ot the transcription machinery in response to changes in intracellular and intranuclear fluxes of metals and radicals and is very ancient evolutionary mechanism of stress adaptation. The role of the NF-kappaB-mediated mechanism in induction or prevention of chronic intlammatory, allergic, degenerative and tumor diseases by zinc, vanadium, manganese, copper, silica, iodine and other trace elements is discussed.

Animals↗

PubMed2001

Effects of low atmospheric CO(2) on plants: more than a thing of the past.

In recent geological time, atmospheric CO(2) concentrations were 25-50% below the current level. Photosynthetic productivity of C(3) plants is substantially reduced at these low CO(2) levels, particularly at higher temperatures and during stress. Acclimation of photosynthesis to reduced CO(2) levels might compensate for some of this inhibition, but plants have a limited capacity to modulate Rubisco and other photosynthetic proteins following CO(2) reduction. Because of this, low CO(2) probably acted as a significant evolutionary agent, selecting plants adapted to CO(2) deficiency. Adaptations to low CO(2) might still exist in plants and might constrain responses to a rising CO(2) concentration.

Carbon Dioxide↗

PubMed2002

Hindsight bias around the world.

Hindsight bias refers to the tendency to overestimate in hindsight what one has known in foresight. Recently, two experiments extended the research to include samples from different cultures (Choi & Nisbett, 2000; Heine & Lehman, 1996). Asking their participants what they would have guessed before they knew the outcome ("hypothetical design"), Choi and Nisbett (2000) found that Koreans, in comparison to North Americans, exhibited more hindsight bias. Heine and Lehman (1996), however, reported that Japanese people in comparison to Canadians showed marginally less hindsight bias. In a second study, in which participants were asked to recall what they had estimated before they knew the outcome ("memory design"), the latter authors found no difference in hindsight bias between Japanese people and Canadians. We extended these studies with 225 Internet participants, in a hypothetical design, from four different continents (Asia, Australia, Europe, and North America). Hindsight bias was large and similar for all samples except for German and Dutch participants who showed no hindsight bias at all. While the latter effect may be based on peculiarities of the material and of the participants, the former underscores the worldwide stability of the phenomenon. In addition a follow-up surprise rating (paper and pencil) in China (35 participants) and Germany (20 participants) revealed that only less surprising items led to hindsight bias while more surprising ones did not. We suggest that the basic cognitive processes leading to hindsight bias are by-products of the evolutionary-evolved capacity of adaptive learning. On top of these basic processes, individual meta-cognitions (e.g., elicited by surprise) or motives (e.g., a self-serving motive) may further moderate the amount of bias, thus explaining the diverging results of Choi and Nisbett (2000), Heine and Lehman (1996), and our own study.

Adolescent↗

PubMed2025

A chromosomal-level genome assembly of Odontolabis cuvera Hope, 1842 (Coleoptera: Lucanidae).

The stag beetle (Coleoptera: Lucanidae) represents a captivating and evolutionarily significant group, regarded as one of the most basal lineages within the superfamily Scarabaeoidea. Despite their importance for studying beetle evolution and ecology, genomic resources for this family remain scarce. Here, we report a chromosome-level genome assembly of Odontolabis cuvera, generated by integrating PacBio HiFi, Illumina, and Hi-C data. The genome assembly spans 908.07 Mb, comprising 66 scaffolds (scaffold N50: 65.36 Mb) and 147 contigs (contig N50: 16.39 Mb). A total of 99.58% (904.22 Mb) of the assembly was anchored to 14 chromosomes. BUSCO analysis (insecta_odb10 dataset, n = 1,367) demonstrated high completeness, with 99.1% of conserved insect orthologs identified (98.3% single-copy, 0.8% duplicated). Repetitive elements accounted for 53.00% (281.28 Mb) of the genome, and a total of 18,332 protein-coding genes were annotated. This high-contiguity genome provides a critical foundation for uncovering the evolutionary mechanisms and ecological adaptations unique to Lucanidae.

Animals↗

PubMed2005

Modeling gene and genome duplications in eukaryotes.

Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.

Arabidopsis↗

PubMed2006

Alternative mutations of a positively selected residue elicit gain or loss of functionalities in enzyme evolution.

All molecular species in an organism are connected physically and functionally to other molecules. In evolving systems, it is not obvious to what extent functional properties of a protein can change to selective advantage and leave intact favorable traits previously acquired. This uncertainty has particular significance in the evolution of novel pathways for detoxication, because an organism challenged with new xenobiotics in the environment may still require biotransformation of previously encountered toxins. Positive selection has been proposed as an evolutionary mechanism for facile adaptive responses of proteins to changing conditions. Here, we show, by saturation mutagenesis, that mutations of a hypervariable residue in human glutathione transferase M2-2 can differentially change the enzyme's substrate-activity profile with alternative substrates and, furthermore, enable or disable dissimilar chemical reactions. Crystal structures demonstrate that activity with epoxides is enabled through removal of steric hindrance from a methyl group, whereas activities with an orthoquinone and a nitroso donor are maintained in the variant enzymes. Given the diversity of cellular activities in which a single protein can be engaged, the selective transmutation of functional properties has general significance in molecular evolution.

Enzyme Stability↗

PubMed2001

Extreme morphological and ecological homoplasy in tropical salamanders.

Fossorial salamanders typically have elongate and attenuated heads and bodies, diminutive limbs, hands and feet, and extremely elongate tails. Batrachoseps from California, Lineatriton from eastern México, and Oedipina from southern México to Ecuador, all members of the family Plethodontidae, tribe Bolitoglossini, resemble one another in external morphology, which has evolved independently. Whereas Oedipina and Batrachoseps are elongate because there are more trunk vertebrae, a widespread homoplasy (parallelism) in salamanders, the genus Lineatriton is unique in having evolved convergently by an alternate "giraffe-neck" developmental program. Lineatriton has the same number of trunk vertebrae as related, nonelongated taxa, but individual trunk vertebrae are elongated. A robust phylogenetic hypothesis, based on sequences of three mtDNA genes, finds Lineatriton to be deeply nested within a clade characterized by generalized ecology and morphology. Lineatriton lineolus, the only currently recognized taxon in the genus, shows unanticipated genetic diversity. Surprisingly, geographically separated populations of L. lineolus are not monophyletic, but are sister taxa of different species of the morphologically generalized genus Pseudoeurycea. Lineatriton, long thought to be a unique monospecific lineage, is polyphyletic. Accordingly, the specialized morphology of Lineatriton displays homoplasy at two hierarchical levels: (i) with respect to other elongate lineages in the family (convergence), and (ii) within what is currently recognized as a single taxon (parallelism). These evolutionary events are of adaptive significance because to invade the lowland tropics salamanders must be either arboreal or fossorial; the repeated evolution of elongation and attenuation has led to multiple lowland invasions.

Animals↗

PubMed1999

Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika.

The current phylogenetic hypothesis for the endemic Lake Tanganyika cichlid fishes of the tribe Eretmodini is based solely on morphology and suggests that more complex trophic morphologies derived only once from a less specialized ancestral condition. A molecular phylogeny of eretmodine cichlids based on partial mitochondrial DNA cytochrome b and control-region sequences was used to reconstruct the evolutionary sequence of trophic adaptations and to test alternative models of morphological divergence. The six mitochondrial lineages found disagree with the current taxonomy and the morphology-based phylogeny. Mitochondrial lineages with similar trophic morphologies are not grouped monophyletically but are typically more closely related to lineages with different trophic phenotypes currently assigned to other genera. Our results indicate multiple independent origins of similar trophic specializations in these cichlids. A pattern of repeated divergent morphological evolution becomes apparent when the phylogeography of the mitochondrial haplotypes is analyzed in the context of the geological and paleoclimatological history of Lake Tanganyika. In more than one instance within Lake Tanganyika, similar morphological divergence of dentitional traits occurred in sympatric species pairs. Possibly, resource-based divergent selective regimes led to resource partitioning and brought about similar trophic morphologies independently and repeatedly.

Animals↗

PubMed1999

Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus).

A paradigm of evolutionary biology is that adaptation and reproductive isolation are caused by a nearly infinite number of mutations of individually small effect. Here, we test this hypothesis by investigating the genetic basis of pollinator discrimination in two closely related species of monkeyflowers that differ in their major pollinators. This system provides a unique opportunity to investigate the genetic architecture of adaptation and speciation because floral traits that confer pollinator specificity also contribute to premating reproductive isolation. We asked: (i) What floral traits cause pollinator discrimination among plant species? and (ii) What is the genetic basis of these traits? We examined these questions by using data obtained from a large-scale field experiment where genetic markers were employed to determine the genetic basis of pollinator visitation. Observations of F2 hybrids produced by crossing bee-pollinated Mimulus lewisii with hummingbird-pollinated Mimulus cardinalis revealed that bees preferred large flowers low in anthocyanin and carotenoid pigments, whereas hummingbirds favored nectar-rich flowers high in anthocyanins. An allele that increases petal carotenoid concentration reduced bee visitation by 80%, whereas an allele that increases nectar production doubled hummingbird visitation. These results suggest that genes of large effect on pollinator preference have contributed to floral evolution and premating reproductive isolation in these monkeyflowers. This work contributes to growing evidence that adaptation and reproductive isolation may often involve major genes.

Journal Article↗

PubMed2001

Identification and structural characterization of nucleus-encoded transfer RNAs imported into wheat mitochondria.

Despite its large size (200-2400 kilobase pairs), the mitochondrial genome of angiosperms does not encode the minimal set of tRNAs required to support mitochondrial protein synthesis. Here we report the identification of cytosolic-like tRNAs in wheat mitochondria using a method involving quantitative hybridization to distinguish among three tRNA classes: (i) those encoded by mitochondrial DNA (mtDNA) and localized in mitochondria, (ii) those encoded by nuclear DNA and located in the cytosol, and (iii) those encoded by nuclear DNA and found in both the cytosol and mitochondria. The latter class comprises tRNA species that are considered to be imported into mitochondria to compensate for the deficiency of mtDNA-encoded tRNAs. In a comprehensive survey of the wheat mitochondrial tRNA population, we identified 14 such imported tRNAs, the structural characterization of which is presented here. These imported tRNAs complement 16 mtDNA-encoded tRNAs, for a total of at least 30 distinct tRNA species in wheat mitochondria. Considering differences in the set of mtDNA-encoded and imported tRNAs in the mitochondria of various land plants, the import system must be able to adapt relatively rapidly over evolutionary time with regard to the particular cytosolic-like tRNAs that are brought into mitochondria.

Base Sequence↗

PubMed2000

The evolution of ADHD: a disorder of communication?

Attention deficit hyperactivity disorder (ADHD) is the most commonly diagnosed psychiatric condition. Many believe that the central disability is impaired inhibition, which leads to reduced abilities in social skills, self-control, organization and time management. The behaviors identified by clinicians as problematic--inattention, hyperactivity and impulsivity--have been incorporated into several evolutionary models as selectively adaptive cognitive skills for surviving the challenges of a variable Pleistocene environment. We propose that the "disabilities" exhibited by individuals with ADHD are maladaptive, and we concur with Barkley that there is a central impairment in the behavioral inhibition system. The underlying neural anatomy and physiology support the possibility that neurotransmitter pathology may have an impact on other interlinked systems (including language), and may also account for the frequent comorbidity of aggression, anxiety, depression, and learning disabilities (many of which are language-related). Language skills compete with other cognitive activities for the attentional system, and thus the evolution of language could not in fact be independent of the evolution of attention. If language represents the ultimate expression of the attentional system, and some individuals with ADHD are seriously impaired in the coordination of interlinked neural systems (including language), then ADHD fits Jerome Wakefield's definition of "harmful dysfunction," and communication impairments should be investigated more thoroughly by clinicians.

Adaptation, Physiological↗

PubMed2000

Testing macro-evolutionary models using incomplete molecular phylogenies.

Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.

Algorithms↗

PubMed2007

Multimodal pattern formation in phenotype distributions of sexual populations.

During bouts of evolutionary diversification, such as adaptive radiations, the emerging species cluster around different locations in phenotype space. How such multimodal patterns in phenotype space can emerge from a single ancestral species is a fundamental question in biology. Frequency-dependent competition is one potential mechanism for such pattern formation, as has previously been shown in models based on the theory of adaptive dynamics. Here, we demonstrate that also in models similar to those used in quantitative genetics, phenotype distributions can split into multiple modes under the force of frequency-dependent competition. In sexual populations, this requires assortative mating, and we show that the multimodal splitting of initially unimodal distributions occurs over a range of assortment parameters. In addition, assortative mating can be favoured evolutionarily even if it incurs costs, because it provides a means of alleviating the effects of frequency dependence. Our results reveal that models at both ends of the spectrum between essentially monomorphic (adaptive dynamics) and fully polymorphic (quantitative genetics) yield similar results. This underscores that frequency-dependent selection is a strong agent of pattern formation in phenotype distributions, potentially resulting in adaptive speciation.

Animals↗

PubMed2003

From biological models to the evolution of robot control systems.

Attempts to formulate realistic models of the development of the human oculomotor control system have led to the conclusion that evolutionary factors play a crucial role. Moreover, even rather coarse simulations of the biological evolutionary processes result in adaptable control systems that are considerably more efficient than those designed by human researchers. In this paper I shall describe some of the aspects of these biological models that are likely to be useful for building robot control systems. In particular, I shall consider the evolution of appropriate innate starting points for learning/adaptation, patterns of learning rates that vary across different system components, learning rates that vary during the system's lifetime, and the relevance of individual differences across the evolved populations.

Adaptation, Physiological↗